Computer networking and chemistry: A symposium sponsored by the Division of Computers in chemistry at the 170th meeting of the American Chemical Society, ... Aug. 26-27, 1975 (ACS symposium series ; 19)
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Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.fw001
Illinois Institute of Technology
A symposium sponsored by the Division of Computers in Chemistry at the 170th Meeting of the American Chemical Society, Chicago, Ill., Aug. 26-27, 1975.
ACS SYMPOSIUM SERIES
AMERICAN
CHEMICAL
WASHINGTON, D. C. 1975
SOCIETY
19
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.fw001
Library of Congress
Data
Computer networking and chemistry. ( A C S symposium series; 19 I S S N 0 0 9 7 - 6 1 5 6 ) Includes bibliographical references and index. 1. Chemistry—Data processing—Congresses. 2. Communication i n chemistry—Congresses. 3. Computer networks—Congresses. I. Lykos, Peter, 1927II. American Chemical Society. D i v i s i o n of Computers i n Chemistry. III. Series: American Chemical Society. A C S symposium series; 19. QD39.3.E46C64 I S B N 8412-0301-6
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.fw001
ACS Symposium Series Robert F. Gould, Series Editor
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.fw001
FOREWORD The A C S
SYMPOSIUM
SERIES
was founded in 1 9 7 4 to provide
a medium for publishing symposia quickly in book form. The format of the IN
CHEMISTRY
SERIES
SERIES
parallels that of the continuing
ADVANCES
except that in order to save time the
papers are not typeset but are reproduced as they are submitted by the authors in camera-ready form.
As a further
means of saving time, the papers are not edited or reviewed except by the symposium chairman, who becomes editor of the book.
Papers published in the A C S
SYMPOSIUM
SERIES
are original contributions not published elsewhere in whole or major part and include reports of research as well as reviews since symposia may embrace both types of presentation.
PREFACE he term "computer networking" conjures up an image of computer A
nodes linked by telecommunications in such a way that all those
computer resources would be accessible to anyone connected to the net and that a single problem could be handled by two or more computers Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.pr001
in the net without human intervention. Actually the computer networks commonly found today are of two general but simple types: (1) star computer networks, whereby a single, central computer has communication lines radiating to terminal devices; and (2) communication networks, whereby a user at a terminal can connect with anyone
from a variety of computer-based services remotely
located, by dialing the appropriate telephone number. Technically, all the components of computer networking could be present in a single chemical apparatus or laboratory or spread over a campus, a region, a country, or the world. There are several motivations for computer networking, including: 1.
Sharing of data and of bibliographic information resources.
2. Sharing of specialized and expensive computing resources, dedicated to a particular mode of problem solving, by users who are geographically dispersed. 3. Provision for loose-coupled computing support for the experimentalist who has a tight-coupled controlled system and occasionally needs additional computer resources. 4. Standardization of protocols and algorithms. T h e variations that now exist, which render software from different sources incompatible, are often idiosyncratic rather than substantive. 5. Sharing of algorithms via a few sites. This means that the best thinking of researchers working in a specific area can be accumulated, used, and continually revised within a common mode of representation. 6. A distributed network of minicomputers at one site may be cheaper, easier to program, and more reliable than one large computer. A report has been published on three E D U C O M - c o n d u c t e d broad and intensive seminars on networking entitled "Networks for Research and Education" ( Greenberger, M . , J. Aronofsky, J. L . McKenny and W . F . Massey, M I T , Cambridge, Mass., 1974) which may be summarized as follows: vii
1. Computer networking must be acknowledged (no person is an island); 2. major inhibitors of the realization of networking potential are political, organizational, and economic—not technological; and 3. networking by itself is not a solution to current deficiencies— user practices, institutional procedures and government policies need to adapt. Networking to enhance scientific education and research will develop in direct proportion to the initiative shown by the scientists themselves. Discipline-oriented computing is most likely to promote diffusion and acceptance of computer-based enhancements to the particular discipline.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.pr001
This follows because the hierarchical leadership structure,
a common
language, the established discipline-based communication media such as journals and conferences—all of which facilitate evolution of a discipline —also provide the natural environment and mechanism for infusing and accepting the comprehensive and pervasive computer impact. Regional, national, or worldwide networking depends on the quality and accessibility of an adequate telecommunications system. Networking within a laboratory, campus, or city can be implemented directly through telephone lines, coaxial cables, microwave links ( line-of-sight, range 50 km) or even infrared beams (line-of-sight, range 10 km, dry and clear atmosphere). For areas with an inadequate terrestrial communications system, the domestic communications satellite will be important.
Because the syn-
chronous orbit satellites will "hover" 22,300 miles above the equator, the total path length of a signal from a terrestrial terminal to a terrestrial computer and back again will be about 90,000 miles. That will require Vz second because of the finite speed of light and will have to be taken into account. Such audio and video communications satellites are already being used experimentally for health care and education in Alaska, covering an area as large as Texas, and for the expansion of medical education into states without a medical school such as Alaska, Montana, and Idaho. The so-called "march of the minis" is an understatement impact of the mini computer—that "shrunk in the wash" general computer
system
of the purpose
now accessible to every university department, every
college, and every high school. T h e mini computer supports not only local interactive computing and batch processing but functions as a remote-job-entry
station as well, facilitating access to remote special
purpose computing facilities via telephone lines—i.e., through networking. Indeed, the hand-held micro computer, as well as "distributed intelligence" microprocessors installed in servo and sensor devices (including all scientific research equipment), puts the choice as well as the comviii
puter into the hands of each teacher and researcher; it effectively removes the administrator from computer service selection just as he is removd from the selection of textbooks for a particular course or of a piece of equipment for a research laboratory.
So-called "intelligent" terminals
give every chemist the opportunity to do local computing and have technologically
transparent access to
remote
computer
services
via
telecommunications. A t the other extreme, no university or chemical industry has on its site today the most powerful computer commercially available. Only the taxpayer-supported National Science Laboratories are that privileged. Computer networking means that those expensive resources could be Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.pr001
realistically accessible,
not only to the in-house scientists physically
located at those national laboratories but also to their peers at universities and in industry throughout the nation. T h e current growing movement toward a National Resource for Computation in Chemistry, if successful, will lead to a truly effective N R C C in direct proportion to the extent that computer networking is involved. The papers comprising this Computer Networking and Chemistry Symposium were selected because they span various important ways in which computer networking is affecting chemistry research and education.
Although most of the authors are chemists, a few are computer
scientists whose work is relevant to chemistry. In some cases the papers are written jointly by chemists and computer scientists, showing what can be done at a well-developed chemistry and computer science interface. Illinois Institute of Technology
PETER LYKOS
Chicago, Ill. M a y 1975
ix
1 C R Y S N E T : A Network for Crystallographic Computing* T. F. KOETZLE, L. C. ANDREWS, F. C. BERNSTEIN and H. J. BERNSTEIN
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch001
Chemistry Department, Brookhaven National Laboratory, Upton, Ν. Y . 11973
The CRYSNET system is comprised of a group of five intelli gent terminals, which primarily are u t i l i z e d to carry out computa tions i n the f i e l d of crystallography, and which communicate with the Control Data Corporation (CDC) model CYBER 70/76 (7600) computing system at Brookhaven National Laboratory (BNL). These terminals are installed i n laboratories geographically distributed from New York to Texas, where they currently are used i n a wide variety of structural investigations. Three out of the five terminals have interactive three-dimensional graphical displays. Structural results can easily be visualized through the medium of computer graphics, and the research programs of groups with access to the CRYSNET graphics terminals have been enhanced greatly. System Organization The basic CRYSNET system organization has been discussed previously (1,2). Here we briefly w i l l review the hardware and software configurations, with emphasis on some recent develop ments. Hardware for the CRYSNET graphics terminals was selected to satisfy two important requirements: 1. The terminal should pos sess a
versatile
communications i n t e r f a c e and be capable of con
nection v i a ordinary telephone lines to a variety of host computers, and 2. The terminal should support a flexible stand -alone interactive graphics package suitable for molecular model ing. The chosen terminal configuration, a D i g i t a l Equipment Corporation (DEC) model PDP 11/40 minicomputer, with 28K words core memory, hardware floating-point processor, a 1.2 M word disk, card reader, magnetic tape and printer/plotter, interfaced with a Vector General three-dimensional display, has the additional *Work performed under the auspices of the Energy Research and Development Administration, and supported by the National Science Foundation under Grants AG-370 and GJ-33248X, and i n part by the National Institutes of Health under grants CA10925 and RR05539. 1
2
COMPUTER
NETWORKING
AND
CHEMISTRY
advantage t h a t the t e r m i n a l i t s e l f p r o v i d e s s u f f i c i e n t computing power t o p e r f o r m s m a l l c r y s t a l l o g r a p h i c c o m p u t a t i o n s . The g r a p h i c s t e r m i n a l s c u r r e n t l y o p e r a t e u n d e r DOS/BATCH v e r s i o n 9 . 2 0 c , w i t h a p p l i c a t i o n s programs almost e n t i r e l y w r i t t e n i n FORTRAN. Use o f a h i g h e r - l e v e l l a n g u a g e e n a b l e s code t o b e t r a n s f e r r e d w i t h r e l a t i v e ease to d i f f e r e n t hardware c o n f i g u r a t i o n s , and a l l o w s p r a c t i c i n g c r y s t a l l o g r a p h e r s t o p r o g r a m t h e s y s t e m . The BNL c o m p u t i n g c e n t e r o p e r a t e s t h e INTERCOM s y s t e m (SCOPE 3 . 4 ) on a CDC 6600 f r o n t - e n d , and SCOPE 2 . 1 on t h e 7 6 0 0 . The CRYSNET t e r m i n a l s communicate w i t h INTERCOM v i a o r d i n a r y t e l e p h o n e l i n e s a t 2 , 0 0 0 b a u d ( s y n c h r o n o u s ) , u n d e r t h e CDC mode 4c o r ANSI 200 U s e r T e r m i n a l p r o t o c o l . INTERCOM p r o v i d e s f l e x i b l e f i l e m a n i p u l a t i o n f a c i l i t i e s , a l l o w s i n t e r a c t i v e p r o c e s s i n g on t h e 6 6 0 0 ' s , and s u b m i s s i o n o f j o b s t o t h e b a t c h queues o f t h e 6 6 0 0 s and 7 6 0 0 . U n d e r CRYSNET, l a r g e c o m p u t a t i o n s may b e p e r f o r m e d a t t h e BNL CYBER 70/76, b y u s e o f p r o g r a m s f r o m an e x t e n s i v e c r y s t a l l o g r a p h i c l i b r a r y , w i t h I/O e s p e c i a l l y t a i l o r e d f o r a r e m o t e u s e r e n v i r o n ment. B e s i d e B N L , t h e CRYSNET t e r m i n a l s h a v e b e e n u s e d t o comm u n i c a t e w i t h CDC s y s t e m s a t C o u r a n t I n s t i t u t e , New Y o r k U n i v e r s i t y , a t L a w r e n c e B e r k e l e y L a b o r a t o r y , and t h e N a t i o n a l C e n t e r f o r A t m o s p h e r i c R e s e a r c h ( B o u l d e r ) , as w e l l as w i t h t h e IBM 360/91 a t UCLA. A n a s y n c h r o n o u s p o r t on two o f t h e t e r m i n a l s has b e e n u s e d t o communicate w i t h a DEC PDP 10 s y s t e m a t t h e N a t i o n a l I n s t i t u t e s of H e a l t h .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch001
1
Molecular Graphics A v e r s a t i l e m o l e c u l a r m o d e l i n g s o f t w a r e package i s under d e v e l o p m e n t f o r t h e PDP 1 1 / V e c t o r G e n e r a l t e r m i n a l s ( 3 ^ 4 ) . Curr e n t l y o p e r a t i o n a l are f i v e major g r a p h i c s programs: 1. PRJCTN, w h i c h a l l o w s r e a l - t i m e r o t a t i o n of s t i c k f i g u r e s of m o l e c u l e s w i t h up t o 740 a t o m s . T h i s program i n c l u d e s o p t i o n a l s i d e - b y - s i d e o r top-bottom m i r r o r - i m a g e s t e r e o , and p r o v i d e s h a r d copy o u t p u t a t a user-designated s c a l e (cm/Sngstrom) o n t h e terminal Versatec p r i n t e r / p l o t t e r . Bond d i s t a n c e s , a n g l e s and t o r s i o n a n g l e s o f i n t e r e s t may be o u t p u t t o t h e c o n s o l e k e y b o a r d o r t h e printer/plotter. A modified v e r s i o n o f P R J C T N , r u n n i n g i n i n t e r a c t i v e mode o n t h e CDC 6600 u n d e r INTERCOM, has b e e n u s e d t o draw m o l e c u l e s o n a T e k t r o n i x m o d e l 4010 s t o r a g e - t u b e g r a p h i c s t e r minal. C r y s t a l l o g r a p h i c s y m m e t r y - g e n e r a t i o n , c u r r e n t l y accomp l i s h e d v i a an independent p r o g r a m GEN w h i c h p r o d u c e s a PRJCTN i n p u t f i l e w i t h s y m m e t r y - r e l a t e d atoms, i s i n the p r o c e s s of being added as an o p t i o n i n P R J C T N . 2. ELLIPS ( 5 ) , a program w h i c h produces r e p r e s e n t a t i o n s of molec u l e s w i t h atoms d r a w n as e l l i p s o i d s t o show a m p l i t u d e s o f a n i s o t r o p i c t h e r m a l m o t i o n . These v i e w s a r e s i m i l a r t o t h o s e p r o d u c e d by t h e ORTEP p r o g r a m (6) commonly u s e d o n a l a r g e computer w i t h a mechanical p l o t t e r .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch001
1.
KEOTZLE
E T
AL.
CRYSNET:
Crystallographic
Computing
3
3· S T I P L , w h i c h d i s p l a y s s p a c e - f i l l i n g models w i t h v a r i a b l e v a n d e r Waals r a d i i . Atoms a r e r e p r e s e n t e d as s t i p p l e d s p h e r e s ; t h e h i d d e n p o r t i o n s o f atoms a r e o p t i o n a l l y n o t d r a w n . A l t h o u g h the d i r e c t i o n of v i e w can be s e l e c t e d by the u s e r , r e a l - t i m e r o t a t i o n i s not p o s s i b l e w i t h t h i s program, because of the r e l a t i v e l y l a r g e amount o f c o r e needed t o s t o r e t h e l a r g e number o f p o i n t s u s e d t o draw most m o l e c u l e s . 4 . BUILDR, a m o d e l - b u i l d i n g p r o g r a m w h i c h g e n e r a t e s s t i c k f i g u r e s o f m o l e c u l e s f r o m a s p e c i f i e d c o n n e c t i v i t y p l u s bond d i s t a n c e s , a n g l e s , and t o r s i o n a n g l e s . T h i s program i s i m p o r t a n t , because i t p r o v i d e s an a l t e r n a t e method f o r s p e c i f y i n g m o l e c u l a r s t r u c t u r e s , b e s i d e s t h e i n p u t o f a known s e t o f a t o m i c c o o r d i n a t e s . 5 . MANIPL ( 7 ) , a p r o g r a m t o a c c o m p l i s h t h e i n t e r a c t i v e f i t o f m o l e c u l a r m o d e l s t o c o n t o u r e d e l e c t r o n - d e n s i t y maps. The u s e r c a n change t h e c o n t o u r - l e v e l o f t h e map, and c o n t r o l t h e p o s i t i o n , o r i e n t a t i o n and c o n f o r m a t i o n o f t h e m o l e c u l e w i t h c o n t r o l - d i a l s . The f u n c t i o n s assumed by t h e s e d i a l s may b e d y n a m i c a l l y r e d e f i n e d i n o r d e r to p r o v i d e f l e x i b i l i t y of o p e r a t i o n . Experiments are underway t o f i t a p r o t e i n m o d e l t o a d e n s i t y map w i t h MANIPL ( s e e b e l o w ) , and i m p r o v e m e n t o f t h i s s o f t w a r e c o n t i n u e s . Applications The c r y s t a l l o g r a p h i c g r o u p s who a r e members o f CRYSNET r e p r e s e n t a w i d e r a n g e o f i n t e r e s t s i n s t r u c t u r a l c h e m i s t r y and b i o chemistry (Table I ) . T h i s b r o a d u s e r community r e q u i r e s a c o m p r e h e n s i v e c r y s t a l l o g r a p h i c s o f t w a r e p a c k a g e t o r u n on t h e CYBER 70/76 a t B N L . C o m p u t a t i o n s r e c e n t l y p e r f o r m e d on t h e CYBER 70/76 have i n c l u d e d , f o r example, phase c a l c u l a t i o n s from m u l t i p l e i s o morphous r e p l a c e m e n t X - r a y d a t a f o r t h e p r o t e i n D - x y l o s e isornerase, f u l l - m a t r i x l e a s t - s q u a r e s refinements of the s t r u c t u r e s o f s e v e r a l c a r b o h y d r a t e s ( 8 , 9 ) and an a n t i - c a n c e r d r u g ( 1 0 ) , and f a s t - F o u r i e r transform c a l c u l a t i o n s of e l e c t r o n - d e n s i t y syntheses f o r various hemoglobins. I n a d d i t i o n , s e v e r a l s t r u c t u r e s have b e e n s o l v e d w i t h c o m p u t a t i o n s p e r f o r m e d e n t i r e l y on t h e PDP 11/40 terminal. T h i s mode o f o p e r a t i o n i s q u i t e q u i c k and c o n v e n i e n t ; f o r example, a complete s t r u c t u r e d e t e r m i n a t i o n f o r g u a n i d i n i u m trans-disulfatotetraaquocobaltate(II), which included data reduct i o n , and l o c a t i o n o f a l l atoms f r o m s e v e r a l s u c c e s s i v e s t r u c t u r e f a c t o r - F o u r i e r c a l c u l a t i o n s , was a c c o m p l i s h e d i n t h i s way w i t h i n t h e s p a c e o f one d a y . The CRYSNET V e c t o r G e n e r a l d i s p l a y s h a v e b e e n u s e d t o p o r t r a y r e s u l t s at v a r i o u s stages i n the process of s t r u c t u r e d e t e r m i n a t i o n and r e f i n e m e n t . The a b i l i t y t o o b t a i n g r a p h i c a l o u t p u t q u i c k l y and e a s i l y , w i t h o p t i o n a l h a r d c o p y , h a s b e e n e s p e c i a l l y u s e f u l i n s u r v e y s o f t r i a l s t r u c t u r e s o l u t i o n s , and i n t h e com p o s i t i o n of f i n a l r e s u l t s f o r p u b l i c a t i o n (Figs 1-3). In addit i o n , t h e d i s p l a y h a s b e e n u s e d t o examine s t r u c t u r e s f r o m t h e c r y s t a l l o g r a p h i c l i t e r a t u r e , by r e t r i e v a l o f i n f o r m a t i o n f r o m t h e
4
COMPUTER
Table I .
AND
CHEMISTRY
R e s e a r c h I n t e r e s t s o f CRYSNET Member G r o u p s
Brookhaven N a t i o n a l Laboratory amino a c i d s and p e p t i d e s carbohydrates clathrate hydrates electron-density studies folate inhibitors metal hydrides nucleosides Johns Hopkins U n i v e r s i t y
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch001
NETWORKING
hemoglobins immunoglobulins
Institute
f o r Cancer
Research
a n t i - c a n c e r agents m o d e l compounds f o r p r o t e i n nucleic acid interactions D-xylose isomerase
M e d i c a l F o u n d a t i o n of
Buffalo
antibiotics prostaglandins steroids
Texas A & M U n i v e r s i t y b i l e pigments c o o r d i n a t i o n compounds porphyrins staphylococcal nuclease
Figure 1.
View of the structure of trimethoprim (9); retraced from Versatec plotter output of program PRJCTN
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch001
KEOTZLE
E T AL.
CRYSNET:
Crystallographic
Computing
Acta Crystallographica
Figure 2.
Drawing of L-phenyManine cation in ^phenylafonine (14); output of program ELLIPS
Figure 3.
hydrochloride
Space-filling model of O-glucaro-3-lactone (8); output of program STIPL
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch001
6
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NETWORKING
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CHEMISTRY
C a m b r i d g e C r y s t a l D a t a F i l e (11) and f r o m t h e P r o t e i n D a t a Bank (12). The d e v e l o p m e n t o f p r o g r a m M A N I P L , t o a c c o m p l i s h i n t e r a c t i v e l y the f i t of m o l e c u l a r models to c o n t o u r e d d e n s i t y maps, has b e e n r e f e r r e d t o a b o v e . To d a t e , segments o f a m o d e l o f s t a p h y l o c o c c a l n u c l e a s e have been f i t t e d w i t h moderate e f f i c i e n c y t o a 1.5 Xngstrom r e s o l u t i o n e l e c t r o n - d e n s i t y map o f t h e p r o t e i n (Fig 4). W i t h an e n t i r e l y d i f f e r e n t s o f t w a r e p a c k a g e , t h e d i s p l a y has b e e n u s e d t o a i d t h e r e f i n e m e n t o f t h e s t r u c t u r e o f l a m p r e y hemoglobin. I n t h i s w o r k , models of p o r t i o n s of the p o l y p e p t i d e c h a i n w h i c h w e r e i d e a l i z e d b y t h e method o f l o c a l change (13), have been v i e w e d superimposed upon c o n t o u r e d s e c t i o n s of e l e c t r o n density (Fig 5). CRYSNET has c u r r e n t l y b e e n i n o p e r a t i o n f o r a p p r o x i m a t e l y two years. D u r i n g t h i s p e r i o d , i t has become c l e a r t h a t a n i n t e l l i g e n t g r a p h i c s t e r m i n a l c a n s a t i s f y t h e c o m p u t a t i o n a l needs o f a t y p i c a l c r y s t a l l o g r a p h i c g r o u p , and t h a t a c c e s s t o g r a p h i c s g r e a t l y enhances r e s e a r c h on c r y s t a l and m o l e c u l a r s t r u c t u r e , f o r s m a l l and l a r g e m o l e c u l e s a l i k e . Acknowledgement The a u t h o r s w i s h t o t h a n k t h e i r c o l l e a g u e s H . M . B e r m a n , H . L . C a r r e l l , J . C. Hanson, E . F . Meyer, J r . , C. N . Morimoto, and R. K . S t o d o l a , a l l o f whom h a v e made i n v a l u a b l e c o n t r i b u t i o n s t o CRYSNET. We a l s o t h a n k M . E . G r e s s f o r s u p p l y i n g one o f t h e Figures.
(Abstract) The CRYSNET system is comprised of a group of five intelligent terminals, which are used primarily for computations in the field of crystallography, and which communicate with the CDC CYBER 70/76 system at Brookhaven. Three out of the five terminals consist of DEC PDP 11/40 minicomputers with 28K words of core memory and interfaced with Vector General three-dimensional displays. An extensive library of interactive molecular-modeling software is being developed for these terminals. Programs are currently available which allow real-time rotation in stereo of stick figures of molecules with up to 740 atoms, display of space-filling models with variable van der Waals radii, generation of stick models from a specified connectivity plus bond distances, angles, and torsion angles, and interactive fit of molecular models to electron-density maps. The terminals provide access to the data files for organic compounds compiled by the Cambridge, England Crystallographic Data Centre, and to the Protein Data Bank, a comprehensive file of crystallographic data for macromolecules, compiled at Brookhaven, which currently includes data for 20 proteins.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch001
KEOTZLE
CRYSNET:
E T AL.
Crystallographic
Computing
Figure 4. Stereomew of thymidine-3'', 5'-diphosphate in single-level 3-D electron-density contours of the ternary complex of thymidine-3',5'diphosphate, Ca , staphylococcal nuclease at 1.5-2.0 A resolution (map courtesy of F. A. Cotton and Ε. E. Hazen). Output of program MANIPL. 2+
Figure 5. Stereomew of a fragment difference-density map for lamprey hemoglobin. An adjustment in the position of the proline ring is clearly indicated (map courtesy of J. C. Hanson).
8
computer networking and chemistry
Literature Cited (1) Bernstein, H. J., Andrews, L. C., Berman, H. M., Bernstein, F. C., Campbell, G. H., C a r r e l l , H. L., Chiang, H. B., Hamilton, W. C., Jones, D. D., Klunk, D., Koetzle, T. F., Meyer, E . F., Morimoto, C. N., Sevian, S. S., Stodola, R. Κ . , Strongson, Μ. Μ., and Willoughby, T. V., Second Annual AEC Scientific Computer Information Exchange Meeting, Proceedings of the Technical Program (1974). 148-158. Report BNL 18803, Brookhaven National Laboratory.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch001
(2) Meyer, E . F., Morimoto, C. N . , V i l l a r r e a l , J., Berman, Η. Μ., C a r r e l l , H. L., Stodola, R. Κ . , Koetzle, T. F., Andrews, L. C., Bernstein, F. C., and Bernstein, H. J., Federation Proceedings (1974). 33, 2402-2405. (3) Andrews, L. C., Pittsburgh Diffraction Conference Programs and Abstracts (1974). (4) Koetzle, T. F., Andrews, L. C., Berman, Η. Μ., Bernstein, H. J., C a r r e l l , H. L., Meyer, E . F., Morimoto, C. N., Stodola, R. Κ . , and V i l l a r r e a l , J., 169th National A.C.S. Meeting Abstracts (1975). Abstract COMP 12. (5) C a r r e l l , H. L. and Stodola, R. Κ . , Pittsburgh Diffraction Conference Programs and Abstracts (1974). (6) Johnson, C. K. (1965). Report ORNL-3794, Oak Ridge National Laboratory. (7) Morimoto, C. N. and Meyer, E . F., i n Proceedings of the Int'l. Summer School on Crystallographic Computing (1975). F. R. Ahmed, ed. (Munksgaard: Copenhagen, in press). (8) Poppleton, B. J., Jeffrey, G. A., and Williams, G. J. B. Acta Cryst. (1975)., i n press. (9) Gress, M. E . and Jeffrey, G. A., Amer. Cryst. Assoc. Meeting Abstracts, Charlottesville, Va (1975). Abstract A2. (10) Williams, G. J. B. and Koetzle, T. F., Amer. Cryst. Assoc. Meeting Abstracts, Charlottesville, Va (1975). Abstract G4. (11) Allen, F. Η . , Kennard, O., Motherwell, W. D. S., Town, W. G . , and Watson, D. G . , J. Chem. Doc. (1973). 13, 119-123. (12) Protein Data Bank, Acta Cryst. (1973).
B29, 1746.
(13) Hermans, J. and McQueen, J. E., Acta Cryst. (1974). A30, 730-739. (14) Al-Karaghouli, A. R. and Koetzle, T. F., Acta Cryst. (1975)., in press.
2
Remote Terminal Computer Graphics DAVID L. BEVERIDGE and ELIAS GUTH
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch002
Chemistry Department, Hunter College of the City University of New York, 695 Park Avenue, Ν. Υ., Ν. Y. 10021
The dominant theme in the development of computer technology in the 1970's is teleprocessing. The interface between user and computer has evolved from punched cards and printed output passed across an input/output desk to job creation and retrieval by i n teractive terminals for individual users and remote batch entry for groups of users. Communication between user and computer is carried out over ordinary telephone lines. Large central proces sors serving local and regional computer needs on a remote basis are now common, and several national networks, both federaly funded (ARPANET) and commercially funded (CDC-CYBERNET) are oper ational. More, including a national center for theoretical chem i s t r y calculations, are contemplated. The s c i e n t i f i c community has greatly benefited from these developments. Improved access to d i g i t a l computer equipment makes possible a vast saving of valuable user time and can significant ly increase individual productivity. In chemistry in particular, scientists carrying out theoretical studies of chemical systems based on quantum mechanics, s t a t i s t i c a l thermodynamics and molec ular dynamics or experiments involving large scale data reduction such as x-ray crystallography and magnetic resonance spectroscopy have been direct beneficiaries of developments in computer tech nology. Quite often, however, the computer output generated by chemical computations is extensive and unwieldy. For interpreta tion of results one often turns to computer graphics, i . e . incre mental plots drawn by a pen under computer control or storage dis plays wherein a plot is generated under computer control on a storage display cathode ray tube. Several examples of computer graphics used in interpreting various calculations on chemical systems are shown in Figs. 1-5. The capabilities for accommodating card input and printed output as well as an interactive link with the central processor for console purposes are provided as standard equipment on mini computer-based intelligent (programmable) remote job entry termi nals. At present however, the f a c i l i t y for routinely dealing with computer graphics on a remote basis i n a convenient and economic 9
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Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch002
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Figure 2. A computer generated stereoscopic view of the chemical neurotransmitter acetylcholine in roughly the geometry preferred in aqueous solution. This drawing was generated using the program ORTEP by C. K. Johnson and was used in studies described by D. L. Beveridge, M. M. Kelly and R. J. Radna, J. Amer. Chem. Soc. (1974) 96,3769.
nuta-ai-CMu
Figure 3. A computer generated conformational energy contour map calculated for acetylcholine in water using theoretical methods. The coordinates r(01-C5-C4-N) and T(C6-01-C5-C4) are dihedral angles referred to Figure 2. The structure in = IKJm Mm Figure 2 correspond to r(01-C5-C4-S) 60° and T(C6-01-C5-C4)
=
180°.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch002
2.
BEVERiDGE A N D G U T H
Remote
Terminal
11
Graphics
manner i s n o t w i d e l y a v a i l a b l e . We d e s c r i b e h e r e i n a method f o r r e m o t e t e r m i n a l c o m p u t e r g r a p h i c s b a s e d o n a s y s t e m d e s i g n e d comp a t i b l e w i t h a l l s t a n d a r d i n t e l l i g e n t j o b e n t r y t e r m i n a l s , and completely independent o f s p e c i a l c o n s i d e r a t i o n from t h e c e n t r a l site. The s y s t e m u s e s s t a n d a r d c o m m e r c i a l l y a v a i l a b l e h a r d w a r e and c a n b e i m p l e m e n t e d w i t h a k n o w l e d g e o f m i n i c o m p u t e r p r o g r a m m i n g commensurate w i t h t h a t r e q u i r e d f o r l a b o r a t o r y t a s k s s u c h a s data a c q u i s i t i o n and instrument c o n t r o l . The remote t e r m i n a l c o m p u t e r g r a p h i c s s y s t e m i s d e s c r i b e d a s i m p l e m e n t e d o n f a c i l i t i e s o f t h e H u n t e r C h e m i s t r y Computer l a b o r a t o r y , where g r a p h i c s c a p a b i l i t i e s h a v e b e e n d e v e l o p e d f o r n e t work enhanced r e s e a r c h and i n s t r u c t i o n a l a c t i v i t i e s based on r e mote a c c e s s t o t h e CDC-6600 c o m p u t e r a t t h e C o u r a n t I n s t i t u t e o f M a t h e m a t i c a l S c i e n c e s (CIMS) a t New Y o r k U n i v e r s i t y a n d t o t h e IBM 370/168 f a c i l i t y o f t h e C i t y U n i v e r s i t y o f New Y o r k (CUNY) Computer C e n t e r . Some b a c k g r o u n d o n g e n e r a l a s p e c t s o f i n t e l l i gent remote j o b e n t r y i s p r o v i d e d i n t h e next s e c t i o n , f o l l o w e d i n S e c t i o n I I b y d e t a i l s o f t h e remote t e r m i n a l c o m p u t e r g r a p h i c s system. I.
Intelligent
Remote J o b E n t r y
Remote t e r m i n a l c o m p u t e r g r a p h i c s i n v o l v e s a d d i t i o n s a n d m o d i f i c a t i o n s t o t h e remote j o b e n t r y t e r m i n a l hardware and s o f t ware. I n t h i s s e c t i o n we d e s c r i b e b r i e f l y t h e h a r d w a r e a n d s o f t w a r e components o f a t y p i c a l r e m o t e j o b e n t r y t e r m i n a l . Addit i o n a l d e t a i l s o f t e l e p r o c e s s i n g f o r c h e m i s t s have been d e s c r i b e d recently elsewhere.1 Hardware. The m i n i m a l e q u i p m e n t c o n f i g u r a t i o n f o r i n t e l l i gent remote j o b e n t r y i s a programmable m i n i c o m p u t e r i n t e r f a c e d to a card r e a d e r , l i n e p r i n t e r , t e l e t y p e w r i t e r ( c o n s o l e ) , and data set f o r telecommunication. A f a c i l i t y o f t h i s t y p e c a n be implemented f o r as l i t t l e as $25,000. A schematic diagram of the H u n t e r C h e m i s t r y Computer L a b o r a t o r y h a r d w a r e i s shown i n F i g . 6 . Note t h a t i n a d d i t i o n t o t h e minimal hardware, t h i s system i n c l u d e s a mass s t o r a g e d i s c , a d d i n g a n a d d i t i o n a l $ 1 0 , 0 0 0 t o t h e c a p i t a l investment. T h i s i s an o p t i o n a l i t e m . The h a r d w a r e r e q u i r e d f o r remote t e r m i n a l computer g r a p h i c s w i l l be d e s c r i b e d i n the f o l l o w i n g s e c t i o n . Software. The c o m p u t e r p r o g r a m r e s i d e n t i n t h e m i n i c o m p u t e r memory d u r i n g t e l e p r o c e s s i n g s e r v e s t h r e e d i s t i n c t f u n c t i o n s : a) t h e management o f i n p u t / o u t p u t a c t i v i t i e s , b ) t h e t r a n s l a t i o n and c o m p r e s s i o n / d e c o m p r e s s i o n o f o u t g o i n g a n d i n c o m i n g c o m m u n i c a t i o n s on the data l i n e , and c) data l i n e p r o t o c o l . These f u n c t i o n s a r e scheduled f o r p a r a l l e l p r o c e s s i n g on a p r i o r i t y i n t e r rupt basis. A schematic diagram of t y p i c a l t e r m i n a l software d e s i g n e d f o r t e l e p r o c e s s i n g i n a n IBM 370/168 e n v i r o n m e n t i s shown i n F i g u r e 7. 2
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AND CHEMISTRY
Figure 4. Computer generated stereoscopic views of the minimum energy structure for (top) a tetrahedrally hydrated K ion and (bottom) tetrahedrally hydrated F~ ion. Produced using the ORTEP program in conjunction with studies described by D. L. Beveridge and G. W. Schnuelle, J . Phys. Chem. (1974) 78, 2064 and un published data.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch002
+
Figure 5. Computer generated perspective views of density difference maps for (top) the ground state and (bottom) the σ „ 2 excited states of Η 2
Figure 6. Schematic of hardware ele ments of the Hunter Chemistry Com puter Laboratory ca. May 1975
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch002
2.
BEVEREDGE
AND GUTH
Remote Terminal
Graphics
13
To f o l l o w t h e f l o w o f e v e n t s i n v o l v e d i n r e m o t e b a t c h p r o c e s s i n g , c o n s i d e r a t y p i c a l b a t c h j o b s u b m i t t e d on c a r d s a t t h e t e r m i n a l and p r o d u c i n g p r i n t e d o u t p u t . Card i n p u t i s p l a c e d i n t h e c a r d r e a d e r a n d t h e r e a d e r i s a c t i v a t e d b y a c o n s o l e command. Cards a r e r e a d under program c o n t r o l o f t h e r e a d e r d r i v e r and copied into the appropriate device b u f f e r . The c a r d image a t t h i s p o i n t i s i n a b i n a r y r e p r e s e n t a t i o n of h o l l e r i t h code. When the c a r d s a r e i n and/or t h e d e v i c e b u f f e r i s f u l l , a f l a g i s s e t . T h i s s c h e d u l e s t h e "READER GET" r o u t i n e w h i c h p i c k s up t h e c a r d image f r o m t h e d e v i c e b u f f e r , c o n v e r t s i t t o EBCDIC, c o m p r e s s e s out b l a n k s and r e p e a t e d c h a r a c t e r s , and p l a c e s t h e t r a n s l a t e d , c o m p r e s s e d code i n t o a c o m m u n i c a t i o n b u f f e r . When t h i s i s comp l e t e , t h e d a t a l i n e t r a n s m i t t e r (DLC XMTR), i s s c h e d u l e d . The t r a n s m i t t e r s e c t i o n o f t h e t e l e p r o c e s s i n g s o f t w a r e p i c k s up t h e c o n t e n t s o f t h e c o m m u n i c a t i o n s b u f f e r , adds t h e a p p r o p r i a t e b i n a r y s y n c h r o n o u s l i n e p r o t o c o l c h a r a c t e r s , a n d o u t p u t s t h e communic a t i o n c h a r a c t e r by c h a r a c t e r t o t h e d a t a l i n e c o n t r o l l e r and thereby onto the telephone l i n e . A communication r e c e i v e d from the c e n t r a l s i t e i s processed u n d e r p r o g r a m c o n t r o l o f t h e d a t a l i n e r e c e i v e r (DLC RCVR) i n t h e teleprocessing software. The r e c e i v e r p i c k s up i n c o m i n g communic a t i o n c h a r a c t e r b y c h a r a c t e r , i n t e r p r e t s a n d s t r i p s away l i n e p r o t o c o l c h a r a c t e r s , assembles the r e c e p t i o n i n a communication b u f f e r , and s c h e d u l e s t h e "PUT r o u t i n e c o r r e s p o n d i n g t o t h e o u t put d e v i c e f o r w h i c h t h e r e c e p t i o n i s i n t e n d e d . The PUT r o u t i n e manages d e c o m p r e s s i o n , t r a n s l a t i o n f r o m EBCDIC t o code a p p r o p r i ate f o r t h e o u t p u t d e v i c e , p l a c e s t h e t r a n s l a t e d , decompressed code i n t h e d e v i c e b u f f e r , a n d s c h e d u l e s t h e a p p r o p r i a t e o u t p u t device d r i v e r . The c o m m u n i c a t i o n s c y c l e i s c o m p l e t e d when a p h y s i c a l r e p r e s e n t a t i o n o f t h e r e c e p t i o n i s d i s p l a y e d on t h e a p p r o p r i a t e output device. For t e l e p r o c e s s i n g i n the environment of another type o f h o s t m a c h i n e s u c h a s t h e CDC 6600 i n v o l v e s an a n a l o g o u s f l o w o f e v e n t s , b u t w i l l d i f f e r i n d e t a i l s s u c h a s l i n e code a n d d a t a line protocol.3 Thus c o m m u n i c a t i o n o f a s i n g l e i n t e l l i g e n t r e mote j o b e n t r y t e r m i n a l w i t h a m u l t i p l i c i t y o f d i f f e r e n t h o s t m a chines i s p o s s i b l e provided the t e r m i n a l software appropriate f o r each d i f f e r e n t environment i s a v a i l a b l e . The f a c i l i t y shown i n F i g . 6 m a i n t a i n s remote b a t c h e n t r y c a p a b i l i t i e s w i t h b o t h t h e CIMS CDC-6600 a n d t h e CUNY-370/168 i n t h i s m a n n e r . 11
II »
Remote T e r m i n a l Computer G r a p h i c s
The o b j e c t i v e o f t h i s p r o j e c t was t o p r o v i d e r e m o t e t e r m i n a l g r a p h i c s c a p a b i l i t i e s a t a l e v e l commensurate w i t h s t a n d a r d r e mote t e r m i n a l i n p u t / o u t p u t a c t i v i t i e s a s c o n v e n i e n t l y a n d economi c a l l y as p o s s i b l e . C o n v e n i e n c e d i c t a t e s t h a t a) t h e s y s t e m s h o u l d be i m p l e m e n t e d w i t h no s p e c i a l e f f o r t r e q u i r e d o n t h e p a r t of t h e system group a t t h e h o s t f a c i l i t y and t h e system s h o u l d o p e r a t e w i t h a minimum o f o p e r a t o r i n t e r v e n t i o n a t t h e t e r m i n a l
14
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end and no operator i n t e r v e n t i o n at the host f a c i l i t y r e q u i r e d . Economics d i c t a t e s that the hardware used should be s h e l f items and not r e q u i r e elaborate i n d i v i d u a l m o d i f i c a t i o n .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch002
Hardware. The device s e l e c t e d f o r our system i s the Tektronix 4010 storage tube d i s p l a y t e r m i n a l , equipped with a hardcopy device f o r production of thermofax-type c o p i e s . This i s i n t e r f a c e d as an a d d i t i o n a l p e r i p h e r a l to the terminal minicomputer. The cost of the graphic u n i t s i s c u r r e n t l y around $5000 f o r the terminal and $3500 f o r the hard copy device, adding an a d d i t i o n a l $9000 to the c a p i t a l o u t l a y i n c l u d i n g i n t e r f a c i n g . Thus v e r s a t i l e remote job and graphics c a p a b i l i t i e s can be obt a i n e d with a t o t a l c a p i t a l o u t l a y of the order of $40,000. A photograph of the remote t e r m i n a l graphics f a c i l i t y i n operation i s shown i n Fig.8. Software. The software i n v o l v e d i n remote t e r m i n a l computer graphics can be conveniently discussed i n terms of a) p l o t genera t i o n and b) p l o t r e t r i e v a l and d i s p l a y . The flow of events i n a remote graphics job i s shown s c h e m a t i c a l l y i n F i g . 9 . This i s t y p i c a l of our production v e r s i o n implemented i n the CUNY IBM 370/168 environment. To f o l l o w the flow of events i n remote t e r m i n a l computer graphics, consider a t y p i c a l batch job i n v o l v i n g the generation of graphic output using c a l l s to Calcomp type incremental p l o t routines.4 The job as submitted from the t e r m i n a l c o n s i s t s of an a p p l i c a t i o n program i n compiler language such as FORTRAN and i n put data. The job i s telecommunicated to the c e n t r a l s i t e as des c r i b e d i n s e c t i o n I I . At the c e n t r a l s i t e the program i s compiled. E x t e r n a l r e f e r e n c e s to Calcomp p l o t r o u t i n e s are s a t i s f i e d using the Calcomp Previewing Routines supported by Tektronix. The Calcomp Previewing Routines reference i n t u r n the T e k t r o n i x Terminal C o n t r o l software r e s i d e n t at c e n t r a l s i t e . Execution of the graphics a p p l i c a t i o n program at the c e n t r a l s i t e causes an input data to be read and generates a standard p r i n t e d output f i l e . C a l l s to the Calcomp subroutines generate c a l l s to the Terminal C o n t r o l Program. The Terminal C o n t r o l Program and attendent d i s p l a y d r i v e r s would i n a l o c a l graphics system manage the c r e a t i o n of a d i s p l a y on the graphics screen, a u t o m a t i c a l l y t a k i n g care of s i z i n g and other housekeeping chores. Here we intervene and r e q u i r e the Terminal C o n t r o l Program to produce an output f i l e (plot f i l e ) c o n s i s t i n g of the arguments to be s u p p l i e d to the graphic d i s p l a y d r i v e r s f o r generating the d i s p l a y . Both the p r i n t e d output and p l o t f i l e are then queued f o r communication back to the t e r m i n a l . Any code conversion scheduled f o r the p l o t f i l e by the c e n t r a l s i t e i s suppressed. A high order b i t i s added to each word of the p l o t f i l e to d i s t i n guish the contents from a c c i d e n t a l coincidence with data l i n k control characters. In the r e t u r n i n g output to the t e r m i n a l , we are r e q u i r e d to
2.
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Remote
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Graphics
READER
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Figure 7. Schematic diagram of tele processing elements, relevant to remote terminal operation. The units READER, CONSOLE, PRINTER, DISPLAY, and DLC are hardware items. Other blocks represent software resident in the ter minal CPU.
CONSOLE ft '
PRINTER
DISPLAY
Figure 8. Hunter Chemistry Computer Laboratory remote batch and graphics facility in operation. Users are from left to right Gary W. Schnuelle, Elias Guth and D. Beveridge.
PLYING
TfWNSHISSION
INPUT
[+|7ηάο»*|+ p f l ^ iEN i
o u
™i
m
RETRIEVAL
Figure 9. Schematic of flow of events commensurate with a remote terminal computer graphics job
OUTPUT
PLOT
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distinguish the plot f i l e from standard printed or console output. The general specification of individual terminal capabilities at the central site may contain provision for any number of peripherals, and customarily IBM 360/20 intelligent terminals and their emulators are support a reader, printer, console and punch. Thus output intended for a certain output device w i l l be preceded by a characteristic data link control character, which is processed upon reception in DLC RCVR. We do not support a card punch l o c a l l y , so plot f i l e s are generated and returned as punch f i l e s from the central site. A plot f i l e received at the terminal from the central site passes through DLC RCVR to the plot/punch "PUT" routine where decompression occurs and the f i l e is placed in the graphics terminal device buffer. No code translation is carried out, since the plot f i l e as generated by the Terminal Control Package is already in a form suitable for further use. The graphics display drivers resident in the terminal minicomputer are then scheduled, and the physical display is generated on the storage tube display screen. The system as described was made operational in the CUNY IBM 370/168 environment in February of 1975. An analogous version has been operational in the CIMS CDC-6600 environment since September 1972. Figs. 1-7 and Fig. 9 of this a r t i c l e were generated on the Hunter Chemistry Computer F a c i l i t y . III.
Acknowledgements
This project was supported by NSF Grant GJ-32969 from the Office of Computing Activities and in part by a Public Health Research Career Development Award 6K04-GM21281 from the National Institute of General Medical Sciences. IV. References 1. Beveridge, D . L . , Guth, E. and Cole, E.H. in Proc. International Conference on Computers in Chemical Research and Education, D. Hadzi, ed. Union of the Chemical Societies of Yugoslavia (1973). 2. The terminal software for this task was assembled from programs written in part by Mr. Mark Ford of the Honeywell Corporation Automotive Branch of Detroit, and in part locally by the authors. 3. Franceschini, E., Feinroth, Y. and Goldstein, M. AEC Research and Development Report #NYO-1480-148 (1970) 4. "Programming Calcomp Electromechanical Plotters", California Computer Products, Inc. August 1974.
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Multiprocessor Molecular Mechanics KENT R. WILSON Department of Chemistry, University of California, San Diego, La Jolla, Calif. 92037 "Chemical phenomena must be treated as if they were problems in mechanics." Lothar Meyer, co-discoverer, with Mendeleev, of the periodic table, 1868. (1) Life is based on marvelous biomolecular machinery, and a central theme in molecular biology has been the role of this machinery's precise molecular architecture. Such molecular architecture, however, is only a static snapshot of a moving, ever changing microscopic world. We are building a macroscopic machine, NEWTON, an internal network of several computer processors, to help the human chemist or molecular biologist investigate and understand the molecular dynamics, the detailed time evolution, as well as the structure of biomolecular systems, for example of enzymes, of membranes, of biomolecular self-assembly. Chemists have long known that such biomolecular behavior is in theory derivable from mechanics, but computational barriers to such a molecular mechanical approach to atomic motions have seemed insurmountable. We have now designed an instrument which will closely interface a human chemist through three-dimensional visual and touch interaction to an extraordinarily powerful networked computer system capable of integrating the classical mechanical coupled differential equations describing the motions of several hundred atoms under their mutual interatomic force fields in such rapid fashion that the chemist can watch the interacting bio- and solvent molecules evolve and reach into a volume of space to actually manipulate simulated atoms, feeling the changing forces upon them, in order to set up and guide the molecular system into the desired chemical pathway. Potential applications span all molecules; their structures, properties and reactions, but particular biomolecular applications include protein conformation, the dynamics of enzyme-substrate interaction, allosteric effects, membrane transport, drug-receptor dynamics and drug design (enzyme blocking agents, antibiotics, specific 17
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c o m p l e x i n g agents), antigen-antibody i n t e r a c t i o n and b i o m o l e c ular self-assembly.
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L
Introduction and B a c k g r o u n d
S i n c e N e w t o n i n the 17th c e n t u r y , i t has b e e n c l e a r that the s t r u c t u r e ( s t a t i c s ) as w e l l as the m o t i o n s ( d y n a m i c s ) of a set of p a r t i c l e s a r e b a s e d o n the f o r c e s b e t w e e n t h e m . Thus, e v e r s i n c e the a t o m i c t h e o r y c r y s t a l l i z e d i n the 19th c e n t u r y , c h e m i s t s h a v e d r e a m e d that the p r o p e r t i e s of m o l e c u l e s w o u l d s o m e d a y be d e r i v a b l e f r o m the f o r c e s between a t o m s . We now k n o w that the p r o b l e m d i v i d e s into two p a r t s : that a q u a n t u m m e c h a n i c a l t r e a t m e n t i s r e q u i r e d f o r the e l e c t r o n s i n o r d e r to d e r i v e the p o t e n t i a l (or f o r c e ) f i e l d w i t h i n w h i c h the n u c l e i m o v e ; but that f o r p u r p o s e s of u n d e r s t a n d i n g m o l e c u l a r s t r u c t u r e o r the m e c h a n i s m of c h e m i c a l r e a c t i o n , o n c e the f o r c e s a r e k n o w n the m o t i o n s of the n u c l e i m a y u s u a l l y be t r e a t e d b y classical mechanics with reasonable accuracy. It i s t h e c l a s s i c a l p a r t of t h e p r o b l e m , the n u c l e a r m o t i o n s , w h i c h w e w i l l discuss here. W h i l e c h e m i s t s h a v e s u c c e s s f u l l y l e a r n e d h o w to u n d e r stand c h e m i c a l reactions by calculating atomic motions i n a f o r c e f i e l d f o r s i m p l e r e a c t i o n s i n v o l v i n g a h a n d f u l of a t o m s , s u c h c a l c u l a t i o n s f o r r e a c t i o n s of o r g a n i c m o l e c u l e s of o r d i n a r y c o m p l e x i t y , l e t a l o n e t h e l a r g e r m o l e c u l e s of b i o c h e m i s t r y , h a v e b e e n too l e n g t h y to h a n d l e w i t h p r e s e n t day c o m p u t e r t e c h nology. A typical organic reaction including solvent effects m i g h t i n v o l v e 100 a t o m s , e a c h s p e c i f i e d i n x , y a n d z , a n d t h u s t h e s o l u t i o n ( i n N e w t o n i a n o r L a g r a n g i a n f o r m ) of 300 c o u p l e d s e c o n d o r d e r d i f f e r e n t i a l e q u a t i o n s , e a c h w i t h u p t o 300 v a r i a b l e s . B i o l o g i c a l p o l y m e r s , e. g . p r o t e i n s a n d n u c l e i c a c i d s , m a y r e q u i r e t h o u s a n d s of a t o m s to r e p r e s e n t t h e i r p r o p e r t i e s a n d reactions. W h i l e the a m o u n t of c o m p u t e r t i m e n e c e s s a r y to i n t e g r a t e s u c h a s e t of c o u p l e d d i f f e r e n t i a l e q u a t i o n s i s i t s e l f a c o n s i d e r a b l e o b s t a c l e , the g r e a t e s t c a l c u l a t i o n a l p r o b l e m w h i c h has p r e v e n t e d a " m e c h a n i c a l m o l e c u l e " a p p r o a c h to o r g a n i c a n d b i o c h e m i c a l r e a c t i o n s is a m o r e subtle one: the e n o r m o u s phase s p a c e of i n i t i a l a t o m i c p o s i t i o n s a n d m o m e n t a w h i c h m u s t b e s e a r c h e d to f i n d the r e g i o n l e a d i n g to c h e m i c a l l y i n t e r e s t i n g results. Most molecular conformations, relative orientations a n d r e l a t i v e a p p r o a c h v e l o c i t i e s do not l e a d to the d e s i r e d chemical reaction. If o n e w e r e t o t a k e a b r u t e f o r c e a p p r o a c h
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and s y s t e m a t i c a l l y s e a r c h t h r o u g h j u s t f i v e d i f f e r e n t i n i t i a l position vectors and five different initial v e l o c i t y vectors for a t y p i c a l 100 a t o m o r g a n i c r e a c t i o n , l o o k i n g f o r t h o s e w h i c h l e a d t o t h e r e a c t i o n i n q u e s t i o n , t h e s e t o f 300 c o u p l e d d i f f e r e n t i a l equations w o u l d h a v e to be i n t e g r a t e d ~ 25*^0 t i m e s J S u c h a b r u t e f o r c e a p p r o a c h is not m e r e l y d i f f i c u l t w i t h p r e s e n t c o m p u t e r s ; it i s i m p o s s i b l e and w i l l r e m a i n so. On the other h a n d , the w e l l t r a i n e d h u m a n c h e m i s t h a s , o r t h i n k s h e h a s , a r e a s o n a b l y g o o d c o n c e p t i o n of w h a t t h e a t o m s m u s t be d o i n g if c h e m i c a l r e a c t i o n i s to o c c u r . If h e c o u l d s o m e h o w w a t c h the atoms i n t h r e e d i m e n s i o n s and r e a c h i n and a d j u s t o r s t e e r the m o l e c u l e s into c h e m i c a l l y r e a s o n a b l e p r o x i m i t y , orientation, conformation and velocity, readjusting the c a l c u l a t i o n i n p r o c e s s , he c o u l d c o l l a p s e an i m p o s s i b l y l a r g e s e a r c h space into a manageable s i z e . We have developed a t e c h n i q u e of m a n - m a c h i n e t o u c h c o m m u n i c a t i o n to do j u s t t h i s , a l l o w i n g us to r e a c h into t h r e e d i m e n s i o n a l s p a c e a n d a d j u s t s i m u l a t e d a t o m s w h i l e f e e l i n g the f o r c e s i n v o l v e d a n d s i m u l t a n e o u s l y w a t c h i n g c o m p u t e r g e n e r a t e d 3D i m a g e s of the i n t e r acting molecules. A c h e m i s t s t e e r i n g the c a l c u l a t i o n and w a t c h i n g the r e s u l t s w i l l q u i c k l y l e a r n , w e b e l i e v e , to c o n v e r g e on the s m a l l e r r e g i o n of c h e m i c a l l y m e a n i n g f u l i n i t i a l c o n d i t i o n s . T h u s a tight m a n - m a c h i n e s y m b i o s i s c a n d e v e l o p , the h u m a n b e i n g p r o v i d i n g h i s s t r o n g p o i n t s of r e c o g n i t i o n of m e a n i n g f u l c h e m i c a l p a t t e r n s , of p u r p o s e , of d i r e c t i o n , of i n t u i t i o n , a n d t h e c o m p u t e r p r o v i d i n g s t o r a g e of p a r a m e t e r s a n d r a p i d a n d e x a c t c a l c u l a t i o n of t h e i r i m p l i c a t i o n s i n t e r m s of m o l e c u l a r d y n a m i c s , i n o t h e r w o r d s , c o m p u t i n g t h e m o t i o n s of t h e a t o m s i n a m o l e c u l a r s y s t e m u n d e r a g i v e n set of i n t e r a t o m i c f o r c e s and s t e e r e d i n i t i a l c o n d i t i o n s . If a h u m a n i s to g u i d e s u c h c h a n g i n g a n d r e a c t i n g m e c h a n i c a l m o l e c u l e s , the c a l c u l a t i o n m u s t be f a s t enough to m a t c h the t i m e s c a l e of h u m a n i n t e r a c t i o n . Even for a molecular system of 100 a t o m s , o n l y a l a r g e , d e d i c a t e d p r o c e s s o r c o u l d k e e p u p with a human partner for such a task. To handle several h u n d r e d a t o m s w o u l d r e q u i r e a c o n v e n t i o n a l p r o c e s s o r of the c o m b i n e d c a l c u l a t i o n a l s p e e d of s e v e r a l d o z e n I B M 3 6 0 / 6 5 ' s . F o r l a r g e r b i o l o g i c a l p o l y m e r s , s i n c e t h e n u m b e r of i n s t r u c t i o n s s c a l e s as N ^ , w h e r e Ν i s the n u m b e r of a t o m s , no p r e s e n t p r o c e s s o r appears adequate. H o w e v e r , as w i l l be d i s c u s s e d b e l o w , the n e e d e d c o m p u t a t i o n a l speeds c a n be obtained w i t h p r e s e n t l y a c h i e v a b l e l o g i c , m e m o r y and b u s s p e e d s b y d i s t r i b u t i n g the c o m p u t a t i o n a l l o a d
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among several fast specialized processors, running in parallel and p i p e l i n e d m o d e s . P r o c e s s o r costs in instructions/dollar s e c o n d h a v e n o w d r o p p e d to the r a n g e w h e r e b i o m o l e c u l a r d y n a m i c s c a n be i n v e s t i g a t e d f o r m o l e c u l a r s y s t e m s w i t h a l a r g e e n o u g h n u m b e r of a t o m s to b e i n t e r e s t i n g a n d i m p o r t a n t . We have designed such a system, have run a much scaled down test, a n d a r e n o w c o n s t r u c t i n g a f i r s t p r o t o t y p e of a f u l l s y s t e m . A. Chemistry. T h e s t u d y of the p r o p e r t i e s of m o l e c u l e s as d e r i v e d f r o m i n t e r a t o m i c f o r c e s has d e v e l o p e d m a i n l y i n two d i v e r s e a r e a s : the m o l e c u l a r d y n a m i c s of v e r y s m a l l m o l e c u l e s i n c h e m i c a l p h y s i c s a n d t h e m o l e c u l a r s t a t i c s , i . e. t h e c o n f i g u r a t i o n , of l a r g e r m o l e c u l e s , p a r t i c u l a r l y t h e s t r u c t u r e of o r g a n i c m o l e c u l e s a n d the c o n f o r m a t i o n of p r o t e i n s . I n c h e m i c a l p h y s i c s , o n e of t h e m a j o r t h e m e s o f t h e p a s t d e c a d e h a s b e e n the u n d e r s t a n d i n g of c h e m i c a l p r o c e s s e s , i n c l u d i n g c h e m i c a l r e a c t i o n s , i n t e r m s of t h e s c a t t e r i n g of a t o m s a n d s m a l l m o l e c u l e s ( 2 , 3). O n e of the m a i n r e a s o n s f o r t h e b l o s s o m i n g of t h i s a p p r o a c h to c h e m i s t r y h a s b e e n t h e d e v e l o p m e n t of e x p e r i m e n t a l t e c h n i q u e s , o f t e n i n v o l v i n g m o l e c u l a r b e a m s a n d m o r e r e c e n t l y l a s e r s , c a p a b l e of s t u d y i n g i n d i v i d u a l m o l e c u l a r events w i t h s u f f i c i e n t d e t a i l and p r e c i s i o n that c o n c l u s i v e t e s t s of t h e o r e t i c a l s c a t t e r i n g p r e d i c t i o n s a r e possible. It i s c l e a r t h a t t h e f u n d a m e n t a l t h e o r e t i c a l b a s i s o f i n t e r a t o m i c and i n t e r m o l e c u l a r f o r c e s m u s t be a n a l y z e d f r o m a q u a n t u m m e c h a n i c a l v i e w p o i n t (4), a s t h e e l e c t r o n s h a v e s m a l l enough m a s s and m o m e n t u m that t h e i r w a v e n a t u r e cannot be i g n o r e d on the m o l e c u l a r s c a l e . It h a s , h o w e v e r , a l s o b e c o m e c l e a r i n the p a s t d e c a d e that i f one h a s i n h a n d a n i n t e r a t o m i c f o r c e f u n c t i o n , u s u a l l y e x p r e s s e d i n t e r m s of a m u l t i d i m e n s i o n a l p o t e n t i a l e n e r g y s u r f a c e u p o n w h i c h the m o r e m a s s i v e n u c l e i m o v e , a surface w h i c h has either been calculated quantum m e c h a n i c a l l y o r a r r i v e d at b y a n a l y s i s of e x p e r i m e n t a l m e a s u r e m e n t s , t h e n the c a l c u l a t i o n of s t a t i c m o l e c u l a r s t r u c t u r e o r dynamic m o l e c u l a r evolution and c h e m i c a l reaction can usually b e h a n d l e d w i t h r e a s o n a b l e a c c u r a c y b y the a p p r o x i m a t i o n of classical mechanics. T h i s type of m o l e c u l a r d y n a m i c s a p p r o a c h (5) h a s b e e n l i m i t e d t o s m a l l m o l e c u l e s o f o n l y a f e w a t o m s b e c a u s e of c o m p u t a t i o n a l d i f f i c u l t y . While in chemical physics, m o l e c u l a r dynamics has been d e r i v e d f r o m i n t e r a t o m i c p o t e n t i a l (or f o r c e ) f u n c t i o n s , i n organic and p o l y m e r c h e m i s t r y m o l e c u l a r structure has been
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studied on this b a s i s . O n the organic m o l e c u l a r scale, researchers have included H i l l , Westheimer, Dashevsky, Kitaigorodsky, Allinger, Lifson, Hendrickson, Wibert, Boyd, S c h l e y e r , M i s l o w a n d m a n y o t h e r s (6, 7, 8 ) . This technique h a s a l s o b e e n e x t e n d e d p a r t of the w a y i n t o d y n a m i c s , to a n a l y s i s of p a t h w a y s b e t w e e n s t r u c t u r e s b y c a l c u l a t i o n of e n e r g i e s at v a r i o u s i n t e r m e d i a t e c o n f i g u r a t i o n s i n o r d e r to s t u d y , f o r e x a m p l e , i s o m e r i z a t i o n (9, 1 0 ) . In p o l y m e r c h e m i s t r y , p a r t i c u l a r l y p r o t e i n c o n f o r m a t i o n , a l a r g e body of r e s e a r c h h a s b e e n c a r r i e d o u t b y m a n y g r o u p s i n c l u d i n g t h o s e of R a m a c h a n d r a n , S c h e r a g a , L i f s o n , F l o r y , L i q u o r i , and H o p f i n g e r (11, 12). P r o t e i n c o n f o r m a t i o n i s u s u a l l y t r e a t e d as a n e n e r g y m i n i m i zation p r o b l e m with constraints. M o s t bonded interactions between atoms are f i x e d as c o n s t r a i n t s i n bond length and bond a n g l e , and a l l o w a b l e d e g r e e s of f r e e d o m a r e u s u a l l y r o t a t i o n s about c e r t a i n bonds. Nonbonded interactions are specified in t e r m s of a s s u m e d p o t e n t i a l f u n c t i o n s . A s e a r c h is then c a r r i e d out to t r y to f i n d the g l o b a l p o t e n t i a l e n e r g y m i n i m u m , s u b j e c t to the c o n s t r a i n t s . T h i s m i n i m u m i s t h e n a s s u m e d to c o r r e s p o n d to the m o s t p r o b a b l e c o n f o r m a t i o n f o r the p r o t e i n , although m o r e r e c e n t l y the l o c a l l y a v a i l a b l e phase s p a c e has b e e n e s t i m a t e d as w e l l i n o r d e r to b e t t e r t a k e n into a c c o u n t the e n t r o p y c o n t r i b u t i o n to the f r e e e n e r g y w h i c h s h o u l d m o r e c o r r e c t l y be m i n i m i z e d . We plan a somewhat different approach, related in c o o r d i n a t e s t o w o r k b y L e v i t t (13) a n d b y H e r m a n s a n d M c Q u e e n (14), w h i c h i s e a s i e r t o g e n e r a l i z e t o n o n p o l y m e r s a n d m u c h s i m p l e r to p r o g r a m a n d to s p l i t i n t o t a s k s f o r m u l t i p l e p r o cessors. Bonded and nonbonded i n t e r a t o m i c interactions w i l l a l l be t r e a t e d b y the s a m e f o r m a l i s m , not as c o n s t r a i n t s , but e x p l i c i t l y as f o r c e f u n c t i o n s , w h i c h m a y h o w e v e r be f u n c t i o n s of the v e c t o r p o s i t i o n s of s e v e r a l n e i g h b o r i n g a t o m s a n d n e e d n o t be r e s t r i c t e d to t w o b o d y i n t e r a c t i o n s . A s f r e q u e n t l y as w e c a n , i n s t e a d of e x p r e s s i n g f o r c e s e x p l i c i t l y i n t e r m s of a n g l e s , t h e y w i l l be e x p r e s s e d i n t e r m s of v e c t o r o p e r a t i o n s s u c h as d i s t a n c e and the i n n e r p r o d u c t , w h i c h c a n be c a l c u l a t e d m u c h f a s t e r than the c o r r e s p o n d i n g t r i g o n o m e t r i c f u n c t i o n s . W e w i l l u s e f o r c e f u n c t i o n s i n s t e a d of the e q u i v a l e n t p o t e n t i a l f u n c t i o n s and w i l l not m i n i m i z e f o r c e o r p o t e n t i a l e n e r g y , but r a t h e r a s s i g n the c o r r e c t m a s s e s to the a t o m s a n d l e t e a c h one m o v e u n d e r the s u m of the f o r c e s u p o n i t . It i s i n t e r e s t i n g t o f u r t h e r c o m p a r e e n e r g y m i n i m i z a t i o n for molecular statics with molecular dynamics. For large
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m o l e c u l e s , e a c h t y p e o f c a l c u l a t i o n m u s t s p e n d m u c h of i t s t i m e i n e v a l u a t i n g the p o t e n t i a l o r f o r c e . T h u s the a d d i t i o n a l c o m p u t e r t i m e i s n o t a s l a r g e a s o n e m i g h t t h i n k t o go f r o m a c a l c u l a t i o n w h i c h s e a r c h e s f o r a static s t r u c t u r e i n w h i c h the a t o m s a r e m o v e d i n o r d e r to f i n d a n e n e r g y m i n i m u m to a calculation involving a molecular dynamic approach in which a c t u a l a t o m i c t r a j e c t o r i e s a r e c a l c u l a t e d f r o m the a c c e l e r a t i o n s of a t o m s of d e f i n e d m a s s u n d e r t h e f o r c e s i m p a r t e d b y o t h e r atoms. Given a machine which will calculate molecular dynamics, one c a n a l s o c a l c u l a t e s t r u c t u r e , b y r e m o v i n g e n e r g y u n t i l a t o m i c m o t i o n s t o p s , t h r o u g h the a d d i t i o n of a v i s c o u s f o r c e p r o p o r t i o n a l to the n e g a t i v e of e a c h a t o m s v e l o c i t y v e c t o r . T h i s r e l a x a t i o n t e c h n i q u e i s e q u i v a l e n t c o n c e p t u a l l y to d u n k i n g an i n i t i a l l y v i b r a t i n g m o l e c u l e into a f l u i d . A s an energy m i n i m u m is a p p r o a c h e d a n d a t o m i c m o t i o n s l o w s d o w n , the v i s c o s i t y c a n be d e c r e a s e d to s p e e d a p p r o a c h to e q u i l i b r i u m . There are two c e n t r a l difficulties w e l l known i n energy m i n i m i z a t i o n p r o t e i n c o n f o r m a t i o n studies w h i c h m u s t be dealt with also i n using our approach. The f i r s t is being trapped i n a l o c a l (but n o t g l o b a l ) e n e r g y m i n i m u m . This is probably less likely than with s i m p l e energy m i n i m i z a t i o n schemes, as o u r a t o m s w i l l h a v e m o m e n t u m a n d a r e l i k e l y to b o u n c e o n t h r o u g h m a n y l o c a l m i n i m a on t h e i r w a y to a d e e p e r m i n i m u m . W e s u s p e c t i n a d d i t i o n that the h u m a n o p e r a t o r w a t c h i n g the 3 D v i s u a l d i s p l a y (8, 9) w i l l b e a b l e t o r e c o g n i z e l o c a l t r a p p i n g a s c l u s t e r s of a t o m s " c a t c h " o n e a c h o t h e r , a n d r e a c h i n w i t h the t o u c h i n t e r f a c e to n u d g e t h e m a p a r t . A further serious d i f f i c u l t y i s o u r l a c k of p r e c i s e k n o w l e d g e of the a p p r o p r i a t e f o r c e f u n c t i o n s t o u s e (7, 1 5 , 1 6 ) . W e expect a long and d i f f i c u l t c o u r s e of r e s e a r c h b e f o r e t h i s i m p r e c i s i o n i s r e s o l v e d for organic and b i o c h e m i c a l molecules i n general and we d i s c u s s s o m e d i r e c t i o n s of a p p r o a c h i n a l a t e r s e c t i o n . Our m a c h i n e s h o u l d b e one m e a n s of s p e e d i n g t h i s r e s e a r c h . C l a s s i c a l c a l c u l a t i o n s of the d y n a m i c s of l a r g e n u m b e r s of p a r t i c l e s h a v e a l s o b e e n m a d e i n at l e a s t t h r e e o t h e r a r e a s : a s t r o p h y s i c s ( 1 7 ) , p l a s m a p h y s i c s (18) a n d t h e s t a t i s t i c a l m e c h a n i c s of a s s e m b l i e s of a t o m s a n d m o l e c u l e s . The stellar and p l a s m a m e c h a n i c s f i e l d s s h a r e m a n y s i m i l a r i t i e s as w e l l as m u t u a l a s p e c t s w h i c h d i f f e r e n t i a t e t h e m f r o m the m o l e c u l a r m e c h a n i c s w e a r e d i s c u s s i n g , s o m e of w h i c h a r e s u m m a r i z e d i n the f o l l o w i n g table. 1
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
AND
3.
WILSON
Molecular
23
Feature
P l a s m a & Stellar
Molecular
i)
Often m a c r o s c a l e , gross effects, many particles needed, less detail.
Microscale, local effects u s u a l l y dominate, .". l e s s p a r t i c l e s n e e d e d , more precision.
S c a l e of Effects
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
Mechanics
-1
ii)
S c a l e of Interaction
Long range; potentials.
iii)
Interaction Complexity
2-body usually sufficient; somet i m e s m a g n e t i c as w e l l as e l e c t r o s t a t i c for plasmas.
2-body sufficient for m a n y i n t e r a c t i o n s , but multibody essential in many cases.
iv)
Particle Complexity
A n y t e s t p a r t i c l e at given location would feel same force with e x c e p t i o n of m a g n i tude and s i g n (plasma).
Different test particles (elements) would feel quite different force fields.
v)
ShortRange Collisions
For many purposes c o l l i s i o n s c a n be ignored.
Collisions
vi)
Calculational Techniques
Fourier Transform methods between configuration and field useful.
Fourier Transform m e t h o d s at l e a s t initially appear less useful.
r
Usually short range; r' potentials or shielded Coulomb.
essential.
M o r e c l o s e l y r e l a t e d to o u r a p p r o a c h a r e s t a t i s t i c a l m e c h a n i c a l c a l c u l a t i o n s o n l a r g e a s s e m b l i e s of a t o m s o r m o l e c u l e s u s i n g c l a s s i c a l m e c h a n i c s to f o l l o w the t r a j e c t o r i e s . W h i l e m o s t w o r k has u s e d v e r y s i m p l i f i e d p o t e n t i a l s , s u c h as h a r d spheres, m o r e recently r e s e a r c h has begun with potentials w h i c h a r e q u i t e i n the s p i r i t of t h o s e n e e d e d to c o n s i d e r m o r e c o m p l e x m o l e c u l a r p r o c e s s e s , f o r e x a m p l e the c e n t r a l f o r c e m o d e l f o r w a t e r b y L e m b e r g a n d S t i l l i n g e r (19) w h i c h a l l o w s f o r the p o s s i b i l i t y of d i s s o c i a t i o n . B. Computer. Our design for a h i e r a r c h i c a l , d i s t r i b uted, s e m i - p a r a i l el, pipelined computer network follows n a t u r a l l y a l o n g t h e h i s t o r i c a l p a t h of c o m p u t e r e v o l u t i o n . A s
24
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L o r i n (20) p o i n t s
NETWORKING
AND
CHEMISTRY
out,
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
" I t i s t h i s p r o c e s s of p e r c e i v i n g the e x i s t e n c e of s m a l l e r a n d s m a l l e r f u n c t i o n s a n d t h e n i m p l e m e n t i n g t h e m i n f u n c t i o n a l l y s p e c i a l i z e d u n i t s that i s the p r o c e s s of ' m a t u r a t i o n ' i n c o m p u t e r d e v e l o p ment. T h e r e d u c t i o n of a v i e w of a s y s t e m f r o m a n u n d i f f e r e n t i a t e d m a s s i n t o a c o l l e c t i o n of d i s c r e t e f u n c t i o n s i s the p r o c e s s b y w h i c h the c o m p u t e r s have matured. M u c h of t h i s h a s b e e n m a d e p o s s i b l e b y t e c h n o l o g y b u t m u c h of i t i s i n d e p e n d e n t . It i s i n t e r e s t i n g to note t h e r e i s a l w a y s a t h r e e - s t a g e c y c l e i n d e s i g n a d v a n c e : (1) R e c o g n i z e t h e f u n c t i o n . (2) I d e n t i f y t h e s t r u c t u r e t h a t c o u l d p e r f o r m i t . (3) B u i l d m o r e r e s o u r c e s i n t o t h i s s t r u c t u r e , i . e . elaborate it, until it evolves into a h i g h l y i n t e l l i gent a s y n c h r o n o u s s u b s y s t e m c a p a b l e of r e l i e v i n g the ' m a i n p a t h ' of c o n s i d e r a b l e b u r d e n . " T h i s is the d i r e c t i o n we have f o l l o w e d . A s s e v e r a l a u t h o r s h a v e i n d i c a t e d (21), h i e r a r c h i c a l s t r u c t u r e s , h i g h e r l e v e l s b e i n g c o m p o s e d of s i m i l a r s u b u n i t s t h e m s e l v e s c o m p o s e d of s m a l l e r s u b u n i t s , e t c . , a r e a n a t u r a l r e s u l t of the e v o l u t i o n of c o m p u t e r h a r d w a r e a n d s o f t w a r e , as w e l l as of the e v o l u t i o n of l i f e a n d of s o c i a l a n d e c o n o m i c organizations (including universities). M a n himself is a d i s t r i b u t e d p a r a l l e l p r o c e s s o r of i n f o r m a t i o n (22), " a c o l l e c t i o n of a s y n c h r o n o u s s u b p r o c e s s o r s w i t h h i g h l y d i s t r i b u t e d i n t e l l i gence t h r o u g h o u t the s u b s y s t e m " (20). M a n y p a r a l l e l p r o c e s s o r s have been proposed and a cons i d e r a b l e v a r i e t y b u i l t (23) f o r u s e i n p a t t e r n r e c o g n i t i o n , associative processing, optical processing, m a x i m u m likelih o o d c a l c u l a t i o n , s i g n a l p r o c e s s i n g a n d the s o l u t i o n of c o u p l e d d i f f e r e n t i a l e q u a t i o n s (24). O u r m a c h i n e , w h i c h w i l l be e m p l o y e d f o r the s o l u t i o n of the c o u p l e d d i f f e r e n t i a l e q u a t i o n s c o r r e s p o n d i n g to N e w t o n ' s S e c o n d L a w (and t h u s the n a m e N E W T O N ) f o r a s e t of i n t e r a c t i n g a t o m s , h a s s e v e r a l a n t e cedents. T h e y i n c l u d e the L o c k h e e d D i f f e r e n t i a l E q u a t i o n P r o c e s s o r ( 2 4 ) , I l l i a c I V a n d i t s S o l o m o n p r e d e c e s s o r s ( 2 3 , 24), a l t h o u g h I l l i a c I V s e e m s b e t t e r s u i t e d due to i t s l o c a l d a t a p a t h s t r u c t u r e to the s o l u t i o n of d i f f e r e n t i a l e q u a t i o n s i n v o l v i n g f i x e d n e i g h b o r s (or i n t e r c o m m u n i c a t i n g c e l l s ) r a t h e r t h a n to o u r p r o b l e m i n w h i c h the s p e c i f i c n e i g h b o r s w i t h w h i c h each a t o m m u s t c o m m u n i c a t e can be continually shifting. A c l o s e r
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
3.
WILSON
Molecular
25
Mechanics
r e s e m b l a n c e i s to the P a r a l l e l E l e m e n t P r o c e s s i n g E n s e m b l e ( P E P E ) b e i n g c o n s t r u c t e d f o r the A r m y A d v a n c e d B a l l i s t i c M i s s i l e Defense Agency in a project w h i c h has involved B e l l L a b s , Systems Development C o r p . , H o n e y w e l l and B u r r o u g h s (23). It i s a h i g h l y p a r a l l e l m a c h i n e c o n s i s t i n g o f a g e n e r a l p u r p o s e h o s t c o m p u t e r ( C D C 7600) a n d m a n y P r o c e s s i n g E l e m e n t s , e a c h of w h i c h c a n t r a c k a n i n c o m i n g m i s s i l e . It r e s e m b l e s N E W T O N i n that it r e q u i r e s v e r y fast floating point s p e e d s (~ 1 m i l l i o n i n s t r u c t i o n s p e r s e c o n d , M I P S ) i n e a c h P r o c e s s i n g E l e m e n t and that an i m p o r t a n t a s p e c t is s p a t i a l d i s c r i m i n a t i o n , the d i s t i n g u i s h i n g of w h i c h o b j e c t s a r e n e a r b y . It d i f f e r s i n t h a t t h e o b j e c t s a r e p r e s u m e d n o n - i n t e r a c t i n g . T h u s , the s t r u c t u r e i s s i n g l e i n s t r u c t i o n s t r e a m , m u l t i p l e data s t r e a m (true p a r a l l e l ) w i t h o u t n e e d f o r d i r e c t e l e m e n t to element c o m m u n i c a t i o n , w h i l e our atoms are interacting and e a c h a t o m i h a s i t s o w n s p e c i f i c f o r c e f u n c t i o n , ^F- ( r . . . J*]\j)W e m u s t t h e r e f o r e u s e a m u l t i p l e (but s i m i l a r ) i n s t r u c t i o n s t r e a m , m u l t i p l e data s t r e a m (semiparallel) distributed s t r u c t u r e and p r o v i d e f o r i n t e r c o m m u n i c a t i o n a m o n g the p r o cessing elements. In a d d i t i o n , P E P E u s e s a s s o c i a t i v e m e m o r y t e c h n i q u e s to d i s t i n g u i s h w h i c h o t h e r o b j e c t s a r e the n e a r n e i g h b o r s of e a c h o b j e c t , w h i l e , f o r r e a s o n s o f c o s t / p e r f o r m a n c e , w e p l a n to u s e a n a c t i v e d i s c r i m i n a t o r . O t h e r p a r a l l e l o r d i s t r i b u t e d s y s t e m s of i n t e r e s t a r e t h e Carnegie-Mellon Multi-Mini Processor (C.mmp), Korn s proposal for a multiple m i n i c o m p u t e r differential equation s o l v e r , and N e i l s e n ' s i m p l e m e n t a t i o n of s u c h a s y s t e m . C.mmp i s a s y m m e t r i c s e t o f u p t o 16 m i n i c o m p u t e r s ( D E C P D P - 1 1 ' s ) w i t h a n e q u i v a l e n t n u m b e r of m e m o r y u n i t s , a l l i n t e r c o n n e c t e d t h r o u g h a c r o s s - b a r s w i t c h so that any p r o c e s s o r c a n a c c e s s a n y m e m o r y a n d u p t o 16 s e p a r a t e a n d s i m u l t a n e o u s p r o c e s s o r m e m o r y connections are possible. It i s d e s i g n e d t o b e m u c h m o r e of a g e n e r a l p u r p o s e c o m p u t e r t h a n N E W T O N , a n d thus requires h a r d w a r e and software flexibility beyond our needs. O n the o t h e r h a n d , it i s not d e s i g n e d f o r l a r g e f l o a t i n g p o i n t number crunching, w h i c h is our need. K o r n (25) i n 1 9 7 2 p r o p o s e d a s y s t e m of s e v e r a l P D P 1 1 / 4 5 ' s w i t h f l o a t i n g p o i n t p r o c e s s o r s a n d s h a r e d m e m o r i e s f o r the o n - l i n e s o l u t i o n of coupled differential equations d e s c r i b i n g d y n a m i c a l s y s t e m s . It w a s d e s i g n e d a s a r e p l a c e m e n t f o r h y b r i d d i g i t a l - a n a l o g differential a n a l y z e r s , and would have been a worthy p r e c u r s o r t o the c o m p u t i n g e n g i n e p a r t of N E W T O N i f h e h a d b e e n a b l e to b u i l d i t . W h i l e w e c a n r u n m u c h f a s t e r , as w i l l be s e e n , 1
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b e c a u s e of o u r s p e c i a l i z e d b a r r e l - r o l l d i s c r i m i n a t o r a n d f l o a t i n g p o i n t a r r a y p r o c e s s o r s , K o r n f o r e s a w m a n y of t h e a s p e c t s o f p a r a l l e l c o m p u t a t i o n a p p l i e d to c o u p l e d d i f f e r e n t i a l e q u a t i o n s o l v i n g w h i c h w e p l a n to i m p l e m e n t . A s y s t e m r e l a t e d te K o r n s w i l l be i m p l e m e n t e d at L o m a L i n d a U n i v e r s i t y b y N e i l s en i n the n e a r f u t u r e and a p p l i e d to c o u p l e d d i f f e r e n t i a l e q u a t i o n s y s t e m s (26). 1
C. Visual Interface. A l r e a d y i n the 1950's, i n r e a l time m i l i t a r y c o m m a n d and control systems, C R T display c o n s o l e s a n d a l i g h t g u n w e r e d e v e l o p e d (27). In the I960 s m o r e sophisticated v i s u a l d i s p l a y and i n t e r a c t i o n s y s t e m s w e r e d e s i g n e d , f o r e x a m p l e S u t h e r l a n d ' s " S k e t c h p a d " (28). Several groups have developed software and hardware for three d i m e n sional computer v i s u a l d i s p l a y , i n c l u d i n g d i g i t a l and h y b r i d graphics systems, a head mounted stereoscopic display which m o v e s w i t h t h e v i e w e r (29) a n d s e v e r a l v i s i b l e s u r f a c e a l g o r i t h m s a n d h a r d w a r e p r o c e s s o r s (30, 31).
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1
T h e s e 3D v i s u a l output s y s t e m s s t i m u l a t e d the d e v e l o p m e n t of i n p u t s y s t e m s f o r c o m m u n i c a t i n g 3D p o s i t i o n to c o m p u t e r s , i n c l u d i n g the L i n c o l n W a n d s y s t e m u s i n g a n u l t r a s o n i c s i g n a l a n d 4 p o i n t m i c r o p h o n e s (32), the 3D s o n i c p e n a n d s t r i p m i c r o phone s y s t e m u s e d b y W i p k e at P r i n c e t o n to i n t e r a c t w i t h m o l e c u l a r i m a g e r y (33), s y s t e m s e m p l o y i n g r o t a t i o n a l a n d translational stages with r a d i a l or linear potentiometers (34), and a " V i c k e r s W a n d " s y s t e m u s i n g t h r e e r e t r a c t a b l e c o r d s (35) , s i m i l a r i n c o n c e p t t o t h e f o u r c o r d s y s t e m w e u s e f o r t h e " T o u c h y F e e l y " , our f i r s t touch interface. B u r t o n and Sutherland developed a s y s t e m ( " T w i n k l e Box") w h i c h a l l o w s the r e a l - t i m e m e a s u r e m e n t of m u l t i p l e 3 D p o s i t i o n s (36) . S m a l l l i g h t s a t t a c h e d t o a n o b j e c t ( w h i c h c a n f o r e x a m p l e be a d a n c i n g m a n ) f l a s h i n s e q u e n c e , and m u l t i p l e one d i m e n s i o n a l s c a n n e r s p i c k u p the p o s i t i o n s . We plan a related s y s t e m to p i c k u p b o t h p o s i t i o n a n d o r i e n t a t i o n w i t h o u r n e x t t o u c h i n t e r f a c e , " T o u c h y T w i s t y " , d e s i g n e d to a l l o w the u s e r to a s s e m b l e objects ( m o l e c u l e s ) w h i l e f e e l i n g t h e i r a n g u l a r and positional interactions. D. T o u c h I n t e r f a c e . In 1965 S u t h e r l a n d s u g g e s t e d t h a t a c o m p u t e r d i s p l a y s y s t e m should s e r v e as m a n y senses as p o s s i b l e if i t i s to p r o v i d e a " w i n d o w into the m a t h e m a t i c a l wonderland constructed i n computer m e m o r y " , and p r e d i c t e d t h e u s e f u l n e s s of a u g m e n t i n g s i g h t a n d s o u n d w i t h f o r c e d i s p l a y
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(37). H e s u g g e s t e d i m p l e m e n t a t i o n of c o m p u t e r c o n t r o l l e d kinesthetic presentation through joysticks and mechanical a r m s . T w o g r o u p s , B a t t e r a n d B r o o k s at the U n i v e r s i t y of N o r t h C a r o l i n a a n d N o l l at B e l l L a b s , f i r s t i m p l e m e n t e d t o u c h c o m munication with computers. B a t t e r a n d B r o o k s (38) b u i l t a n d p r o g r a m m e d G R O P E - 1 , an on-line interactive computer display s y s t e m i n v o l v i n g two d i m e n s i o n a l input to the c o m p u t e r and b o t h v i s u a l and f o r c e f e e d b a c k to the u s e r . G R O P E - 1 was a p i l o t s y s t e m h a v i n g o n l y t w o d e g r e e s of f r e e d o m , χ a n d y , a n d w a s d e s i g n e d to t e s t the c o n c e p t of k i n e s t h e t i c o u t p u t b y e x e r t i n g p r o g r a m m a b l e f o r c e s on the f i n g e r s as one m o v e d a k n o b i n a p l a n e , thus e n a b l i n g the u s e r to e x a m i n e e l e m e n t a r y force fields by e x p e r i e n c i n g p o s i t i o n dependent f o r c e s p r o p o r t i o n a l to f o r c e s that w o u l d be e x e r t e d on a p a r t i c l e i n a f i e l d . T h e u s e r c o u l d b o t h c h a n g e the p o s i t i o n of a p a r t i c l e i n c o n c e p t u a l s p a c e a n d f e e l the f o r c e n e e d e d to m o v e the p a r t i c l e i n the f i e l d . In a d d i t i o n to G R O P E - 1 , B a t t e r a n d B r o o k s d i s c u s s the i m p l e m e n t a t i o n of k i n e s t h e t i c d i s p l a y t h r o u g h a m e c h a n i c a l a r m , w h i c h they h a v e c o n t i n u e d to d e v e l o p . N o l l (34) d u r i n g t h e s a m e p e r i o d b u i l t a n d t e s t e d a 3 D touch c o m m u n i c a t i o n s y s t e m , r e p o r t i n g on it i n his thesis i n 1971. Orthogonally m o v i n g stages are used, culminating i n a knob g r a s p e d b y the h a n d . P o s i t i o n is p i c k e d off b y t h r e e l i n e a r potentiometers and force exerted by three torque m o t o r s linking the s t a g e s . S o f t w a r e w a s w r i t t e n i n o r d e r to s i m u l a t e o b j e c t s and s u r f a c e s ( s p h e r e , c u b e , s p h e r e w i t h i n a cube). N o l l d i s c u s s e s m a n y a s p e c t s of t o u c h c o m m u n i c a t i o n , f r o m p r a c t i c a l to p h i l o s o p h i c a l , a n d s u g g e s t s a v a r i e t y of a p p l i c a t i o n s i n c l u d i n g s t u d i e s i n p e r c e p t u a l p s y c h o l o g y of c l a s h b e t w e e n v i s i o n and touch, investigations b y m o t o r - s k i l l p s y c h o l o g i s t s , l a t c h i n g onto o b j e c t s b y t o u c h as a m e a n s of i m p r o v i n g v i s u a l d i s p l a y s , t e s t i n g of m a n u a l d e x t e r i t y , e d u c a t i o n , d e s i g n of o b j e c t s s u c h as t e l e p h o n e s w i t h p r o p e r " f e e l " to the h a n d s , a i d to the b l i n d , a n d m a n - t o - m a n t o u c h c o m m u n i c a t i o n (for e x a m p l e , a cloth purchaser in New Y o r k remotely feeling a manufacturer's cloth in Tokyo). II.
System
Design
O u r t a s k i s to f i n d the set of f o r c e f u n c t i o n s · · · -£n^' i = 1 to Ν w h i c h d e s c r i b e the i n t e r a t o m i c f o r c e s as f u n c t i o n s o f a t o m i c p o s i t i o n s jc\ o f Ν a t o m s i n a b i o m o l e c u l a r s y s t e m a n d then integrate Newton' s Second L a w ,
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-1
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1 to Ν
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t o g i v e t h e t r a j e c t o r i e s of t h e a t o m s w i t h a d d i t i o n a l i n i t i a l s t e e r i n g f o r c e s a d d e d b y the u s e r t h r o u g h the t o u c h i n t e r f a c e . C a r r y i n g out the t a s k c a n b e d i v i d e d i n t o t w o p a r t s : f i n d i n g the f o r c e functions and i n t e g r a t i n g the equations, c h e m i s t r y and computation. A. Chemistry. T h e m o s t d i f f i c u l t q u e s t i o n , one w i t h m a n y c l u e s a n d a d e a r t h of a c c u r a t e a n s w e r s , i s , " w h a t a r e reasonable interatomic force functions which describe inter atomic interactions?" T h e i r nature is w e l l described by L i f s o n a n d W a r s h e l l (39). " I t i s c o m m o n l y a s s u m e d that the u s e of e m p i r i c a l and s e m i - e m p i r i c a l energy functions i n c o n f o r m a t i o n a l a n a l y s i s is ' c l a s s i c a l , i n c o n t r a d i s t i n c t i o n to q u a n t u m mechanical calculations. W e suggest that the b a s i c d i f f e r e n c e is that the l a t t e r i s a d e d u c t i v e m e t h o d , s e e k i n g to p r e d i c t o b s e r v a b l e p h e n o m e n a f r o m a f u n d a m e n t a l l a w (the S c h r o d i n g e r e q u a t i o n ) , w h i l e t h e f o r m e r is an inductive method, seeking a c o m m o n analytical r e p r e s e n t a t i o n to a l a r g e s e t of o b s e r v a b l e p h e n o m e n a . In fact, t h e r e is nothing ' c l a s s i c a l ' i n these functions, as they a r e not d e d u c e d f r o m c l a s s i c a l p h y s i c s . They m a y j u s t as w e l l be c o n s i d e r e d as a n e m p i r i c a l r e p r e s e n t a t i o n of t h e B o r n - O p p e n h e i m e r a p p r o x i m a t i o n , a c c o r d i n g to w h i c h the g r o u n d s t a t e of m o l e c u l e s i s a c o n t i n u o u s f u n c t i o n of the a t o m i c c o o r d i n a t e s . " 1
T h e b a s i c a s s u m p t i o n w h i c h w e m a k e , one w h i c h i n d e e d i s t h e b a s i s of o u r g e n e r a l u n d e r s t a n d i n g of l a r g e r m o l e c u l e s , i s t h a t m o l e c u l e s to a r e a s o n a b l e d e g r e e of a c c u r a c y c a n be d e s c r i b e d h i e r a r c h i c a l l y , as a s s e m b l e d f r o m s u b u n i t s w h i c h at least approximately preserve their properties (including force f u n c t i o n d e s c r i p t i o n ) f r o m m o l e c u l e to m o l e c u l e . These subunits are usually functional groups or m o n o m e r s . (This division of m o l e c u l e s i n t o f u n c t i o n a l g r o u p s a n d m o n o m e r s i s so i n g r a i n e d i n u s as c h e m i s t s that i t f o r m s t h e b a s i s of o u r m o l e c u l a r n o m e n c l a t u r e . ) T h e c o r o l l a r y to t h i s a s s u m p t i o n i s that the
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f o r c e s w h i c h affect an a t o m are l o c a l , i n that t h e r e is s o m e s p h e r e w h i c h one c a n d r a w a r o u n d an a t o m , s u c h that the p o s i t i o n s of a t o m s o u t s i d e the s p h e r e h a v e a n e g l i g i b l e d i r e c t effect on the c e n t r a l a t o m . ( T h i s i s not to s a y t h e y d o n ' t i n d i r e c t l y affect i t b y a f f e c t i n g a t o m s i n s i d e the s p h e r e w h i c h i n t u r n a f f e c t the c e n t r a l a t o m . ) T h i s l o c a l i z a t i o n of i n t e r a t o m i c e f f e c t i s a t l e a s t i m p l i c i t i n o u r u s u a l a n a l y s e s of m o l e c u l a r s t r u c t u r e a n d o n l y f o r the c a s e of e x t e n d e d c o n j u gated s y s t e m s o r u n s h i e l d e d c h a r g e s i s the s p h e r e l i k e l y to be very large. T h e i m p l i c a t i o n i s that one c a n f i n d the f o r c e o n a p a r t i c u l a r a t o m i f one k n o w s the p o s i t i o n s a n d n a t u r e s of t h e o t h e r a t o m s w i t h i n i t s s p h e r e , i n d e p e n d e n t of t h e p o s i t i o n s of a l l the o t h e r a t o m s o u t s i d e the s p h e r e . T h u s one c a n h o p e to d e v e l o p l i b r a r i e s of s u b u n i t f o r c e f u n c t i o n s w h i c h c a n p r o v i d e at l e a s t s t a r t i n g p o i n t s f o r f o r c e f u n c t i o n d e s c r i p t i o n s of l a r g e r m o l e c u l e s . T h e r e a r e two m a j o r paths one c a n take to t r y to f i n d these force functions: calculate t h e m or deduce t h e m f r o m experimental measurements. 1. Forces - Theoretical. S i n c e the q u a n t u m r e v o l u t i o n i n the late 1920's and e a r l y 1930's, w e h a v e k n o w n h o w i n t h e o r y to c a l c u l a t e the n e e d e d i n t e r a t o m i c p o t e n t i a l (or f o r c e ) f u n c t i o n s (4). Despite the i m m e n s e growth i n c o m p u t e r power i n the p a s t two d e c a d e s , w e s t i l l cannot p r a c t i c a l l y h a n d l e the f u l l ab i n i t i o f o r c e f u n c t i o n c a l c u l a t i o n s f o r l a r g e r m o l e c u l e s even on the l a r g e s t c o m p u t e r s . We can, however, handle subu n i t s l i k e the f u n c t i o n a l g r o u p s and s i m p l e r m o n o m e r s to reasonable a c c u r a c y , and this approach has been and c e r t a i n l y w i l l c o n t i n u e to be a s i g n i f i c a n t s o u r c e of f o r c e d a t a . In a d d i t i o n , it h a s m o r e r e c e n t l y b e c o m e c l e a r that the f o r c e s b e t w e e n n o n - c h e m i c a l l y i n t e r a c t i n g a t o m s and g r o u p s of atoms can quite reasonably be d e r i v e d f r o m l o c a l i z e d c a l c u l a t i o n s w h i c h r e q u i r e o n l y the w a v e f u n c t i o n s of the s e p a r a t e a t o m s o r g r o u p s as i n p u t (40, 41). This is an i m p o r t a n t step f o r w a r d , b e c a u s e it r e d u c e s a p r o b l e m w h i c h s c a l e d as N ^ , i n w h i c h Ν i s the n u m b e r of i n t e r a c t i n g a t o m s o r g r o u p s , to one s c a l i n g as N . In a d d i t i o n to the ab i n i t i o a p p r o a c h e s , t h e r e a r e v a r i o u s s e m i - e m p i r i c a l theoretical approaches w h i c h can be useful. F i r s t , t h e r e a r e s e m i - e m p i r i c a l m e t h o d s f o r s o l v i n g the q u a n t u m m e c h a n i c a l equations t h e m s e l v e s . S e c o n d , the l o n g r a n g e r e g i o n of i n t e r a t o m i c f o r c e s i s f a i r l y w e l l u n d e r s t o o d , f o r
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e x a m p l e C o u l o m b r~ f o r charge interaction and V a n der W a a l s r " ^ for L o n d o n d i s p e r s i o n f o r c e s , and we can calculate such l o n g r a n g e f o r c e s at l e a s t a p p r o x i m a t e l y f r o m c h a r g e d i s t r i butions and p o l a r i z a b i l i t i e s . 2. F o r c e s - E x p e r i m e n t a l . M o s t of o u r f o r c e i n f o r m a t i o n , h o w e v e r , w i l l h a v e to c o m e at t h i s s t a g e f r o m p o s t u lating reasonable adjustable force functions and then tuning t h e m to m a t c h e x p e r i m e n t a l o b s e r v a t i o n s of p a r a m e t e r s w h i c h depend upon these forces. S u c h methodology has been the b a s i s of m u c h of the c o n f o r m a t i o n a l c a l c u l a t i o n w o r k i n o r g a n i c c h e m i s t r y a n d p o l y m e r c h e m i s t r y (6, T, <8, 1 1 , 1 2 , 4 2 , 4 3 ) . M a n y t y p e s of p h y s i c a l a n d c h e m i c a l m e a s u r e m e n t s c a n be u s e d to p r o v i d e f o r c e f u n c t i o n i n f o r m a t i o n a n d to tune f o r c e functions. F o r example, molecular b e a m scattering can p r o v i d e i n f o r m a t i o n o n b o t h l o n g a n d s h o r t r a n g e f o r c e s (2, 3) a n d f r o m t r a n s p o r t p r o p e r t y m e a s u r e m e n t s one c a n d e r i v e l o n g range forces. T h e r m o c h e m i s t r y can provide bond strengths and thus w e l l depth i n f o r m a t i o n . M a n y s p e c t r o s c o p i c measurem e n t s a r e p h y s i c a l l y l i n k e d to f o r c e f u n c t i o n s . X-ray diffract i o n p r o v i d e s s t r u c t u r a l i n f o r m a t i o n a n d thus the e q u i l i b r i u m geometry where forces balance. Rotational (microwave) spectroscopy can p r o v i d e accurate e q u i l i b r i u m geometry, bond lengths and a n g l e s , and b a r r i e r s to i n t e r n a l r o t a t i o n . Vibrat i o n a l ( i n f r a - r e d a n d R a m a n ) s p e c t r o s c o p y p r o v i d e s the s h a p e s of f o r c e c u r v e s n e a r the e q u i l i b r i u m g e o m e t r y . Electronic spectroscopy (visible and u l t r a - v i o l e t ) can p r o v i d e potential or force function information over a broader internuclear distance range. In f a c t , a n y f o r m of s p e c t r o s c o p y , O R D , C D , N M R , e t c . , i n w h i c h m e a s u r e m e n t s depend on s t r u c t u r e , can be u s e d to t u n e f o r c e f u n c t i o n s (44). T h u s , one c a n h y p o t h e s i z e r e a s o n a b l e f o r c e f u n c t i o n s f o r m o l e c u l e s , c o m p a r e these p r e d i c t i o n s against p h y s i c a l and c h e m i c a l m e a s u r e m e n t s a n d r e f i n e the f o r c e f u n c t i o n s f o r b e s t m a t c h (39). B y c o m p a r i n g the r e s u l t s a c r o s s s e t s of m o l e c u l e s w i t h the s a m e f u n c t i o n a l g r o u p s o r m o n o m e r s one c a n b u i l d up subunit force function l i b r a r i e s . We can with N E W T O N calculate any interatomic force a l g o r i t h m , w h e t h e r g i v e n i n f u n c t i o n a l o r t a b u l a r f o r m , and do it e x t r a o r d i n a r i l y r a p i d l y . F o r computational efficiency, h o w e v e r , w e i n t e n d to c a r e f u l l y t h i n k about the m o s t e f f i c i e n t w a y to h a n d l e f o r c e s f o r m o l e c u l a r m e c h a n i c a l c a l c u l a t i o n s . It i s b y n o m e a n s c l e a r t h a t t h e u s u a l f u n c t i o n a l f o r m s f o r
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p o t e n t i a l s as u s e d i n s p e c t r o s c o p y a r e the m o s t c o n v e n i e n t f o r molecular mechanical calculations. A t l e a s t f o r a s t a r t , f r o m the p o i n t of v i e w of a n y g i v e n a t o m , w e c a n d i v i d e the other a t o m s into f o u r c a t e g o r i e s :
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a
>> ο S
i)
t h o s e too f a r a w a y to d i r e c t l y a f f e c t i t (most other atoms i n l a r g e r molecules),
ϋ)
those w h o s e effect c a n be t r e a t e d b y a two b o d y i n t e r a c t i o n w h i c h d e p e n d s o n l y on the c l a s s to w h i c h e a c h of the t w o a t o m s b e l o n g s (for e x a m p l e nonbonded i n t e r a c t i o n b e t w e e n an H a t o m on aliphatic C and a ketone Ο atom),
iii)
t h o s e w h i c h a r e s p e c i f i c a l l y b o n d e d to the a t o m i n question by bonds w h i c h don't change t h e i r f o r c e f u n c t i o n c h a r a c t e r d u r i n g the c h e m i c a l p r o c e s s , and
iv)
t h o s e a t o m s w h o s e i n t e r a c t i o n w i t h the a t o m in question changes i n force function nature a s a f u n c t i o n of t h e p o s i t i o n s of o t h e r a t o m s , in other words full multibody interactions, f o r e x a m p l e bond w e a k e n i n g and f o r m a t i o n due to the a p p r o a c h of o t h e r a t o m s at a c t i v e s i t e s in chemical reactions.
eu
3· eu u m &D
•Η
CO eu
u υ
S o m e of the a b o v e c l a s s i f i c a t i o n s c h e m e c a n b e r e f l e c t e d i n the c o m p u t e r h a r d w a r e and s o f t w a r e i n s u c h a w a y as to vastly increase its calculational speed B. Computational System. We are now i n an era i n w h i c h i f one c a n u n d e r s t a n d the s t r u c t u r e of a c o m p u t a t i o n a l p r o b l e m , one c a n often d e s i g n a s p e c i a l i z e d c o m p u t a t i o n a l s y s t e m w h i c h d i s t r i b u t e s the v a r i o u s p a r t s of the c a l c u l a t i o n a m o n g v e r y e f f i c i e n t s u b u n i t s , s u c h that the c o m p u t a t i o n c a n be h a n d l e d m u c h f a s t e r and m u c h l e s s e x p e n s i v e l y than w i t h a general purpose computer. F o r example, our molecular dynamics computation has t h r e e l e v e l s w h i c h s c a l e q u i t e d i f f e r e n t l y w i t h N , the n u m b e r of atoms. T h e f i r s t i s the e x p l o r a t i o n a n d c h o i c e of i n i t i a l c o n d i t i o n s ( c o o r d i n a t e s a n d v e l o c i t i e s o r m o m e n t a ) of the a t o m s , w h i c h s c a l e s as V ^ , i n w h i c h V i s the v o l u m e of p h a s e s p a c e to be e x p l o r e d f o r e a c h a t o m . T h i s s e a r c h s p a c e of i n i t i a l
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a t o m i c c o n d i t i o n s i n c r e a s e s as the N t h p o w e r , and a b r u t e f o r c e approach quickly becomes unmanageable for any computer. The c h o i c e of i n i t i a l c o n d i t i o n s i s t h u s m u c h b e t t e r h a n d l e d b y c l o s e l y i n v o l v i n g a h u m a n c h e m i s t and r e l y i n g on h i s c a l i b r a t e d i n t u i t i o n , h i s s p a t i a l , g e o m e t r i c a l s e n s e of w h a t i s c h e m i c a l l y appropriate. T h i s i s the r e a s o n f o r the c l o s e a t t e n t i o n to v i s u a l and touch interfaces: to i n v o l v e the h u m a n c h e m i s t i n a c o n venient, comfortable symbiotic relationship with a computer s y s t e m i n s u c h a w a y as to g r e a t l y m a g n i f y h i s a b i l i t y to s o l v e problems in molecular mechanics. S e c o n d i s the d i s c o v e r y of w h i c h a m o n g the o t h e r N - l a t o m s a r e n e a r enough to the a t o m u n d e r c o n s i d e r a t i o n to d i r e c t l y c o n t r i b u t e to the f o r c e o n i t . T h i s p a r t of t h e p r o b l e m s c a l e s as N ^ , a n d f o r l a r g e r m o l e c u l e s q u i c k l y d o m i n a t e s the computational load. A s shown below, we have designed a s p e c i a l b a r r e l - r o l l d i s c r i m i n a t o r w h i c h c a n s o l v e t h i s p a r t of the c o m p u t a t i o n so r a p i d l y that it no l o n g e r r e p r e s e n t s a m a j o r d i f f i c u l t y , at l e a s t f o r the r a n g e of Ν u p to a t h o u s a n d w h i c h w e are now considering. T h i r d , g i v e n the s e t of n e i g h b o r i n g a t o m s w h i c h a r e i m p o r t a n t i n d e t e r m i n i n g the f o r c e on the i t h a t o m , w e m u s t e v a l u a t e the f o r c e f u n c t i o n (r^ . . . f o r the i t h a t o m a n d i n t e g r a t e t h e p o s i t i o n j : - of t h e a t o m o n e s t e p f o r w a r d i n t i m e . T h i s c a l c u l a t i o n f o r a l l Ν a t o m s s c a l e s as N , and i s m o s t c o n v e n i e n t l y c a r r i e d out on a g e n e r a l p u r p o s e c o m p u t e r s i n c e f o r d i f f e r e n t a t o m s t h e JT^ c a n h a v e a v a r i e t y of a l g o r i t h m i c f o r m s . T h i s p a r t of t h e c a l c u l a t i o n w e t u r n o v e r t o a n e x p a n d a b l e s e t of p a r a l l e l a n d p i p e l i n e d f l o a t i n g p o i n t a r r a y p r o c e s s o r s w i t h c o n t r o l , coordination and c o m m u n i c a t i o n handled by a s u p e r v i s o r y c o m p u t e r , as i s s h o w n i n F i g . 1. A l l t h e p a r t s of t h i s m a n - m a c h i n e s y m b i o s i s m u s t w o r k s m o o t h l y t o g e t h e r , to e f f e c t t h e s t e e r e d s o l u t i o n to the c o u p l e d differential equations. It i s a n i n i t i a l v a l u e p r o b l e m w i t h m a n s u p p l y i n g the i n i t i a l v a l u e s i n r e a l h u m a n t i m e and r e l y i n g on r a p i d r e s p o n s e f r o m the m a c h i n e to g i v e h i m f e e d b a c k so he c a n t r i m h i s i n p u t . T h e m a c h i n e m u s t r e l y on m a n to h a n d l e the i n i t i a l v a l u e s e l e c t i o n (the N t h p o w e r p r o b l e m ) w h i c h i s b e y o n d m a c h i n e c a p a b i l i t y , a n d the m a n m u s t r e l y o n the m a c h i n e to s h o w h i m t h e c a l c u l a t e d r e s u l t s of h i s c h o i c e r a p i d l y e n o u g h s o h e c a n u s e the r e s u l t s to s t e e r the m o l e c u l e s i n t o the d e s i r e d initial pathway. W h e n the h u m a n c h e m i s t p u s h e s on c e r t a i n a t o m s , t h e r e s t of t h e m o l e c u l e m u s t f o l l o w , a n d t h u s t h e d i f f e r e n t i a l equations m u s t be s o l v e d r a p i d l y on a h u m a n t i m e
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scale. O u r p r e l i m i n a r y t e s t s i n d i c a t e t h a t to m a t c h m a n ' s v i s u a l a n d t o u c h p e r c e p t i o n s , the t i m e to s o l v e one s t e p i n t h e i n t e g r a t i o n s h o u l d be a m a x i m u m of a p p r o x i m a t e l y 0. 1 s e c o n d , and this sets m i n i m u m p e r f o r m a n c e standards for our m a c h i n e .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
1. Molecular Manipulation - Touch Interface. Touchy F e e l y I, w h i c h i n p u t s 3D p o s i t i o n to a c o m p u t e r a n d o u t p u t s 3 D f o r c e , h a s b e e n b u i l t . T o u c h y F e e l y II, w h i c h i n p u t s 3D f o r c e and outputs 3D p o s i t i o n , i s b e i n g d e s i g n e d , a l o n g w i t h T o u c h y T w i s t y I w h i c h w i l l i n p u t t h r e e d i m e n s i o n s of p o s i t i o n a n d t h r e e of o r i e n t a t i o n a n d o u t p u t t h r e e d i m e n s i o n s of f o r c e a n d t h r e e of torque. T h e s e touch i n t e r f a c e s s h o u l d be sufficient f o r m o s t molecular applications. 2. Molecular P o r t r a y a l - Visual Interface. The v i s u a l i n t e r f a c e , the E v a n s & S u t h e r l a n d P i c t u r e S y s t e m , i s i n o p e r a t i o n and the software f o r this a p p l i c a t i o n is r u n n i n g . The P i c t u r e S y s t e m a l l o w s u s to b u i l d 3D m o l e c u l a r i m a g e s , to c o n t r o l a t o m a n d b o n d p o s i t i o n s f r o m e x t e r n a l c o m p u t e r s l i k e N E W T O N , to t r a n s l a t e and r o t a t e the m o l e c u l e s , to z o o m into s e l e c t e d p o r t i o n s , c l i p p i n g and w i n d o w i n g to see o n l y the c h o s e n r e g i o n , and to v i e w the m o l e c u l e s i f d e s i r e d i n p e r s p e c t i v e , s t e r e o a n d color. 3. Distributed M u l t i p r o c e s s o r N e t w o r k . A s shown in F i g . 1, the h a r d w a r e to i n t e g r a t e the c o u p l e d d i f f e r e n t i a l equations d i v i d e s into t h r e e p a r t s : the s u p e r v i s o r y p r o c e s s o r , the b a r r e l - r o l l d i s c r i m i n a t o r a n d a set of f l o a t i n g p o i n t processors. a) Supervisory Processor. The s u p e r v i s o r y p r o c e s s o r w i l l be r e s p o n s i b l e f o r s y s t e m s s o f t w a r e , f o r l o a d i n g and i n t e r r o g a t i n g the b a r r e l - r o l l d i s c r i m i n a t o r , f o r c o m p i l i n g and l o a d i n g m i c r o c o d e for the floating point a r r a y p r o c e s s o r s , for l o a d i n g t h e i r d a t a , f o r s u p e r v i s i n g c o m m u n i c a t i o n a m o n g the b a r r e l - r o l l d i s c r i m i n a t o r , the f l o a t i n g p o i n t p r o c e s s o r s , the v i s u a l and t o u c h i n t e r f a c e s and the h i e r a r c h i c a l s y s t e m and its n e t w o r k , a n d f o r c a r r y i n g out o r s u p e r v i s i n g o n - l i n e s u b s i d i a r y c a l c u l a t i o n s b a s e d on the t r a j e c t o r i e s . It n e e d s t o b e a r e l a t i v e l y f a s t p r o c e s s o r , to h a v e s u f f i c i e n t f a s t a n d a c c e s s i b l e m e m o r y to be a b l e to t r a n s f e r m i c r o c o d e a n d d a t a r a p i d l y e n o u g h to k e e p the d i s c r i m i n a t o r and a r r a y p r o c e s s o r s b u s y , a n d to h a v e enough f i x e d h e a d d i s k o r e q u i v a l e n t m e m o r y to r a p i d l y
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Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
store t r a j e c t o r y i n f o r m a t i o n for later o f f - l i n e analysis if desired, a n d a w a y , p e r h a p s a f l o p p y d i s k , to c o n v e n i e n t l y l o a d a n d s t o r e individual p r o g r a m s and data. b) D i s c r i m i n a t o r . A s shown i n F i g . 2, w h e n the n u m b e r of a t o m s , N , b e c o m e s s i z e a b l e , m o s t of the a r i t h m e t i c o p e r a t i o n s a r e t a k e n u p b y t h e p r o c e s s of l o c a t i n g the s u b s e t of a t o m s c l o s e enough to the a t o m u n d e r c o n s i d e r a t i o n to d i r e c t l y c o n t r i b u t e to the f o r c e it f e e l s . In a d y n a m i c s y s t e m the i d e n t i t i e s of t h e n e a r n e i g h b o r s c a n be c o n t i n u a l l y c h a n g i n g . We n e e d o n l y a f e w o u t of the s e v e r a l h u n d r e d o r a t h o u s a n d a t o m s for further consideration. The selection task, w h i c h increases as ~ Ν , s o o n d o m i n a t e s p r o c e s s i n g t i m e . T h i s p r o b l e m c o u l d b e h a n d l e d i n s e v e r a l w a y s : i) b y building an appropriate associative m e m o r y , ii) by building a s p e c i a l p r o c e s s o r , and iii) by being m o r e sophisticated and c o m p l e x i n the p r o g r a m m i n g to take into account " f r a m e c o h e r e n c e " , a s i n the v i s i b l e s u r f a c e p r o b l e m i n g r a p h i c s (30), t r y i n g to f i n d w a y s to u s e the f a c t that the i n t e g r a t i o n f r a m e s a r e n o t i n d e p e n d e n t so that w e d o n ' t h a v e to d o t h e w h o l e d i s c r i m i n a t i o n job o v e r a g a i n at e a c h s t e p . T h e s e c o n d a l t e r n a t i v e , b u i l d i n g a s p e c i a l p r o c e s s o r to do the d i s c r i m i n a t i o n , a p p e a r s the m o s t c o s t e f f e c t i v e . If w e a r r a n g e the c o o r d i n a t e d a t a ( p r o b a b l y c o n v e r t e d to f i x e d p o i n t n u m b e r s w h i c h w e n e e d to do a n y w a y f o r the P i c t u r e S y s t e m ) i n the f o r m of a t a b l e ,
y
i
z
i
we can then load it into shift r e g i s t e r s or i n c r e m e n t a l l y a d d r e s s e d m e m o r y and s e q u e n t i a l l y p r o c e s s it to d i s c o v e r w h i c h a t o m s a r e w i t h i n a c u b e o f s i z e x^ ± Δ, y^ ± Δ, z^ ± Δ c e n t e r e d o n a t o m i a t (x^, y ^ , z^). A s a f i r s t a l t e r n a t i v e , w e c a n r o l l the table into a b a r r e l w i t h Xj^ f o l l o w i n g Xj,, yj^ f o l l o w i n g y^ a n d z j ^ f o l l o w i n g Z j a n d r o t a t e t h e b a r r e l b y s h i f t i n g t h e s h i f t r e g i s t e r s a r o u n d a h o r i z o n t a l a x i s s o t h a t t h e ( X J , y - , Zj) p a s s b y a set of p a r a l l e l c o m p a r a t o r s w h i c h c h e c k s i m u l t a n e o u s l y to see i f X j , y j a n d Zj f a l l w i t h i n the s i x l i m i t s . S e v e r a l s e t s of p a r a l l e l c o m p a r a t o r s l o a d e d w i t h c o o r d i n a t e s of t h e c u b e s s u r r o u n d i n g d i f f e r e n t i a t o m s c a n a l l s i m u l t a n e o u s l y b e f e d the
3.
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DISTANT COMPUTERS
/ \
SUPERVISORY PROCESSOR
\ J
FLOPPY DISK
CAM AC CRATE
HIERARCHICAL
FAST DISK
VISUAL PROCESSOR!
WITH
2
9 PROCESSORS
TOUCH (PROCESSOfl
CAMAC CRATE
Ε
as
PICTURE SYSTEM
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(^PERIP^ERA^^
TTY
CAMAC CRATE
mm
VISUAL INTERFACE
TOUCH INTERFACE
IATIN6 1POINT RAY PROCESSO
NETWORK
)ATIN6 POINT ?AY PROCESSOI
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Figure 1. Block diagram of NEWTON. There are six basic subsystems. The Visual and Touch Interfaces provide on-line communication with the user, while the already existing Hierarchical Computer Network, shown in more detail in Figure 5, provides less direct user communication through standard peripherals and also provides network access to other computers on and off campus. The Barrel-Roll Discriminator provides very fast selection of those atoms near enough to each atom to warrant further computation. The Floating Point Array Processors provide very fast (167 nsec pipelined add and multiply) floating point calculation. The Supervisory Processor handles systems software, compiling of floating point array processor microcode, and supervision of other subsystems including their hading and intercommunication as well as error checking. Several of the subsystems already exist: the Hierarchical Computer Network and peripherals, the Evans &• Sutherland Picture System, and an initial crude version of the Touch Interface.
5 10" 2 5 10" 2 5 10 NUMBER OF ATOMS, N
Figure 2. Approximate number of arithmetic oper ations per integration step as a function of N , the number of atoms. The formula used is: Τ = N [ R ( N — m) + ™P + I] in which Τ = total num ber of arithmetic operations, R = number of opera tions for each neighbor rejected by the discrimina tor, Ρ = average number of operations for each near neighbor through calculation of x, y and ζ components of force on ith atom, I = number of operations for integration (predictor-corrector), and m = aver, number of near neighbors selected after cubic and spherical discrimination. The figure is drawn using R = 10, Ρ = 70, I = 45 and m = 6, and corresponds to force evaluation using an aver age of 6 near neighbors, each of which takes three functional evaluations by table look-up on higher order bits and linear interpolation on lower order bits. Predictor-corrector integration (Adams-Bashforth) of moderate order is assumed. As can be seen, for Ν in the range of hundreds or thousands of atoms, most operations can be handled by the discriminator, freeing the more flexible array processors for force evaluation and integration.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
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t a b l e of j a t o m c o o r d i n a t e s as the b a r r e l r o l l s . A s e c o n d a l t e r n a t i v e i s to r o l l the t a b l e so that f o l l o w s ζ γ, . . . , a n d X j ^ f o l l o w s z-jvj a n d r o t a t e t h e b a r r e l a r o u n d a v e r t i c a l a x i s b y Ν s e t s of s e r i a l a d d e r s , e a c h a l s o b e i n g f e d ( x j , y ^ , z ^ ) . I n e i t h e r a l t e r n a t i v e , a l l w e n e e d out of the d i s c r i m i n a t o r f o r e a c h a t o m i i s a l i s t of i n d e x n u m b e r s t e l l i n g u s w h e r e i n m e m o r y t o f i n d its near neighbors' coordinates. E i t h e r the p a r a l l e l o r the s e r i a l v e r s i o n c a n be c o n s t r u c t e d f r o m r e l a t i v e l y i n e x p e n s i v e c o m p o n e n t s a n d a r e l a t i v e l y m o d e s t s y s t e m c a n k e e p a h e a d of the a r r a y p r o c e s s o r s , e v e n f o r N ' s of o v e r a t h o u s a n d , r e l i e v i n g t h e m , a s c a n b e s e e n i n F i g . 2 , of t h e g r e a t m a j o r i t y o f t h e arithmetic operations. F o r a t h o u s a n d a t o m s , at 10 i n t e g r a t i o n s t e p s p e r s e c o n d , the d i s c r i m i n a t o r m u s t h a n d l e ^ 1 0 ^ a r i t h m e t i c o p e r a t i o n s p e r s e c o n d . W h i l e t h i s s o u n d s v e r y l a r g e at f i r s t h e a r i n g , the a r i t h m e t i c t a s k c a n be s h a r e d a m o n g m a n y c o m p a r a t o r s w h i c h c a n r u n i n p a r a l l e l . In r e a l i t y the d i s c r i m i nator c a n be b u i l t r e l a t i v e l y i n e x p e n s i v e l y . c) Array Processors. T h e e v a l u a t i o n of the f o r c e f u n c t i o n ^ F i ( r ^ . . . jr-^) g i v e n t h e i n d e x n u m b e r s i d e n t i f y i n g t h e n e a r n e i g h b o r s f o r t h e i t h a t o m a n d t h e i n t e g r a t i o n of the acceleration d r. 2
L."
1
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...
r )
dt to g i v e the t r a j e c t o r y f o r e a c h a t o m w i l l be c a r r i e d out b y the floating point a r r a y p r o c e s s o r s . In a d d i t i o n , to r e m o v e a n g u l a r b i a s , a s e c o n d d i s c r i m i n a t i o n w i l l be d o n e , to c h o o s e t h o s e n e i g h b o r s f a l l i n g w i t h i n the s p h e r e i n s c r i b e d w i t h i n the b a r r e l r o l l d i s c r i m i n a t o r ' s c u b e , i . e. t h o s e n e i g h b o r s f o r w h i c h ' W e e x p e c t to u s e c o m m e r c i a l f l o a t i n g p o i n t a r r a y p r o c e s s o r s , s u c h as those b e i n g d e s i g n e d and b u i l t b y C S P I , b y Datawest and by F l o a t i n g P o i n t S y s t e m s . For example, Floating Point Systems' a r r a y p r o c e s s o r is r e a l l y an e x t r a o r d i n a r i l y f a s t , r a t h e r g e n e r a l p u r p o s e p r o c e s s o r , w i t h 38 b i t f l o a t i n g p o i n t a d d t i m e of 167 n s e c ( 3 3 3 n s e c n o n - p i p e l i n e d ) a n d m u l t i p l y t i m e of 167 n s e c (500 n s e c n o n - p i p e l i n e d ) , a n d s e v e r a l f a s t memories. I t s 64 b i t m i c r o c o d e a l l o w s s e v e r a l o p e r a t i o n s t o p r o c e e d s i m u l t a n e o u s l y (for e x a m p l e a d d , m u l t i p l y , b r a n c h ) . W e ' v e c o d e d up s o m e s h o r t s e g m e n t s to e s t i m a t e r u n n i n g t i m e s , and i t s s p e e d i s i n the c l a s s of the l a r g e s t g e n e r a l p u r p o s e r
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Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
processors, yet the a r r a y p r o c e s s o r fits c o m f o r t a b l y on a desk top. A n e a r l i e r v e r s i o n is a l r e a d y running p l a s m a p a r t i c l e c a l c u l a t i o n s (45) a n d u s e o f a n e t w o r k o f s u c h a r r a y p r o c e s s o r s is being considered by L a w r e n c e L i v e r m o r e L a b o r a t o r y for large s c a l e c a l c u l a t i o n s of t h e c l a s s n o w b e i n g r u n o n C D C 7 6 0 0 a n d S T A R c o m p u t e r s (46). d) I n t e r p r o c e s s o r C o m m u n i c a t i o n . In the e v o l u t i o n t o w a r d m o r e and m o r e p a r a l l e l u n i t s , the t i m e spent i n i n t e r p r o c e s s o r c o m m u n i c a t i o n m u s t be c o n t r o l l e d , or it can s w a m p the s y s t e m . F o r t h i s r e a s o n , one n e e d s a c o m m u n i c a t i o n n e t w o r k a l l o w i n g b o t h s p e c i f i c and b r o a d c a s t m o d e s , so that a p r o c e s s o r can a c c e s s and be a c c e s s e d by any other s p e c i f i c p r o c e s s o r o n the one h a n d and a l s o b r o a d c a s t i n f o r m a t i o n n e e d e d b y a l l p r o c e s s o r s s i m u l t a n e o u s l y , f o r e x a m p l e the set of c o o r d i n a t e s of t h e a t o m s at e a c h p r e d i c t o r o r c o r r e c t o r s u b step. W e p l a n to b u i l d t h i s d u a l c o m m u n i c a t i o n m o d e c a p a b i l i t y into the C A M A C s y s t e m w e n o w u s e f o r i n t e r p r o c e s s o r c o m m u n i c a t i o n , a n d to i n c r e a s e the s p e e d to m a t c h the f a s t e r m e m o r y speeds. The above h a r d w a r e represents an e x t r a o r d i n a r i l y fast computational system for molecular dynamics calculations. N E W T O N , as is s h o w n i n the f o l l o w i n g table, c a n p e r f o r m t h e s e c a l c u l a t i o n s at r a t e s f a r f a s t e r t h a n e v e n a C D C 7 6 0 0 , d u e to N E W T O N s specialized hardware. 1
ROUGH COMPARISONS OF MILLIONS OF FLOATING I N S T R U C T I O N S P E R S E C O N D (MIPS) NEWTON C D C 7600 I B M 360/195 C D C 6400 I B M 360/65 D E C P D P 10 ( K I - 1 0 ) I B M 370/158 I n t e r d a t a 8/32 Data General Eclipse Digital Scientific Meta 4 D E C P D P 11/70 D E C L S I 11 m i c r o c o m p u t e r
POINT
100 M I P S 10 6 0. 6 0. 6 0. 6 0.4 0.4 0. 16 0 . 10 0. 10 0. 0 2
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N o t e : N E W T O N c a n be e x p a n d e d to s e v e r a l h u n d r e d , o r even a thousand M I P S by adding m o r e d i s c r i m i n a t o r s and f l o a t i n g p o i n t a r r a y p r o c e s s o r s , a n d c o u l d t h e n handle a few thousand atoms. N E W T O N will probab l y a c c o m p l i s h t h o s e o p e r a t i o n s to be done i n the discriminator by converting coordinates f r o m f l o a t i n g to f i x e d p o i n t .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
T h i s i s i n d i c a t i v e of a n e w p e r i o d i n c o m p u t e r s c i e n c e , i n w h i c h s p e c i a l i z e d c o m p u t a t i o n s c a n be c a r r i e d out on r e l a t i v e l y e a s y to c o n s t r u c t s p e c i a l i z e d c o m p u t e r s at s p e e d s m u c h g r e a t e r t h a n with general purpose machines. e) Algorithm. In concept, o u r task is s t r a i g h t f o r w a r d . A f t e r b e i n g p r e s e n t e d w i t h the n e i g h b o r s w h i c h m a t t e r , the a r r a y p r o c e s s o r m u s t c a l c u l a t e t h e f o r c e F ^ ( X i · · · J^-^) o n t h e i t h a t o m a s a f u n c t i o n of i t s v e c t o r p o s i t i o n a n d t h o s e of the neighbors. F o r c e f u n c t i o n e v a l u a t i o n w i l l n o r m a l l y be by table l o o k - u p and i n t e r p o l a t i o n for speed. Then, using Newton s second law, 1
the a c c e l e r a t i o n m u s t be u s e d to m o v e f o r w a r d the t r a j e c t o r y of t h e i t h a t o m one t i m e s t e p . T h i s m u s t be a c c o m p l i s h e d f o r a l l Ν a t o m s w i t h i n a f i x e d r e a l t i m e Δ τ, so that to the h u m a n o p e r a t o r the a t o m s a p p e a r to m o v e e v e n l y w i t h t i m e . Predictorc o r r e c t o r i n t e g r a t i o n m e t h o d s a p p e a r to be the l o g i c a l c h o i c e (47, 48). If o n l y t h e t r a j e c t o r y i n c o o r d i n a t e s p a c e i s d e s i r e d , d i r e c t s e c o n d d e r i v a t i v e m e t h o d s w h i c h s k i p t h e e v a l u a t i o n of t h e f i r s t d e r i v a t i v e (velocity) m a y be u s e d f o r i n c r e a s e d s p e e d . If velocity dependent f o r c e s are used for structure calculations by r e l a x a t i o n , o r p h a s e s p a c e i n f o r m a t i o n i s d e s i r e d , then the i n t e g r a t i o n c a n be p e r f o r m e d as two f i r s t o r d e r equations ( H a m i l t o n i a n ) . D i s c r i m i n a t i o n p r o b a b l y n e e d o n l y be p e r f o r m e d on the p r e d i c t i o n and not the c o r r e c t i o n s u b s t e p . The equations a r e not p a r t i c u l a r l y stiff, as the i n t r i n s i c t i m e constants f o r the b o n d l e n g t h c h a n g i n g m o d e s f a l l w i t h i n a r e a s o n a b l y s m a l l range. S t i l l , w e i n t e n d to i n v e s t i g a t e w a y s to s p e e d up c a l c u l a t i o n , e i t h e r b y stiff e q u a t i o n m e t h o d s o r b y t r e a t i n g the f a s t Η atom vibrations separately.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
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W h i l e w e d o n ' t k n o w and p r o b a b l y n e v e r w i l l k n o w the basic force functions with great accuracy, we must still proceed i n o u r n u m e r i c a l c o m p u t a t i o n w i t h s u f f i c i e n t p r e c i s i o n so as not to l o s e m e a n i n g . T r u n c a t i o n e r r o r i n the a l g o r i t h m c a n be m a d e n e g l i g i b l y s m a l l b y p r o p e r c h o i c e of i n t e g r a t i o n o r d e r a n d s t e p size. E r r o r p r o p a g a t i o n e s t i m a t e s (47) b a s e d o n p r e s e n t l y a v a i l a b l e f l o a t i n g point a r r a y p r o c e s s o r w o r d lengths (for e x a m p l e 38 b i t s , 28 b i t m a n t i s s a , 10 b i t e x p o n e n t , f o r f l o a t i n g point s y s t e m s ) i n d i c a t e that they a r e l o n g enough f o r i n i t i a l w o r k , but that a l o n g e r w o r d l e n g t h w i l l p r o b a b l y u l t i m a t e l y be desirable. One s o l u t i o n w o u l d be to c a l c u l a t e the f o r c e w i t h s i n g l e p r e c i s i o n and a c c u m u l a t e the i n t e g r a l w i t h double p r e c i s i o n (25). N u m e r o u s c h e c k s c a n be m a d e on c a l c u l a t i o n a l a c c u r a c y , i n c l u d i n g i) c h a n g e i n i n t e g r a t i o n s t e p s i z e , i i ) t i m e r e v e r s a l , i i i ) c o n s e r v a t i o n l a w s s u c h as e n e r g y , l i n e a r m o m e n t u m and a n g u l a r m o m e n t u m and iv) p r e - and p o s t - o p e r a t i o n by a G a l i l e a n t r a n s f o r m a t i o n , i . e. to a n d f r o m a f r a m e w i t h a f i x e d v e l o c i t y w i t h r e s p e c t to the o r i g i n a l f r a m e (49). One of the i m p o r t a n t a r e a s to s t u d y w i l l be w h a t p r a c t i c a l t r a d e o f f s t o m a k e b e t w e e n n u m b e r o f a t o m s , c o m p l e x i t y of f o r c e functions, speed and a c c u r a c y . III.
P r e l i m i n a r y Test
A c r u d e t e s t of the N E W T O N c o n c e p t h a s b e e n a s s e m b l e d using available equipment, and is i l l u s t r a t e d i n F i g s . 3-6. Our f i r s t t o u c h i n t e r f a c e , s h o w n i n F i g . 6, i s u s e d t o m o v e a s e l e c t e d a t o m i n a m o l e c u l e , and to s i m u l t a n e o u s l y f e e l the f o r c e s w h i c h that a t o m e x p e r i e n c e s f r o m the other a t o m s and its own i n e r t i a . T h e m o t i o n s of the a t o m s i n the t i m e e v o l v i n g m o l e c u l e a r e v i e w e d i n 3D on an E v a n s & S u t h e r l a n d P i c t u r e S y s t e m , i n stereo and c o l o r if d e s i r e d . The differential equations are integrated by a fast m i c r o - p r o g r a m m a b l e m i n i - c o m p u t e r , a M e t a - 4 , with m i c r o - c o d e d floating point instructions. For 5 atoms interacting by L e n n a r d - J o n e s 1 2 - 6 potentials and a n o n optimized F O R T R A N p r o g r a m using low order Adams-Bashforth p r e d i c t o r - c o r r e c t o r i n t e g r a t i o n , the M e t a - 4 a c h i e v e s i n t e g r a t i o n t i m e s o f 0. 0 5 s e c p e r s t e p o r o s c i l l a t i o n p e r i o d s o f t h e f a s t e s t atoms i n about a second w i t h r e a s o n a b l e a c c u r a c y . This integ r a t i o n t i m e i s a b o u t i n t h e b a l l p a r k o f t h e m a x i m u m of 0 . 1 s e c p e r s t e p n e c e s s a r y f o r r e a s o n a b l e i n t e r f a c e to o u r h u m a n v i s u a l a n d t o u c h p e r c e p t i o n s of m o t i o n . T e s t s o f t h e v i s c o u s d a m p i n g a p p r o a c h to m o l e c u l a r s t r u c t u r e d e t e r m i n a t i o n s h o w that s u c h a
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Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
EÔS PICTURE SYSTEM
TTY
VISUAL INTERFACE
TOUCH INTERFACE
Figure 3. Block diagram of system used to test crudely the concept of NEWTON. The touchstone of the touch interface drives the central carbon atom of a methane molecule, allowing it to be moved and the forces on it from the other atoms to be felt by the user. The molecule is displayed on the Evans à- Sutherland Picture System and the differential equations are integrated in real (human) time by the Meta-4 computer to give the trajectories displayed on the Picture System. The Meta-4 is linked through three CAMAC crates and an IBM 1800 to the COP 135 visual processor emulating a DEC POP-11/40 which in turn runs symbiotically with the Picture System Processor.
Figure 4. Preliminary test of version of NEWTON using minicomputers, as diagrammed in Figure 3
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s i m p l e m o l e c u l e r e l a x e s w i t h i n a f e w s e c o n d s to i t s e q u i l i b r i u m geometry. R e l a x a t i o n i s so f a s t that the s t r u c t u r a l i m p l i c a t i o n s of v a r y i n g the i n t e r a t o m i c f o r c e f u n c t i o n s c a n be s e e n a l m o s t a s f a s t as one t u r n s the c o n t r o l l i n g d i a l . S i n c e the c o m p u t a t i o n s c a l e s as ~ N ^ , w h e r e Ν i s t h e n u m b e r of a t o m s , i t c a n be s e e n that to h a n d l e b i o m o l e c u l a r s y s t e m s w i t h attendant s o l v e n t m o l e c u l e s , w i t h h u n d r e d s o r t h o u s a n d s of a t o m s , w e n e e d a m u c h f a s t e r w a y of c a r r y i n g out the c o m p u t a t i o n t h a n e v e n a f a s t m i n i c o m p u t e r . N E W T O N i s d e s i g n e d to p r o v i d e s u c h speeds.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
IV.
Applications
A. M o d e s of A p p l i c a t i o n . There are three basic modes of a p p l i c a t i o n w h i c h w e e n v i s i o n f o r N E W T O N : s t a t i c s , d y n a m ics and statistics. 1. Statics - M o l e c u l a r Structure. A s described above, and tested w i t h s m a l l m o l e c u l e s , once an inter m o l e c u l a r f o r c e f i e l d i s s p e c i f i e d , the a t o m s m o v e d into r o u g h l y t h e i r c o r r e c t positions and a v i s c o u s d a m p i n g applied, they m o v e smoothly and q u i c k l y to a m i n i m u m e n e r g y s t r u c t u r e . If t h e u s e r p e r c e i v e s that this s t r u c t u r e is a l o c a l and not a g l o b a l m i n i m u m , he c a n r e a c h i n w i t h the t o u c h i n t e r f a c e and nudge the a t o m s a l o n g , out of the l o c a l m i n i m u m . 2. D y n a m i c s - C h e m i c a l R e a c t i o n s a n d E v o l u t i o n of Molecular Systems. O n c e the u s e r h a s s p e c i f i e d the i n t e r m o l e c u l a r f o r c e s to b e u s e d a n d g u i d e d the m o l e c u l e s i n t o the d e s i r e d i n i t i a l c o n d i t i o n s , he c a n w a t c h the s y s t e m evolve i n t i m e , r e a c h i n g i n to t r i m i t u p en r o u t e i f h e w i s h e s . He can slow it d o w n o r f r e e z e f r a m e it at a n y m o m e n t to e x a m i n e it m o r e t h o r o u g h l y , a n d r e v e r s e i t a n d s t e p b a c k i n t i m e to c o r r e c t mistakes or repeat a sequence. The i n i t i a l c o n d i t i o n s c a n be s t o r e d and the r u n r e p e a t e d o r a l t e r e d , s t a r t i n g w i t h the b a s i s of a n y p r e v i o u s r u n . H e c a n t u r n k n o b s a n d z o o m i n to w a t c h j u s t t h e d y n a m i c s at the a c t i v e s i t e i n m o r e d e t a i l . Subsidiary p a r a m e t e r s or t h e i r functions can be c a l c u l a t e d and d i s p l a y e d a l o n g w i t h the e v o l v i n g s y s t e m , f o r e x a m p l e the c h a n g i n g f o r c e v e c t o r s o r v e l o c i t y v e c t o r s of a t o m s a s a r r o w s , b o n d l e n g t h s o r a n g l e s as n u m b e r s , e n e r g y f l o w w i t h i n o r b e t w e e n m o l e c u l e s , and p r o g r e s s along u s e r defined r e a c t i o n coordinates.
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TERMINAL SYSTEM
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Figure 5. Existing Hierarchical Computer Network used in test. NEWTON will depend upon the Hierarchical Network for large disk support and for most peripherals such as card reader/punch, line printer, tape, and plotter, as well as for links to the campus computer center and off-campus computers and users. The Hierarchical Network links 10 different minicomputers from seven different manufacturers (California Data Processors, DEC, Digital Scientific, IBM, Modcomp, Texas Instruments, and Varian) into a hierarchical three-level system. Level one is composed of various processors running laboratory experiments, and the Evans 6- Sutherland Picture System. Level two joins together three processors, one providing disk operating systems for all the processors as well as data management out of large disk storage, a second providing local processing on a time shared basis and a third handling the peripherals. Level three is a link to the campus computer center and its Burroughs B6700 and, at least for the moment, a link to the ARPANET. Communication from processor to processor, processor to peripheral and processor to experiment is by a universal hardware system based on the CAMAC convention. This project has involved the design and fabrication of ~ 30 different CAMAC modules, of which ~ 100 units have been built using ~ 10,000 integrated circuits.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch003
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3. S t a t i s t i c s - D i s t r i b u t i o n s of M o l e c u l a r P a r a m e t e r s . In r e a l i t y , m o l e c u l e s d e f i n e d b y m a c r o s c o p i c c o n d i t i o n s do not h a v e one s t r u c t u r e but r a t h e r a d i s t r i b u t i o n of s t r u c t u r e s . They do not r e a c t b y a s i n g l e r e a c t i o n p a t h , b u t r a t h e r b y a b u n d l e of trajectories. B y c a r r y i n g out s e t s of r u n s w i t h N E W T O N , w e c a n a p p l y c l a s s i c a l s t a t i s t i c a l m e c h a n i c s to a r r i v e at s u c h d i s t r i b u t i o n f u n c t i o n s . W e c a n i n v e r t the u s u a l v i e w of t h e E r g o d i c T h e o r e m , and m a k e the connection between m e a s u r e m e n t s w e d e r i v e o v e r the t i m e e v o l u t i o n of m o l e c u l e s to t h e d i s t r i b u t i o n s t o b e f o u n d i n a n e n s e m b l e o f m o l e c u l e s ( 5 0 , 51 ). To insure a g a i n s t b e i n g t r a p p e d i n l o c a l r e g i o n s of p h a s e s p a c e , w e c a n start different runs f r o m different initial conditions, all c o r r e s p o n d i n g to t h e s a m e m a c r o s c o p i c set of c o n d i t i o n s . T e m p e r a t u r e c a n be set b y i m m e r s i n g the m o l e c u l e s i n a bath of A r a t o m s o r Η £ θ m o l e c u l e s w i t h w r a p a r o u n d b o u n d a r y c o n d i t i o n s and i n j e c t i n g energy, k i c k i n g t h e m u n t i l the A r a t o m s o r H 2 O m o l e c u l e s (and the m o l e c u l e s of i n t e r e s t i n e q u i l i b r i u m w i t h them) r e a c h the d e s i r e d t e m p e r a t u r e . In this w a y e n t r o p y , t h e r m o d y n a m i c p r o p e r t i e s and t i m e c o r r e l a t i o n functions c a n be studied. B. Specific Biomolecular Applications. A l l molecules, their s t r u c t u r e s , d y n a m i c s , reactions, and statistical m e c h a n i c s , are potential applications for N E W T O N and its s u c c e s s o r s . We w i l l e m p h a s i z e h e r e t h e s t u d y of t h e d y n a m i c , a s c o n t r a s t e d t o the s t a t i c , f u n c t i o n of b i o m o l e c u l e s . T h e v e r s i o n of N E W T O N h e r e i n d e s c r i b e d s h o u l d be a b l e to h a n d l e s e v e r a l h u n d r e d a t o m s , and it c a n be e x p a n d e d to h a n d l e s e v e r a l t h o u s a n d a t o m s b y a d d i n g m o r e of t h e s a m e d i s t r i b u t e d p r o c e s s o r m o d u l e s . Many of the a p p l i c a t i o n s w h i c h a r e d i s c u s s e d b e l o w c a n be h a n d l e d b y the o r i g i n a l N E W T O N , w h i l e o t h e r s w i l l h a v e to w a i t f o r i t s m o r e p o w e r f u l p r o g e n y (son of N E W T O N = S O N o r d a u g h t e r of N E W T O N = D O N E ? ), d e p e n d i n g u p o n t h e n u m b e r o f a t o m s involved. Before we discuss particular biomolecular applications, w e s h o u l d c l e a r l y f o c u s o n the f a c t that a l m o s t a l l of t h e s e m o l e c u l a r s y s t e m s e x i s t and e v o l v e i n aqueous s o l u t i o n and that w a t e r m o l e c u l e s and often H , O H " and other ions are i m p o r tantly involved i n what happens. One c a n t r y to take into a c c o u n t the s o l v e n t e f f e c t s i n v a r i o u s w a y s (11), b u t the m o s t a p p e a l i n g to us i s to t r y to d i r e c t l y i n v o l v e the w a t e r m o l e c u l e s a n d i o n s by s u r r o u n d i n g the b i o m o l e c u l e s w i t h a b o x f i l l e d w i t h w a t e r m o l e c u l e s a n d o c c a s i o n a l i o n s ; the b o x h a v i n g p e r i o d i c o r w r a p a r o u n d b o u n d a r y c o n d i t i o n s s o t h a t , f o r e x a m p l e , e a c h e d g e of +
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DRIVER
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Figure 6. Block diagram of Touchy-Feely I touch interface, with touchstone (central hall) and suspension cables extending to the four corners of a tetrahedron. The position input section measures cable length by means of four cable winches with shaft encoders and reversing counters. The output section impresses force upon the touchstone by driving torque motors on the winch shafts. The computer transforms position and force by matrix operations be tween ordinary cartesian coordinates and the distorted tetrahedral coordinate system of the touchstone.
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the b o x is a l s o its opposite edge. w i l l r e q u i r e the a b i l i t y to p r o c e s s can provide this ability.
45 E x p l i c i t l y i n c l u d i n g the s o l v e n t m a n y a t o m s , but N E W T O N
S o m e of the m a n y p o s s i b l e b i o m o l e c u l a r a p p l i c a t i o n s
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g i v e n i n the f o l l o w i n g l i s t . 1. Protein Structure. A c l a s s i c a l a r e a of b i o m o l e c u l a r s t u d i e s i s the a t t e m p t to u n d e r s t a n d a n d p r e d i c t the r e l a t i o n s h i p b e t w e e n p r i m a r y p r o t e i n s t r u c t u r e o n the one h a n d a n d s e c o n d a r y , t e r t i a r y and e v e n q u a t e r n a r y s t r u c t u r e o n the o t h e r h a n d . Using the v i s c o u s r e l a x a t i o n d a m p i n g t e c h n i q u e , w h i c h i s a r a p i d l y c o n v e r g e n t p r o c e s s , N E W T O N c a n be a p p l i e d to the s t u d y of t h e s e r e l a t i o n s h i p s . A p r a c t i c a l a p p l i c a t i o n of N E W T O N w o u l d b e to t h e r e f i n e m e n t of p r o t e i n s t r u c t u r e s d e r i v e d f r o m x - r a y d i f f r a c t i o n (13, 52). In a d d i t i o n , c o n f o r m a t i o n a l t r a n s i t i o n s and p r o t e i n f o l d i n g c a n be o b s e r v e d a n d one c a n s t u d y c o o p e r a t i v e effects, m e t a s t a b l e i n t e r m e d i a t e s , t r a n s i t i o n v e l o c i t i e s and the p a t h to f i n a l s t a t e s (11). C o n f o r m a t i o n a l f l u c t u a t i o n s c a n be s t u d i e d a s w e l l a s t h e i r s t a t i s t i c a l m e c h a n i c s (11). Nucleic acid s t r u c t u r e c o u l d be t r e a t e d i n a n a l o g o u s f a s h i o n . 2. Protein Function. A s nearly all chemical reactions i n l i v i n g s y s t e m s are c o n t r o l l e d by e n z y m e s , the u n d e r s t a n d i n g of t h e d y n a m i c f u n c t i o n of t h e s e m a r v e l o u s m a c h i n e s i s a n obvious goal for N E W T O N u s e r s . A l l o s t e r i c effects m a y w e l l i n v o l v e a t o m i c m o t i o n s w h i c h r e q u i r e a d y n a m i c a n a l y s i s . It i s a t r u i s m that i f one c o u l d u n d e r s t a n d and c o n t r o l e n z y m e f u n c t i o n , one c o u l d c o n t r o l l i f e a n d i t s d i s e a s e s . Antigen-antibody specif i c i t y c o u l d be r e s e a r c h e d . T h e s e l f - a s s e m b l y of p r o t e i n s a n d other m o l e c u l e s into m o r e c o m p l e x s t r u c t u r e s s u c h as m e m branes, r i b o s o m e s , organelles, and v i r u s e s m u s t have a d y n a m i c c h a r a c t e r , w h i c h could be investigated. _3. Membrane Transport. T h e t r a n s p o r t of i o n s and molecules across membranes is an inherently dynamic process. I o n t r a n s p o r t a p p e a r s t o i n v o l v e e l e c t r o s t a t i c i n t e r a c t i o n s (53) w h i c h a r e d i f f i c u l t to u n d e r s t a n d o n the b a s i s of p l a s t i c , w o o d e n o r m e t a l m o d e l s h e l d i n the h a n d , but c a n be t r e a t e d j u s t as e a s i l y as s t e r i c f o r c e s b y N E W T O N . T h e a c y l c h a i n s i n the i n t e r i o r of a l i p i d b i l a y e r m e m b r a n e c a n p r o b a b l y l a r g e l y be m o d e l l e d o n the b a s i s of t h e w e l l - e x p l o r e d e q u i l i b r i u m f o r c e f i e l d s f o r a l k y l m o l e c u l e s (8). Perhaps membrane permeation i n v o l v e s not just i n d i v i d u a l m o l e c u l a r effects, but c o l l e c t i v e
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m u l t i m o l e c u l a r e f f e c t s as w e l l , i n a n a l o g y to the c o l l e c t i v e e f f e c t s c o m m o n i n s t e l l a r a n d p l a s m a d y n a m i c s ( 1 7 , 18) w h i c h w o u l d r e q u i r e the m o d e l l i n g of m a n y i n t e r a c t i n g m o l e c u l e s s i m u l t a n e o u s l y . M o d e l s f o r m o l e c u l e s w h i c h act as c a r r i e r s a c r o s s m e m b r a n e s (54, 55) c a n b e s t u d i e d , a n d s e r i e s o f a r t i f i c i a l c a r r i e r s ( 5 6 , 57) t r i e d o u t b e f o r e t h e l a b o r i o u s s y n t h e s i s of the m o s t p r o m i s i n g o n e s . T h e e f f e c t s of a p p l i e d e l e c t r i c f i e l d s c a n be o b s e r v e d , f o r e x a m p l e i n m o d e l s f o r the f i e l d c o n t r o l l e d o p e n i n g o r c l o s i n g of m e m b r a n e c h a n n e l s . 4. Pharmacology-Toxicology. A s mentioned above, c o n t r o l of e n z y m a t i c a c t i o n c o u l d b e a n a l m o s t u n i v e r s a l t o o l i n d i s e a s e c o n t r o l . D r u g - r e c e p t o r i n t e r a c t i o n c o u l d be s t u d i e d i n t e r m s of s t r u c t u r e a n d d y n a m i c s . D r u g d e s i g n c o u l d be a i d e d b y N E W T O N i n t h e c r e a t i o n of e n z y m e b l o c k i n g a g e n t s , a n t i b i o t i c s , c o m p l e x i n g a g e n t s ( 5 6 , 57) f o r s p e c i f i c m o l e c u l e s , f o r example particular metabolites. S u c h a b r o a d l i s t of a p p l i c a t i o n s , s p a n n i n g m u c h of b i o c h e m i s t r y a n d m o l e c u l a r b i o l o g y , i s of c o u r s e m o r e t h a n a n y investigator can tackle alone. We envision extensive collabor a t i o n w i t h o t h e r c h e m i s t s a n d b i o l o g i s t s a n d i n t i m e the r e p l i c a t i o n of m o r e N E W T O N S b y o t h e r s , p a r t i c u l a r l y a s the c o s t of l a t e r v e r s i o n s c a n be e x p e c t e d to d r o p p r e c i p i t o u s l y . C. Other Uses. N E W T O N i s a l s o a p p l i c a b l e to coupled differential equation p r o b l e m s .
other
1. Chemical Kinetics. E n z y m e kinetics and c o m p a r t ment m o d e l s c o u l d be treated, although stiff equation techniques ( 4 7 , 48) m i g h t b e n e c e s s a r y . 2. Mechanical System A n a l y s i s . Prosthetic device design and p h y s i o l o g i c a l m o d e l l i n g i n c l u d i n g blood c i r c u l a t i o n and o r g a n m e c h a n i c s s t u d i e s m i g h t be c a r r i e d out. 3. Electrical System Analysis. vide a tool for neural network analysis.
N E W T O N might pro-
4. F o u r i e r A n a l y s i s . In a d d i t i o n to c o u p l e d d i f f e r e n t i a l equation application, N E W T O N ' s floating point a r r a y p r o c e s s o r s w i l l ejctraordinarly quickly p e r f o r m Fast Fourier Transforms and t h u s c o u l d be a p p l i e d to x - r a y d i f f r a c t i o n a n a l y s i s f o r b i o molecular structure.
3.
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Conclusion
A. N e t w o r k i n g . W e a r e at the b e g i n n i n g of a n e w e r a in computer usage by scientists. Until recently a computer has b e e n s o m e t h i n g one p u r c h a s e d f r o m a m a n u f a c t u r e r , a m a c h i n e d e l i v e r e d off the s h e l f a n d d e s i g n e d to " d o a l l t h i n g s f o r a l l m e n . " N o w w e a r e g i v e n the o p p o r t u n i t y b y t h e a d v a n c e of c o m p u t e r technology to b u i l d o u r o w n c o m p u t e r s y s t e m to f i t o u r o w n specific needs, m u c h better and l e s s expensively than any general purpose machine. Thus scientists can build special c o m p u t e r s f o r s p e c i a l t a s k s , j u s t as t h e y t r a d i t i o n a l l y b u i l d o t h e r s p e c i a l i n s t r u m e n t a t i o n to f i t t h e i r n e e d s . We can p u r c h a s e s u b u n i t s on m a n y l e v e l s , f r o m i n t e g r a t e d c i r c u i t s to p r o c e s s o r s , or design our own subunits again ranging f r o m i n t e g r a t e d c i r c u i t s to p r o c e s s o r s . A s t h e p r i c e of t h e s u b u n i t s d r o p , a t t e n t i o n i n e v i t a b l y t u r n s to i n t e r - r e l a t i o n s h i p s ; h o w b e s t to a s s e m b l e s u b u n i t s i n t o h i g h e r l e v e l s of h i e r a r c h i c a l s y s t e m s , a n d i n p a r t i c u l a r , to t h e intercommunication among subunits. T h u s n e t w o r k i n g of s u b u n i t s i n t o l a r g e r s y s t e m s n a t u r a l l y c o m e s to o c c u p y o u r f o c u s as the s u b u n i t s b e c o m e m o r e e a s i l y a v a i l a b l e . T h i s a r t i c l e p r e s e n t s one e x a m p l e of s u c h a n e t w o r k e d system. N E W T O N , a t i g h t n e t w o r k of p r o c e s s o r s , s o m e p u r c h a s e d as u n i t s a n d s o m e b u i l t f r o m c o m p o n e n t s , w i l l h a n d l e a specific molecular dynamics task. It i s s u p p o r t e d b y a l o o s e h i e r a r c h i c a l n e t w o r k of p r o c e s s o r s w h i c h p r o v i d e d a t a m a n a g e ment, p e r i p h e r a l s and c o m m u n i c a t i o n for N E W T O N and for m a n y other tasks. In t u r n , the h i e r a r c h i c a l n e t w o r k r e a c h e s out a c r o s s the c o u n t r y to a c c e s s a n e t w o r k of c o m p u t e r i n s t a l l a t i o n s w h i c h c a n p r o v i d e a b r o a d m e n u of a d d i t i o n a l c a p a b i l i t i e s . B. Significance. The relation between structure and f u n c t i o n i n b i o m o l e c u l e s h a s p r o v i d e d one of the m o s t s t i m u l a t i n g a r e a s of s c i e n c e i n the p a s t t w o d e c a d e s . W e m a y n o w be at the b e g i n n i n g of a n e q u a l l y e x i c i t i n g n e w p e r i o d , the e l u c i d a t i o n of structure-dynamics-function. W e b e l i e v e that i n s t r u m e n t s s u c h as N E W T O N c a n be i m p o r t a n t t o o l s f o r s u c h e l u c i d a t i o n , a l l o w i n g the c o m p u t a t i o n a n d s t u d y of the d y n a m i c (and s t r u c t u r a l ) c o n s e q u e n c e s of i n t e r a t o m i c f o r c e f i e l d s a s r e f l e c t e d i n the t i m e e v o l u t i o n of b i o m o l e c u l a r s y s t e m s . W e f o r e s e e the t i m e w h e n w e c a n u n d e r s t a n d the m o v i n g m a c h i n e r y of l i f e : t h e m e c h a n i c a l molecular motions which are involved in transport across m e m -
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branes, in muscle contraction, in protein folding, in enzyme catalysis, in allosteric effects and in molecular self-assembly. Given such understanding, one can then attempt to design particular molecular machines for specific tasks in living systems. If one understands viral self-assembly, perhaps one can build a molecule which will disrupt this assembly. If one understands the action of an enzyme used by bacteria and not by man, perhaps one can build a substrate-substitute which will jam the active site mechanism, blocking its use. If one can understand the difference between the molecular genetic machinery in normal and malignant cells, perhaps one can design a molecular machine to shut down malignant cells. A l l these are very difficult tasks, perhaps a long way from realization. Yet their significance is great, both intellectually to our understanding of life and practically to our control of dis ease. Acknowledgement Support by the Division of Computer Research of the National Science Foundation and by the National Institutes of Health is gratefully acknowledged. We thank J. Cornelius and the staff of the Chemistry Department Computer Facility for the development of the Hierarchical Computer Network. Abstract Chemists have long dreamed that chemical properties could be derived in detail from classical equations of motion based on interatomic forces, but computational difficulties have blocked such calculations for larger molecules. The first difficulty is the large space of initial atomic positions and momenta which must be searched for those leading to chemically interesting results. The second problem is the computational time necessary to solve the coupled differential equations. We plan to collapse this search space with closer man-machine symbiosis based on visual and touch communication of spatial and dynamic chemical information and achieve sufficient computational speed with a network of computers, each handling specialized tasks. The internal computer network will handle this particular calculation several times as fast as a CDC 7600, and will interface with our existing local hierarchical network of computers interconnected through CAMAC modules. Preliminary
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simulation involving 3D man-machine visual and touch communication and computation on a minicomputer indicates that a practical system can rapidly handle calculations of structure, statistical mechanics and molecular dynamics of reaction for molecules involving several hundred to a thousand atoms. Literature Cited 1.
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2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15.
Dickerson, R. Ε . , Gray, Η. Β . , and Haight, G. P . , J r . , "Chemical Principles," W. A. Benjamin, Menlo Park, California, 1974, second edition. Ross, J., ed., "Molecular Beams: Advances in Chemical Physics," Interscience Publishers, New York, 1966. Schlier, C . , "Molecular Beams and Reaction Kinetics," Academic Press, New York, 1970. Margenau, Η., and Kestner, K. R., "Theory of Intermolecular Forces," Pergamon Press, Oxford, 1969. Levine, R. D., and Bernstein, R. Β . , "Molecular Reaction Dynamics," Oxford University Press, New York, 1974. Williams, J. D., Stand, P. J., and Schleyer, P.v.R., Ann. Rev. Phys. Chem. (1968) 19, 531. Kitaigorodsky, A. I., "Molecular Crystals and Molecules," Academic Press, New York, 1973. Engles, Ε. Μ., Andose, J. D., and Schleyer, P. v. R., J. Amer. Chem. Soc. (1973) 95, 8005. Andose, J. D., and Mislow, K . , J. Amer. Chem. Soc. (1974) 96, 2168. Hutchings, M. G . , Andose, J. D., and Mislow, Κ., "Empirical Force Field Calculations of Tetraarylmethanes and -silanes. II. Dynamic Stereochemistry," in press. Hopfinger, A. J., "Conformational Properties of Macromolecules," Academic Press, New York, 1973. Blout, E. R., Bovey, F. A . , Goodman, Μ., and Lotan, Ν., eds., "Peptides, Polypeptides and Proteins," John Wiley & Sons, New York, 1974. Levitt, M . , J. Mol. Biol. (1974) 82, 393. Hermans, J., J r . , and McQueen, J. E., J r . , Acta Cryst. (1974) A30, 730. Ramachandran, G. Ν . , in Bergmann, E. D., and Pullman, Β., eds., "Conformation of Biological Molecules and Polymers," p. 1, Israel Academy of Sciences and Humani ties, Jerusalem, 1973.
50 16. 17. 18. 19. 20.
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computer networking and chemistry Hagler, A. T . , Lifson, S., and Huler, Ε . , in Ref. 12, p. 35. Proceedings of the I. A. U. Colloquium No. 12, Cambridge, England, appearing as Astrophys. Space Sci. (1971) 13, 279-495. Alder, B., Fernbach, S., and Rotenberg, Μ., eds., Meth. Comp. Phys. (1970) 9. Lemberg, H. L., and Stillinger, F. H . , J. Chem. Phys. (1975) 62, 1677. Lorin, Η., "Parallelism in Hardware and Software," Prentice-Hall, Inc., Englewood Cliffs, New Jersey, 1972. Pattee, Η. Η., ed., "Hierarchy Theory," George Braziller, New York, 1973. Arbib, Μ. Α . , "The Metaphorical Brain," John Wiley & Sons, New York, 1972. Comptre Corporation, Enslow, Philip Η., J r . , ed., "Multiprocessors and Parallel Processing," John Wiley & Sons, New York, 1974. Murtha, J. C . , Adv. Computers (1966) 7, 1. Korn, G. Α . , Simulation ( 1972) 19, 2. Neilsen, I. R., Loma Linda University, private commu nication. Sackman, H . , "Man-Computer Problem Solving," Auerbach, Princeton, 1970. Sutherland, I. E., Proc. AFIPS, SJCC (1963) 23, 329. Sutherland, I. Ε . , Proc. AFIPS, FJCC (1968) 33, 757. Sutherland, I. E., Sproull, R. F., and Schumacher, R. Α., ACM Comput. Surv. (1974) 6, 1. Newman, W. Μ., and Sproull, R. F., "Principles of Interactive Computer Graphics," McGraw-Hill, New York, 1973. Roberts, L. G . , MIT Lincoln Laboratory Report, Lexington, Mass., June 1966. Wipke, W. T . , and Whetstone, Α . , SIGGRAPH Report (1971) 5. Noll, Α. Μ., "Man-Machine Tactile Communication," unpublished Ph. D. thesis, Polytechnic Institute of Brooklyn (1971); J. Soc. Inform. Dis. (1972) 1, (2). Vickers, D. L., "Sorcerer's Apprentice: Head Mounted Display and Wand," unpublished Ph. D. thesis, Dept. of Elec. Engineering, University of Utah (1973).
3. Wilson 36. 37. 38. 39. 40. 41.
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Burton, R. P . , "Real-time Measurement of Multiple Three-dimensional Positions," unpublished Ph. D. thesis, Computer Science Division, University of Utah (1973). Sutherland, I. Ε . , Proc. IFIP (1965) 2, 506. Batter, J., and Brooks, F. P . , J r . , Inform. Process. (1972) 71, 759. Lifson, S., and Warshel, Α . , J. Chem. Phys. (1968) 49, 5116. Kim, Y. S., and Gordon, R. G . , J. Chem. Phys. (1974) 60, 4323. Kim, Y. S., and Gordon, R. G . , J. Chem. Phys. (1974) 61, 1. Bergmann, E. D., and Pullman, Β . , eds., "Conformation of Biological Molecules and Polymers," Israel Academy of Sciences and Humanities, Jerusalem, 1973. Fraser, R. D. Β . , and MacRae, T. P . , "Conformation in Fibrous Proteins," Academic Press, New York, 1973. Madison, S., in Ref. 12, p. 89. Culler-Harrison, Inc., Santa Barbara, California, private communication. Rudy, Τ. Ε . , submitted to IEEE Special Issue on Parallel Processing, and private communication. Gear, C. W., "Numerical Initial Value Problems in Ordinary Differential Equations," Prentice-Hall, Inc., Englewood Cliffs, New Jersey, 1971. Gear, C. W., Comm. ACM (1971) 14, 176. Armstrong, T. P . , Harding, R. C . , Knorr, G . , and Montgomery, D., Meth. Comp. Phys. (1970) 9, 29. Tolman, R. C . , "The Principles of Statistical Mechanics," Oxford University Press, London, 1938. Rushbrooke, G. S., "Introduction to Statistical Mechanics," Oxford University Press, London, 1949. Levitt, Μ., and Lifson, S., J. Mol. Biol. (1969) 46, 269. Diamond, J. Μ., and Wright, Ε. Μ., Ann. Rev. Physiol. (1969) 31, 581. Szabo, G . , Eisenman, G . , Laprade, R., Ciani, S. Μ., and Krasne, S., in "Membranes, a Series of Advances," Vol. 2, G. Eisenman, ed., p. 179, Dekker, New York, 1972. Eisenman, G . , Szabo, G . , Ciani, S., McLaughlin, S., and Krasne, S., in "Progress in Surface and Membrane Science," J. F. Danielli, M. D. Rosenberg, and D. A. Cadenhead, eds., p. 139, Academic Press, New York, 1973.
52 56.
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57.
computer networking and chemistry Lehn, J.-Μ., in "Structure and Bonding," J. D. Dunitz, P. Hemmerich, J. A. Ibers, C. K. Jørgensen, J. B. Neilands, D. Reinen and R. J. P. Williams, eds., Springer-Verlag, Berlin, 1973. Cram, D. J., and Cram, J. Μ., Science (1974) 183, 803.
4
Geologic Applications of N e t w o r k Conferencing:
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C u r r e n t E x p e r i m e n t s w i t h the
FORUM
System
JACQUES VALLEE Institute for the Future, 2740 Sand Hill Rd., Menlo Park, Calif. 94025 GERALD ASKEVOLD U.S. Geological Survey, 345 Middlefield Rd., Menlo Park, Calif. 94025 Computer-based teleconferencing is a mode of communication which enables geographically separated users to jointly manage long-term projects, to organize "instant meetings" without the need for costly transportation, and to exchange documents and review position papers between face-to-face sessions. It thus fulfills a function quite different from that of the telephone, TELEX, electronic mail, or facsimile transmission. Since 1973, the Institute for the Future and a group within the U.S. Geological Survey have been jointly experimenting with this medium of communication. The experiments have used a family of systems--known as FORUM and PLANET--which the Institute implemented first on the ARPA network, later on a commercial network, and most recently on the Survey's own PDP-10 computer in Denver, Colorado. The experience of the Survey in using computer teleconferencing is typical of what can be anticipated when other scientific communities, such as chemists or physicists, begin to use such media, and thus provides some specific examples illustrating the design and use of these systems. The Conferencing System The basic idea of FORUM is to allow unhampered interaction of participants under the guidance of an organizer who defines a topic of discussion, assembles a panel of participants on that topic, and presents the material relevant to the subject. Each participant establishes communication with the computer network via a portable terminal with a standard typewriter keyboard. FORUM is able to convey questions and answers, assemble group opinions, protect anonymous statements, and supply other information to, and within, the group while the organizer monitors the proceedings and intervenes as necessary. In order to illustrate the nature of the interaction made possible by FORUM, i t is appropriate to imagine a hypothetical discussion among a group of experts on the subject of the projected availability of mineral and energy resources in the period 53
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1980-1990. The p a r t i c i p a n t s are about 20 i n number. Among them are planners, economists, g e o l o g i s t s , and petroleum experts. Two are s p e c i a l i s t s i n computerized data bases. In a d d i t i o n , there might be r e p r e s e n t a t i v e s from power and u t i l i t y companies and the p r e s i d e n t o f a mining c o r p o r a t i o n . The o r g a n i z e r o f the conference has experience i n d e a l i n g with groups and i s f a m i l i a r with the v a r i o u s techniques which can be brought t o bear on the e l i c i t a t i o n o f f o r e c a s t s and i n t u i t i v e judgments i n areas o f high technology. This h y p o t h e t i c a l conference d i f f e r s from the usual workshop i n t h a t the p a r t i c i p a n t s are not meeting f a c e - t o - f a c e . Instead, they are g e o g r a p h i c a l l y separated and use a v a r i e t y o f communicat i o n media. Some are s i t t i n g around a t e r m i n a l i n a Washington, D.C., o f f i c e b u i l d i n g . A g e o l o g i s t i s i n the computer room o f the Branch o f Computations o f the U.S. G e o l o g i c a l Survey i n Denver. One o f the economists i s i n h i s o f f i c e a t Stanford Univ e r s i t y . Another one may be s i t t i n g i n h i s study a t home i n New J e r s e y o r i n London, f o r t h a t matter. (These experts are i n telephone communication with a c e n t r a l operator who can i n s t a n t l y advise them o f the s t a t u s o f the conference, o f the progress o f work done i n subcommittees, or o f the reasons f o r any p a r t i c u l a r d i f f i c u l t y o r delay.) The substantive p a r t o f the i n t e r a c t i o n takes p l a c e through e n t r i e s typed on standard t e r m i n a l s . A l l o f the terminals are connected t o the network and are c o n t r o l l e d by a computer. The c e n t r a l problem o f implementing such a computer conferencing system c l e a r l y reduces t o that o f i d e n t i f y i n g , d e f i n i n g , and implementing a range o f s t r u c t u r e s under which the p a r t i c i pants are able t o share i n f o r m a t i o n and enter comments i n t o a common computer-storage file. The implementation o f a system l i k e FORUM r a i s e s unusual problems o f design: a group o f experts o r decision-makers typi c a l l y does not have much knowledge o f , o r i n t e r e s t i n , computer technology p e r se. There i s no opportunity t o t r a i n them i n the use o f a t e x t - o r i e n t e d language before the conference. And i t i s not f e a s i b l e t o ask them to i n t e r f a c e with t h e i r peers through information s p e c i a l i s t s because each p a r t i c i p a n t has a unique awareness o f the problem a t hand and needs t o experience d i r e c t contact with h i s data and with other p a r t i c i p a n t s i n order t o perform a t the " c u t t i n g edge" o f h i s t h i n k i n g . When a group o f conferees communicates v i a FORUM, each part i c i p a n t uses a t e r m i n a l o f the type t h a t can be rented f o r $150 a month o r l e s s . Once the t e r m i n a l has been logged i n t o the network, the user i s presented with a l i s t o f d i s c u s s i o n s which he can attend ( j u s t as he would i f he were t o walk i n t o the lobby o f a convention center t o review the day s program). Having s e l e c t ed an a c t i v i t y , the conferee i s given a s h o r t background s t a t e ment d e s c r i b i n g the a c t i v i t y . He i s then free t o observe the ongoing d i s c u s s i o n , t o review p a s t comments entered i n t o the conference, o r t o s t a r t t y p i n g h i s own remarks. A t any p o i n t d u r i n g 1
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the d i s c u s s i o n , a conferee can send a p r i v a t e message t o another p a r t i c i p a n t or make an anonymous entry. A l l of these communicat i o n modes can be entered without the p a r t i c i p a n t ' s having t o l e a r n a s i n g l e command, thus avoiding a major problem o f most i n t e r a c t i v e systems i n existence; namely, t h a t system commands get i n the way o f the person who types and c l u t t e r the t r a n s c r i p t with extraneous l i n e s that only have meaning f o r the machine. An important f a c e t o f FORUM conferences l i e s i n the ease with which the p a r t i c i p a n t s have access t o s e r v i c e s outside o f the d i s c u s s i o n i t s e l f : they can, f o r i n s t a n c e , submit a prepared statement t o the r e s t o f the group o r i n s e r t p a r t s o f the d i s c u s s i o n i n t o a personal f i l e . They can a l s o draw responses from a data-base system and enter them i n t o the general d i s c u s s i o n . C l e a r l y , the l e v e l o f i n t e r a c t i o n thus reached i s one not found i n f a c e - t o - f a c e meetings where experts are c u t o f f from t h e i r f i l e s and personal notes. The i n i t i a l tasks i n the FORUM p r o j e c t i n c l u d e d an a n a l y s i s o f the a v a i l a b l e resources and a review o f the e x i s t i n g t e r m i n a l technology i n terms o f character s e t , p l o t t i n g symbols, s i z e of frame, speed o f p r e s e n t a t i o n , and i n t e r f a c e standards. A decis i o n i n v o l v i n g the programming language t o be used had t o be made e a r l y ; a f t e r e x p l o r a t i o n o f the languages a v a i l a b l e on the PDP-10 under the ΤΕΝΕΧ o p e r a t i n g system, we r e l u c t a n t l y concluded t h a t assembly language was the only s u i t a b l e medium t o g a i n access t o shared f i l e s and t o c o n t r o l terminal behavior, both functions being c r i t i c a l t o our g o a l . A d d i t i o n a l requirements were speed and low c e n t r a l - p r o c e s s o r u t i l i z a t i o n . A c t u a l development o f the conferencing program proceeded through a s e r i e s o f stages i d e n t i f i e d as " r e l e a s e s . " Release 5 (FORUM-5) was thé f i r s t v e r s i o n t h a t could conveniently support heavy usage by r e a l - w o r l d p a r t i c i p a n t s . The code had been modif i e d t o make the e n t i r e program sharable. Performance measurements showed i t s c e n t r a l - p r o c e s s o r u t i l i z a t i o n r a t i o t o be e x c e l l e n t (one minute o f CPU time f o r two hours o f synchronous d i s c u s s i o n p e r p a r t i c i p a n t ) . Most command-language features became a v a i l a b l e t o the user w i t h i n the d i s c u s s i o n i t s e l f , and use o f c o n t r o l characters was p r a c t i c a l l y e l i m i n a t e d . The a b i l i t y t o r e t r i e v e and d i s p l a y past e n t r i e s by date, name, content, and range was made a v a i l a b l e . Network-wide d i s c u s s i o n s were conducted r o u t i n e l y and i n c l u d e d such t o p i c s as the design o f advanced t e l e c o n f e r e n c i n g systems, the transportation/communicat i o n t r a d e o f f s , and i n i t i a l exchanges o f research information with the Communications Study Group i n London. F0RUM-6, which was introduced on an experimental b a s i s i n August 1974 and was t e s t e d u n t i l December 1974, features a s i n g l e , i n t e g r a t e d command language, a g e n e r a l i z a t i o n o f the concept o f a conference t o make j o i n t authorship and other management tasks p o s s i b l e , and a scheme f o r handling p r i v a t e messages i n a persona l user f i l e r a t h e r than as p a r t o f the main d i s c u s s i o n . In October 1974, the I n s t i t u t e converted the FORUM program
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to a commercial network. This r e l e a s e i s t a i l o r e d e s p e c i a l l y t o the business environment and i s known as PLANET-1.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch004
Approach t o E v a l u a t i o n The I n s t i t u t e ' s approach t o e v a l u a t i o n has been founded on the concept o f computer conferencing as a means o f communication. The c r i t e r i a f o r e v a l u a t i o n o f a medium o f communication t y p i c a l l y i n v o l v e comparison with other media. And s i n c e the medium most f a m i l i a r to the m a j o r i t y o f us i s f a c e - t o - f a c e communication, there i s a tendency f o r i t t o become the standard o f judgment. One needs to e x h i b i t great care i n such comparisons because t e l e communications media are not n e c e s s a r i l y surrogates f o r f a c e - t o face p a t t e r n s . I t seems more l i k e l y that each medium has its own inherent characteristics which should not be expected to mimic f a c e - t o - f a c e p a t t e r n s . A t the same time, computer-based systems are too o f t e n evaluated and analyzed s o l e l y i n t h e i r own terms. In the case o f FORUM, we have sought t o r e l a t e observations o f the medium t o an e x t e r n a l s t a n d a r d — o n e which can apply t o many m e d i a — a s much as f e a s i b l e . In t u r n i n g t o the l i t e r a t u r e o f group communication, however, we do not r e a d i l y d i s c o v e r general p r i n c i p l e s o r procedures which are e a s i l y adopted as "standard." C e r t a i n l y the l i t e r a t u r e o f group process i s broad and p r o v o c a t i v e , and the p o t e n t i a l f o r r e l a t i n g group process research t o communication research i s r e a l , though complicated by many f a c t o r s . In designing our r e s e a r c h , we have sought t o answer two sets of q u e s t i o n s : 1.
What are the o p e r a t i o n a l c h a r a c t e r i s t i c s o f FORUM as a communications medium? What are the c h a r a c t e r i s t i c s o c i a l p a t t e r n s o f FORUM communication, and how might these be a l t e r e d ?
2.
What are the l i k e l y s o c i a l e f f e c t s o f communicating v i a FORUM on the i n d i v i d u a l and on the group? How can these s o c i a l e f f e c t s be measured? How can FORUM be compared to other media?
To answer the f i r s t s e t o f questions, we have devised a method f o r p l o t t i n g c h a r a c t e r i s t i c s o c i a l patterns and f o r analyzi n g the r e s u l t i n g graphs. A sample o f t h i s graph appears i n F i g u r e 1. In the second s e t o f questions, the problem o f comparison with other media has l e d t o a search f o r a general taxonomy—that i s , a comprehensive c l a s s i f i c a t i o n system f o r elements o f group communication—which could be employed across media i n various group communications s i t u a t i o n s . The e x i s t i n g taxonomies o f group process are p r i m a r i l y o r i ented toward communication between two persons (dyadic
VALLÉE
AND
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KEY Average message
Q
Geologic
length:
500
characters
CD-
Arrows
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conference
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facilitator
i n d i c a t e exchange patterns
f o r p r i v a t e messages
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Participation map showing characteristic social patterns
150
-
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communication). Even though a number o f experiments have been c a t e g o r i z e d as "group" communication, most of these have d e a l t with the i n t e r c o n n e c t i o n o f two f a c e - t o - f a c e groups ( i . e . , an i n d i v i d u a l i n f a c e - t o - f a c e contact with h i s own group and i n cont a c t v i a e l e c t r o n i c media with a s i n g l e d i s t a n t group). Extrapol a t i o n from dyadic p a t t e r n s t o group p a t t e r n s , however, i s quest i o n a b l e . The p r i n c i p l e s simply cannot be assumed t o be t r a n s ferable . In our i n i t i a l attempt to c o n s t r u c t a taxonomy, we have not t r e a t e d the dynamic aspects o f the communication, but have conc e n t r a t e d i n s t e a d on the elements i n a communication s i t u a t i o n before the i n t e r p e r s o n a l process begins. Our f i r s t , p a r t i a l taxonomy has thus been arranged to suggest a v a r i e d weighting among f i v e key factors—medium, task, r u l e s , person, and group—none o f which w i l l be completely d i s c r e t e . For i n s t a n c e , i f members of a given group have a very high need t o communicate, they are more l i k e l y t o make appropriate e f f o r t s to g a i n access to any medium, even i f i t i s d i f f i c u l t to use or u n f a m i l i a r t o them. Conversely, f a m i l i a r i t y with a p a r t i c u l a r medium i s l i k e l y to be a very imp o r t a n t f a c t o r i n the choice o f t h a t medium f o r p r a c t i c a l communication . The p r e l i m i n a r y r e s u l t s o f t h i s s o c i a l e v a l u a t i o n o f comput e r conferencing are presented i n Group Communication through Computers, Volume 2: A Study of Social Effects. More d e f i n i t i v e r e s u l t s are forthcoming. Review of Some E a r l y Experiments
with the U.S.G.S.
The Survey's i n t e r e s t i n c r e a t i n g and u s i n g data bases prompted us to begin our experiments by l i n k i n g mineral resource experts i n Washington, Denver, and Menlo Park i n t e l e c o n f e r e n c e s d i s c u s s i n g the present and f u t u r e a v a i l a b i l i t y o f f o s s i l f u e l and other commodities. Two data-base systems were a v a i l a b l e o n l i n e to the p a r t i c i p a n t s ; one of them was a data base o f petroleum reserves which was on the INFONET network, and the other was a catalogue o f Alaskan mineral resources s t o r e d i n the Stanford computer. (Transfer o f i n f o r m a t i o n i n and out o f the conference was achieved simply by having two s i t e s operate two t e r m i n a l s , one f o r the conference and one f o r the r e t r i e v a l system.) The t e l e c o n f e r e n c i n g system f o r these experiments was an e a r l y v e r s i o n of the FORUM system on the ARPA network. Although the d e t a i l s of the p r o j e c t have been reported elsewhere (1), i t i s u s e f u l t o review b r i e f l y i t s c o n c l u s i o n s , which encouraged us to enlarge the scope o f our j o i n t experimentation: 1.
The major advantage o f computer conferencing f o r these a p p l i c a t i o n s i s the a b i l i t y t o introduce human judgment at a new l e v e l i n an i n f o r m a t i o n system, l i n k i n g together not only users and sources o f data but i n f o r m a t i o n experts as w e l l .
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2.
In computer conferencing s i t u a t i o n s , group leaders can o b t a i n more d e l i b e r a t e answers to s p e c i f i c t e c h n i c a l questions, backed up by f a c t s and with l e s s delay. Both questions and answers are captured on r e c o r d and can l a t e r be reviewed.
3.
Computer conferencing appears to be e s p e c i a l l y u s e f u l i n c o o r d i n a t i n g t e c h n i c a l p r o j e c t s , when p a r t i c i p a n t s are widely disseminated (or t r a v e l i n g e x t e n s i v e l y ) and have a c o n t i n u i n g need f o r r e p o r t i n g and s h a r i n g notes.
4.
Users o f the medium have reported an a b i l i t y to d e a l with a l a r g e r amount of information more e f f i c i e n t l y than through the use of conventional media, such as m a i l and the telephone.
On the negative s i d e , a major drawback of the e a r l y system was the u n r e l i a b i l i t y of the experimental computer network we were u s i n g . Access was l i m i t e d , and frequent hardware f a i l u r e s made " r e a l " work a l l but impossible. In response to t h i s problem, we i n i t i a t e d two new approaches; namely, reimplementation of an advanced v e r s i o n of FORUM on the Survey's own hardware and research on the f e a s i b i l i t y o f i n t e r n a t i o n a l conferences using a commercial network. The FORUM System a t the U.S.G.S.:
Some I n i t i a l A p p l i c a t i o n s
During February and March 1975, a dedicated v e r s i o n of FORUM was mounted on the Survey's own PDP-10 computer i n Denver. T h i s i n s t a l l a t i o n marked the f i r s t instance i n which an advanced t e l e conferencing system had been completely turned over to an operat i o n a l group. Figure 2 shows a t y p i c a l entry process f o r a FORUM a c t i v i t y . C u r r e n t l y a v a i l a b l e conferences are presented as a m u l t i p l e choice l i s t f o r the p a r t i c i p a n t s . Once a conference has been s e l e c t e d , the agenda i s reviewed. In t h i s example, the user (Askevold) was up-to-date i n both p a r t s of the d i s c u s s i o n . He went to p a r t 1 and requested a l i s t i n g o f the e n t r i e s made so far. Three e n t r i e s were found (Figure 3). At t h i s p o i n t , another user (Betsy Yount) j o i n e d the d i s c u s s i o n from her own t e r minal, and p r i v a t e messages were exchanged (Figure 4 ) . Such messages are not r e t r i e v a b l e . Moving to the second p a r t of the conference, the user again reviewed the t r a n s c r i p t from Menlo Park and added an entry r e questing t h a t a f i l e of mineral i n f o r m a t i o n be loaded i n t o d i s k storage i n Denver (Figure 5). The data base systems under d i s cussion i n t h i s conference d e a l with the chemical analyses o f rock samples. An i n t e r a c t i v e storage and r e t r i e v a l system named GRASP (developed by Botbol and Bowen o f the U.S.G.S.) i s used f o r general g e o l o g i c a p p l i c a t i o n s (Figure 6 ) .
COMPUTER
NETWORKING
A N D CHEMISTRY
[ 7 2 1 , 7 2 2 ]
RUN FORUM
We1 c o m e . Please
-
type
your
last
name
(and then
strike
t h e CR k e y ) .
prints
on
Askevold
Please
type
your
password.
Good.
A r e you using
a
terminal
that
paper?
- Yes
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch004
Thank y o u . You
may a t t e n d 1.
Comments
2.
Background
3.
FORUM
k.
Canada
Please -
Figure
any one o f t h e f o l l o w i n g
type
o n FORUM
Users Test
o n RASS
and T e s t
on t h e Denver
System
Session o f FORUM
t h e number o f t h e a c t i v i t y
you wish
to join.
2
2. The FORUM
System at USGS: Joining a
The t i t l e o f t h e a c t i v i t y i s : B a c k g r o u n d o n RASS a n d T e s t o n t h e D e n v e r The
activities:
parts i nthe a c t i v i t y are: 1. General I n f o r m a t i o n o n RASS 2. I n s t r u c t i o n s o n How t o A c c e s s
Conference
System
RASS R e m o t e l y
(Using
GRASP)
(To FORUM) - GO ( t o p a r t ) 1 Part 1 General You
Information
o n RASS
a r e up t o d a t e .
(To FORUM) - REVIEW ( e n t r i e s ) a l l [1] A s k e v o l d ( O r g ) 1 5 - A p r - 7 5 9:23 AM The p u r p o s e o f t h i s a c t i v i t y i s t o g e t some i n f o r m a t i o n o n RASS w h i c h I d o n ' t h a v e , b u t n e e d p r i o r t o my d e p a r t u r e t o E u r o p e t o m o r r o w . I w i l l be s i t t i n g i n o n a m e e t i n g o f a n a d h o c Working Group o n Rock C h e m i c a l Data a t t h e UNESCO h e a d q u a r t e r s i n P a r i s o n A p r i l 29 a n d 30 a n d w o u l d l i k e t o c o n t r i b u t e s o m e t h i n g o n w h a t RASS i s a l l a b o u t , how i t i s u s e d , a n d t h e r o l e GRASP m i g h t h a v e ( a s R o g e r a n d J o e e n v i s i o n i t ) . [2] A s k e v o l d ( O r g ) 1 5 " A p r - 7 5 9:30 AM In p a r t 2 I h a v e l i s t e d my u n d e r s t a n d i n g o f how I s h o u l d a r r a n g e t o p u l l o f f a n A l a s k a s u b s e t o f t h e f i l e a s w e l l a s how t o a c c e s s w h a t i s c u r r e n t l y a v a i l a b l e f o r t e s t i n g ; I w o u l d a p p r e c i a t e c o n f i r m a t i o n f r o m someone o n t h i s a l o n g w i t h a n y t h i n g e l s e t h a t m i g h t be h e l p f u l . [3]
Askevold
Joe,
R o g e r m e n t i o n e d a n a r t i c l e o n RASS
shoot
(Org)
1 5 " A p r - 7 5 9:32 AM (that you authored);
could you
me t h e r e f e r e n c e ?
3 e n t r i e s were
found.
Figure 3.
Reviewing the conference transcript
VALLÉE
Geologic
A N D ASKEVOLD
Applications
(To FORUM) - STATUS ( o f p a r t i c i p a n t s ) Name Askevold Bowen Botbol Yount
L a s t Time E n t e r e d 15-Apr-75 3:^9 PM 15~Apr-75 6:25 AM Never e n t e r e d 15-Apr-75 3:36 PM
L a s t E n t r y Seen 6 4 6
(To FORUM) You
a r e now back i n t h e d i s c u s s i o n .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch004
(To Y o u n t ) - B e t s y , maybe y o u c a n g i v e me some o f t h e h e a v i e s t u s e r s o f RASS h e r e i n - M e n l o P a r k f o r f u t u r e r e f e r e n c e , and some o f t h e p r o b l e m s t h e y r u n i n t o - by h a v i n g t o o p e r a t e i n a b a t c h mode, and how g o i n g o n l i n e m i g h t s o l v e - some o f t h e s e p r o b l e m s . [7] Yount Some o f t h e h e a v i e s t u s e r s o f RASS h e r e i n Menlo P a r k a r e : t h e people a s s o c i a t e d w i t h t h e w i l d e r n e s s programs and t h e PAMRAP p e o p l e . The p e o p l e a s s o c i a t e d w i t h PAMRAP have no p r o b l e m s , o r r a t h e r , few p r o b l e m s i n u s i n g RASS b e c a u s e e a c h q u a d r a n g l e h a s a Denver r e s e a r c h c h e m i s t w o r k i n g w i t h t h e team l e a d e r a n d t h e y a r e t h e RASS i n t e r f a c e . Anyone e l s e w a n t i n g t o use RASS d a t a w h i c h t h e y have c o n t r i b u t e d t o — b y t h a t I mean t h e a n a l y t i c a l r e s u l t s o f t h e i r own s a m p l e s — h a s d i f f i c u l t y g e t t i n g t h e d a t a i n . (To Y o u n t ) -That's g r e a t , Betsy, thanks a l o t .
Figure 4.
Fragments of a synchronous discussion with private and public messages
(To FORUM) - GO ( t o p a r t ) 2 Part 2 I n s t r u c t i o n s on How t o A c c e s s
RASS R e m o t e l y
( U s i n g GRASP)
You a r e up t o d a t e . (To FORUM) - Review ( e n t r i e s ) a l 1 [ I ] A s k e v o l d ( O r g ) 15~Apr-75 9 : 3 3 AM My i n s t r u c t i o n t o t e s t GRASP on RASS i s t o : Run IRIS f r o m t h e Denver mac h i n e ; how l o n g w i l l t h i s be a v a i l a b l e ? I g o t i n t o i t o n c e , a n d have t o go b a c k t o t h e s e a r c h e x a m p l e s Roger s e n t me t o c o m p l e t e a v a l i d t e s t . [2] A s k e v o l d (Org) 15~Apr-75 9 : 3 6 AM The d a t a s e t s f o r ALASKA a r e : FI0RD.DAT, NEBESN.DAT, and YUKON.DAT. are protected.
They
[3] A s k e v o l d (Org) 15~Apr-75 9 : ^ 0 AM I am t o go i n t o SYS F a n d r e q u e s t MOUNT T 6 5 8 , c o r r e c t ? T h i s s h o u l d be f o r a few m i n u t e s . S h o u l d have two d i s c s mounted. I'm n o t r e a l l y s u r e I have a l l t h i s r i g h t , s o p l e a s e c o n f i r m . 3 e n t r i e s were
found.
(To FORUM) You a r e now b a c k i n t h e d i s c u s s i o n . [k] Askevold (Org) - R o g e r , c o u l d y o u p l e a s e do t h e above s o t h a t t h i s f i l e c o u l d be r e a d - o n t o t h e d i s c s p a c e t h a t Mony has s e t a s i d e f o r me, and g e t i t o f f h i s - hands? You may have t o g e t i n t o u c h w i t h h i m t o g e t e v e r y t h i n g - straight.
Figure 5.
Sample transcript with request for a file of mineral information
COMPUTER
NETWORKING
AND
CHEMISTRY
? While
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch004
may
in
the a c t i v i t y
you
can
type
an
entry
at
any
time.
To e d i t ,
you
type: Control
A to
delete
the
last
character
Control
W to
delete
the
last
word
last
line
Control
Q to
delete
the
Control
X to
delete
the whole
you
typed
entry
I η add i t i o n ,
To
Control
R will
retype
the
last
Control
S will
retype
the
entire
end
You
the
can
thesis
send "(",
message. vate (To -
entry, a
strike
private
followed
You can
message
to
also
FORUM
the c a r r i a g e
message
by
line
his gain
as
corrected
message
as
return
(CR)
to
a
participant
name,
a
carriage
access
itself
or
to
typing
special a
key
by
twice.
typing
r e t u r n , and services
[CTRL]
a
left
then
by
paren
your
sending
a
pri
F.
FORUM)
?
The
FORUM GO
services
(to
listed
below a r e
available
to
part)
you: FEEDBACK
QUIT
JOIN
(entries)
(activity)
REVIEW
(entries)
STATUS
REVIEW
(entries)
ADD
STATUS
(of
REVISE
(contents)
DELETE
(entries)
SAVE
participants)
(entries)
SUBMIT ASK If
corrected
(file)
(the
you
do
not
return
to
the
ERASE
following wish
to
(of
participants)
(participant)
(activity)
question)
use
any
of
these
services,
strike
the
CR
discussion.
Figure 6.
General user instructions amilable outline
key
to
4.
VALLÉE
AND
ASKEVOLD
Geologic
Applications
63
The a b i l i t y present i n FORUM to e l i c i t o n l i n e votes and t o feedback p r o b a b i l i t y d i s t r i b u t i o n s r e f l e c t i n g group judgment i n s i t u a t i o n s i n v o l v i n g reserve estimates o r e x p l o r a t i o n d e c i s i o n s represents a new dimension i n the use of i n f o r m a t i o n systems. These and other user options are r e a d i l y a v a i l a b l e t o any p a r t i c i p a n t i n a FORUM conference. The system i s self-documenting, so t h a t a p a r t i c i p a n t can type a question mark, e i t h e r during the d i s c u s s i o n or i n the FORUM s e r v i c e s mode, to r e c e i v e a l i s t of options a v a i l a b l e at t h a t p o i n t . F u r t h e r documentation i s provided when s p e c i f i c s e r v i c e s are requested. Figure 6 shows two general overviews o f the communication or r e t r i e v a l options a v a i l a b l e to the FORUM user.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch004
I n t e r n a t i o n a l Networking During 1974, we began moving the computer conferencing concept "out o f the l a b o r a t o r y " by implementing a conferencing program on a commercial timesharing network. The name o f t h i s new program i s PLANET, r e f l e c t i n g the major emphasis on j o i n t p l a n ning among disseminated user groups. At t h i s w r i t i n g , the PLANET system has been o p e r a t i o n a l f o r seven months. I t i s used by educ a t i o n a l i n s t i t u t i o n s i n France and i n the United States i n the c o o r d i n a t i o n o f j o i n t computing p r o j e c t s . We have a l s o had exp e r i e n c e with s e v e r a l a c t u a l "conferences" i n which p a r t i c i p a n t s made e n t r i e s through remote terminals over a two- o r three-week p e r i o d i n s t e a d of t r a v e l i n g to a c e n t r a l l o c a t i o n ; f o r such conferences, we have observed a c o s t r e d u c t i o n o f 50 to 60 percent over s i m i l a r f a c e - t o - f a c e conferences. Since A p r i l 1975, we have been h o l d i n g a continuous computer conference, intended as a computing experiment among members o f the COGEODATA community i n North America and Western Europe. F i g u r e 7 i l l u s t r a t e s the nature of the dialogue i n t h i s conference. The reader w i l l note from the time stamps t h a t some ent r i e s were made while a user was "alone" i n the conference, but others were "synchronous" (entries 20 to 28) with users i n P a r i s and i n Menlo Park p a r t i c i p a t i n g a t the same time. Conclusion In t h i s paper, we have d e s c r i b e d two communication systems i n c u r r e n t use by a s c i e n t i f i c community s h a r i n g geochemical and geol o g i c a l i n f o r m a t i o n . The f i r s t system, named FORUM, i s running on the computer of the U.S.G*S. i n Denver. The second system, named PLANET, i s a v a i l a b l e to commercial and e d u c a t i o n a l o r g a n i z a t i o n s on an i n t e r n a t i o n a l network. Such systems represent a s i g n i f i c a n t t o o l f o r the management o f j o i n t p r o j e c t s among disseminated groups. They make p o s s i b l e a r e d u c t i o n i n t r a v e l costs while promoting t i m e l y and accurate exchange o f data. They a l s o represent an a l t e r n a t i v e means o f p u b l i c a t i o n and a powerful medium f o r the dissemination o f s c i e n t i f i c i d e a s .
64
COMPUTER
[13] •
V a l l e e
Y o u r
t r i p
t e l e p h o n e s •
f r o m be
t o
b e
t o
t i m e .
t h e W o r l d
AND
CHEMISTRY
1:39 P M
o f f
a r e t h e w o r s t
t i m e
a t
22-Apr-75
seems
NETWORKING
t o
A l s o ,
F u t u r e
a
v e r y
p r o b l e m
g o o d
i n
B o b J o h a n s e n
S o c i e t y
i n
s t a r t .
E u r o p e ,
Y o u w i l l
b u t w e h o p e
w o u l d
l i k e
t o
p r o b a b l y t o
know
h e a r i f
f i n d
f r o m
t h a t
y o u
y o u e x p e c t
t o
J u n e ?
• [14] •
Y o u n t
G e r r y ,
I
h o w e v e r , •
R o g e r be
• Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch004
T h a d
u n t i l
s o o n
w i t h
p h o n e d
f o r
a r e g o i n g
o u r
a s
y o u r
B r u c e
•
y o u
•
T h a n k s
a
t h a n
MODEM.
i n
a n d l e t y o u know
g e t
[15]
b a c k ,
I
w i l l
A s k e v o l d
a
PM
i s
n o t
t h e a c c o u n t
n o w a r r a n g e d . a l r e a d y
h e r e .
3:30
I
a n d k e y w o r d
w i l l
PM h e r e .
O n e q u e s t i o n
f e e l i n g
i s
g e t t i n g
t h a t
more
w r i t e
( O r g )
b u t i s
i n f o r m a t i o n ;
n o t b e
a b l e
t o
I
t h a t
t h a t
h o p e
p h o n e w i l l
p u r p o s e s .
B r u c e ' s
i n t e r e s t
•
i t
s m o o t h l y
S t a n f o r d .
c o n f i r m
3 : 2 1
m a n u a l
a n d a l l
t o m o r r o w ,
e n o u g h
T h i n g s •
22-Apr-75
h a d t h e P L A N E T
a b o u t a
W i l l
A p p e a r s
t o
s e r v i c e . I f
h e r e I
w i l l
a n y t h i n g
r e g a r d i n g
s h o u l d
w r i t e
c h e c k
n e e d s
t o
c o n n e c t i o n a
memo
t o
f u r t h e r
w i t h
b e
b e f o r e
d o n e
f o r y o u .
9 : M
k e e p
b e
h a s a r i s e n
s o m e o n e
i t .
memo
23~Apr-75
l o t , J a c q u e s .
t h a t
A M
t h i s
g o i n g
s h o r t .
A m u s i n g
a
c o u p l e r
n o w
r a t h e r
o k a y .
• [16] •
A s k e v o l d
P l e a s e do
w i t h
a
• F O R U M , • [ 1 7 ]
•
b u t
• a n d
•
•
t h e r e I
g e t
t h a n k s ,
o n e
r e q u e s t
f o r m a l l y
p r e f e r
me t o
( w h i c h
a t t e n d
I
w i l l
w i t h
i t .
a
l i n e
f o r
h i g h e r
s p e e d
w o r k
w i t h
d o s o .
9 : 4 8 A M
w e n t
v e r y
e f f o r t .
w i t h
h i m more
c a n s e e f o r
i n , p l e a s e
e v e r y o n e ,
t o u c h
t o
w a y h e
d e f i n i t e l y
f o r m a l l y
s t u d y
a
9 : 4 7 A M
23-Apr-75
good
i n
i s
w o u l d
e v e r y t h i n g
a
Many t o
w e l l — b e y o n d
W i l l
t r y
t o
a n d t h e p e o p l e
R o g e r
B o w e n .
e x p e c t a t i o n s — i n
come
h e r e
W i l l
f i l l
y o u r
p a s t
i n
f r o m
a n d a t h i m i n
L o n d o n ,
P a ri s . . .
A T L A S a s
a r e
s o o n
a s
l e a v e
v e r y I
g e t
b a c k .
[ 1 9 ]
Bowen
G e r a l d — I •
( O r g )
l i k e
9 : 4 5 A M r e s p o n d i n g
2 3 " A p r - 7 5
We s h o u l d
r e p o r t
t o m o r r o w . a n x i o u s
i f
n o t
y o u c a n s h o o t
A s k e v o l d
l o o k s
b u t
( O r g )
I f
t o
23~Apr-75 B o b f o r
p h y s i c a l l y ,
B e t s y .
P l e a s e d
•
n o t
t h e C R T ' s .
[ 1 8 ]
t o
l e t t e r ) ,
A s k e v o l d
T h a n k s , •
( O r g )
a p o l o g i z e
t h a t
2 4 - A p r - 7 5
h a v e
t h e
y o u d i d n ' t
9 : 4 3A M
i m p r e s s i o n
g e t
t h e
i n f o
f r o m i n
r e a d i n g
t i m e
s o
I
a m g o i n g
t o
e n t r i e s
i n
FORUM
r e p e a t
i t
h e r e
( D e n v e r ) j u s t
c a s e .
• •
For RASS d a t a , t h e s y s t e m h a s b e e n r e n a m e d t h e s y s t e m , y o u a c c e s s IRIS b y : RUN I R I S ,
•
T h e r e
•
•
•
a r e 5
d a t a
s e t s
u p .
T h e y
a r e a s
(1)
RASS1
-
A n
i n i t i a l
d a t a
s e t f r o m
(2)
A L S K A
-
A l l A l a s k a
RASS
d a t a
(3)
YUKON
-
D a t a
f r o m
t h e Y u k o n
NABSN
-
D a t a
f r o m
t h e N a b e s n a
( 5 )
FIORD
-
D a t a
f r o m
t h e F i o r d
Figure 7.
O n c e y o u a r e l o g g e d ( f o l l o w e d b y C R )
f o l l o w s :
J e s s i e
(7000
(4)
I R I S . e t c .
r e g i o n
(>3000
r e g i o n
r e g i o n
W h i t l o w .
r e c s )
(<300
(<3000
r e c s ) r e c s ) r e c s )
Sample transcript
o n t o
i n
4.
VALLÉE
AND
ASKEVOLD
Geologic
Applications
65
Data s e t s 1 and 4 a r e ο η - l î n e in the p u b l i c a r e a ; data s e t s 2 , 3 , and 5 w i l l r e q u i r e a p r i v a t e d i s k to be mounted. I suggest that ( i n IRIS) a f t e r g i v i n g the f i l e command to i d e n t i f y a p a r t i c u l a r data base, the names command be issued to examine the s t r u c t u r e o f RASS data s e t s . Or i f you l e t me know, I ' l l send a copy of the output you w i l l get u s i n g t h i s command.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch004
[20] V a l l é e 24-Apr-75 4:18 PM G e r r y , I am p r e p a r i n g the d r a f t o f the paper f o r the American Chemical S o c i e t y meeting on computer networking and c h e m i s t r y . I am going over the m a t e r i a l we assembled. What about a t i t l e l i k e : "Network t e l e c o n f e r e n c i n g and M i n e r a l Resource I n f o r m a t i o n : Current Experiments w i t h the FORUM System?" [21] Askevold (Org) 28-Apr-75 9:47 AM I am a t t h i s moment in F o n t a i n e b l e a u a t the Centre de Recherche Informatique of the Ecole des Mines de P a r i s . Looking on w i t h me a r e : M. Kremer, M. B l o c h , and M. L e n c i . T y p i c a l problem now s o l v e d : t e r m i n a l s , but u s u a l l y hard w i r e d . An IBM, but w i t h a French keyboard. Solution: a teletype-vo i 1 a ! [22] Askevold (Org) 28-Apr-75 9:49 AM A c t u a l l y , the phone n o i s e i s not apparent a t a l l . G r e e t i n g s , Jacques and Thad. See your ESP radar i s s t i l l on t r a c k . . . a p l e a s a n t s u r p r i s e . What's happening? [23] Wilson 28-Apr-75 9:50AM Hi Gerry! Summer f i n a l l y has a r r i v e d in Menlo. grance o f s p r i n g ?
Is P a r i s f u l l of the f r a -
[24] V a l l e e 28-Apr-75 9:50AM G e r a l d , I am working on the f i r s t d r a f t o f the Chemical S o c i e t y paper. Perhaps I c o u l d t e l l you something about t h e . o u t l i n e , and you c o u l d g i v e me some f i r s t - o r d e r r e a c t i o n s before I proceed w i t h i t . Would you have time f o r t h a t ? As an a l t e r n a t i v e I can put t h i s i n t o the conference and you can react in the next few days. Which do you p r e f e r ? [25] Askevold (Org) 28-Apr-75 9:52 AM I should add t h a t the main purpose o f t h i s d i s c u s s i o n d o e s n ' t have to c e n t e r around RASS and G R A S P . . . . t h i s was o n l y f o r a s p e c i a l request p e r i p h e r a l to t h i s C0GE0DATA c o n f e r e n c e . [26] Wilson 28-Apr-75 9 : 5 3 A M Time f o r me to get back to computing s t a t i s t i c s , G e r r y . you. W i l l drop in l a t e r .
Good t a l k i n g w i t h
[27] Askevold (Org) 28-Apr-75 9:55 AM J a c q u e s , the t i t l e sounds f i n e . A c t u a l l y I have to c a t c h a bus back to P a r i s i n 15 minutes. I w i l l have access to t h i s same t e r m i n a l tomorrow, i f you can e n t e r what you have and I w i l l review i t tomorrow and g i v e you some immediate feedback. Okay? Good t a l k i n g w i t h y o u , and w i l l check back tomorrow. [28] V a l l e e 28-Apr-75 9:56AM Re 27: W i l l do. B o n s o i r , et s a l u t a l ' é c o l e des mines.
Figure 7.
(Continued)
66
computer networking and chemistry
This work has been supported by the U.S. Geological Survey and the National Science Foundation, Division of Computer Research. Literature Cited
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch004
A N e t w o r k o f R e a l - T i m e Mini C o m p u t e r s WILLIAM J. LENNON
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
Computer Sciences Department, Northwestern University, Evanston, Ill. 60201
INTRODUCTION The principal justification for having a mini or micro computer is the cost effective control and monitoring of real-time systems. A second justification is the relative ease with which independent, dedicated computers can be moulded to fit particular requirements. A common problem which can arise, however, is that when care is taken to improve user interaction or attention is paid to facilitating new program development, expensive additional resources are required. We solved this problem by building a flexible, resource distribution network to avoid two problems inherent in the routine procedure of expanding the peripheral complement of dedicated computers. First, because the truly expensive resources -printers, access to the University computer, etc. -- are required only intermittently, these resources will be used inefficiently and generally cannot benefit from economy of scale considerations. Second, and most important, each installation must invest in maintenance and development personnel eventually competing with one another for precious personnel support funds. It has been our experience that we can realize most of the economy of scale inherent in being a computing center without including most of the problems normally associated with use of such an installation* The network has been used routinely since the summer of 1971* The Computer Science Laboratory at the Technological Institute of Northwestern University is unusual, primarily because it was designed and is maintained, for the convenience of its users* It is a network of mini-computers, which has been designed to provide to remote computers easy access to commonly used peripherals and to the University's CDC 6400 and to support research in distributed resource computing (see figure 1)* The continuing growth of the system, and occasional changes that occur, are 67
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e f f e c t e d with minimum user inconvenience, as changes to the system do not r e q u i r e concomitant changes i n every e x i s t i n g program* Laboratory usage i n v o l v e s both real-time computing and computer system reseach* With few exceptions, software and l o c a l l y designed hardware are the work of volunteer or student p r o j e c t labor and t h e i r c o n t r i b u t i o n to the success of the l a b o r a t o r y cannot be overemphasized* They, i n t u r n , receive experience a t a nuts-and-bolts l e v e l not a t t a i n a b l e elsewhere* The s t i m u l a t i n g atmosphere of the l a b o r a t o r y f o s t e r s the development of these e n t h u s i a s t s who spend hours of t h e i r own time on p r o j e c t s f o r f a c u l t y members or fellow students* Their volunteer l a b o r , i n a d d i t i o n t o c e r t a i n design features of the system, make the network operation exceedingly economical* T e c h n i c a l l y , the laboratory houses a star-shaped network of real-time mini-computers, which i s interconnected to remote computers, most of which are DEC PDP-8 computers, although there i s no r e s t r i c t i o n as to computer type* The i n t e r c o n n e c t i o n hardware t r a n s e e i v e s characters using asynchronous s e r i a l communication a t a s u b s t a n t i a l rate (about 14,000 characters per second) with the r e c e i v i n g computer c o n t r o l l i n g the transmission of each c h a r a c t e r * This r e c e i v e r c o n t r o l e l i m i n a t e s the software overhead normally associated with such high speed communication by e l i m i n a t i n g the need f o r complex message handling and character s t r i n g b u f f e r i n g * Also, u t i l i t i e s and g e n e r a l l y needed programs are w r i t t e n to run i n the remote, rather than the c e n t r a l computer* The " i n t e l l i g e n c e " of the network i s thus d i s t r i b u t e d throughout the system, considerably s i m p l i f y i n g the maintenance and minimizing the impact of evolving s e r v i c e s and f a c i l i t i e s * The advantages of i n t e r c o n n e c t i n g a computer to the network are manyfold* The computer gains the a b i l i t y t o perform both q u a l i t a t i v e l y and q u a n t i t a t i v e l y beyond i t s own c a p a b i l i t i e s by using Network Central resources* The cost per computer i s very low — l e s s than that f o r paper tape equipment, while only under heavy load c o n d i t i o n s does i t s performance degrade to paper tape speeds* Interconnection hardware and software overhead i s minimal and the i n t e r c o n n e c t i o n i s e a s i l y accomplished* Many of the remote computers have only an instrument i n t e r f a c e , a t e l e t y p e console and a pseudo paper tape connection to the network* In t u r n , each interconnected computer strengthens Network Central by being a v a i l a b l e as a d i s t r i b u t e d i n t e l l i g e n c e resource to support other computers, when i t i s not otherwise being used* The c e n t r a l i z e d c l u s t e r of computers and p e r i p h e r a l s i s r e f e r r e d to as "Network C e n t r a l " t o d i s t i n g u i s h i t and the programs r e q u i r e d i n i t s operation from the "network" programs, which are g e n e r a l l y run i n remote computers that are supported by Network Central*
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PROCEDURES
Objectives
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
The goals of the network were to f a c i l i t a t e the design and implementation of new programs as well as g e n e r a l l y provide the necessary enhancement to dedicated, real-time computers to make them more f l e x i b l e , a c c e s s i b l e and g e n e r a l l y e a s i e r to use. These goals were a t t a i n e d by meeting the following four design o b j e c t i v e s both for l a r g e r machines and minimum c o n f i g u r a t i o n c o n t r o l computers which b e n e f i t most from access to shared resources. 1. Create an economical system by pooling expensive resources and by p r o v i d i n g easy access to i t with minimum hardware cost and minimum software overhead. 2. Run a l l e x i s t i n g programs without m o d i f i c a t i o n . 3. Provide a monitor which, while transparent to most programs, would provide f u l l access to a l l network resources for newly developed programs. 4. Evolve new f a c i l i t i e s without i n t e r f e r i n g with e x i s t i n g facilities. These o b j e c t i v e s have been met for both the minimum c o n f i g u r a t i o n c o n t r o l computer, which b e n e f i t s the most from access to shared resources, and the l a r g e r c o n f i g u r a t i o n computers.
Network Hardware
The key hardware for the network i s a u n i v e r s a l s e r i a l i n t e r f a c e [1] which by s u i t a b l e l o g i c card or connector changes w i l l transceive 11-unit, 8 - b i t s e r i a l characters at rates between 110 and 153,000 baud i n t o current loops, EIA RS232 i n t e r f a c e s , c o a x i a l cable or twisted p a i r transmission l i n e s . The hardware uses a reverse channel permission to send s i g n a l (see f i g u r e 2). Thus, i r r e s p e c t i v e of baud r a t e , the r e c e i v i n g device or computer d i c t a t e s character r a t e . Time c o n s t r a i n t s are e f f e c t i v e l y removed from high-speed communication with an attendant s i m p l i f i c a t i o n of the required software. The problem of character overruns has been e l i m i n a t e d . The reverse channel i s used by each r e c e i v e r to grant i t s corresponding t r a n s m i t t e r permission to send one character. In our c o n f i g u r a t i o n , four twisted p a i r interconnect computers using differential line driver/receivers. Commonly used p e r i p h e r a l s are i n s t a l l e d along with a s i x m i l l i o n word, moving head d i s k on a c e n t r a l machine. Time c r i t i c a l or temporary p e r i p h e r a l s are i n s t a l l e d on two a d d i t i o n a l c e n t r a l
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CDC 6400
(phone)
4k PDP-8/E
Network Central 8K PDP-8/I— (Graphics)
4K PDP-8/L (Editing) —32K PDP-8/E (Teaching Lab)
12K PDP-8/E(Graphics)
—VARIAN 73 (Microprogramming) —PDP-11 Network ( P r o t e i n Sequencing)
PDP-9 (Bio Med) D17B (Missle) 4K PDP-8/E(EE)
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
Imlac PDS-1 Display
— 8 K PDP-12 (Chem* Eng*) 8 K PDP-8/E 8K PDP-8/E -8K PDP-8/E ( M a t e r i a l Science)
8 K PDP-8/E8 K PDP-8/E(Freshmen) [DG NOVA 8 4 0 ] — [RAYTHEON 704]lChemistry)
— 8 K PDP-8/E (Bio Med)
4K PDP-8/M— (Interfacing)
--Intel Intellec-80 (Micro- computer)
Present Configuration of the Computer Science Research Network [Systems scheduled f o r 1975 expansion are i n brackets] Figure 1.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
D i r e c t access to p e r i p h e r a l s i s c u r r e n t l y denied, although inter-computer communication i s allowed for access to s p e c i a l i z e d equipment. The d e t a i l e d c o n f i g u r a t i o n of Network C e n t r a l i s shown i n f i g u r e 3. The c e n t r a l computer complex i s located i n the T e c h n o l o g i c a l I n s t i t u t e . I t communicates with a dedicated PDP-8/E i n an adjacent b u i l d i n g which i s i n t e r f a c e d to the CDC 6400 and the Imlac PDS-1 computers. The d i s k i s used to store working programs as w e l l as temporary f i l e s . A d i r e c t o r y records, by f i l e name, storage parameters, as well as c r e a t i o n and usage h i s t o r y . F i l e s are simple l i n k e d - l i s t s t r u c t u r e s of 384, 8 - b i t or 512, 6-bit character blocks stored as 256, 12-bit words. Data transmission to remote users i s s i n g l e buffered on a block b a s i s . Character transmissions are executed i n a foreground, i n t e r r u p t handler. Remote communication i n t e r r u p t s are serviced on a round r o b i n b a s i s to provide f u l l - d u p l e x monitor command d i a l o g without degradation during heavy load periods. Buffer completions r e s u l t i n a request to the background support program to i n i t i a t e d i s k i / o . Only inter-computer t r a n s f e r s which by-pass the d i s k approach the hardware design l i m i t of 14K characters a second ( i . e . 36 blocks of 384 c h a r a c t e r s ) . The maximum rate i n v o l v i n g d i s k t r a n s f e r s i s about 7.5 blocks a second. This maximum i s r e a l i z e d when only one one-way channel i s active (e.g. reading an e d i t o r f i l e when no other machines are making demands upon Network C e n t r a l ) . While t h i s low density operation i s g e n e r a l l y the case, transmission r a t e degrades to about 1 block a second e i t h e r when a s i n g l e user runs an input/output bound program or two independent users v i e for d i s k access. L i t t l e degradation beyond t h i s f i r s t l i m i t i s reached by a d d i t i o n a l users because the d i s k requests are e f f e c t i v e l y sorted by p o s i t i o n and queued during heavy load periods. The d i s k track access time i s the p r i n c i p a l factor i n t h i s degradation. The system design has been p u r p o s e f u l l y kept simple to permit changes with minimum user inconvenience. Only monitor command processing l o g i c i s o v e r l a i d on request to f a c i l i t a t e new command feature development. These overlays and the d i r e c t o r y are located i n the center of the moving head d i s k . The maximum delay i n decoding a request and i n i t i a t i n g s e r v i c e c u r r e n t l y i s two seconds during peak loads. Without any design changes a d d i t i o n a l users are e a s i l y served by a d d i t i o n a l b u f f e r memory and mass storage. The Network C e n t r a l program r e s i d e s i n a 12,288 word PDP-8/E i n which 5120 words are used as twenty-one disk/user b u f f e r s . Each a d d i t i o n a l 4096 words w i l l provide an a d d i t i o n a l s i x t e e n b u f f e r s . A user computer w i l l r e q u i r e at most two b u f f e r s at Network C e n t r a l . During peak loads when s i x of the remote machines are performing input/output, CPU u t i l i z a t i o n approaches 50%. The d a i l y average r a r e l y approaches 10%.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
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******* *
* 6M
«
* »
WORD DISK
* *
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Printer
*
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Paper Tape
cartridge Mag Tape
{ DEC Tape j _ [ 4K PDP-8/E j
\/ to CDC 6400's PDP-8/E
{ 8K PDP-8/E j -
\/
CDC 8090 ι — /
Synchronous Modem Controller
"ROM" Writer
to remote computers
Network C e n t r a l C o n f i g u r a t i o n (8090 P e r i p h e r a l s i n t e r f a c e d t o s i m u l a t e d PDP-8 e x t e r n a l busses)
Figure 3.
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Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
Network Programming C h a r a c t e r i s t i c s
The p r i n c i p a l o b j e c t i v e to e f f e c t i v e l y share resources was e a s i l y met. Most paper tape oriented programs can be run without m o d i f i c a t i o n . To take advantage of recent manufacturer emphasis on d i s k operating systems, the command s t r u c t u r e of the Network C e n t r a l monitor includes random access memory operations. A r o u t i n e complement of d r i v e r programs f o r the "systems device", mass storage, and s e r i a l f i l e s w i l l g e n e r a l l y s a t i s f y the needs of a user seeking to run unmodified mass memory operating system programs — with or without l o c a l mass memory. Simple communication between computers provides access to unique resources and i d l e computers to allow the easy a d d i t i o n of new support f a c i l i t i e s . F i n a l l y , the usual complement of u t i l i t i e s and system programs were w r i t t e n to run i n remote computers. This f a c i l i t a t e s the development of u t i l i t i e s p r i o r to assessing whether a p a r t i c u l a r f u n c t i o n should be included w i t h i n the complement of Network C e n t r a l command a c t i o n s . Transparency, as w e l l as concepts of r e l a t i v e e f f i c i e n c y or e f f e c t i v e n e s s , are best discussed by examining the i n d i v i d u a l c l a s s e s of computer support provided. In t h i s context, transparency i s taken to mean the user program i s g e n e r a l l y unaware of the support provided by the operating system. In p a r t i c u l a r , only changes e x p l i c i t l y requested are ever made to the remote computer memory holding the user program. R e a l i z i n g t h i s o b j e c t i v e i s p a r t i c u l a r l y important when s t r i v i n g to run unmodified vendor programs designed for minimum c o n f i g u r a t i o n c o n t r o l computers. Because most programs w r i t t e n for minimum c o n f i g u r a t i o n mini-computers ( i n c l u d i n g s i m i l a r micro-computers) include paper tape as well as teletype i/o support, network communication paths use c o n t r o l hardware which responds to high-speed paper tape i n s t r u c t i o n s . A unique c h a r a c t e r i s t i c of the operating system t r a d i t i o n a l l y used by t h i s c l a s s of computer i s i t s minimal r e s i d e n t . While obviously true for a paper tape based c o n t r o l computer, the philosophy i s g e n e r a l l y retained as mass memory based systems are introduced for the same machine — programs which ran with only paper tape support are expected to run with the new system. These a p p l i c a t i o n programs w i l l often be a v a i l a b l e only i n absolute binary form and cannot be moved to make room f o r any resident other than one f i t t i n g the minimal space o r i g i n a l l y reserved for the paper tape loader. This philosophy places severe r e s t r i c t i o n s on any network-connected system designed to support computers running t h i s c l a s s of programs. "Paper Tape" Based Computers
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
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Transparency i s achieved by having a resident monitor i n the remote computer occupy the area normally reserved for a paper tape loader. The monitor resident e f f e c t i v e l y connects the remote computer console d i r e c t l y to a Network Central machine where the majority of the monitor l o g i c r e s i d e s . Network Central r e p l i e s are p r e f i x e d and/or followed by non-printing command codes which are i n t e r p r e t e d by the r e s i d e n t while typing the message to the user. These non-printing characters may be used to automate system access without r e s o r t i n g to an a n a l y s i s of the character s t r i n g s designed for remote user communication. The resident includes a modified loader which i s c o n t r o l l e d by Network C e n t r a l . A f t e r a program i s loaded, a Monitor d i a l o g e s t a b l i s h e s a source of characters for the paper tape "reader", as well as a d e s t i n a t i o n for those "punched." A f t e r t h i s d i a l o g , an unmodified program operates as i f i t had a 14,000 character per second paper tape system. Since the same channel i s used for data and c o n t r o l information, Network C e n t r a l and l o c a l l y developed remote programs monitor data streams f o r an escape sequence (2 ASCII "CAN" codes) which never a r i s e s i n standard "paper-tape" transmissions. The remainder of the remote programs are u s u a l l y s e n s i t i v e to a "reader time-out" to s i g n a l end of f i l e . F i l e s which might a c c i d e n t a l l y contain the escape sequence are transmitted i n a 6-bit mode. Most of the Network Central commands are summarized at the end of the paper. An examination of the commands w i l l confirm the fact that t h i s c l a s s of computers requires the greatest l e v e l of support. The majority of the commands are oriented toward a user communicating with the Network C e n t r a l monitor to obtain programs and manipulate serial files. II
Paper Tape" program examples
In the f i r s t example, an unmodified program, the Focal language i n t e r p r e t e r , i s loaded and the Network Central f i l e s named OUTPUT and INPUT are assigned to serve the f u n c t i o n of paper tape punch and reader expected by the i n t e r p r e t e r . The Network Central Monitor prompts the user with a carriage r e t u r n / l i n e feed and sharp sign ("#"). Example 1.
#GET FOCAL
Load FOCAL i n t e r p r e t e r .
#ASSIGN OUTPUT
'/G i s the command to s t a r t a f t e r assignment.
CONGRATULATIONS ! ! !
Initial
f
d i a l o g of F o c a l .
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HAVE SUCCESSFULLY e t c . ( T y p i c a l time to d i a l o g i s 15 seconds)
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
A small mini-monitor (the resident l e s s loader l o g i c ) i s imbedded i n commonly used programs (e.g. E d i t o r s , Assemblers, Compilers) and the network d r i v e r s of l a r g e r , s e l f - s u p p o r t i n g operating systems. The following example shows the monitor and mini-monitor d i a l o g for a a modified "paper tape" assembler used to t r a n s l a t e a source program approximately 3000 characters long. The assembler obtains the date and time from Network Central f o r the l i s t i n g output. T r a n s l a t i o n under i d l e network c o n d i t i o n s takes about 40 seconds with the l i s t i n g pass taking an a d d i t i o n a l 65 seconds. As should be expected f o r a program designed for paper tape, the f i l e c o n t a i n i n g the source i s read three times. The second pass produces a binary tape image i n the Network Central f i l e "BINARY." The t h i r d pass produces a character s t r i n g stored i n the f i l e named "LISTING." When a l i s t i n g f i l e i s d i v e r t e d to the p r i n t e r , i t s name i s placed i n a queue which must be emptied by an operator at Network C e n t r a l . In a d d i t i o n , the l i s t i n g can be viewed using the standard e d i t o r program. The "%" symbol i s used to d i s t i n g u i s h mini-monitor from f u l l monitor d i a l o g s . Example 2.
#RUN PAL Ν
Load and s t a r t assembler.
%ASSIGN SOURCE
S t a r t pass 1.
%ASSIGN
Pass 2.
BINAR¥<SOURCE
%ASSIGN LISTING<SOURCE
Pass 3.
#DIVERT LPKLISTING
Queue the l i s t i n g for p r i n t out at #
Network C e n t r a l The normal e v o l u t i o n of a Network C e n t r a l f a c i l i t y begins with a remote computer program that provides s e r v i c e while we obtain usage data, suggestions and an assessment of i t s usefulness. Few u t i l i t i e s have demonstrated s u f f i c i e n t s t a b i l i t y to be included i n new v e r s i o n s of the c e n t r a l program. A s i m i l a r e v o l u t i o n occurs for programs which are modified to use network resources more e f f i c i e n t l y . The present assembler has s t a b i l i z e d as the example shows because most users f e e l that l i t t l e more would be gained f o r
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the e f f o r t involved to automate the d i a l o g . Four years experience i n d i c a t e s improvement i s due but that i t i s not a t r i v i a l task as the following example shows. Example
3.
#RUN PALΝ
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
%ASSIGN SOURCE1 %ASSIGN BINARY<S0URCE1
Remote command.
OUTPUT FILE EXISTS
Error
%SCRAP YOUR DIRECTORY
Remote command.
SAME TO YOU FELLA!!
Error
report.
retort.
%PURGE BINARY %ASSIGN BINARY<S0URCE1 etc.
At present, any programmed computer may have the same l e v e l of support as a PDP-8 c l a s s computer. Adequate disk space must be a v a i l a b l e to store e s s e n t i a l systems and a p p l i c a t i o n s programs. A r e s i d e n t , as w e l l as a mini-monitor, must be w r i t t e n f o r each unique computer. One powerful feature of the network i s the growing number of c e n t r a l l y maintained systems and u t i l i t y programs. To gain access to these older programs, as w e l l as provide access to newer programs f o r users of the o l d computers, p r o v i s i o n must be made to c o n t r o l programs running on one computer from another. The communications c a p a b i l i t y i s present and as more computers evolve to a size which can support mass memory operating systems having t r u l y device independent input/output, t h i s problem diminishes. Any user at any computer w i l l have the a b i l i t y to seek out an i d l e machine to run a program r e q u i r i n g a p a r t i c u l a r configuration. We are adding micro computers to the network as i f they were inexpensive mini computers. They t y p i c a l l y have a network r e s i d e n t and read/write memory. However, as p a r t i c u l a r a p p l i c a t i o n s are d e f i n e d , there w i l l be a growing number of dedicated processors using read-only memory to support a fixed a p p l i c a t i o n — say, e d i t i n g . A f t e r meeting t h e i r p r i n c i p a l requirement, the network r e s i d e n t w i l l then be used to communicate with and c o n t r o l other computers running a p p l i c a t i o n programs. Successful upgrade of most
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network machines to the general c a p a b i l i t i e s of those supporting operating systems w i l l mean a general trend away from machine language to higher l e v e l language programming. Newly developed u t i l i t y programs w i l l tend to become more machine independent. Mass Memory Operating System
Support
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
A network connection w i l l simultaneously support e i t h e r two s e r i a l f i l e s or up to s i x t y - f o u r random f i l e s . The random f i l e commands request the t r a n s f e r of e i t h e r subsequent blocks or s p e c i f i c blocks r e l a t i v e t o the beginning of a f i l e . These commands may be issued by program modules i n the remote computer to support a mass memory operating system. When c o n s i d e r i n g the support of a mass memory operating system i n the network, three d i s t i n c t l e v e l s are p o s s i b l e . Simplest of a l l i s supplying a s e r i a l f i l e d r i v e r to perform pseudo paper tape support to computers already capable of running the operating system. Second, mass memory d r i v e r s can be supplied which t r e a t i n d i v i d u a l f i l e s or groups of f i l e s as separate mass memory devices. F i n a l l y , a s p e c i a l "systems device" d r i v e r can be defined to use Network C e n t r a l resources i n l i e u of any l o c a l mass memory. The d e t a i l s concerning which combination i s p r e f e r r e d c l e a r l y depends upon the p a r t i c u l a r computer c o n f i g u r a t i o n and i t s base operating system. In the case of the PDP-8, we were able to run the OS/8 operating system using one t h i r d of the recommended minimum d i s k c a p a c i t y by adding one or both of the f i r s t two l e v e l s of support. The q u a l i t y of the "pseudo paper tape" software a l s o makes i t d e s i r a b l e to q u i c k l y boot i n and out of the operating system. By t r e a t i n g access to Network C e n t r a l as access to 64 separate devices we are able to overcome a severe operating system r e s t r i c t i o n . Blocks i n a f i l e are stored contiguously i n OS/8 so that i t i s i m p r a c t i c a l f o r OS/8 to allow more than one open output f i l e on a device. The second major operating system i n t e r f a c e d has been D i g i t a l Equipments's RSX-ll/M f o r the PDP-11. We have not attempted to use Network C e n t r a l to simulate the mass memory "systems device" but have concentrated on contiguous f i l e transmissions to gain access to the shared p e r i p h e r a l s and the CDC 6400. The approach to be taken, and the d e s i r a b i l i t y of mass memory s i m u l a t i o n i s a f u n c t i o n of the p a r t i c u l a r operating system to be supported. A f t e r a c e r t a i n l e v e l of s o p h i s t i c a t i o n i s passed, i t may no longer be cost e f f e c t i v e to simulate a mass memory device used f o r swapping and general overlay support. As operating systems become more complex, f i l e manipulation, d i r e c t o r y processing and access permission code maintenance may force the
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mount of l o c a l suport software to be excessive. In a l l cases we have achieved s u b s t a n t i a l performance improvements at minimal hardware and software overhead. I f more s o p h i s t i c a t e d systems than we have supported appear important enough f o r the a d d i t i o n a l e f f o r t , our approach would be to add an a d d i t i o n a l computer at the c e n t r a l s i t e to provide the a d d i t i o n a l algorithms r e q u i r e d f o r the several machines to be i n t e r f a c e d . We would adopt t h i s more conservative approach over making s u b s t a n t i a l changes to the c e n t r a l machine because of the ease with which the interconnected network computers could provide the required support i n a d i s t r i b u t e d fashion.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
Distributed
Computing
There are three a p p l i c a t i o n s areas which u t i l i z e the d i s t r i b u t e d c a p a b i l i t i e s of the network. F i r s t , a running CDC 6400 program can a c t i v e l y communicate with a program running e i t h e r i n a network computer or i n a p a r t i t i o n i n our time-shared PDP-8. The network-based program g e n e r a l l y acts as an i n t e l l i g e n t terminal for the 6400 program. Experimental r e s u l t s are frequently transmitted to the 6400 a f t e r which the a n a l y s i s i s d i r e c t e d from the remote computer. Second, a new p e r i p h e r a l i s often i n s t a l l e d on a remote computer rather than the Network C e n t r a l complex u n t i l i t s d r i v e r philosophy or f i n a l hardware i n t e r f a c e i s defined. Communication with a Network Central f i l e or another remote computer i s e s t a b l i s h e d to read from, or write to, the new p e r i p h e r a l . F i n a l l y , new program functions w i l l often be programmed to run i n a second remote computer which communicates with the f i r s t . In many cases the code to support a new f u n c t i o n w i l l e i t h e r not f i t or w i l l degrade the o r i g i n a l program performance below acceptable l e v e l s . In a recent a n a l y s i s of program behavior, a small data taking routine was imbedded i n a small time-sharing system. The data was logged at Network C e n t r a l where a second computer read i t , performing preliminary data r e d u c t i o n . In t h i s instance, minimal change to the monitored program took p l a c e . The performance of the program was m a r g i n a l l y a f f e c t e d by the data taking and far more s o p h i s t i c a t e d logging was p o s s i b l e because the i n i t i a l data reduction routine was not forced i n t o the already t i g h t program being analyzed. FUTURE DEVELOPMENTS
The system has reached a point of development during which the experience with current computers i s being applied to i n t e r f a c e new models. As f i g u r e 1 i n d i c a t e s , we expect to i n t e r f a c e Data General Nova's, DEC PDP-11's, and a Raytheon 704. We a n t i c i p a t e each unique computer or operating system w i l l require about
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500,000 words of d i s k storage. At the other extreme we some micro-computers.
79 are adding
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
One of the network computers supports a l o c a l l y developed time-sharing system used f o r l a b o r a t o r i e s i n computer o r g a n i z a t i o n and software fundamentals. We a n t i c i p a t e new a p p l i c a t i o n programs w i l l be developed to support t e r m i n a l , rather than computer, access to network resources. The communication between Network C e n t r a l and the CDC 6400 uses a t r a n s i e n t program running i n a computer i n the c e n t r a l complex. The d i a l o g with the 6400 i s more complicated than that used i n the remainder of the network. P a r a l l e l developments i n the computing center and i n our laboratory w i l l r e s u l t i n e f f e c t i n g simultaneous communications between s e v e r a l network-based programs and corresponding programs running on the CDC 6400. The r e s u l t a n t communications d i s c i p l i n e w i l l be such that we expect to support telephone-connected computers, as w e l l as the 6400, i f we add a dedicated computer for these tasks. CONCLUSIONS
The network has two key f e a t u r e s : F i r s t , the u n i v e r s a l s e r i a l i n t e r f a c e with r e c e i v e r c o n t r o l of character transmissions which minimizes i n t e r c o n n e c t i o n hardware and software, and secondly, the fact that " i n t e l l i g e n c e " i s d i s t r i b u t e d uniformly throughout the l o o s e l y connected remote machines. The r e s u l t i s an economical system which provides a marked increase i n f l e x i b i l i t y and a c c e s s i b i l i t y without s a c r i f i c i n g e s s e n t i a l real-time c a p a b i l i t i e s . The next l o g i c a l step i s to increase the connectiveness of i d l e machines to address the p a r t i t i o n i n g and d i s t r i b u t i o n of large data processing tasks. Our network design can be contrasted with networks of l a r g e r , s e l f s u f f i c i e n t batch processing or time-sharing computer systems where load l e v e l i n g or access to unique resources has been the aim, as a major f u n c t i o n of our mini-computers continues to be real-time o p e r a t i o n . Present intercomputer speeds allow us to r e l a x somewhat the common sense r e s t r i c t i o n that data storage and program execution f a c i l i t i e s r e s i d e i n the same l o c a t i o n . However, for real-time and o n - l i n e experiment c o n t r o l s , use of l o c a l storage i s encouraged for guaranteed response time and data i n t e g r i t y . Using Network C e n t r a l to store the only copy of a data f i l e e s s e n t i a l for achieving Nobel Laureate, tenure, or Ph. D. status i s proscribed. Within our mixed environment of real-time computing and computer system research, i t i s d i f f i c u l t to e n v i s i o n an approach which d i f f e r s other than i n d e t a i l from our present system. The two key
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features of our network can be easily achieved by other laboratories for much more powerful computing systems-. Because our experience emphasizes the desirability of initial homogeneity for maintaining adequate control of the evolution to a heterogeneous network, the existing population of mini-computers and their operating system should be considered when designing an initial configuration» LITERATURE CITED
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
1. Barrett R.C. and Lennon W.J. "A Universal Serial Interface for Data Set, Teletype, and Intercomputer Connection." May 1971 DECUS Symposium Proceedings. 2. Lennon W.J., Barrett R.C., and Spies J.T. "Northwestern's Mini-Computer Research Network." May 1972 DECUS Symposium Proceedings. 3.Lennon W.J., Henderson K.F., and Spies J.T. "A Read Only Memory peripheral for S-NET." November 1973 Decus Symposium Proceedings. Note: DECUS Symposium Proceedings reprints are available from either the author of the DECUS Headquarters in Maynard, Massachusetts. In addition, the Proceedings of the Society are available from University Microfilms. APPENDIX EXTRACT OF NETWORK USER'S GUIDE (Serial files) All commands may be specified by the first two letters of the command* The remaining letters until the first space character are ignored* Exceptional, one letter commands are noted* All command sequences must end with a carriage return* NOTATION: Character sequences a user must type are enclosed in single quotes* Sequences generated by Network Central are enclosed in double quotes* Optional sequences are bracketed* Parameters or strings will be indicated by lower case words* When required, non-printing characters will be denoted by three digit octal numbers in parentheses* IDENTIFICATION COMMANDS; 'LOGOFF' This command will close out all account data taking for this
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t e r m i n a l and ( u s u a l l y ) c a u s e t h e computer t o h a l t * When a new u s e r r e s t a r t s t h e c o m p u t e r , i n s t e a d o f t h e s t a n d a r d "#" prompt c h a r a c t e r from t h e Network C e n t r a l m o n i t o r , t h e l o c a l t e l e t y p e w i l l c o p y t h e f o l l o w i n g from Network C e n t r a l : "LOG ON! #"
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
The u s e r must t h e n t y p e i n h i s p a s s w o r d * Once l o g g e d o n , t h e accounting procedures then maintain a l o g of a l l data t r a n s f e r s from t h a t t e r m i n a l and a s s o c i a t e t h a t u s e r s i n t e r n a l a c c o u n t number w i t h a l l f i l e s c r e a t e d w h i l e u s i n g t h e c o m p u t e r * A u s e r s p a s s w o r d i s " s e c r e t " w h i l e t h e a c c o u n t number i s p u b l i c information* SERIAL F I L E MANAGEMENT AND GENERAL COMMANDS
~
F I L E NAMES: A f i l e name c o n s i s t s o f up t o t e n c h a r a c t e r s f o l l o w e d by an o p t i o n a l '•' f o l l o w e d by two c h a r a c t e r s c a l l e d an e x t e n s i o n * EXAMPLES: FROG
TEMP*PA
The e x t e n s i o n h e l p s t o i d e n t i f y what t y p e o f f i l e i s t h e r e * W i t h one e x c e p t i o n , t h e e x t e n s i o n i s used f o r u s e r i n f o r m a t i o n o n l y * The "*IM" e x t e n s i o n i s appended t o t h e program name a u s e r t y p e s when i s s u i n g a "RUN" o r "GET" command* Some commonly used extensions follow: •SY *IM *SV • 89 *PA *BN • FT *DA *LS *CR •TM • FC *BA *WU *TX *YF •WL *BS •01-.77
NETWORK SYSTEM F I L E NETWORK CORE IMAGE OS/8 CORE IMAGE 8090 BIOCTAL PROGRAMS PAL SOURCE NON-RELOCATABLE ( L I K E PAL) BINARY FORTRAN SOURCE DATA L I S T I N G , PROBABLY TEMPORARY CROSS REFERENCED L I S T I N G , TEMPORARY TEMPORARY FOCAL BASIC PROGRAM WRITEUP TEXT WJL'S, PURGE THIS — YOU'RE FIRED! NOT AS SEVERE AS *YF ABOVE PERSONAL, PROBABLY PHILOSOPHY F I L E S LOCAL TO A TERMINAL
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'ASSIGN' [ f i l e 2 ] 'ASSIGN' [ f i l e l ] '<' 'ASSIGN' [ f i l e l ] '<' [ f i l e 2 ] Assign Network Central f i l e s , f i l e l and f i l e 2 as output and input f i l e s , r e s p e c t i v e l y (the bracketed names are o p t i o n a l ) * Characters punched to a n u l l output f i l e are ignored while the end of information sequence, two ASCII CAN (230 o c t a l ) codes w i l l be read from a n u l l input f i l e . I f the " " character appears immediately a f t e r the f i l e name, that f i l e w i l l pack or be unpacked from the 1 2 - b i t word s i x b i t s at a time* Otherwise 8 - b i t packing i s assumed, three 8 - b i t characters to every two 1 2 - b i t computer words* Since Network Central monitors a l l received data transmissions f o r the end of information sequence, f i l e s which might a c c i d e n t l y contain that sequence are transmitted i n 6 - b i t mode*
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
Λ
'DIVERT' [odev] '<' [ f i l e ] D i v e r t the f i l e to the queue of an output device* [odev] stands for a s e q u e n t i a l output device and can be replaced by "LPT" or "PTP" under the current hardware c o n f i g u r a t i o n * An operator at the c e n t r a l s i t e must i n i t i a t e dumping of t h i s f i l e from the queue* The f i l e must be e x p l i c i t l y "PURGED" f o l l o w i n g the a c t u a l output operation* 'RUN' (OR 'R') [program name] Load the binary image f i l e i n t o core, r e l e a s e Network Central b u f f e r s and branch t o the program's s t a r t i n g address* The assumed extension on the f i l e i s 'ΙΜ'* An e x p l i c i t extension may be used to o v e r r i d e the assumed extension — E*G* "*89" f o r 8090 programs* 'GET'
[program name]
Load the binary image f i l e i n t o core but do not branch to the s t a r t i n g address* Return to the network command mode to enter more commands before s t a r t i n g * When a s e r i e s of "GET's" are typed i n , the s t a r t i n g address saved by the network r e s i d e n t i n the remote s i t e i s the l a s t one r e c e i v e d * The characters "/G" may be typed a f t e r e i t h e r an assignment or "ASSIGN" or "OFF" command causing the Network Central Monitor to s i g n a l the remote r e s i d e n t to s t a r t the remote computer a t the most r e c e n t l y received s t a t i n g address* 'STATUS' argument Where "argument" can be: 'FREE' P r i n t out how many f r e e blocks ( o c t a l ) are on the d i s k * 'CORE'
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P r i n t out how many 256 word b u f f e r s are l e f t * 'USER'
P r i n t the user (terminal) numbers f o r a l l computers a l l o c a t e d core b u f f e r s *
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
'DATE'
P r i n t today's date* 'TIME' P r i n t the current time* 'TNUM' P r i n t out your terminal number (The one logged by the USER s t a t u s command above)* 'LOG' P r i n t out how many un-dumped blocks of the system l o g are on the disk* 'VER' P r i n t out the current v e r s i o n number* 'ACCT' P r i n t out the account number c u r r e n t l y a c t i v e at t h i s t e r m i n a l * Account numbers are p u b l i c whereas the passwords are secret* 'FNT' [character] Included f o r completeness, t h i s command i s used only when performing "random access" input output with Net Central f i l e s *
'TALK' [ s t r i n g ] This allows a terminal to send messages to the network c e n t r a l console TTY* An a l e r t w i l l sound a t the c e n t r a l s i t e u n t i l acknowledged there* [ s t r i n g ] w i l l then p r i n t out at the console* The remote s i t e and console w i l l then be "short c i r c u i t e d " to allow f u r t h e r communications* A c o n t r o l χ terminates communication* 'OK' Type t h i s when a b u l l e t i n has been received to turn i t o f f * B u l l e t i n s are entered a t the c e n t r a l s i t e and broadcast to a l l newly logged on users* 'NAME' [ f i l e l ] 'NAME' [ f i l e l ] '<' [ f i l e 2 ] The f i r s t form of t h i s command creates an empty d i r e c t o r y entry with the name f i l e l * The second form renames the f i l e , f i l e 2 , to filel* 'OFF'
or '0'
Release a l l Network Central b u f f e r s * This command should be used
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to fr-ee up the two pages of core used f o r s t o r i n g the command s t r i n g . The network program w i l l e i t h e r r e t u r n to the system monitor of the machine a t the remote s i t e or w i l l h a l t * 'PURGE' [ f i l e ] Remove a l l traces of the f i l e from the network d i s k * I f the f i l e i s i n use by any remote s i t e or be on any output queue a "FILE BUSY" d i a g n o s t i c w i l l be issued* 'LINKS'
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch005
Make sure that the l i n k block pointers to a l l f i l e s are now stored on the disk* 'MERGE' [ f i l e l ]
',' [ f i l e 2 ]
Concatenate f i l e l and f i l e 2 with n u l l (000 o c t a l ) f i l l between* F i l e 2 w i l l disappear from the d i r e c t o r y and the merged f i l e w i l l be named f i l e l * MESSAGE TRANSMISSIONS: E r r o r messages and the l i n e r e s u l t i n g from a 'STATUS' request are preceeded by the message command character (004)* They are only one l i n e long and are terminated by a c a r r i a g e r e t u r n and l i n e feed (215,212)* They are then followed by the prompting sequence which ends i n the command character (005)· For any given command, the f i r s t character of p o s s i b l e error messages i s unique* The f o l l o w i n g i s a l i s t of a l l e r r o r messages: BAD DATE [Net Central only] BUSY FILE DEVICE BUSY [Net Central only] DISK FULL FILE NOT FOUND INVALID COMMAND INVALID DEVICE LOAD ERR LOG 75$ FULL [Net Central only] NO! NO CORE (OOPS) NOT ACTIVE [Net Central only] NOT IN QUEUE [Net Central only] OUTPUT FILE EXISTS QUEUE EMPTY [Net Central only] SYNTAX ERROR SAME TO YOU!! TOO FEW ARGS TYPE 'DATE MM*DD*YY' [Net Central
only]
6
A Computer Utility for Interactive Instrument C o n t r o l *
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch006
PAUL DAY Argonne National Laboratory, Argonne, Ill. 60439
I.
INTRODUCTION
With few exceptions, laboratory automation has proceeded by the interfacing of a mini-computer to each instrument that requires some type of real-time service; data acquisition, experiment control and/or the analysis of an on-going experiment. To those willing to invest considerable programming effort for each system or those whose needs may be satisfied by a commercially available package, this approach appears attractive. However, limited system f l e x i b i l i t y is the price paid for such systems, which price is derived from the inherent limitations of mini-systems; 16 b i t word size, fixed system resources, custom tailored programs (not modular), inherent difficulty of program development on a teletype, and unavailability of the computer for experiment control during code generation. The recent trend toward interconnecting several minis together into a network overcomes the limitations of fixed system size and provides the possibility of generating new code while real-time service is being provided. However, there is a class of instruments which require, and others which could greatly benefit by, real-time support which included the storage and analysis of large amounts of data (25K bytes/sec.) using such routines as fast fourier transformations, multi-point smoothing, least squares analysis and
*Work performed under the auspices of the U. S. Energy Research and Development Administration. 85
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matrix manipulation. T h i s type o f s u p p o r t cannot g e n e r a l l y be p r o v i d e d by a mini-computer network u n l e s s a computer w i t h s i g n i f i c a n t l y more c a p a b i l i t y than a m i n i i s connected t o t h e network. T h i s computer s h o u l d p r o v i d e s u f f i c i e n t s t o r a g e c a p a c i t y and c o m p u t a t i o n a l a b i l i t y (32 and 64 b i t f l o a t i n g p o i n t a r i t h m e t i c ) t o p e r m i t t h e r e a l - t i m e e x e c u t i o n o f 20 t o 30K word FORTRAN programs, and i t c o u l d f u r t h e r i n c r e a s e s c i e n t i f i c p r o d u c t i v i t y i f a l l t h e f i n a l a n a l y s i s f o r each experiment c o u l d be performed on the same system. Rather than a network, our approach i s more analogous t o an o c t o p u s , i n which a l l r e a l - t i m e s u p p o r t i s p r o v i d e d by d i r e c t c o n n e c t i o n t o a c e n t r a l computer. A c a r e f u l study o f the r e a l - t i m e r e q u i r e m e n t s o f our C h e m i s t r y D i v i s i o n i n 1967 i n d i c a t e d t h a t a c e n t r a l computer w i t h s u i t a b l e hardware f e a t u r e s , p r o p e r l y c o n t r o l l e d by an o p e r a t i n g system, c o u l d p r o v i d e a l l the advantages o f a l a r g e computer w i t h o u t s a c r i f i c i n g the i s o l a t i o n advantage o f t h e mini-computer i n t h e l a b o r a t o r y {!) . The o p e r a t i n g system must u t i l i z e t h e s e hardware f e a t u r e s i n a manner which w i l l p r o v i d e each u s e r w i t h t h e l e v e l o f r e a l - t i m e and o t h e r s e r v i c e r e q u i r e d t o run h i s experiment, w h i l e a t t h e same time i n s u r i n g a l e v e l o f d a t a and program i n t e g r i t y e n j o y e d by the i s o l a t e d mini-computer u s e r . To d a t e i t has not been n e c e s s a r y t o enhance our c e n t r a l comp u t e r ' s s e r v i c e by t h e a d d i t i o n o f a mini-computer between t h e c e n t r a l computer and t h e remote i n s t r u m e n t . However, some o f our remote i n t e r f a c e s do p e r f o r m c o m p u t e r - l i k e f u n c t i o n s which i n t e r a c t w i t h an i n s t r u ment on a m i c r o s e c o n d time s c a l e . At f i r s t g l a n c e , t h e i s o l a t e d m i n i - s y s t e m has t h r e e advantages o v e r a l a r g e r system ( i n c l u d i n g a m i n i - n e t w o r k ) : i s o l a t i o n i n s u r e s no c o m p e t i t i o n f o r r e s o u r c e s ; d a t a and program i n t e g r i t y are as good as the s t a n d - a l o n e s o f t w a r e package; s i n c e hardware f a i l u r e r a t e i s somewhat p r o p o r t i o n a l t o t h e number of components i n a system, t h e m i n i w i l l be o u t o f service less often. However, our system has demons t r a t e d t h a t i t i s p o s s i b l e t o meet t h e above s e r v i c e and i n t e g r i t y a s p e c t s . The o n l y d i s a d v a n t a g e o f our c e n t r a l system i s a hardware f a i l u r e r a t e o f about once i n 20 days compared t o m i n i s which o f t e n run f o r many months w i t h o u t f a i l u r e . However, our o n - l i n e u s e r s c o n s i d e r t h i s i n s i g n i f i c a n t compared t o t h e f o l l o w i n g advantages o f our c e n t r a l system: 1.
The system i s o f s u f f i c i e n t s i z e and speed t o p e r f o r m most d a t a a n a l y s i s i n r e a l - t i m e o r a t
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the c o m p l e t i o n o f an experiment. In the r a r e case t h a t more computing c a p a c i t y i s r e q u i r e d , 9 - t r a c k magnetic tape i s used f o r d a t a t r a n s f e r t o a l a r g e r computer. Dynamic s h a r i n g p r o v i d e s more r e s o u r c e s (CPU, c o r e , d i s k , magnetic tape) per experiment f o r a g i v e n c a p i t a l investment. F a s t program g e n e r a t i o n and debugging w i t h h i g h speed c a r d r e a d e r and l i n e p r i n t e r , a l o n g w i t h t h e use of modular programming t e c h n i q u e s makes program u p g r a d i n g easy enough t o keep up w i t h the r e s e a r c h s c i e n t i s t ' s changing needs. A t l e a s t seven of our o n - l i n e experiments a r e c o n s i d e r e d s t a t e - o f - t h e - a r t systems. Time-shared e x e c u t i o n of 25K word FORTRAN programs i n r e a l - t i m e . Batch e x e c u t i o n o f up t o 40K word programs f o r f i n a l a n a l y s i s . O n - l i n e keyboard d i s p l a y s and i n t e r a c t i v e g r a p h i c s r u n n i n g a t 9600 baud f o r w o r k i n g with data. D i s k s t o r a g e (75 megabytes) f o r d a t a (FORTRAN a c c e s s i b l e ) , programs and program o v e r l a y storage. Open-shop b a t c h - p r o c e s s i n g p e r m i t s o n - l i n e u s e r s t o d e v e l o p and debug t h e i r own FORTRAN programs which then have d i r e c t a c c e s s t o t h e i r data. Only a s m a l l programming s t a f f i s r e q u i r e d . A programming investment of 15 man-years has completed t h e o p e r a t i n g system and a p p l i c a t i o n s programs f o r 21 o n - l i n e e x p e r i m e n t s . An a d d i t i o n a l 8 man-years was i n v e s t e d i n t h e d e s i g n and c o n s t r u c t i o n o f the hardware i n t e r faces .
A l l c o n t r o l and o r g a n i z a t i o n a l a s p e c t s o f the System were d e s i g n e d , coded and implemented by our Chemist r y D i v i s i o n (2) . The f o l l o w i n g Xerox s o f t w a r e was i n t e r f a c e d t o t h e system; l o a d e r (BCM), assembler (SYMBOL), c o m p i l e r (FORTRAN IV-H) and FORTRAN r u n - t i m e / a r i t h m e t i c s u b r o u t i n e package. The c e n t r a l f a c i l i t y has been s e I f - r u n n i n g (no computer o p e r a t o r ) f o r over f i v e y e a r s 24 hours/day, 7 days/week w i t h t h e e x c e p t i o n of 8 h o u r s : 4 hours o f p r e v e n t i v e maintenance f o l l o w e d by 4 hours o f System development each week. The s y s tem i s c o n t i n u a l l y e v o l v i n g t o s u p p o r t new p e r i p h e r a l s (disks, i n t e r a c t i v e t e r m i n a l s , array processors, etc.) and t o p r o v i d e new s e r v i c e s as t h e needs a r i s e . Prov i s i o n s have been b u i l t i n f o r a u t o m a t i c r e c o v e r y from power f a i l u r e s , t o r e s t a r t f a u l t y p e r i p h e r a l s and t o cease u s i n g f a u l t y memory when d e t e c t e d . System uptime
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averages 157 hours p e r week w i t h one system c r a s h (down time averages about 40 minutes) about e v e r y 10 days ( h a l f a r e hardware r e l a t e d and t h e o t h e r system s o f t ware) . Automatic r e s t a r t f o r u s e r s i s a v a i l a b l e a f t e r weekly maintenance or a c r a s h . D a i l y c o p y i n g t o mag n e t i c tape o f a l l program and d a t a f i l e s s t o r e d on the d i s k s and RAD (Rapid Access Device - f i x e d head p e r track disk) insures users against c a t a s t r o p h i c f a i l u r e . A p a r t i a l l o s s o f d a t a c o l l e c t e d o v e r s e v e r a l hours has o c c u r r e d t h r e e times i n f i v e y e a r s as a r e s u l t o f h a r d ware f a i l u r e .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch006
II.
System S e r v i c e s
Computer C o n f i g u r a t i o n . The p r e s e n t computer conf i g u r a t i o n (Table I) has been i n c r e m e n t a l l y expanded from a 24K word system, w i t h o u t d i s k , s u p p o r t i n g 8 experiments t o t h e p r e s e n t system s u p p o r t i n g 21 e x p e r i ments and s i x independent g r a p h i c s / k e y b o a r d t e r m i n a l s . Sigma 5
CPU
Memory MIOP (2) CIOP Disk RAD ( f i x e d - h e a d d i s k ) 9 - t r a c k mag tape (2) Card Reader Line Printer Card Punch Paper Tape Digital Plotter TABLE I .
Central Processing Unit/ floating point arithmetic 56K 32 b i t words p l u s p a r i t y 750K b y t e s / s e c . bandwidth, 32 channels 21 110 baud t e l e t y p e , 2 1200 & 8 9600 baud t e r m i n a l s 251K b y t e s / s e c . t r a n s f e r , 25 megabytes χ 3 s p i n d l e s 170 K b y t e / s e c , 6 megabytes 60 K b y t e s / s e c , 800 b p i 1500 cpm 650 1pm 300 cpm 120 cps r e a d e r : 300 cps Punch: CALCOMP 565
Hardware C o n f i g u r a t i o n
Data T r a n s f e r . A l l u s e r and system d a t a i s han d l e d by i n p u t / o u t p u t hardware (MIOP) t h a t i n t e r a c t s with a l l devices running c o n c u r r e n t l y ; being capable of t r a n s f e r r i n g d a t a a t an aggregate r a t e of 750K b y t e s / sec. Thus, a d e v i c e seldom w a i t s more than a few mi c r o s e c o n d s f o r t r a n s f e r of a datum a f t e r i t s i g n a l s t h e MIOP t h a t i t i s r e a d y . Each u s e r ' s d a t a i s moved d i r e c t l y between h i s a s s i g n e d program c o r e memory and a d e v i c e ; t h e r e i s no system overhead r e q u i r e d beyond the time r e q u i r e d f o r MIOP t r a n s f e r .
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Real-Time Response. A s o f t w a r e p r i o r i t y i s a s s o c i a t e d w i t h each program c o n t r o l l i n g an i n t e r f a c e d i n strument. These p r i o r i t i e s a r e a s s i g n e d on t h e b a s i s o f i n s t r u m e n t r e q u i r e m e n t s a t system b o o t - i n t i m e . Upon r e c e i p t o f a r e q u e s t f o r program e x e c u t i o n (e.g. u s e r ' s d e v i c e s i g n a l s "done"), t h e u s e r ' s r e a l - t i m e program w i l l commence e x e c u t i o n a f t e r a time l a p s e t h a t depends on i t s p r i o r i t y . The h i g h e s t p r i o r i t y program w i l l commence e x e c u t i o n w i t h i n 160 microseconds, whereas the l o w e s t p r i o r i t y may not s t a r t e x e c u t i o n u n t i l up t o 200 m i l l i s e c o n d s l a t e r , i f one o r more h i g h e r p r i o r i t y programs a r e c u r r e n t l y " r e a d y - t o - r u n " . A s i m p l i f i e d r e a l - t i m e e x e c u t i o n s e r v i c e c y c l e may be r e p r e s e n t e d by t h e f o l l o w i n g : 1. Program r e q u e s t s a system s e r v i c e (e.g. s t a r t r e a d i n g d a t a from my d e v i c e ) 2. Program c a l l s e n d - o f - s e r v i c e (EOS) (program has n o t h i n g t o do u n t i l d a t a t r a n s f e r i s complete) 3. An MIOP i n t e r r u p t f o r t h i s d e v i c e i n d i c a t e s t r a n s f e r complete 4. Program p r o c e s s e s d a t a 5. Proceed t o s t e p "1" Custom Designed C o n t r o l Programs. Even though our e n g i n e e r s have e s t a b l i s h e d a b a s i c i n t e r f a c e d e s i g n and our programmers have d e v e l o p e d e f f e c t i v e t e c h n i q u e s f o r a c q u i r i n g d a t a and c o n t r o l l i n g i n s t r u m e n t s , each new system i s custom d e s i g n e d a t a l e v e l which w i l l b e s t s e r v e the u s e r ' s c u r r e n t and p r o j e c t e d needs. A command language i s e s t a b l i s h e d w i t h which the u s e r can e a s i l y communicate w i t h h i s programs i n a n a t u r a l manner. Program prompts a r e p r o v i d e d (e.g. "how many scans") so the u s e r does not have t o memorize an unfami l i a r mneumonic scheme. While our programming s t a f f d e s i g n s and w r i t e s t h e d a t a a c q u i s i t i o n and i n s t r u m e n t c o n t r o l p o r t i o n s of t h e package, u s e r s f a m i l i a r w i t h FORTRAN may code and use t h e i r own FORTRAN programs f o r r e a l - t i m e p r o c e s s i n g and/or f i n a l a n a l y s i s . User Communication and C o n t r o l . Human communicat i o n w i t h the computer system i s p r o v i d e d a t each r e mote e x p e r i m e n t a l s i t e v i a a KSR33 t e l e t y p e . At system b o o t - i n t i m e , i n p u t r e q u e s t s are i n i t i a t e d t o a l l comm u n i c a t i o n s t e r m i n a l s . A t any subsequent time, a u s e r may l o g - o n t o the system; a t which time s u f f i c i e n t c o r e memory space i s a s s i g n e d f o r t h e c o r e r e s i d e n t p o r t i o n o f h i s s p e c i f i c i n s t r u m e n t c o n t r o l program and i n t e r a c t w i t h h i s i n s t r u m e n t through t h i s program. Some o f the remote s i t e s a l s o have i n t e r a c t i v e g r a p h i c s t e r m i n a l s . In a d d i t i o n , s e v e r a l g r a p h i c s t e r m i n a l s and keyboard
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d i s p l a y s are s t r a t e g i c a l l y l o c a t e d f o r s h a r e d use. A u s e r may s i m i l a r l y l o g - o n and i n t e r a c t w i t h h i s graphi c s and/or computation programs from t h e s e t e r m i n a l s . The system p r o v i d e s the u s e r w i t h complete c o n t r o l of h i s i n s t r u m e n t i n t e r f a c e through the c o n s t r u c t i o n and e x e c u t i o n of any I/O command sequence t h a t can be e x e c u t e d by the MIOP and h i s d e v i c e . This permits the b u f f e r i n g of d a t a i n t o a u s e r ' s c o r e a r e a , w i t h i n t e r rupt i n d i c a t i o n s being passed t o the user's c o n t r o l program as each b u f f e r f i l l s , w h i l e t h e MIOP may initiate f u r t h e r d a t a t r a n s f e r i n t o another u s e r - s p e c i f i e d a r e a w i t h i n l e s s than 10 microseconds a f t e r a b u f f e r fills. System i n t e g r i t y i s i n s u r e d by c h e c k i n g f o r c o r e bounds v i o l a t i o n b e f o r e an I/O o p e r a t i o n i s i n i t i a t e d on the u s e r ' s a s s i g n e d d e v i c e . Mass S t o r a g e Usage. The system was d e s i g n e d t o maximize d a t a t h r o u g h p u t . T h e r e f o r e , d i s k (and RAD) f i l e s t r u c t u r e s were s i m p l y d e s i g n e d t o p r o v i d e random a c c e s s i n r e c o r d s i z e s o f t h e u s e r ' s c h o i c e . When d e f i n i n g a new f i l e , t h e u s e r p r o v i d e s t h e name and s i z e o f the f i l e t o be d e f i n e d . The system a s s i g n s a b l o c k o f c o n t i g u o u s s e c t o r s and r e c o r d s t h e f i l e name, l o c a t i o n , s i z e and c r e a t i o n d a t e i n t h e u s e r ' s d i s k r e s i d e n t f i l e index. The f i l e may be "opened" a t any subsequent t i m e , which t h e n p l a c e s t h e f i l e ' s s e c t o r bounds i n the r e q u e s t i n g l e v e l ' s PDT (program d e s c r i p tion table). The f i l e space w i t h i n t h e s e bounds may then be used i n any manner t h e u s e r chooses; however, d a t a t r a n s f e r always commences a t t h e b e g i n n i n g o f t h e l o g i c a l d i s k s e c t o r (LDS) s p e c i f i e d (one s e c t o r = 256 words). Each r e q u e s t c o n t a i n s t h e LDS, the c o r e add r e s s f o r d a t a t r a n s f e r and t h e number o f words t o transfer. The a c t u a l s t a r t i n g s e c t o r address i s t h e n d e r i v e d by t h e a d d i t i o n o f the LDS t o t h e lower s e c t o r bound ( c o r e - r e s i d e n t a f t e r f i l e i s "opened"). After i n s u r i n g t h a t t h e u s e r ' s c o r e and f i l e bounds w i l l not be exceeded, t h e o p e r a t i o n i s i n i t i a t e d . To f a c i l i t a t e t h e r a p i d u p d a t i n g o f l a r g e h i s t o grams, o n l y a p o r t i o n o f which can r e s i d e i n c o r e memo r y a t one t i m e , a w r i t e - r e a d f e a t u r e has been p r o v i ded. T h i s p e r m i t s t h e w r i t i n g back on t h e d i s k ( o r RAD) o f a j u s t - u p d a t e d p o r t i o n o f a h i s t o g r a m and the r e a d i n g i n t o the same c o r e a r e a o f t h e a d j a c e n t p o r t i o n of the d i s k - s t o r e d h i s t o g r a m ; a l l i n one d i s k r o t a t i o n . Non-Resident Program E x e c u t i o n . Our r e a l - t i m e c o m p u t a t i o n a l r e q u i r e m e n t s v a r y o v e r a wide range. p u l s e d NMR experiment r e q u i r e s scan a v e r a g i n g a 16K word h i s t o g r a m e v e r y 300 m i l l i s e c o n d s , t a k i n g about m i l l i s e c o n d s p e r update. While t h i s i s t h e h i g h e s t
Our 100
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usage r e q u i r e d by t h i s e x p e r i m e n t , i t i s needed o c c a sionally. Other experiments r e q u i r e t h e e x e c u t i o n o f a 25K word h i s t o g r a m t r a n s f o r m a t i o n program ( n u c l e a r f i s s i o n d e t e c t o r s ) e v e r y minute, t a k i n g about 5 s e c onds. Other u s e r s r e q u i r e t h i s t y p e o f e x e c u t i o n e v e r y 10 minutes f o r times r a n g i n g from a few seconds to 30 seconds. To s a t i s f y t h i s v a r i e t y o f demand w i t h o u t r e q u i r i n g an i n o r d i n a t e amount o f c o r e memory, t h e o p e r a t i n g system p r o v i d e s f o r the t i m e - s h a r e d e x e c u t i o n o f nonr e s i d e n t programs (not always i n core) i n t h e b a c k ground core a r e a . These programs are d i s k - r e s i d e n t core images o f r e l a t i v e l y l a r g e programs r e q u i r e d i n f r e q u e n t l y and w i t h o u t s e v e r e time c o n s t r a i n t s . Two queues are p r o v i d e d : one w i t h a 1 and t h e o t h e r w i t h a 32 second e x e c u t i o n time l i m i t . These programs are u s u a l l y FORTRAN which are u s e r - w r i t t e n o r from u s e r group l i b r a r i e s . T h i s system f u n c t i o n a l s o makes i t easy f o r the c a s u a l u s e r , who i s c o n v e r s a n t w i t h FORTRAN, t o perform h i s own r e a l - t i m e p r o c e s s i n g . P r i o r t o e x e c u t i o n , a n o n - r e s i d e n t program must be "opened",which c o n s i s t s o f c r e a t i n g and s t o r i n g the c o r e image on a d i s k f i l e and s e t t i n g t h e r e l e v a n t f i l e i n f o r m a t i o n i n t h e u s e r ' s PDT. M u l t i p l e programs may be opened and/or open a t one t i m e . At execution r e q u e s t t i m e , u s i n g the c o r e r e s i d e n t s i z e i n d i c a t i o n , the system w r i t e s a s u f f i c i e n t p o r t i o n o f t h e c u r r e n t lower p r i o r i t y t a s k on t h e d i s k and t h e n reads i n t h e c o r e image n o n - r e s i d e n t program. The t o t a l time r e q u i r e d between t h e r e q u e s t and t h e s t a r t o f nonr e s i d e n t e x e c u t i o n i s about 250 msec, f o r a 15K word program, i f no o t h e r r e q u e s t i s pending; o t h e r w i s e i t must w a i t i t s t u r n i n t h e queue. S e v e r a l o p t i o n s a r e a v a i l a b l e a t e x e c u t i o n t i m e ; c o r e page s i z e i f l a r g e r than the code, a u t o m a t i c "opening" o f u s e r ' s c u r r e n t f o r e g r o u n d f i l e s t o t h e n o n - r e s i d e n t program, queue s e l e c t i o n (1 or 32 s e c . time l i m i t ) and a "save" o p t i o n ( w r i t e program back on d i s k a t e x i t t i m e ) . The "save" o p t i o n a l l o w s s t e p - w i s e e x e c u t i o n . A t e n t r y time, a r e g i s t e r c o n t a i n s t h e address o f t h e r e q u e s t o r ' s c a l l i n g f u n c t i o n parameter t a b l e (which may c o n t a i n an argument l i s t of any l e n g t h ) f a c i l i t a t i n g argument t r a n s f e r . N o n - r e s i d e n t memory w r i t e l o c k s are "ORed" w i t h t h e r e q u e s t i n g l e v e l ' s w r i t e l o c k s , p e r m i t t i n g m o d i f i c a t i o n of the foreground core. C o n c u r r e n t User O p e r a t i o n s . A u s e r ' s program has the o p t i o n o f o v e r l a p p i n g d i f f e r e n t system s e r v i c e s . T h i s i s e f f e c t e d t h r o u g h a " t y p e " o p t i o n i n each c a l l a program makes t o t h e system, s p e c i f y i n g t h e t y p e o f
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a c t i o n t h e system s h o u l d t a k e a f t e r i n i t i a t i n g t h e request: 1. I n i t i a t e r e q u e s t and r e t u r n immediately 2. I n i t i a t e r e q u e s t and r e t u r n when r e q u e s t i s completed 3. Return i f o r when t h e p r e v i o u s r e q u e s t o f t h i s k i n d i s completed 4. I n i t i a t e r e q u e s t , c a l l e n d - o f - s e r v i c e and r e t u r n when r e q u e s t f i n i s h e d 5. I n i t i a t e r e q u e s t , r e t u r n immediately and r e t u r n when r e q u e s t f i n i s h e d M u l t i p l e " r e q u e s t f i n i s h e d " i n d i c a t o r s a r e saved i n t h e r e q u e s t o r ' s PDT, w i t h u s e r n o t i f i c a t i o n b e i n g p r o v i d e d on a f i r s t - i n - f i r s t - o u t b a s i s . Using combinations o f t h e above " t y p e s " , a u s e r program may o v e r l a p a number of o p e r a t i o n s t h a t do n o t have t o be completed i n a s p e c i f i c order. F o r example: 1. S t a r t d e v i c e r e a d i n g i n t o next d a t a b u f f e r 2. Move p r e v i o u s d a t a t o magnetic t a p e 3. Write data t o disk 4. Execute a n o n - r e s i d e n t program which g e n e r a t e s display data 5. Computation Having t h e o p t i o n o f b e i n g n o t i f i e d about t h e complet i o n o f t h e v a r i o u s p r o c e s s e s , t h e u s e r program can p r o c e e d as r e q u i r e d . Graphics F a c i l i t i e s . Graphics f a c i l i t i e s c o n s i s t o f a CALCOMP 565 d i g i t a l p l o t t e r and e i g h t T e k t r o n i x 4010 g r a p h i c s u n i t s , t h r e e o f which have 4610 h a r d copy units. T h e i r r e s p e c t i v e FORTRAN c a l l a b l e d r i v e r subr o u t i n e s w r i t e c a l c u l a t e d move-data t o t h e u s e r ' s d i s k plotter-file. A f t e r e x e c u t i n g t h e FORTRAN program i n the b a t c h mode, a r e a l - t i m e CALCOMP u t i l i t y program i s i n i t i a t e d , which r e a d s t h e move-data from t h e d i s k f i l e and w r i t e s t h i s d a t a t o t h e MIOP-coupled CALCOMP. Thus t h e slow moving CALCOMP p l o t t i n g i s performed w h i l e other batch jobs are running. The T e k t r o n i x i n t e r a c t i v e g r a p h i c s u n i t s a r e supp o r t e d w i t h d r i v e r r o u t i n e s t h a t execute a t a f o r e ground l e v e l which i n t u r n makes c a l l s t o t h e u s e r ' s n o n - r e s i d e n t code, r e t u r n t o t h e f o r e g r o u n d l e v e l r e a d s the move d a t a from t h e d i s k and t r a n s m i t s i t t o t h e T e k t r o n i x s c r e e n . Or, t h e f o r e g r o u n d w r i t e s an i n q u i r y on t h e s c r e e n and, a f t e r a subsequent u s e r r e s p o n s e r e t u r n s t h e r e s p o n s e t o t h e n o n - r e s i d e n t program v i a a new execute n o n - r e s i d e n t program r e q u e s t . Thus, nonr e s i d e n t core i s a v a i l a b l e f o r other users during w r i t i n g , r e a d i n g o r w a i t i n g f o r a u s e r t o r e s p o n d t o an i n quiry. P r o v i s i o n i s a l s o made f o r t h e u s e r ' s program t o a s c e r t a i n t h e c o o r d i n a t e s o f thumbwheel c o n t r o l l e d f
6.
DAY
Instrument
c u r s o r c r o s s h a i r s , p r o v i d i n g the u s e r f u r t h e r a c t i o n w i t h h i s program.
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Time-Sharing. P r e v i o u s l y c o m p i l e d and s t o r e d (batch mode) FORTRAN IV-H programs can be e x e c u t e d i n a t i m e - s h a r e d mode from any remote keyboard t e r m i n a l (numbering 31). The keyboard t e r m i n a l i s t r e a t e d as the I/O d e v i c e i n p l a c e o f the c a r d r e a d e r and l i n e printer. A c t u a l code e x e c u t i o n t a k e s p l a c e i n b a c k ground c o r e as a n o n - r e s i d e n t program between I/O statements. Programs e x e c u t e d i n such a manner a l s o have a c c e s s t o d i s k and RAD s t o r a g e . In a d d i t i o n t o the u s e r s ' s p e c i a l i z e d programs a l i b r a r y o f c o n v e r s a t i o n a l programs i s a v a i l a b l e . Routines f o r i n t e r a c t i v e g r a p h i c s t e r m i n a l s i n c l u d e : peak r e s o l v i n g , d a t a smoothing, s p e c t r a l d i s p l a y i n g . Interactive routines are a l s o a v a i l a b l e f o r m a n u s c r i p t g e n e r a t i o n u s i n g a t e x t - e d i t i n g package. Open-Shop B a t c h - P r o c e s s i n g . A very important f e a t u r e o f t h e system i s t h e s u p p o r t o f an open-shop b a t c h - p r o c e s s i n g s e r v i c e i n which jobs a r e queued through the c a r d r e a d e r . T h i s t y p e o f queuing p r o v i d e s the c a s u a l u s e r w i t h immediate feedback f o r the r a p i d debugging of h i s programs. B a t c h i s t h e o n l y l e v e l i n the system which has a c c e s s t o t h e " b a t c h p e r i p h e r a l s " ; c a r d r e a d e r , l i n e p r i n t e r , c a r d punch and paper tape reader/punch. The b a t c h l e v e l a l s o has a c c e s s t o d i s k , RAD and magnetic t a p e . A l t h o u g h t h e o n - l i n e u s e r has the o p t i o n o f p e r f o r m i n g e x t e n s i v e a n a l y s i s o f h i s experiment from h i s remote t e r m i n a l , t h e b a t c h l e v e l i s o f t e n u t i l i z e d where l a r g e amounts o f o u t p u t a r e i n v o l v e d and f o r the t r a n s f e r r i n g o f f i l e d a t a onto magn e t i c tape f o r a r c h i v i n g o r t r a n s p o r t t o a n o t h e r computer. The b a t c h l e v e l i s a l s o used e x t e n s i v e l y t o generate and debug code f o r t h e c o n t r o l o f o n - l i n e experiments. The b a t c h l e v e l uses a l l CPU c y c l e s not used by on-going f o r e g r o u n d p r o c e s s e s w h i l e no h i g h e r p r i o r i t y use (e.g. n o n - r e s i d e n t e x e c u t i o n , f o r e g r o u n d l o a d i n g , c o r e image g e n e r a t i o n ) i s r e q u i r e d of the background core a r e a . Under normal daytime system l o a d i n g , t h e f o r e g r o u n d u s e r s r e q u i r e about 10 p e r c e n t o f t h e CPU c y c l e s and the n o n - r e s i d e n t program e x e c u t i o n about another 40 p e r c e n t . Thus, i t appears t o t h e b a t c h u s e r t h a t h i s program i s e x e c u t i n g on a computer w i t h about h a l f t h e speed o f a Sigma 5 computer which was d e d i c a ted to batch-processing. Long-Term Computation. CPU u t i l i z a t i o n seldom exceeds 30 p e r c e n t i n a 24 hour p e r i o d even w i t h heavy r e a l - t i m e and b a t c h usage. The r e m a i n i n g CPU c y c l e s
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are made a v a i l a b l e f o r e x e c u t i n g v e r y l o n g (hours t o weeks) b a t c h - t y p e computations r u n n i n g a t a p r i o r i t y l e v e l below b a t c h p r o c e s s i n g . These j o b s d i f f e r from normal b a t c h i n t h a t t h e y o n l y have a c c e s s t o d i s k and RAD f i l e s , not t h e "batch p e r i p h e r a l s " . Once i n i t i a t e d (from t h e c a r d r e a d e r ) , the job i s r o l l e d i n t o b a c k ground c o r e anytime t h e r e i s s u f f i c i e n t c o r e space and h i g h e r p r i o r i t y usage p e r m i t s . The d a i l y s a v i n g o f f i l e s onto magnetic t a p e a l s o c o p i e s t h e c u r r e n t c o r e image (now s t o r e d on d i s k ) o f t h e l o n g term j o b a l o n g w i t h i t s d i s k and RAD f i l e s . A u t o m a t i c f i l e (and l o n g term) r e s t o r a t i o n a t system b o o t - i n s u p p o r t s e x e c u t i o n s e x t e n d i n g over l o n g p e r i o d s . Incremental Expansion. As more experiments a r e added t o t h e system, one i s concerned w i t h two t y p e s of system e x p a n s i o n ; hardware and s o f t w a r e . The Xerox hardware a r c h i t e c t u r e i s such t h a t e s s e n t i a l l y a l l hardware c a p a b i l i t y i s m o d u l a r l y expandable e x c e p t t h e CPU. For example memory can be expanded i n i n c r e m e n t s of 8K words t o a maximum o f 128K; I/O c h a n n e l s can be added i n groups o f 8 up t o 64 (2 MIOPS) u n t i l a n o t h e r memory p o r t i s added which would t h e n p e r m i t up t o another 64 c h a n n e l s . The a d d i t i o n o f a new i n t e r f a c e d instrument requires the p h y s i c a l connection of i t s a s s o c i a t e d d e v i c e c o n t r o l l e r t o t h e MIOP bus s t r u c t u r e , a one hour j o b , d u r i n g which computer power i s s h u t down. S o f t w a r e e x p a n s i o n need o n l y be c o n c e r n e d w i t h the g e n e r a t i o n of a p p l i c a t i o n s programs f o r each newly i n t e r f a c e d i n s t r u m e n t . The o p e r a t i n g system does n o t r e q u i r e any m o d i f i c a t i o n f o r a new e x p e r i m e n t . At system b o o t - i n time, a l l of t h e r e q u i r e d PDT's a r e g e n e r a t e d from l e v e l parameter cards,one p e r i n t e r f a c e . T h e r e f o r e , a new i n s t r u m e n t r e q u i r e s t h e a d d i t i o n o f o n l y one c a r d t o t h e boot-deck. The a p p l i c a t i o n s programs f o r a new i n s t r u m e n t a r e d e s i g n e d and w r i t t e n i n c l o s e c o n s u l t a t i o n w i t h t h e u s e r s w h i l e t h e new i n t e r f a c e i s b e i n g d e s i g n e d and c o n s t r u c t e d . T o t a l time from c o n c e p t i o n t o o p e r a t i o n runs about 3 t o 6 months. III.
C u r r e n t On-Line
Experiments
The 21 experiments p r e s e n t l y i n t e r f a c e d t o t h e Sigma 5 r e q u i r e w i d e l y d i f f e r i n g t y p e s and amounts o f service. Data t r a n s m i s s i o n r a t e s v a r y from one b y t e per minute t o 100,000 b y t e s p e r second o v e r s h o r t intervals. C o n t r o l r e q u i r e m e n t s v a r y from none, t o computing t h e a n g u l a r c o o r d i n a t e s o f a goniometer from a c r y s t a l l o g r a p h i c o r i e n t a t i o n matrix, to providing p u l s e s e q u e n c i n g f o r r a d i o f r e q u e n c y g e n e r a t o r s . Mass s t o r a g e r e q u i r e m e n t s v a r y from 1000 t o 1,000,000 words.
6. D A Y
Instrument
95
Control
R e a l - t i m e p r o c e s s i n g i n c l u d e s ; scan a v e r a g i n g 16K c h a n n e l s p e c t r a , p e r f o r m i n g mass-energy t r a n s f o r m a t i o n s on c o r r e l a t e d p u l s e - h e i g h t e v e n t s , f a s t f o u r i e r t r a n s f o r m s , l e a s t squares a n a l y s i s , d a t a smoothing and peak f i n d i n g . Table I I i s a l i s t o f the c u r r e n t l y s u p p o r t e d programs w i t h t h e i r a s s o c i a t e d i n s t r u m e n t s . Quantity 5 2
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch006
1 1 1 1 1 1
1 1 1 1 1 1 1 1
Research
Program
Instrument
Type
P a c k a r d 45 p u l s e height analyzer mass s p e c t r o m e t e r s routine chemical analysis (12 i n . 60° sec) B i o m a t i o n 8100 pulsed r a d i o l y s i s transient recorder B i o m a t i o n 802 stopped-flow k i n e t i c s transient recorder V i d a r 520 4 d a t a p r e c i s i o n heat c a p a c i t y a c q u i s i t i o n system time-of-flight c r o s s e d m o l e c u l a r beams detector neutron d i f f r a c crystal structures tometer b i o l o g i c a l system s t r u c t u r e s V a r i a n HR220 super-con p u l s e d NMR Nuclear Chicago very f a s t k i n e t i c s M u l t i s c a l a r (400) Cary 14 s p e c t r o chlorophyll studies photometer Cary 17H s p e c t r o matrix i s o l a t i o n photometer 30 f t . g r a t i n g s p e c t r o m e t e r p l a t e measuring comparator V a r i a n E-9 ESR primary photosynthesis spectrometer V a r i a n E-700 ENDOR p l a n t pigment s t u d i e s spectrometer e n v i r o n m e n t a l r a d i o a c t i v i t y m u l t i - d e t e c t o r (22) c o u n t i n g system e f f u s a t e spectromhigh-temperature chemistry eter fission
and n u c l e a r s p e c t r a
TABLE I I .
Current Interfaced
Instruments
P u l s e d N u c l e a r M a g n e t i c Resonance S p e c t r o s c o p y . T h i s system c o n s i s t s o f a V a r i a n HR220 s u p e r - c o n NMR o p e r a t i n g i n p u l s e d mode f o r p r o d u c i n g f o u r i e r t r a n s form 1h and l 3 c m s p e c t r a (3^£) . Automation i s p r o v i d e d t o c o n t r o l p u l s e s e q u e n c i n g w i t h up t o 10 interval-width pairs: p u l s e - w i d t h s o f 0.5 t o 511 m i c r o s e c o n d i n 0.5 m i c r o s e c o n d s t e p s and i n t e r v a l s o f r
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N
Μ x 2 (where M and Ν range o v e r 0 t o 31) . Data i s d i g i t i z e d w i t h an ADC (8 t o 13 b i t s e l e c t i o n ) and t r a n s m i t t e d d i r e c t l y t o computer memory i n groups o f up t o 16,384 c h a n n e l s w i t h d w e l l times o f as low as 16 y s e c w i t h o u t l o s i n g more than 5 p e r c e n t o f the s c a n s . Data l o s s i s hardware d e t e c t e d and s o f t w a r e compensa t e d ; i n c o m p l e t e scans are d i s c a r d e d . For shorter d w e l l time a h a r d w a r e / s o f t w a r e i n t e r l a c e f e a t u r e has been p r o v i d e d which t a k e s e v e r y N-th (N = 2, 4, 8, 16) d a t a p o i n t from Ν s u c c e s s i v e scans i n an a d v a n c i n g manner, r e q u i r i n g up t o 16 times l o n g e r a c c u m u l a t i o n p e r i o d s , but p e r m i t t i n g a c q u i s i t i o n o f s p e c t r a w i t h d w e l l t i m e s as s h o r t as 1 y s e c . Data i s s c a n - a v e r a g e d i n r e a l - t i m e onto a d i s k - s t o r e d h i s t o g r a m . After a c c u m u l a t i n g the d e s i r e d number o f scans t h e d a t a i s b a s e - l i n e c o r r e c t e d , apodized, f o u r i e r - t r a n s f o r m e d (4K c h a n n e l s r e q u i r e s 3 sec.) and phase c o r r e c t e d . S p e c t r a may be s t o r e d f o r f u t u r e comparison o r a n a l y sis. A " t a u " mode i s p r o v i d e d which w i l l a u t o m a t i c a l l y c o l l e c t and a n a l y z e s p e c t r a at up t o 10 s p e c i f i e d intervals. The s p e c t r o m e t e r i s p r i m a r i l y used f o r n a t u r a l products chemical s t u d i e s , e s p e c i a l l y i n photos y n t h e t i c pigments and i n e l e c t r o n t r a n s p o r t p r o t e i n s . Neutron D i f f r a c t o m e t e r . We have an e x t e n s i v e program i n v e s t i g a t i n g c r y s t a l and m o l e c u l a r s t r u c t u r e s i n t h e 10-300°K t e m p e r a t u r e range on t h e f o l l o w i n g types of m a t e r i a l s : hydrogen bonded such as h y d r a t e d p r o t o n s ; h i g h c o n d u c t i v i t y i n o r g a n i c complexes; b o n d i n g e l e c t r o n d e n s i t y s t u d i e s on i n o r g a n i c and b i o l o g i c a l compounds. Sigma 5 s u p p o r t f o r t h i s e f f o r t i n c l u d e s automation o f a f o u r - c i r c l e n e u t r o n d i f f r a c t o m e t e r (5^6_) , l o c a t e d one m i l e from the computer, which i s c o n t r o l l e d a t any l e v e l o f i n t e r a c t i o n s e l e c t e d by the experimentalist. T h i s i n t e r a c t i o n can be e i t h e r a t the r e a c t o r or i n the u s e r ' s r e m o t e l y l o c a t e d o f f i c e (not a t the r e a c t o r ) . User commands range o v e r t h e following: move c i r c l e "X" t o N-degrees, t a k e a count, scan a d i f f r a c t i o n peak i n a s p e c i f i e d r e g i o n and s t o r e i t s c o o r d i n a t e s , compute a p r e l i m i n a r y o r i e n t a t i o n matrix, determine the l o c a t i o n s of a s e t of r e f l e c t i o n s u s i n g the p r e l i m i n a r y m a t r i x , compute a least-squares adjusted o r i e n t a t i o n matrix u s i n g s e l e c t e d r e f l e c t i o n s , scan r e f l e c t i o n s (up t o 10,000) i n s e l e c t e d r e g i o n s o f r e c i p r o c a l s p a c e . These o p e r a t i o n s may e x t e n d o v e r p e r i o d s from minutes t o weeks (the program i s a u t o m a t i c a l l y r e s t a r t e d a t the a p p r o p r i a t e p o i n t a f t e r system shut-down o r c r a s h ) w i t h o u t human i n t e r v e n t i o n o r t h e y may be suspended, d i s c o n t i n u e d o r t e r m i n a t e d at any t i m e . With t y p i c a l c r y s t a l s i z e s ,
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about 150 t o 400 r e f l e c t i o n s a r e scanned p e r day. P r o v i s i o n i s a l s o made f o r r e a l - t i m e i n t e r a c t i v e e d i t i n g and g r a p h i c d i s p l a y o f d a t a . A n a l y s i s o f s t r u c t u r e s c o n t a i n i n g up t o 50 atoms i n t h e u n i t c e l l a r e g e n e r a l l y run i n b a t c h mode. The a n a l y s i s i n c l u d e s usage o f : the C a n t e r b u r y f o u r i e r program f o r o b t a i n i n g 3 - d i m e n s i o n a l f o u r i e r a n a l y s i s o f i n t e n s i t y ; ORFLS-3 l e a s t squares r o u t i n e w i t h i s o t r o p i c temperature f a c t o r s ; ORFFE-3 f o r o b t a i n i n g atom d i s t a n c e s , a n g l e s and d i h e d r a l a n g l e s . These programs may be run d u r i n g the d a t a a c q u i s i t i o n phase t o a s s i s t i n e s t a b l i s h i n g t h e measurement s t r a t e g y o f a p a r t i c u l a r l y d i f f i c u l t c r y s t a l system. Pulse R a d i o l y s i s . A broad range o f p u l s e r a d i o l y s i s experiments i s c o n d u c t e d a t t h e "LINAC" ( e l e c t r o n a c c e l e r a t o r ) l o c a t e d about 1200 f e e t from t h e computer. They have d e v e l o p e d a new method t o r e c o r d t h e time dependence a b s o r p t i o n o r e m i s s i o n spectrum produced by a single pulse of electrons. The time r e s o l v e d s p e c trum i s produced by an image c o n v e r t e r camera w i t h a s t r e a k c a p a b i l i t y (7_) . The s t r e a k image on t h e phosphor, which i s a two d i m e n s i o n a l a r r a y o f t h e a b s o r p t i o n (or e m i s s i o n ) , i s scanned by a TV camera and s t o r e d on a v i d e o d i s k . Under computer c o n t r o l : t h e v i d e o d i s k image i s scanned one l i n e a t a time; t h e scan i s d i g i t i z e d and s t o r e d as 2000 p o i n t s i n a B i o mation t r a n s i e n t r e c o r d e r ; t h e B i o m a t i o n d a t a i s t h e n t r a n s m i t t e d t o a d i s k f i l e on t h e computer. This p r o c e s s i s r e p e a t e d u n t i l t h e d a t a from about 100 s c a n l i n e s has been s t o r e d . The d a t a from one s c a n l i n e r e p r e s e n t s the l i g h t i n t e n s i t y a t one wavelength as a f u n c t i o n o f t i m e . The e x p e r i m e n t e r may view t h i s d a t a and i n t e r a c t w i t h h i s a n a l y s i s programs v i a a T e k t r o n i x g r a p h i c d i s p l a y u n i t , which has a 4610 h a r d copy u n i t . A f t e r f u r t h e r p r o c e s s i n g , a FORTRAN program i s u s e d t o generate a 3 - d i m e n s i o n a l d i s p l a y o f i n t e n s i t y v e r s u s wavelength and t i m e . A l t e r n a t e programs a r e a v a i l a b l e to g i v e 2 - d i m e n s i o n a l p l o t s o f i n t e n s i t y v e r s u s wavel e n g t h . The e n t i r e p r o c e s s o f o b t a i n i n g t h e d a t a and s t o r i n g i n t h e Sigma 5 t a k e s a matter o f minutes comp a r e d t o days by t h e c o n v e n t i o n a l methods and makes working w i t h h i g h l y r a d i o a c t i v e m a t e r i a l s more f e a s i b l e . In measuring f a s t k i n e t i c s (50 p i c o s e c o n d r i s e t i m e ) which a r e i n i t i a t e d by a p u l s e o f e l e c t r o n s , s i g n a l s a r e o f t e n s m a l l and s i g n a l - t o - n o i s e r a t i o s a r e l i m i t e d by s h o t n o i s e , which means a g r e a t d e a l o f s i g n a l a v e r a g i n g may be n e c e s s a r y . The computer system a l l o w s the s a v i n g o f p a r t i a l a v e r a g e s , so t h a t l o n g a v e r a g i n g t i m e s may be used w i t h o u t f e a r o f l o s i n g e v e r y t h i n g caused by an e x p e r i m e n t a l problem i n the l a s t f i v e
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minutes. Good p a r t i a l averages a r e a v e r a g e d and k i n e t i c d a t a are e x t r a c t e d u s i n g n o n - l i n e a r l e a s t squares c u r v e f i t t i n g ; e d i t i n g and d i s p l a y a r e p r o v i d e d on an i n t e r a c t i v e g r a p h i c s t e r m i n a l l o c a t e d a t the experimental s i t e . T h i s scan a v e r a g i n g system i s e f f e c t e d through an i n t e r f a c e d 400 c h a n n e l N u c l e a r Chicago m u l t i - s c a l i n g a n a l y z e r . ENDOR and ESR S p e c t r o s c o p y . A s i g n i f i c a n t p o r t i o n of our e f f o r t s t o c h a r a c t e r i z e p r i m a r y p h o t o s y n t h e s i s i s b e i n g s u p p o r t e d by two i n t e r f a c e d s p i n resonance spectrometers : a V a r i a n E-700 ENDOR ( e l e c t r o n n u c l e a r double resonance) and a V a r i a n E-9 ESR ( e l e c t r o n s p i n resonance) b u f f e r e d by a N i c o l e t 1074 CAT ( s i g n a l a v e r a g e r ) . The uniqueness o f t h e s e spectrome t e r systems d e r i v e s from the l a r g e memory and computat i o n a l speed ( f l o a t i n g p o i n t a r i t h m e t i c ) o f t h e Sigma 5 which a l l o w s the a c q u i s i t i o n and m a n i p u l a t i o n o f l a r g e q u a n t i t i e s o f t h r e e d i m e n s i o n a l d a t a (3-D) v i a two ADC's. A s i n g l e 3-D e x p e r i m e n t may be composed o f up t o 6 40,000 d a t a p o i n t s . F o r example i n the ENDOR mode s i g n a l i n t e n s i t y and r a d i o f r e q u e n c y a r e r e c o r d e d as a f u n c t i o n o f magnetic f i e l d . In t h e ESR mode, t h e t y p i c a l i n t e n s i t y v e r s u s f i e l d spectrum i s r e c o r d e d as a f u n c t i o n o f a t h i r d d i m e n s i o n , such as time f o r k i n e t i c s t u d i e s , or l i g h t i n t e n s i t y f o r p h o t o c h e m i c a l s t u d i e s . Furthermore, s p e c t r o m e t e r o p e r a t i o n i s c o n t r o l l e d by t h e computer; f o r example, i n t h e ENDOR mode t h e comp u t e r s y n t h e s i z e s t h e r a d i o f r e q u e n c y v a l u e , makes d e c i s i o n s about d a t a v a l i d i t y , and t e r m i n a t e s spectrome t e r o p e r a t i o n i f t h e r a d i o f r e q u e n c y power i s i n s u f f i c i e n t . A l l data c a l c u l a t i o n s , i n c l u d i n g s o p h i s t i c a t e d spectrum s i m u l a t i o n s as w e l l as FFT ( f a s t f o u r i e r t r a n s f o r m ) a n a l y s i s i s performed i n r e a l - t i m e by u s e r w r i t t e n FORTRAN programs. These unique f a c i l i t i e s have g r e a t l y s i m p l i f i e d and speeded up t h e u n r a v e l i n g of v a r i o u s fundamental a s p e c t s o f p r i m a r y p h o t o s y n t h e s i s i n our l a b o r a t o r y . Stopped-Flow K i n e t i c s . Using the stopped-flow t e c h n i q u e , k i n e t i c s t u d i e s a r e b e i n g made on systems w i t h s h o r t - l i v e d r e a c t a n t s and p r o d u c t s a t a q u a n t i t a t i v e l e v e l never b e f o r e a c h i e v e d (10,11). Current s t u d i e s c o v e r a v a r i e t y o f a c t i n i d e rêHbx r e a c t i o n s , i n c l u d i n g work w i t h N p ( V I I ) , one o f t h e most p o w e r f u l o x i d a n t s known i n a c i d s o l u t i o n . The a p p a r a t u s c o n s i s t s o f a Durrum model D-110 s t o p p e d - f l o w s p e c t r o p h o t o m e t e r whose o u t p u t i s d i g i t i z e d and s t o r e d i n a B i o m a t i o n 80 2 t r a n s i e n t r e c o r d e r , which i n t u r n i s i n t e r f a c e d t o t h e computer. One t h o u sand d a t a p o i n t s s p a n n i n g a time range o f 0.5 msec, t o
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20 s e c . are c o l l e c t e d per e x p e r i m e n t . R e a l - t i m e s t o r a g e and a n a l y s i s o f the d a t a a l l o w o u t p u t o f the l e a s t s q u a r e s f i t r e s u l t s a t t h e remote s i t e w i t h i n 30 s e c . of the end o f the e x p e r i m e n t . The f a s t t u r n around a l l o w s the e x p e r i m e n t e r t o a d j u s t c o n d i t i o n s c o n t i n u a l l y f o r optimum r e s u l t s . S p e c t r o s c o p i c P l a t e Reading. The s p e c t r o s c o p i c group i s u s i n g a 30 f o o t g r a t i n g s p e c t r o m e t e r t o i n t e r p r e t a c t i n i d e s p e c t r a , each o f which may have up t o 100,000 s p e c t r a l l i n e s . An a u t o m a t i c comparator measures t h e p o s i t i o n o f spectrum l i n e s on an exposed p h o t o g r a p h i c p l a t e by moving i t c o n t i n u o u s l y under a s c a n n i n g s l i t and p h o t o c e l l ; t h e l o c a l b l a c k e n i n g a t s e l e c t e d i n t e r v a l s i s o b t a i n e d by d i g i t a l v o l t m e t e r (DVM) r e a d i n g s o f the p h o t o c e l l c u r r e n t . About 60,000 r e a d i n g s are t a k e n on one scan o f a 250 mm. plate, r e q u i r i n g about 4 m i n u t e s . The d i g i t i z e d (DVM) data i s t r a n s m i t t e d d i r e c t l y t o the computer, s t o r e d and analyzed i n real-time using non-resident execution. The smoothed r e a d i n g s and d e r i v a t i v e s are scanned f o r peaks, and the peak p o s i t i o n s are c o n v e r t e d t o wavel e n g t h by a p o l y n o m i a l f o r m u l a d e r i v e d i n a s e p a r a t e scan o f known s t a n d a r d w a v e l e n g t h s . An i m p o r t a n t c o n v e n i e n c e i s a d i s k f i l e o f s t a n d a r d wavelengths and p o s i t i o n s ; o n l y one p a i r o f knowns i s r e q u i r e d as i n p u t c a l i b r a t i o n , so the system r e q u i r e s much l e s s e f f o r t than manual measurement and a t the same time g i v e s i n c r e a s e d a c c u r a c y (1 i n 1 0 ) . 7
Nuclear P a r t i c l e Detection. A broad area of r e s e a r crTlifirôrt""^^ i s concerned w i t h e l i c i t i n g the d e t a i l s o f the f i s s i o n p r o c e s s . In s t u d y i n g the dynamics o f a m u l t i - n u c l e o n fissioning system, i t i s n e c e s s a r y t o measure t h e changes i n t h e fragment mass and k i n e t i c energy as t h e i n i t i a l e x c i t a t i o n energy, a n g u l a r momentum, and t a r g e t mass and s p i n are a l t e r e d . The i n i t i a l c o n d i t i o n s are most e a s i l y v a r i e d by u s i n g d i r e c t - i n t e r a c t i o n i n d u c e d f i s s i o n r e a c t i o n s such as (d,pf) which a l l o w t h e s i m u l taneous o b s e r v a t i o n o f e x c i t a t i o n e n e r g i e s from below t o 10 MeV above t h e f i s s i o n b a r r i e r . C h a r a c t e r i z i n g t h e s e r e a c t i o n s r e q u i r e s a f i v e parameter e v e n t - b y e v e n t c o r r e l a t i o n o f t h e f i s s i o n fragment e n e r g i e s as w e l l as the l i g h t p a r t i c l e t y p e and e n e r g y . These q u a n t i t i e s a r e c o n v e r t e d t o mass and k i n e t i c energy d i s t r i b u t i o n s i n r e a l - t i m e by u s e r - w r i t t e n programs ( e x e c u t i n g as n o n - r e s i d e n t programs), p e r m i t t i n g s u f f i c i e n t i n t e r a c t i o n between the e x p e r i m e n t a l i s t and a real-time d i s p l a y of h i s transformed data; f a c i l i t a t i n g optimum use o f t h e e x p e r i m e n t a l i s t ' s and a c c e l e r a t o r time.
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The computer system s u p p o r t s f i v e d a t a a c q u i s i t i o n areas l o c a t e d i n t h e C h e m i s t r y b u i l d i n g , C y c l o t r o n b u i l d i n g and a t t h e Van De G r a a f f a c c e l e r a t o r i n t h e P h y s i c s b u i l d i n g l o c a t e d about 2,000 f e e t d i s t a n t . Experiments range from s i n g l e p u l s e h e i g h t s p e c t r a ( u s i n g Packard 45 memories and model 160 ADC's), r e c o r d i n g o f e v e n t - t i m e d a t a (at r e s o l u t i o n s o f 40 y s e c . ^ t o m u l t i - p a r t i c l e p u l s e h e i g h t s p e c t r a on up t o s i x ADC's. S i n g l e s , c o r r e l a t e d and t r a n s f o r m e d s p e c t r a a r e g e n e r a t e d i n r e a l - t i m e and a u t o m a t i c a l l y d i s p l a y e d a t a selected interval. An o p t i o n i s a l s o p r o v i d e d f o r s t o r i n g event d a t a p u l s e - h e i g h t s (one o r more ADC's) on magnetic tape f o r subsequent a n a l y s i s i n b a t c h mode or on t o the d i s k f o r r e a l - t i m e d i s p l a y , e d i t i n g and analysis. E v e n t r a t e s o f up t o 10,000 ADC-events/sec. may be p r o c e s s e d . UV, V i s i b l e and I n f r a r e d S p e c t r o s c o p y . Two i n t e r f a c e d Cary s p e c t r o p h o t o m e t e r s (14 and 17H) s u p p o r t t h e D i v i s i o n ' s c h l o r o p h y l l and s u r f a c e s t u d i e s groups. D i g i t a l d a t a from the Cary 14 i s s e n t d i r e c t l y t o t h e computer f o r subsequent d e c o n v o l u t i o n and p l o t t i n g on t h e Calcomp p l o t t e r . On the Cary 17H, t h e scan speed, c h a r t speed and i n t e n s i t y range a r e under computer c o n t r o l (12,13). D i r e c t d i g i t i z a t i o n of the photom u l t i p l i e r o u t p u t has enhanced t h e absorbance a c c u r a c y by a t l e a s t a f a c t o r o f two. Automatic absorbance s c a l e r a n g i n g i s a l s o p r o v i d e d d u r i n g a s p e c t r a l sweep such t h a t t h e u s e f u l absorbance range has been i n c r e a s ed from 0.3 t o 0.4. In a d d i t i o n , t h e problem o f d a t a f i d e l i t y depending on scan speed has been e l i m i n a t e d . R e p e t i t i v e scans w i t h d a t a a v e r a g i n g p r o v i d e s a ready means o f i m p r o v i n g s i g n a l - t o - n o i s e r a t i o s . The d i g i t i zed d a t a are a v a i l a b l e f o r a n a l y s i s by programs which i n c l u d e base l i n e c o r r e c t i o n , G a u s s i a n - L o r e n t z i a n d e c o n v o l u t i o n , peak a r e a measurement, and p l o t t i n g o f t h e o r i g i n a l or program-modified d a t a . Heat C a p a c i t y Measurements. T h i s system i s used f o r t h e p r e c i s e measurement o f t h e heat c a p a c i t i e s o f v a r i o u s c h e m i c a l compounds between 0,1°K and 350°K, a p l a t i n u m r e s i s t a n c e thermometer b e i n g used between 4°K and 350°K and a germanium r e s i s t a n c e thermometer between 0.1°K and 25°K (14,15). Thermometer r e s i s t a n c e s a r e measured w i t h a 6-dTgIt* p o t e n t i o m e t e r whose d i a l p o s i t i o n s a r e a u t o m a t i c a l l y t r a n s m i t t e d t o t h e computer on command. A f i f t e e n t h o r d e r p o l y n o m i a l ( f o r germanium) which c o n v e r t s v o l t a g e t o temperature i s s o l v e d by a n o n - r e s i d e n t program, r e t u r n i n g the time, temperat u r e and temperature d r i f t . A f t e r d r i f t i n g becomes c o n s t a n t , a h e a t i n g c y c l e i s e n t e r e d i n which r e a d i n g s
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o f h e a t e r power and time a r e r e a d a u t o m a t i c a l l y by an i n t e r f a c e d V i d a r 5204D-DAS and t r a s m i t t e d t o t h e computer. F o l l o w i n g h e a t i n g , t h e thermometer c u r r e n t and r e s i s t a n c e s a r e a g a i n f o l l o w e d , u n t i l d r i f t s become constant. The system makes t h e r e c o r d i n g o f t h e d a t a much e a s i e r and more r e l i a b l e and i n a d d i t i o n i t i s much e a s i e r f o r t h e e x p e r i m e n t e r t o d e c i d e when e q u i l i b r i u m has been a t t a i n e d a f t e r t h e h e a t i n g p e r i o d , s o t h a t a n o t h e r h e a t i n g can be i n i t i a t e d .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch006
IV.
New
Directions
Our c e n t r a l computer system has s u p p o r t e d p r e s e n t day i n s t r u m e n t a t i o n q u i t e w e l l . However, as t h e a r t of automation advances, e x p e r i m e n t a l i s t s ' l e a r n t o b e t t e r u t i l i z e t h e i r new s o p h i s t i c a t e d t o o l s and new i n s t r u m e n t c a p a b i l i t i e s e v o l v e , i t i s c l e a r t h a t new and more d i f f i c u l t d a t a a c q u i s i t i o n problems w i l l continue t o a r i s e . One o f t h e more demanding problems i s the scan-averaging o f s p e c t r a acquired a t r a t e s a p p r o a c h i n g a m i l l i o n c h a n n e l s p e r second. Another i s more s o p h i s t i c a t e d r e a l - t i m e c o n t r o l o f e x p e r i m e n t s r e q u i r i n g l o g i c d e c i s i o n s (computation) on a m i c r o second time s c a l e . One might t r y t o s o l v e t h e s e p r o b lems by a d d i n g a mini-computer between t h e s e new i n struments and t h e c e n t r a l system. However, one i s then f a c e d w i t h t h e problem o f programming t h e s e i n d i v i d u a l computers ( p r o b a b l y o f d i f f e r e n t manufacture) and d e s i g n i n g an i n t e r f a c e t o t h e c e n t r a l system. I n a d d i t i o n , a mini-computer's r e s p o n s e time i s f a s t e r than a c e n t r a l computer o n l y by v i r t u e o f t h e f a c t t h a t i t t a k e s 4 nanoseconds p e r f o o t (2 way t r a n s m i s s i o n ) f o r d a t a t r a n s m i s s i o n and communication. We a r e i n t e n d i n g t o p r o v i d e h i g h e r speed c a p a b i l i t i e s i n t h e f u t u r e by u s i n g m i c r o p r o c e s s o r s u p p o r t a t the e x p e r i m e n t a l s i t e . Xerox has a System C o n t r o l U n i t which has a wide v a r i e t y o f c o n f i g u r a t i o n s and o p t i o n s including 8 r e g i s t e r s , interrupts, stacks, clocks, r e a d - o n l y and w r i t a b l e memory (16 b i t , 350 and 700 nanosecond) i n i n c r e m e n t s o f IK words, and o p t i o n a l f l o a t i n g p o i n t . We w i l l l o a d t h e s e computers w i t h code from t h e c e n t r a l computer f o r each phase o f i t s d a t a a c q u i s i t i o n e f f o r t , u s i n g them more as a s o p h i s t i c a t e d i n p u t / o u t p u t d e v i c e than as a computer. T h i s w i l l keep t h e programming l o g i c a l l y simple and thus e f f i c i e n t . In a d d i t i o n , t h i s t y p e o f usage w i l l n o t r e q u i r e much memory, thus k e e p i n g t h e c o s t down below t h a t which would be r e q u i r e d by u s i n g a mini-computer.
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Summary
The s u c c e s s f u l o p e r a t i o n o f our system o v e r t h e past f i v e years i s a c l e a r demonstration that a c e n t r a l computer, w i t h o u t remote mini-computers, can p r o v i d e very s o p h i s t i c a t e d real-time support without s u f f e r i n g the disadvantages o f u n r e l i a b i l i t y o f t e n experienced i n l a r g e systems. Users never e x p e r i e n c e t h e consequences o f a n o t h e r u s e r ' s e r r a n t program, o n l y t h e i r own. The l e v e l o f system i n t e g r i t y i s such t h a t we t e s t a comp l e t e l y new i n s t r u m e n t c o n t r o l program d u r i n g normal system l o a d i n g , w i t h o u t h a v i n g t o be c o n c e r n e d about i n t e r f e r r i n g w i t h any o t h e r u s e r ' s i n t e r e s t s . Evidence of t h e system's a c c e p t a n c e as u s e r s have been added o v e r t h e y e a r s , i s t h a t we c o n t i n u e t o have 6-8 new u s e r s w a n t i n g t o be i n t e r f a c e d as funds become a v a i l able. The t o t a l c a p i t a l i n v e s t m e n t f o r t h e e n t i r e system i s about $50K p e r experiment, which compares f a v o r a b l y t o the c o s t o f s o p h i s t i c a t e d mini-systems. But, one has much more r e s o u r c e and c a p a b i l i t y t o supp o r t each e x p e r i m e n t : p r o v i d i n g f u l l experiment cont r o l i n a f l e x i b l y i n t e r a c t i v e manner; f u l l y i n t e r a c t i v e g r a p h i c s c a p a b i l i t y w i t h o n - g o i n g and completed e x p e r i m e n t s ; c o m p u t a t i o n a l a b i l i t y f o r complete f i n a l a n a l y s i s o f experiments. APPENDIX Memory Bus S t r u c t u r e . The 960 nanosecond c o r e memory (32 b i t s p l u s p a r i t y ) i s modular; each 16K words has i t s own r e a d - w r i t e and address r e c o g n i t i o n c a p a b i l i t y and may have up t o s i x p o r t s . The CPU and each p r o c e s s o r (MIOP's and CIOP) i s c o n n e c t e d t o i t s own " p o r t b u s " made by j o i n i n g one p o r t from each memory bank. S i m u l t a n e o u s a c c e s s i s a c h i e v e d when r e q u e s t s a r e i n d i f f e r e n t banks and c y c l e s t e a l i n g t a k e s p l a c e when more than one r e q u e s t c o e x i s t s f o r a s i n g l e memory bank. Memory P r o t e c t i o n . A 2 - b i t l o c k and key f e a t u r e p r e v e n t s a u s e r ' s program from m o d i f y i n g u n a s s i g n e d c o r e , w h i l e p e r m i t t i n g t h e e x e c u t i o n o f r e e n t r a n t code. The "key" r e s i d e s i n t h e c u r r e n t PSD (program s t a t u s doubleword), t h e page (512 words) l o c k s a r e s e t i n f a s t memory i n t h e CPU v i a a s i n g l e i n s t r u c t i o n by t h e s c h e d u l e r each time a program l e v e l commences e x e c u tion. Implementation o f t h e p r o t e c t i o n f e a t u r e w i l l t r a p a c o r e - m o d i f y i n s t r u c t i o n b e f o r e e x e c u t i o n and y e t does n o t i n c r e a s e i n s t r u c t i o n e x e c u t i o n t i m e .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch006
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Data Flow. Each MIOP ( m u l t i p l e x o r i n p u t / o u t p u t p r o c e s s o r ) may handle an aggregate d a t a f l o w of 375K memory a c c e s s e s p e r second (one o r f o u r b y t e s ) on up t o 32 c o n c u r r e n t l y a c t i v e d a t a c h a n n e l s ( t y p i c a l l y one per e x p e r i m e n t ) . Only a s i n g l e i n s t r u c t i o n must be executed by t h e CPU t o i n i t i a t e a d a t a t r a n s f e r between any c o r e memory a r e a and a s p e c i f i e d d e v i c e ; a l l subsequent d a t a movement and communication w i t h t h e remote d e v i c e i s h a n d l e d by the MIOP. A t t h e t e r m i n a t i o n o f d a t a t r a n s f e r (up to 65,536 b y t e s ) , the MIOP g e n e r a t e s a single interrupt. Upon r e c o g n i t i o n o f the i n t e r r u p t , the CPU a s c e r t a i n s t h e c h a n n e l number and t h e c h a n n e l end c o n d i t i o n s by e x e c u t i n g a s i n g l e i n s t r u c t i o n . Thus, h i g h speed d a t a t r a n s f e r t o i n d i v i d u a l l y s e l e c t e d c o r e areas ( s p e c i f i e d by each u s e r ' s program) i s comp l e t e l y handled by t h e MIOP, f r e e i n g the CPU t o p e r form u s e f u l computations c o n c u r r e n t l y w i t h d a t a transfers. T e r m i n a l Communications. The CIOP (communications i n p u t / o u t p u t p r o c e s s o r ) h a n d l e s up t o 128 l i n e s of mixed speeds from 110 t o 9600 baud; c u r r e n t l y d r i v i n g 21 t e l e t y p e s , 8 i n t e r a c t i v e g r a p h i c u n i t s and 2 k e y board d i s p l a y s . T h i s p r o c e s s o r works w i t h t h e CPU i n a manner s i m i l a r t o t h a t used w i t h the MIOP. Thus message t r a n s f e r s t a k e p l a c e t o any c o r e memory a r e a w h i l e the CPU i s p e r f o r m i n g computations. Experiment I n t e r f a c e s . Each of t h e r e m o t e l y l o c a t e d o n - l i n e experiments i s i n t e r f a c e d t o a remote controller. The s i m p l e s t c o n t r o l l e r s c o n s i s t o f a one b y t e b u f f e r and a few l o g i c l i n e s . The more complex ones have up t o s i x t e e n b y t e b u f f e r s , computer i n i t i a ted timing c i r c u i t r y to c o n t r o l instrument f u n c t i o n s to a p r e c i s i o n of 0.1 m i c r o s e c o n d and numerous l o g i c l i n e s . For t r a n s m i s s i o n r a t e s up t o 100,000 b y t e s per second a t d i s t a n c e s up t o 1500 f e e t , a remote c o n t r o l l e r i s connected t o a d e v i c e c o n t r o l l e r v i a a b u n d l e o f c o - a x i a l c a b l e (8 b i t wide d a t a p a t h ) . F o r t r a n s m i s s i o n r a t e s o f up t o 4K b y t e s / s e c o n d and a t d i s t a n c e s o f up t o one m i l e , f o u r t w i s t e d p a i r a r e used. The d e v i c e c o n t r o l l e r s were d e s i g n e d by Argonne e n g i n e e r s and a r e connected t o the MIOP bus s t r u c t u r e i n t h e computer main frame, weekly d a t a t r a n s m i s s i o n v a l i d i t y t e s t s on a l l i n t e r f a c e s r u n n i n g c o n c u r r e n t l y f o r about an hour never d e t e c t a t r a n s m i s s i o n f a u l t . About e v e r y e i g h t months one of t h e i n t e r f a c e s f a i l s s o l i d l y because o f component f a i l u r e , which i s r e a d i l y f i x e d w i t h i n a few hours.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch006
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Core Memory Assignment. With t h e e x c e p t i o n o f system a r e a s , c o r e memory i s a s s i g n e d d y n a m i c a l l y . As u s e r s l o g - o n from t h e i r t e r m i n a l s , s u f f i c i e n t c o r e i s assigned f o r the r e s i d e n t p o r t i o n of t h e i r data a c q u i s i t i o n program, which i n c l u d e s t h e i r own d a t a b u f f e r areas. The programs a r e s t r u c t u r e d i n t o u s e r c o n t r o l l e d o v e r l a y s which a r e t y p i c a l l y w r i t t e n o n t o t h e i r d i s k f i l e and r o l l e d i n t o t h e i r c o r e a r e a as they require. U s i n g t h i s o v e r l a y t e c h n i q u e , t h e average core r e s i d e n c y r e q u i r e d p e r program runs between 2 and 5 pages (page = 5 1 2 w o r d s ) . To p e r f o r m r e a l - t i m e computations u s i n g FORTRAN, t h e f o r e g r o u n d code may c a l l f o r e x e c u t i o n o f a " n o n - r e s i d e n t " program. Foreground c o r e a r e a i s a s s i g n e d from t h e t o p o f c o r e down i n t h e f i r s t a v a i l a b l e b l o c k o f continguous c o r e pages. Background c o r e (batch and system t a s k s ) i s a s s i g n e d from lower c o r e upward. T h i s p e r m i t s t h e maximum b a c k ground c o r e a r e a t o extend on up t o 42,600 words when no r e a l - t i m e t a s k s a r e l o a d e d . W h i l e background c o r e i s v a r i a b l e i n s i z e , t h e u s e r i s always guaranteed an a r e a o f a t l e a s t 15,900 words. R e a l - t i m e j o b l e n g t h s v a r y from minutes t o weeks. On a t y p i c a l day, about 60% o f t h e i n s t r u m e n t s a r e o n - l i n e a t any one time, r e q u i r i n g about 14,400 words o f c o r e . T h i s l e a v e s about 28,200 words o f background c o r e . R e e n t r a n t Code. The Xerox w r i t e - l o c k f e a t u r e , which p e r m i t s t h e e x e c u t i o n o f code anywhere i n memory y e t f o r b i d s t h e m o d i f i c a t i o n o f memory w i t h o u t t h e p r o p e r "key", f a c i l i t a t e s t h e u t i l i z a t i o n o f r e e n t r a n t code t o p e r f o r m many u s e r f u n c t i o n s . R e e n t r a n t code i s d e f i n e d as code t h a t does n o t m o d i f y i t s e l f . About 800 words o f r e e n t r a n t code a r e i n permanent r e s i d e n c e f o r p e r f o r m i n g such f u n c t i o n s as two-way t r a n s l a t i o n o f keyboard I/O and b i n a r y - c o d e d - d e c i m a l c o n v e r s i o n f o r some o f t h e i n t e r f a c e d m u l t i - c h a n n e l a n a l y z e r s . I n a d d i t i o n , t h e r e a r e 12 8 words o f EBCDIC-ASCII c o n v e r sion tables available. Program D e s c r i p t i o n T a b l e s . I n p r o v i d i n g a m u l t i prog raîmnëd~ênvTr^nn^ number ( c u r r e n t l y 41) o f c o n c u r r e n t l y r u n n i n g programs ( u s e r and system), i t was found t h a t a program d e s c r i p t i o n t a b l e (PDT) a s s o c i a t e d w i t h each p r i o r i t y l e v e l was an e f f i c i e n t method o f k e e p i n g t r a c k o f system s e r v i c e r e q u e s t s and i n d i v i d u a l program s t a t u s . B e s i d e s s i m p l i f y i n g p r i o r i t y queuing and l e v e l t e r m i n a t i o n a t e n d - o f - j o b , a PDT s t r u c t u r e a l s o s i m p l i f i e s t h e a d d i t i o n o f a new program l e v e l t o t h e system. PDT g e n e r a t i o n i s c o n t r o l l e d a t system b o o t - i n by one l e v e l - p a r a m e t e r c a r d p e r t e r m i n a l .
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Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch006
The PDT f o r each p r i o r i t y l e v e l i s 80 words l o n g p l u s two words f o r each I/O command p a i r needed by the l e v e l ( r a n g i n g from 1 t o 16) t o c o n t r o l i t s a s s o c i a t e d device. The t a b l e c o n t e n t a l s o i n c l u d e s ; u s e r ID number, l e v e l s t a t u s , program s t a t u s double words (PSD), memory w r i t e - l o c k image, time r e m a i n i n g , c o r e bounds, d i s k memory f i l e bounds and r e g i s t e r v a l u e s . These t a b l e s a r e s t o r e d i n a w r i t e - p r o t e c t e d a r e a o f c o r e memory. Scheduling. The system s t r u c t u r e / o p e r a t i o n and usage s t r a t e g y have been d e v e l o p e d c o n c u r r e n t l y . Thus a system has e v o l v e d which maximizes t h e system work per u n i t time i n such a manner as t o p r o v i d e t h e r e q u i r e d l e v e l o f r e a l - t i m e i n t e r a c t i o n between t h e u s e r , h i s keyboard and h i s i n s t r u m e n t . However, t h e s p e c i f i c s t r a t e g y used f o r any p a r t i c u l a r a p p l i c a t i o n i s not d i c t a t e d by t h e system as l o n g as programs make r e q u e s t s which conform i n time, c o r e memory, dev i c e o p e r a t i o n and f i l e bounds. A hardware t r a p i s s e t t o d i s a l l o w t h e e x e c u t i o n of p r i v i l e g e d i n s t r u c t i o n s by u s e r code. The b a s i c s c h e d u l i n g a l g o r i t h m runs each t a s k t o c o m p l e t i o n , c o n t i n g e n t upon i t s p r i o r i t y . The schedul e r d e t e r m i n e s what p r i o r i t y l e v e l w i l l e x e c u t e n e x t , t h r o u g h t h e p r o c e s s i n g of a l l I/O i n t e r r u p t s from t h e MIOP, and the maintenance o f s o f t w a r e p r i o r i t y l e v e l s t a t u s u s i n g the PDT's. Once the i d e n t i t y and s t a t u s o f the l e v e l a s s o c i a t e d w i t h an i n t e r r u p t i s d e t e r mined, the s c h e d u l e r compares i t s p r i o r i t y w i t h t h a t o f the l e v e l i n t e r r u p t e d . I f i t i s o f lower p r i o r i t y , t h e i n t e r r u p t e d l e v e l i s resumed. O t h e r w i s e , t h e e x e c u t i o n dependent p o r t i o n (PSD, e x e c u t i o n time and r e g i s t e r s ) o f i t s c u r r e n t s t a t e v e c t o r i s moved t o i t s PDT. Refere n c i n g t h e new ( i n t e r r u p t s i g n a l l e d ) l e v e l ' s PDT, i t s e x e c u t i o n i s i n i t i a t e d by s e t t i n g the memory w r i t e p r o t e c t l o c k s , e x e c u t i o n t i m e , r e g i s t e r s and t h e PSD. Upon r e c e i v i n g an e n d - o f - s e r v i c e (EOS) request from a l e v e l , the s c h e d u l e r r e c o r d s t h i s i n i t s PDT. Then i t scans down t h e p r i o r i t y c h a i n t h r o u g h t h e PDT's u n t i l i t f i n d s another l e v e l t h a t i s " r e a d y - t o - r u n " . S t a t e v e c t o r s are t h e n a d j u s t e d as above t o i n i t i a t e execution. A n e c e s s a r y f e a t u r e i n a multi-programmed system i s t h e p r e v e n t i o n of p r o c e s s i n g l o c k o u t by some h i g h e r p r i o r i t y l e v e l l o o p i n g e n d l e s s l y . A maximum s e r v i c e c y c l e time ( e x e c u t i o n : f o r e g r o u n d = l s e c , n o n - r e s i d e n t = 1 or 32 s e c . , b a t c h and l o n g term=no l i m i t ) and a time r e m a i n i n g v a l u e are s t o r e d i n each PDT. Any time a l e v e l i s e x e c u t i n g , the t i m e - r e m a i n i n g v a l u e i s d e c r e mented by a CPU c l o c k (2000 Hz). But each time a l e v e l
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calls EOS, the maximum service value is moved into the time-remaining PDT location. By breaking processing into logical service cycles, a program can readily perform its function forever, but w i l l be terminated by time-out i f i t malfunctions time-wise.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch006
ABSTRACT A careful study of our laboratory automation needs in 1967 led us to the conclusion that a central compu ter could support all of the real-time needs of a diverse collection of research instruments. A suitable hardware configuration would require an operating sys tem to provide effective protection, fast real-time response and efficient data transfer. An SDS Sigma 5 satisfied all our hardware c r i t e r i a , however i t was necessary to write our own operating system; services include program generation, experiment control real -time analysis, interactive graphics and final analysis. Our system is providing real-time support for 21 concurrently running experiments, including an automa ted neutron diffractometer, a pulsed NMR spectrometer and multi-particle detection systems. It guarantees the protection of each user's interests and dynamically assigns core memory, disk space and 9-track magnetic tape usage. Multiplexor hardware capability allows the transfer of data between a user's device and assigned core area at rates of 100,000 bytes/sec. Real-time histogram generation for a user can proceed at rates of 50,000 points/sec. The facility has been self-running (no computer operator) for five years with a mean time between failures of 10 days and an uptime of 157 hours/ week. Literature Cited 1.
Day, P. and Krejci, Η., Proc. AFIPS FJCC (1968) 33 1187-1196 2. Day, P. and Hines, J., Operating Systems Review (1973) 7 (4) 28-37 3. Scheer, H. and Katz, J. J., Proc. Natl. Acad. S c i . USA (1974) 71 (5) 1626-1629 4. Crespi, H. L., Kostka, A. G. and Smith, U . , Biochem. Biophys. Res. Comm. (1974) 61 (4) 14071414 5. Peterson, S. W., Willett, R. D. and Huston, J. L., J. Chem. Phys. (1973) 59 (1) 453-459 6. Williams, J. Μ., Petersen, J. L., Gerdes, Η. Μ., and Peterson, S. W., Phys. Rev. Lett. (1974) 33 (18) 1079-1081
6. DAY Instrument Control 7. 8. 9. 10. 11. 12.
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13. 14. 15.
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Gordon, S., Schmidt, Κ. H. and Martin, J. E., Rev. Sci. Instrum. (1974) 45 (4) 552-558 Norris, J. R., Uphaus, R. A. and Katz, J. J., Chem. Phys. Lett. (1975) 31 157-161 Norris, J. R., Druyan, M. E. and Katz, J. J., J. Am. Chem. Soc. (1973) 95 1680-1682 Watkins, Κ. O., Sullivan, J. C. and Deutsch, E., Inorg. Chem. (1974) 13 1712 Weschler, C. J., Sullivan, J. C. and Deutsch, E., Inorg. Chem. (1974) 13 2360 Gruen, D. M., Gaudioso, S. L., McBeth, R. L., and Lerner, J. L., J. Chem. Phys. (1974) 60 (1) 89-99 Green, D. W. and Gruen, D. M., J. Chem. Phys. (1974) 60 (5) 1797-1801 Osborne, D. W., Schreiner, F., Flotow, H. E. and Malm, J. G., J. Chem. Phys. (1972) 57 (8) 3401-3408 Osborne, D. W., Flotow, H. E., Fried, S. Μ., and Malm, J. G., J. Chem. Phys. (1974) 61 1463-1468
7
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S u p p o r t as a
M e t h o d o l o g i c a l A i d to the L a b o r a t o r y Investigator R. L. ASHENHURST Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch007
Institute for Computer Research, The University of Chicago, Chicago, Ill. 60637 Over the last decade the use of computers as an integral part of laboratory instrumentation has become routine. Technol o g i c a l developments, however, continue to influence the style of computer-based "laboratory automation." Initially, the connection of a battery of laboratory instruments to a single computer with provision for handling realtime processes on a m u l t i -programming basis was the norm. Subsequently the availability of the minicomputer, with its ever decreasing cost, and now the introduction of the microcomputer, have engendered more of a trend toward one-on-one computer-to-instrument design. A t the same time, the l i m i t e d capabilities of m i n i m a l m i n i c o m puter and microcomputer configurations, along with the decreasing cost of digital communications, have led to the idea of connecting individual laboratory computers into backup c o m puter configurations, thereby enhancing the computing services available at the laboratory site. Although many such "laboratory automation support systems" exist, they differ considerably in their general approach, not to mention their detailed implementation. It is also true that such systems are often not reported adequately in the literature, and even if information is available as to hardware configuration the all-important software configuration features are not made clear. In this a r t i c l e some aspects of such systems are discussed from the point of view of the laboratory user. The discussion is framed in terms of a particular system, with which the author has been involved, that has been consciously designed from the ground up from a user-oriented perspective. The system having been developed on a university campus for general research use in the physical and biological sciences, it happens that the discipline of chemistry has figured import108
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antly a m o n g its e a r l y u s e s . T h e p r i n c i p l e s a c c o r d i n g to w h i c h the s y s t e m is s t r u c t u r e d , h o w e v e r , a r e e s s e n t i a l l y " d i s c i p l i n e f r e e , " and it c a n be a r g u e d that t h i s a p p r o a c h p r e s e n t s s o m e a d v a n t a g e s e v e n i f t h e s y s t e m w e r e o n l y to b e u s e d i n a s i n g l e d i s c i p l i n a r y context, such as c h e m i s t r y .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch007
A Hierarchical System O v e r the p a s t t h r e e y e a r s the M i n i c o m p u t e r I n t e r f a c i n g S u p p o r t S y s t e m ( M I S S ) h a s b e e n d e v e l o p e d a t the I n s t i t u t e f o r C o m p u t e r R e s e a r c h a t the U n i v e r s i t y o f C h i c a g o , u n d e r a g r a n t f r o m the N a t i o n a l S c i e n c e F o u n d a t i o n . * The MISS project was d e v e l o p e d i n the c o n t e x t of m i n i c o m p u t e r s u s e d i n the l a b o r a t o r y , a l t h o u g h i t i s a d a p t a b l e to o t h e r u s e s a s w e l l , s u c h a s o n l i n e m o n i t o r i n g of i n s t i t u t i o n a l o p e r a t i o n s (JJ. T h e c o n f i g u r a t i o n d e s i g n is h i e r a r c h i c a l , w i t h the l a b o r a t o r y m i n i c o m p u t e r s a t t h e l o w e s t l e v e l ( l e v e l 0 ) , c o n n e c t e d to a n i n t e r m e d i a t e l e v e l s y s t e m d e d i c a t e d t o t h e i r s u p p o r t ( l e v e l 1), w h i c h i n t u r n i s c o n n e c t e d to a g e n e r a l - p u r p o s e f a c i l i t y s e r v i n g t h e s e a n d o t h e r n e e d s ( l e v e l 2). T h u s the c o n n e c t i o n s a r e as s h o w n s c h e m a t i c a l l y i n F i g u r e 1.
level 2
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level 1
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level 0
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*NSF Grant N o .
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A s c o n c e i v e d , t h e l e v e l 0 m i n i c o m p u t e r s c a n b e of a v a r i e t y of t y p e s a n d c a p a b i l i t i e s (at p r e s e n t P D P - 1 1 s e r i e s a n d N o v a 8 0 0 s e r i e s a r e s u p p o r t e d , w i t h P D P - 8 s e r i e s s o o n to b e a d d e d ) , a n d the l e v e l 2 g e n e r a l - p u r p o s e f a c i l i t y c o u l d be a c o m p u t e r n e t w o r k i n s t e a d of a s i n g l e s y s t e m (but i n f a c t i s o n l y the l a t t e r , the 370/168 s y s t e m o p e r a t e d b y t h e U n i v e r s i t y of C h i c a g o C o m p u tation Center). T h e l e v e l 1 s y s t e m i s the h e a r t of the c o m p l e x , s i n c e i t s o p e r a t i o n i s t h e k e y to t h e b l e n d i n g of t h e h i g h - a n d low-level capabilities o f f e r e d b y the c o m p l e t e system. A l t h o u g h i m p l e m e n t e d on a m i n i c o m p u t e r , it a c t u a l l y is a m e d i u m - s i z e d s y s t e m (a P D P - l l / 4 5 w i t h 6 4 K c o r e a n d c a r d r e a d e r , l i n e p r i n t e r , d i s k s t o r a g e and m a g n e t i c tape p e r i p h e r a l s ) . Although some might desire a more detailed system descript i o n at t h i s p o i n t , t h i s w o u l d f a l l i n t o the c o m m o n e r r o r of p r e o c c u p a t i o n w i t h s y s t e m s i n s t e a d of u s e . H e n c e the d e t a i l s w i l l b e o m i t t e d i n f a v o r of a d i s c u s s i o n o f g e n e r a l c o n s i d e r a t i o n s . Some more configuration details are given in a recent article (2). F u n c t i o n s of L e v e l s . F o u r p a r t i c u l a r a s p e c t s w h i c h p l a y a n i m p o r t a n t p a r t i n t h e w a y M I S S i s s t r u c t u r e d a r e (a) t h e e x i s t e n c e of the i n t e r m e d i a t e l e v e l ( r a t h e r t h a n h a v i n g m i n i c o m p u t e r s c o n n e c t e d d i r e c t l y t o g e n e r a l - p u r p o s e f a c i l i t i e s ) ; (b) t h e c o n c e p t of t h e i n t e r m e d i a t e l e v e l p r o v i d i n g a " n o n r e s i d e n t o p e r a t i n g s y s t e m " f o r t h e m i n i c o m p u t e r s ; (c) t h e p r o v i s i o n f o r c o n n e c t i n g a v a r i e t y of m i n i c o m p u t e r s , w i t h a s l i t t l e as p o s s i b l e s p e c i a l i z e d to t h e i n d i v i d u a l t y p e s ; (d) t h e g e n e r a l i t y o f t h e c o n n e c t i o n to t h e g e n e r a l - p u r p o s e s y s t e m , so that a v a r i e t y of u s e s c a n be e n t e r tained. I n b r i e f , t h e r e a s o n s f o r t h e i m p o r t a n c e of t h e s e a s p e c t s i s as f o l l o w s : (a) T h e i n t e r m e d i a t e l e v e l , d e d i c a t e d a s i t i s to t h e o n l i n e s u p p o r t f u n c t i o n , a f f o r d s t h e p o s s i b i l i t y of g r e a t e r r e l i a b i l i t y a n d f l e x i b i l i t y i n that f u n c t i o n , a s w e l l a s p r o v i s i o n of m o r e p a r t i c u l a r s e r v i c e s t h a n m i g h t b e a v a i l a b l e i n the g e n e r a l - p u r p o s e f a c i l i t y . N o t the l e a s t a d v a n t a g e h e r e i s a n o n t e c h n i c a l but n e v e r t h e l e s s v e r y r e a l o n e , that w i t h the i n t e r m e d i a t e l e v e l s y s t e m i s a s s o c i a t e d a s t a f f s u p p o r t g r o u p o r g a n i z e d a r o u n d the p r o v i s i o n of s e r v i c e s f o r o n l i n e m i n i c o m p u t e r s . The interm e d i a t e l e v e l , h o w e v e r , c a n be v i e w e d i n a n e v e n b r o a d e r c o n t e x t - - i n a v e r y r e a l s e n s e it " m e d i a t e s " b e t w e e n l o w e s t a n d h i g h e s t l e v e l s , a n d e n h a n c e s both i n so d o i n g . F o r e x a m p l e , it c a n g i v e t h e m i n i c o m p u t e r a t t h e l o w e s t l e v e l a c c e s s to e x t e n d e d c o m p i l i n g a n d a s s e m b l i n g c a p a b i l i t i e s c a r r i e d out at the h i g h est l e v e l , a n d a l s o h a n d l e the p r o b l e m s of s y s t e m a c c e s s
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b e t w e e n the l e v e l s , m a k i n g i t u n n e c e s s a r y f o r the m i n i c o m p u t e r u s e r to g r a p p l e w i t h t h e m . T h i s function is significant even in the p r e s e n t c a s e of a s i n g l e s y s t e m a t the h i g h e s t l e v e l , the 3 7 0 / 1 6 8 . I f t h i s w e r e e x t e n d e d t o a c c e s s to a g e n e r a l n e t w o r k , s u c h as A R P A N E T , the m e d i a t i n g f u n c t i o n w o u l d be e v e n m o r e important. (b) R a t h e r t h a n f u n c t i o n i n g m e r e l y a s a " c o m m u n i c a t i o n s c o n t r o l l e r " o r " f r o n t - e n d " f o r a c c e s s to g e n e r a l - p u r p o s e f a c i l i t i e s , as is t r u e i n s o m e h i e r a r c h i c a l s y s t e m s , the i n t e r m e d i a t e l e v e l i s s p e c i f i c a l l y d e s i g n e d to s u p p o r t a r a n g e of f u n c t i o n s that w o u l d be c h a r a c t e r i s t i c of a m e d i u m - s i z e d , a n d hence in general greatly expanded, m i n i c o m p u t e r configuration. R e f e r e n c e to o p e r a t i n g s y s t e m c h a r a c t e r i s t i c s , t h e n , i s m a d e to d e t e r m i n e w h i c h o f t h e m d o n o t n e e d to b e r e s i d e n t i n t h e c o m p u t e r w h i c h t h e o p e r a t i n g s y s t e m s u p p o r t s . A l t h o u g h the n o r m a l i d e a of a n o p e r a t i n g s y s t e m i s that it r u n s i n a c o m p u t e r s y s t e m to r e n d e r i t m o r e u s a b l e , i t t u r n s o u t t h a t a s u r p r i s i n g l y l a r g e n u m b e r of i t s f u n c t i o n s c a n be p r o v i d e d r e m o t e l y , a l l o r i n p a r t . T h i s a s p e c t is s p e c i f i c a l l y d i s c u s s e d i n a p a p e r p r e s e n t e d at a s y m p o s i u m o n c o m p u t e r s y s t e m s (3). (c) T h e d e s i g n o f t h e h a r d w a r e a n d s o f t w a r e i n t e r f a c e f r o m t h e l o w e s t l e v e l to t h e i n t e r m e d i a t e i s m a d e g e n e r a l , e m p h a sizing m a x i m u m flexibility and m i n i m u m cost. This results in a m i n i m a l communication/terminal package being designed for each minicomputer variety, w h i c h communicates in a standard ( l o g i c a l ) w a y w i t h the i n t e r m e d i a t e l e v e l s y s t e m . Thereafter an a t t e m p t i s m a d e to h a v e t h e s y s t e m d e p e n d a s l i t t l e a s p o s s i b l e on w h a t v a r i e t y of m i n i c o m p u t e r it i s . E v e n w h e r e this d i s t i n c tion m u s t be m a d e , for e x a m p l e in a s s e m b l y p r o g r a m s r u n n i n g at the h i g h e s t l e v e l , the m a n n e r of i n v o k i n g the a s s e m b l e r i s c o m m o n to a l l m i n i c o m p u t e r s . H e n c e t h e e f f e c t , a s s h o w n b y (b) a b o v e , i s a s i f e a c h m i n i c o m p u t e r u s e s a s t a n d a r d b u t m e d i u m - s i z e d operating system. (d) R a t h e r t h a n u s i n g o n e o f the m o r e s p e c i a l i z e d e n t r y m o d e s to t h e h i g h e s t l e v e l , s u c h a s " t e r m i n a l a c c e s s " o r " r e m o t e j o b e n t r y , " the p h y s i c a l c o n n e c t i o n i s g e n e r a l ( i . e . c h a n n e l i n t e r f a c e ) , s o t h a t the i m m e d i a t e l e v e l s y s t e m a p p e a r s a s a p e r i p h e r a l p r o c e s s o r to t h e g e n e r a l - p u r p o s e f a c i l i t y . T h i s p e r m i t s v a r i o u s m o r e s p e c i a l i z e d a c c e s s m o d e s to b e s u p p o r t e d b y t h e m e d i a t i n g s o f t w a r e i n the i n t e r m e d i a t e l e v e l s y s t e m . C e n t r a l i z e d / L o c a l i z e d C o m p u t i n g . A s p e c t s (c) a n d t a k e n t o g e t h e r , r e p r e s e n t a c r u c i a l o b j e c t i v e f r o m the v i e w o f the l a b o r a t o r y a p p l i c a t i o n . N a m e l y , t h e u s e r to M I S S f r o m the l a b o r a t o r y c a n u s e t h e m i n i c o m p u t e r e r a l s t a n d a l o n e d e v i c e , o r a s a t e r m i n a l to a c c e s s t h e
(d) a b o v e , p o i n t of connected as a gengeneral-
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p u r p o s e f a c i l i t y , b o t h w i t h o u t e x c e s s i v e o v e r h e a d to w h a t t h e s e functions w o u l d r e q u i r e in any case. T h u s on the s p e c t r u m of l o c a l i z e d / c e n t r a l i z e d c o m p u t i n g , the u s e r h a s b o t h e x t r e m e s a v a i l a b l e (the s t a n d a l o n e l o c a l i z e d m i n i c o m p u t e r , t h e t e r m i n a l a c c e s s e d c e n t r a l i z e d f a c i l i t y ) . N o i n i t i a l c h o i c e n e e d be m a d e to " g o c e n t r a l i z e d " o r " g o l o c a l i z e d , " w h i c h d i c h o t o m y h a s c a u s e d m u c h c o n t r o v e r s y a n d e x p e n d i t u r e of e n e r g y i n the p o l i t i c a l a r e n a of c a m p u s c o m p u t i n g . B y v i r t u e of h a v i n g b o t h t h e s e e x t r e m e s p r e s e n t i n the c o m p l e t e s y s t e m , the u s e r c a n get the a d v a n t a g e of a b l e n d of t h e m , t h a t i s , a d j u s t to a n a p p r o p r i a t e p o i n t on the l o c a l i z e d / c e n t r a l i z e d s p e c t r u m . T h i s i s the m e a n s by w h i c h M I S S " e n h a n c e s " m o r e s t a n d a r d f a c i l i t i e s . T h e q u e s t i o n t h e n a r i s e s , w h a t a r e the r e a s o n s f o r w a n t i n g these two e x t r e m e s i n c o m b i n a t i o n ? A l t h o u g h it m a y s e e n o b v i o u s that l o c a l i z e d c o m p u t i n g is b e t t e r f o r s o m e p u r p o s e s a n d c e n t r a l i z e d c o m p u t i n g f o r o t h e r s , to a p p r o a c h t h e q u e s t i o n o f the p r o p e r c o m b i n a t i o n r e q u i r e s that a n a n a l y s i s be m a d e . Laboratory Methodology F o r p r e s e n t p u r p o s e s , e x p e r i m e n t a l m e t h o d o l o g y m a y be c h a r a c t e r i z e d b y f u n c t i o n s i n f i v e c a t e g o r i e s , n a m e l y : (i) d a t a c o l l e c t i o n ; (ii) a u t o m a t i c c o n t r o l ; (iii) h u m a n - m e d i a t e d c o n t r o l ; ( i v ) a n c i l l a r y a n a l y s i s ; (v) f o l l o w u p a c t i v i t y . T h e f i r s t t h r e e o f t h e s e a r e the f u n c t i o n s w h i c h h a v e b e e n so r e v o l u t i o n i z e d b y the m i n i c o m p u t e r , r e c o r d i n g data f r o m instrumentation sensors, a n d p e r f o r m i n g o n l i n e the n e c e s s a r y c a l c u l a t i o n s to d o a u t o m a t i c a l l y such things as i n s t r u m e n t m o n i t o r i n g and adjustment, o r to g u i d e a n i n v e s t i g a t o r i n d o i n g t h e s e t h i n g s d u r i n g t h e c o u r s e of a n e x p e r i m e n t . The latter two, which may require extensive c a l c u l a t i o n d u r i n g the e x p e r i m e n t a l r u n o r a f t e r w a r d , c a n be c a r r i e d out o n the s a m e m i n i c o m p u t e r if it h a s the c o m p u t i n g c a p a c i t y a n d the r i g h t s o r t of m u l t i p r o g r a m m i n g c a p a b i l i t y , b u t g e n e r a l l y s e e m m o r e a p p r o p r i a t e f o r p r o c e s s i n g by a g e n e r a l p u r p o s e f a c i l i t y , d u e to v o l u m e of c a l c u l a t i o n a n d p o s s i b l e o u t put r e q u i r e m e n t s . One c o u l d i m a g i n e as a f i r s t step at a s a t i s f a c t o r y s y s t e m s o l u t i o n f o r l a b o r a t o r y n e e d s one w h e r e the i n v e s t i g a t o r h a s i n the l a b o r a t o r y a m i n i c o m p u t e r f o r h a n d l i n g (i), ( i i ) , a n d ( i i i ) , and w h i c h does double-duty as a t e r m i n a l device a c c e s s i n g a g e n e r a l - p u r p o s e f a c i l i t y f o r h a n d l i n g (iv) a n d (v). Capabilities o f c o n t e m p o r a r y m i n i c o m p u t e r s a r e c e r t a i n l y s u c h a s to p e r m i t t h e k i n d s o f p h y s i c a l i n t e r f a c i n g n e c e s s a r y , b o t h to e x p e r i m e n t a l a p p a r a t u s a n d to a c o m m u n i c a t i o n s n e t w o r k , a n d f u r t h e r m o r e t h e m i n i c o m p u t e r c a n r e a d i l y b e s e t u p to p e r f o r m b o t h r o l e s c o n c u r r e n t l y , g i v e n the a p p r o p r i a t e d e s i g n of i n t e r r u p t h a n d l i n g
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Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch007
p r o c e d u r e s ( w h i c h h e r e w o u l d h a v e to b e " r e a l - t i m e d e p e n d e n t " f o r b o t h r o l e s , a l t h o u g h m o r e c r i t i c a l l y so i n the f i r s t one). T h e r e i s , h o w e v e r , a n a d d i t i o n a l p r o b l e m f o r b o t h g r o u p s of f u n c t i o n s , that of d e v e l o p i n g o r o b t a i n i n g the n e c e s s a r y p r o g r a m s to c a r r y o u t t h e t a s k s , a n d f o r the l a t t e r g r o u p t h e a d d i t i o n a l p r o b l e m o f h a n d l i n g t h e i n p u t to a n d o u t p u t f r o m t h e c e n t r a l i z e d f a c i l i t y e f f i c i e n t l y f r o m the l a b o r a t o r y . H e r e is an i m p o r t a n t a s p e c t of l a b o r a t o r y a p p l i c a t i o n s of m i n i c o m p u t e r s - - i t m u s t be a s s u m e d that p r o g r a m m i n g i s a c o n t i n u i n g p r o c e s s , as e x p e r i ments p r o g r e s s or new ones a r e e m b a r k e d upon. T h i s is in c o n t r a s t to t h e " t u r n k e y " a p p l i c a t i o n s i n t h e i n d u s t r i a l c o n t e x t , w h e r e a n a p p l i c a t i o n i s d e s i g n e d to f u n c t i o n i n d e f i n i t e l y w i t h o u t reprogramming. If t h e c o m b i n e d l o c a l i z e d / c e n t r a l i z e d c a p a b i l i t y d e s c r i b e d i s a l s o a p p l i e d to p r o g r a m d e v e l o p m e n t , s a y to p r o v i d e e d i t i n g , a s s e m b l y a n d c o m p i l a t i o n o n t h e c e n t r a l i z e d f a c i l i t y for p r o g r a m s to b e t e s t e d a n d r u n o n t h e l o c a l i z e d o n e , t h i s w o u l d s e e m to r o u n d out the n e e d s of the e x p e r i m e n t e r . B u t m e r e p r o v i s i o n of c a p a b i l i t i e s d o e s not r e n d e r t h e m e f f i c i e n t a n d e f f e c t i v e , a n d the a p p r o p r i a t e s t r u c t u r e of the h a r d w a r e / s o f t w a r e c o n f i g u r a t i o n c o m b i n i n g the l o c a l i z e d a n d c e n t r a l i z e d f a c i l i t i e s i s d i c t a t e d by c o n s i d e r a t i o n s w h i c h m u s t take i n t o a c c o u n t the c h a r a c t e r i s t i c s of the l a b o r a t o r y a p p l i c a t i o n . Efficiency and Effectiveness. T h e q u e s t i o n s of e f f i c i e n c y a n d e f f e c t i v e n e s s h a v e m a n y f a c e t s . A l t h o u g h the t e r m " c o s t effective" is often h e a r d i n this context, w h e r e r e s e a r c h is c o n c e r n e d t h e r e i s no m o n e t a r y m e a s u r e of the e f f e c t i v e n e s s , and the r e s e a r c h e r i s o f t e n l i m i t e d i n w h a t c a n be p u r c h a s e d b y somewhat a r b i t r a r y c o n s i d e r a t i o n s such as grant p o l i c i e s and the l i k e . O b v i o u s l y the " o v e r h e a d c o s t " of i n c o r p o r a t i n g a l a b o r a t o r y m i n i c o m p u t e r into a h i e r a r c h i c a l support s y s t e m cannot be e x c e s s i v e , o r e l s e m a n y r e s e a r c h e r s w i l l be p r e v e n ted f r o m u s i n g it even if it s e e m s d e s i r a b l e . A prominent part of t h i s c o s t i s i n the c o m m u n i c a t i o n s l i n k b e t w e e n the l a b o r a t o r y a n d the r e s t of the s y s t e m . But balanced'against this cost and t h e c o s t of i n t e r f a c i n g i s the f a c t that the h i e r a r c h i c a l s y s t e m m a y p e r m i t a r e s e a r c h e r to a c q u i r e a s m a l l e r m i n i c o m p u t e r c o n f i g u r a t i o n to o b t a i n e q u i v a l e n t c a p a b i l i t y to a s t a n d a l o n e . T h i s i s o f t e n the m o s t i m m e d i a t e b e n e f i t p e r c e i v e d , a n d i t i s t h e r e f o r e i m p o r t a n t to e m p h a s i z e t h a t s h a r e d p e r i p h e r a l s a t a s i t e not too f a r r e m o v e d f r o m the l a b o r a t o r y a r e a n a t t r a c t i v e p r o s p e c t f o r the u s e r w h o h a s o n l y o c c a s i o n a l n e e d f o r t h e m . In the M I S S d e s i g n , it i s a s s u m e d that m i n i c o m p u t e r s i t e s c a n b e h a r d w i r e d to t h e i n t e r m e d i a t e f a c i l i t y , w h i c h r e p r e s e n t s
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a s u b s t a n t i a l s a v i n g o v e r the e q u i v a l e n t c a p a b i l i t y s u p p o r t e d t h r o u g h the t e l e p h o n e s y s t e m , b u t o f c o u r s e r e q u i r e s s o m e f o r m of c a b l e n e t w o r k t o b e a v a i l a b l e . T h i s c o n c e p t i s w e l l s u i t e d to a geographically coherent university campus, and in connection w i t h the M I S S p r o j e c t ( a n d i n c o o r d i n a t i o n w i t h s o m e o t h e r c a m p u s p r o j e c t s w i t h s i m i l a r n e e d s f o r a c c e s s to the C o m p u t a t i o n C e n t e r ) , a b a s i c c a b l e n e t w o r k h a s b e e n l a i d o n the U n i v e r s i t y of C h i c a g o c a m p u s c o n n e c t i n g the c o m p u t e r b u i l d i n g ( w h i c h h o u s e s b o t h the I n s t i t u t e f o r C o m p u t e r R e s e a r c h a n d the C o m p u t a t i o n C e n t e r ) to o t h e r s e l e c t e d s i t e s w h i c h a r e c l o s e to the l o c a t i o n s of p o s s i b l e u s e r s . T h i s n e t w o r k c o n s i s t s of t w i s t e d p a i r s , t e r m i n a t e d by r e l a t i v e l y i n e x p e n s i v e l i n e d r i v i n g a p p a r a t u s to h a n d l e t h e d e s i r e d t r a n s m i s s i o n s p e e d o f 9 6 0 0 b a u d b e t w e e n the l o w e s t a n d i n t e r m e d i a t e l e v e l s . A n o t h e r p o s s i b i l i t y a l l o w e d f o r i n the d e s i g n i s that of r e m o t e c o n c e n t r a t o r s at s i t e s c l o s e to s e v e r a l l a b o r a t o r i e s w h e r e M I S S users exist. T h e s e w o u l d be m i n i c o m p u t e r s w i t h a s u b s e t of p e r i p h e r a l s , n a m e l y those input/output devices for w h i c h p r o x i m i t y to t h e u s e r i s i m p o r t a n t , s u c h a s o u t p u t p r i n t e r s . User
Needs
F o r the p r e s e n t d i s c u s s i o n t h e r e m a y b e d i s t i n g u i s h e d t h r e e t y p e s of u s e r : the i n v e s t i g a t o r , the r e s e a r c h a s s i s t a n t a n d the technician. T h e i n v e s t i g a t o r is i n t e r e s t e d i n the c o m p u t e r setup o n l y i n i t s f u n c t i o n of f a c i l i t a t i n g l a b o r a t o r y w o r k , a n d i s g e n e r a l l y u n w i l l i n g to e x p e n d m u c h e f f o r t i n a b s o r b i n g s y s t e m details, and impatient with what may seem awkward or slow system response. T h e r e s e a r c h a s s i s t a n t c a n b e p e r s u a d e d to get m o r e i n v o l v e d i n s y s t e m d e t a i l s , if the i n v e s t i g a t o r i s c o n v i n c e d that it is r e a l l y n e c e s s a r y , but is s t i l l p r i m a r i l y i n t e r e s t e d i n w h a t t h e s y s t e m c a n d o to s u p p o r t t h e s c i e n t i f i c e f f o r t . The t e c h n i c i a n can f o l l o w d e t a i l e d p r e s c r i p t i o n s but r e m a i n s l a b o r a t o r y - o r i e n t e d r a t h e r than c o m p u t e r - o r i e n t e d . These characteristics are purposely made a little dogmatic, and s h a d e d t o w a r d the a p p l i c a t i o n s s i d e . A l t h o u g h e x c e p t i o n s do e x i s t , w h e r e the i n v e s t i g a t o r o r the r e s e a r c h a s s i s t a n t b e c o m e s e n t h u s i a s t i c a l l y i m m e r s e d i n s y s t e m d e t a i l s , p e r h a p s to a f a u l t , c l e a r l y s y s t e m d e s i g n s h o u l d a i m t o w a r d h a n d l i n g the s i t u a t i o n w h e r e the u s e r n e e d s m i n i m a l c o m p u t e r p r o f i c i e n c y . W h e n c o n s i d e r i n g the a c t u a l u s e r n e e d s i n t h i s w a y , c e r t a i n s e e m i n g l y c o n f l i c t i n g d e s i d e r a t a c o m e to t h e f o r e . These can be a p p r e c i a t e d b y c o n s i d e r i n g the w o r d s " r e l i a b i l i t y " a n d " f l e x i b i l i t y " used i n two different s e n s e s . R e l i a b i l i t y can m e a n d e p e n d a b i l i t y f o r s y s t e m a t i c o p e r a t i o n a c c o r d i n g to i i x e d b u t possibly inconvenient standards and schedules, as with c e n t r a -
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l i z e d s y s t e m s , o r it c a n m e a n a v a i l a b i l i t y at t i m e s m o s t c o n v e n i e n t to u s e r s a n d u n d e r t h e i r c o n t r o l , b u t w i t h o u t p r o v i s i o n of s u p p o r t i n g s e r v i c e s , a s w i t h l o c a l i z e d s y s t e m s . S i m i l a r l y , f l e x i b i l i t y c a n m e a n v e r s a t i l i t y i n b e i n g a b l e to r u n a w i d e v a r i e t y o f r o u t i n e t a s k s p e r f o r m e d a c c o r d i n g to g e n e r a l s y s t e m s t a n d a r d s , as w i t h c e n t r a l i z e d s y s t e m s , or c a p a b i l i t y of b e i n g m o d i f i e d o v e r s h o r t t i m e p e r i o d s i n r e s p o n s e to u s e r specified r e q u i r e m e n t s , as with l o c a l i z e d s y s t e m s .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch007
A n a t t e m p t h a s b e e n m a d e i n the d e s i g n of M I S S to a c h i e v e a b l e n d o f t h e s e a d v a n t a g e s i n b o t h s e n s e s , a n d i n a d d i t i o n to make t h e m e a s i l y a c c e s s i b l e to t h e s c i e n t i f i c u s e r b y l e t t i n g t h e i n t e r m e d i a t e l e v e l s e r v e a s f a c i l i t a t o r . S o m e of the s y s t e m c h a r a c t e r i s t i c s r e l e v a n t to t h i s a i m w i l l n o w b e d e s c r i b e d . Reliability. The separate i n t e r m e d i a t e l e v e l is a significant f a c t o r i n p r o m o t i n g r e l i a b i l i t y . T h e set of f u n c t i o n s it p r o v i d e s a r e f i x e d , a n d the d e m a n d s o n t h e m r e l a t i v e l y p r e d i c t a b l e , so that o p e r a t i o n c a n be e x p e c t e d to b e s t a b l e . T h e f a c t that u s e r p r o g r a m s a r e not r u n o n the i n t e r m e d i a t e l e v e l m i g h t be r e g a r d e d a s a m i s s e d o p p o r t u n i t y b y s o m e , b u t s e r v e s to m a k e t h e s y s t e m l e s s s u b j e c t to u n e x p e c t e d l o a d v a r i a t i o n s , w h i c h w o u l d also render performance less dependable. R e l i a b i l i t y of the i n t e r m e d i a t e l e v e l d i s k a n d m a g n e t i c tape s t o r a g e a r e p a r t i c u l a r l y i m p o r t a n t f o r the l a b o r a t o r y i n v e s t i g a t o r , w h o m u s t m a k e the d e c i s i o n a s to h o w m u c h of the c a r e o f e x p e r i m e n t a l l y d e r i v e d d a t a s h o u l d b e t r u s t e d to t h e m . The h a r d w i r e d a c c e s s c o n n e c t i o n s , the e r r o r m o n i t o r i n g l o g i c b u i l t i n t o the l i n e h a n d l i n g s o f t w a r e r u n n i n g a t the i n t e r m e d i a t e l e v e l , a n d the d e s i g n of the o p e r a t i n g s y s t e m a t that l e v e l to i s o l a t e independent functions as separate " p r o c e s s e s " a l l contribute to r e n d e r i n g the i n s t r u m e n t - d a t a - t o - b a c k u p - s t o r a g e p r o c e d u r e a d e p e n d a b l e o n e . It s h o u l d b e e m p h a s i z e d , h o w e v e r , t h a t t h e 9 6 0 0 b a u d t r a n s m i s s i o n r a t e f r o m t h e m i n i c o m p u t e r to t h e P D P - l l / 4 5 i s not i n t e n d e d to s e r v e the t o t a l r a n g e of e x p e r i m e n t a l data rates found in p r a c t i c e . F o r v e r y high data r a t e s , i t i s a p p r o p r i a t e f o r t h e m i n i c o m p u t e r to b e e q u i p p e d w i t h i t s o w n p e r i p h e r a l d i s k , s o that the r e s p o n s i b i l i t y f o r r e t e n t i o n of d a t a i n m a s s i v e a m o u n t s i s n o t r e l e g a t e d to t h e s h a r e d s y s t e m b u t r a t h e r to t h e d e d i c a t e d o n e u n d e r t h e i m m e d i a t e c o n t r o l o f the e x p e r i m e n t e r . R e l i a b i l i t y a t the h i g h e s t s y s t e m l e v e l i s e n h a n c e d b y t h e p r o v i s i o n f o r m o n i t o r i n g , at the i n t e r m e d i a t e l e v e l , the s e r v i c e s p r o v i d e d b y the g e n e r a l - p u r p o s e f a c i l i t y . T h e p u r v e y i n g of a c e r t a i n s e t o f " p a c k a g e d " s e r v i c e s a p p r o p r i a t e to t h e m i n i computer user (such as compilation and assembly) is regarded
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a s p a r t of the m i s s i o n of M I S S m a i n t e n a n c e g r o u p , w h i c h t h e r e b y f r e e s t h e u s e r s f r o m t h e b u r d e n of d e a l i n g w i t h t h e a n d o u t s of s u c h s e r v i c e s " o n t h e i r o w n .
ins
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch007
M
Flexibility. In c o n t r a s t w i t h s u c h " s t a n d a r d " s e r v i c e s , w h i c h m a y be m a d e a v a i l a b l e by the i n t e r m e d i a t e l e v e l i n a w a y s u c h t h a t the u s e r i s n o t e v e n a w a r e o f t h e i r s o u r c e , t h e r e m a y be s p e c i a l needs f o r w h i c h a n i n v e s t i g a t o r m u s t d e a l d i r e c t l y w i t h the g e n e r a l - p u r p o s e s y s t e m , a n d h e r e it i s i m p o r t a n t that the a c c e s s m e c h a n i s m not l i m i t s u c h d e a l i n g . T h e p r e v i o u s l y m e n t i o n e d a s p e c t (d) o f t h e h i e r a r c h i c a l s y s t e m p e r m i t s s u c h f l e x i b i l i t y to b e a c h i e v e d . In f a c t , one p a r t i c u l a r l i s t of d e v e l o p m e n t i n the M I S S p r o j e c t c o n c e r n s the w a y s i n w h i c h a c c e s s to l a r g e j o b - o r i e n t e d f a c i l i t i e s s h o u l d b e t a i l o r e d to t h e p a r t i c u l a r ( n o n s t a n d a r d ) c a s e of the u s e r w i t h o n l y a m i n i c o m p u t e r a n d t e l e t y p e ( t h u s no c a r d r e a d e r a n d l i n e p r i n t e r ) . F i n a l l y , t h e a s p e c t (c) o f t h e h i e r a r c h i c a l s y s t e m c i t e d e a r l i e r p e r m i t s c o n s i d e r a b l e l a t i t u d e i n the w a y the m i n i c o m p u t e r c a n be o p e r a t e d i n the l a b o r a t o r y . B e s i d e s p e r m i t t i n g it to f u n c t i o n e i t h e r a s a s t a n d a l o n e e x p e r i m e n t c o n t r o l l e r o r a s m e r e l y a t e r m i n a l to the g e n e r a l - p u r p o s e f a c i l i t y , the i n t e r f a c e i s d e s i g n e d to a l l o w t h e s e m o d e s t o b e m a i n t a i n e d c o n c u r r e n t l y (by p r o g r a m m i n g s o t h a t the m i n i c o m p u t e r c o m m u n i c a t i o n p a c k a g e h a n d l e s a l l r e a l t i m e i n t e r r u p t s ) . A c c e s s to the s p e c i a l i z e d s e r v i c e s of the i n t e r m e d i a t e l e v e l i s a n a d d e d b o n u s h e r e . B u t the l a t t e r a l s o m a k e s o t h e r c o m b i n e d m o d e s p o s s i b l e , s u c h a s r u n n i n g p r o g r a m a s s e m b l i e s i n the m i n i c o m p u t e r w h i l e l e t t i n g the i n t e r m e d i a t e l e v e l d i s k s t o r a g e be the r e p o s i t o r y f o r s o u r c e p r o g r a m and object code. T h i s a l l o w s t h e u s e r w i t h the m i n i m a l m i n i c o m p u t e r c o n f i g u r a t i o n to u s e i t f o r p r o g r a m d e v e l o p m e n t w i t h o u t t h e b u r d e n t h a t t h e l a c k of p e r i p h e r a l f a c i l i t i e s w o u l d o r d i n a r i l y e n t a i l , w h i c h r e p r e s e n t s a n a l t e r n a t i v e to d e l e g a t i n g the a s s e m b l y of p r o g r a m s to the g e n e r a l - p u r p o s e f a c i l i t y . Experience. T h i s b r i e f d i s c u s s i o n h a s i n d i c a t e d s o m e of the w a y s that h i e r a r c h i c a l m i n i c o m p u t e r s u p p o r t s u c h a s that p r o v i d e d b y M I S S c a n be m a d e r e l i a b l e a n d f l e x i b l e , w i t h o u t the s a c r i f i c e of e f f i c i e n c y a n d e f f e c t i v e n e s s . Experience with i n i t i a l u s e r s d u r i n g the d e v e l o p m e n t p h a s e h a s i n d i c a t e d h o w m u c h the c l o s e i n t e r a c t i o n b e t w e e n u s e r s a n d d e v e l o p e r s c a n f a c i l i t a t e the e x p l o r a t i o n of t h e s e s y s t e m a d v a n t a g e s . A l t h o u g h t h e d i s c u s s i o n h a s n o t b e e n o r i e n t e d to a n y p a r t i c u l a r a p p l i c a t i o n s , i t s r e l e v a n c e to e x p e r i m e n t a l c h e m i s t r y i s a t l e a s t a s g r e a t i f n o t g r e a t e r t h a n to o t h e r f i e l d s . I n f a c t , t h e f i r s t l a b o r a t o r y u s e o f the s y s t e m h a s b e e n i n c o n n e c t i o n w i t h
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that discipline. The initial external connection of MISS was to the PDP-11 in the molecular beam laboratory of L. Wharton in the University of Chicago Franck Institute. Here MISS not only has provided a particular investigator with useful support even in its development phase, but the user feedback obtained in this way has been invaluable for the project. At this writing MISS is still in an advanced stage of development as a complete system, although several users have been getting useful work from it for some time. There are currently nine minicomputers connected to it, with plans for fourteen more in the near future. Recent completion of the campus cable network has made MISS accessible from a variety of locations on the University of Chicago campus, and the total of twenty-three minicomputers now or about to be connected are located in a total of five buildings. Applications of these minicomputers cover a range of uses, both laboratory and operational, in the Physical Sciences and Biological Sciences Divisions. Literature Cited 1. Ashenhurst, R.L., and Vonderohe, R . H . , Datamation, (1975) 21 (2) 40-44. 2. Ashenhurst, R.L., Federation Proceedings (1974) 33 (12) 2405-7. 3. Ashenhurst, R.L., in "Computing Systems" (conference proceedings), University of Texas at Austin (1973).
8
C o m p u t e r N e t w o r k i n g at
UMR
D. W. BEISTEL, Department of Chemistry R. A. MOLLENKAMP, Department of Chemical Engineering H. J. POTTINGER, Department of Computer Science J. S. deGOOD and J. H. TRACEY, Department of Electrical Engineering Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch008
University of Missouri, Rolla, Mo. 65401 The University of Missouri - Rolla (UMR) employs two levels of computer networking in its educational and research activities. The IBM 360/50 of the UMR Computer Center and the other computer facilities of the four-campus, University System are linked via 50 KB data lines to a central IBM 370/168 computer at Columbia. That U-wide network was established to provide the maximum, affordable computer power to every potential user in the University while reducing duplication and its added costs. Figure 1 shows the hardware locations and manner of linkage for the U-wide network, referred to as the Macronetwork by the authors in this paper. In additions to the batch and special jobs processed by Chemistry and Chemical Engineering on the macronetwork, the computer expertise on the UMR campus has drawn together the minicomputers of several academic departments in what we call the UMR Mininet, diagrammed in Figure 2. The two levels of computer networking provide the potential of a vast range of computer services for the chemistry - chemical engineering programs and we will examine present and planned applications. Teaching and research applications of computers in chemistry and chemical engineering at UMR in the I960's were accomplished by batch processing at a central, campus facility and by RJE. The Department of Chemistry assembled a software package for spectroscopy (1) that included infrared, ultraviolet and magnetic resonance spectral applications plus an overview of current molecular orbital approximation methods. The programming was developed for student use and provided for the immediate application of theoretical principles to the analysis of complex spectral data. A Packard model 901A multichannel analyzer was assembled to control repetitive scan, NMR experiments and acquire data in CAT and kinetic studies. The configuration, as shown in Figure 3, allowed for indirect interfacing to the IBM 360/50 via nine-track magnetic tape when complex intensity or frequency analysis was
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William. Woods
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch008
IBM 3780
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Figure 1.
U-wide computer network con figuration ca. 1975
Figure 2.
UMR Mininet
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required. Software was developed to accommodate those a p p l i c a t i o n s using m o d i f i c a t i o n s of LA0C00N III (2), DECOMP and ASSIGN (3) and other programming developed i n house. Further computer a p p l i c a t i o n s to chemistry included paper tape output from a s c i n t i l l a t i o n counter and readout from the Reynolds 60 degree s e c t o r mass spectrometer, along with curve f i t t i n g - p l o t t i n g routines f o r the p h y s i c a l chemistry and instrumental methods l a b o r a t o r i e s . The programming was r e s i d e n t on disk at the UMR Computer Center and i n i t i a t e d as a batch j o b . Remote job entry v i a terminal was l i m i t e d to l e s s than one per cent of the computer a c t i v i t y of the Department. In the Chemical Engineering Department, batch computer a p p l i c a t i o n s included a wide range of s i m u l a t i o n and data analysis projects. The undergraduate c l a s s e s i n process design made extensive use of design programs such as CHESS, and considerable work was done to expand program options and capabilities. D i s t i l l a t i o n p r o j e c t s included development of a s i m u l a t i o n program a p p l i c a b l e to multi-component, sidestream columns. Control studies involved dynamic s i m u l a t i o n o f processes and c o n t r o l systems f o r design of optimal and sampleddata c o n t r o l s t r a t e g i e s . A n a l y s i s of experimental data was of prime importance to research on mixing and on enzyme r e a c t i o n k i n e t i c s . The mixing studies included the modeling of l a s e r - d o p p l e r anemometer data to p r e d i c t mixing patterns i n process v e s s e l s . That research generates a l a r g e amount of data i n looking f o r time v a r i a t i o n s and very high frequency f l u c t u a t i o n s . Enzyme r e a c t i o n k i n e t i c s s t u d i e s have involved the modeling of r e a c t i o n r a t e s with a mass spectrophotometer. Some o f the r e a c t i o n s studied are q u i t e slow and r e q u i r e d e i g h t to twelve hours f o r a s i n g l e experimental r u n . Computer a n a l y s i s of data required manual d i g i t i z i n g , card punching and batch processing using the IBM S c i e n t i f i c Subroutine package as well as user developed programs f o r regression a n a l y s i s . In 1973 a l l batch processing c o n t r o l was t r a n s f e r r e d to the macronetwork and only p l o t t i n g and s p e c i a l i z e d jobs were spooled to the IBM 360/50. Remote terminals were l i n k e d d i r e c t l y to the IBM 370 system under TS0. During t h i s period the computer graphics c a p a b i l i t i e s o f the UMR Computer Center and the Department o f E l e c t r i c a l Engineering were expanded by a c q u i s i t i o n of Data General Nova 800 units and the two f a c i l i t i e s were l i n k e d by phone l i n e . The slow data rates (110 B) o f the d i a l - u p l i n e were unacceptable to the users i n E l e c t r i c a l E n g i n e e r i n g , however. Because several stand alone Nova 800 computers were i n operation i n other departments on campus, the long-range p o t e n t i a l of a mininetwork was evaluated and r e l a t i v e l y high speed (19.2 KB) data l i n e s were i n s t a l l e d to permit i t s development. Link up was accomplished by the s t a f f s o f the computer center and e l e c t r i c a l engineering and a number
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of innovative programs were i n i t i a t e d . (4) In 1974 the Departments of Chemistry and Chemical Engineering purchased major computer hardware, extending the mininetwork to i t s present configuration. The linkup of the Texas Instruments 980A computer o f the Department o f Chemistry provided a number of c h a l l e n g e s . First, the computer was purchased from JEOL to support a JEOLJMS D-100 high r e s o l u t i o n mass spectrometer. The programming system f o r i t s dedicated f u n c t i o n was developed by JEOL i n a coded format that d e f i e d ready i n t e r p r e t a t i o n and i t required c a s e t t e input v i a Texas Instruments ASR 733 d e v i c e . I t was obvious to us that no stand-alone computer a p p l i c a t i o n s could be developed before the mass s p e c t r a l f a c i l i t y was converted to a d i s k operating system. Several software approaches were taken before the Texas Instruments bootstrap program, MHBOOT, was used to read the mass spectral programming i n t o core as data from d i s k , avoiding the f i v e minute load time from c a s e t t e . Another reason f o r that approach may be l e s s obvious to a p o t e n t i a l user of a dedicated system. The operator o f the mass spectrometer has acquired data from the Varian 2700 gas chromatograph and the JMS-D100 mass spectrometer f o r as many as two hundred, 4K word scans. He must normalize the mass s p e c t r a l data and choose his output device and formats before h i s study i s completed, a time-consuming process. A f t e r the data are stored on disk the operator can r e t u r n to the analyses a t his convenience and i s l i m i t e d o n l y by the a v a i l a b l e disk storage of his u n i t . The TI980A computer system as supplied by JEOL had a Calcomp 565 p l o t t e r . The p l o t t e r was not a Texas Instruments - optional accessory a t the time o f purchase, so i t s use i n the stand alone operation required some software development. Using notes supplied by JEOL and output from the IBM 360 p l o t t e r package an assembly language r o u t i n e was w r i t t e n . I t provides the same q u a l i t y o f p l o t s p r e s e n t l y o f f e r e d by the IBM 360/50 system at the UMR Computer Center. The p l o t t e r i s used i n support of l i n e a r l e a s t squares programming a t the present time. Its primary support f u n c t i o n remains i n mass s p e c t r a l output. To f a c i l i t a t e mass s p e c t r a l f i l e storage and searching as well as planned, off-campus communication, a communications package was developed to provide a v i a b l e l i n k to the M i n i n e t . We found that the communications module a v a i l a b l e from Texas Instruments was not capable o f m u l t i l i n k i n g , although i t i s a v e r s a t i l e module because o f i t s software support. The s t a f f at Washington U n i v e r s i t y was kind i n p r o v i d i n g the c i r c u i t diagram f o r an adaptation o f the TI module, but on examining t h e i r schematic i t was concluded that s i g n i f i c a n t improvements could be made at reduced c o s t . The f u l l schematic on our communicat i o n s module w i l l be published at a l a t e r date, but meanwhile a working c o n f i g u r a t i o n i s shown i n Figure 4. The t r a n s m i t t e r r e c e i v e r f u n c t i o n s provide communications over two o n e - h a l f m i l e
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2 |OSC
TI 980A
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Figure 3. Repetitive scanning magnetic reso nance facility
IBM J60/5C
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Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch008
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data l i n e s . This new communications module has the advantage of m u l t i - d a t a rate and m u l t i - d a t a l i n e hookup at one I/O board l o c a t i o n on the computer. We a c t u a l l y b u i l t two modules — one f o r external communications l i k e the Mini net and one f o r i n t e r n a l , remote s i t e s w i t h i n the Chemistry - Chemical Engineering b u i l d i n g . One u n i t i s dedicated to the Mininet at present. The planned development o f the second communications module i s shown i n Figure 5. The f i r s t stage l i n k to the Packard 901 m u l t i channel analyzer required no a d d i t i o n a l i n t e r f a c i n g at the a n a l y z e r , because the analyzer i s equipped with a Packard 970 p a r a l l e l - t o - s e r i a l converter with f r o n t panel switching of I/O options. For t h i s l i n k only the cable connectors f o r the high speed paper tape option were needed and a 1000 c h a r a c t e r - p e r second data r a t e was employed f o r 1/0. The present 1/0 from a !H or 1*F magnetic resonance experiment proceeds as f o l l o w s : The analyzer system acquires magnetic resonance d a t a , s t o r i n g each scan on an assigned magnetic tape r e c o r d . The data are then t r a n s f e r r e d v i a a data l i n e to TI980A d i s k , t r a n s f e r r e d v i a the i n i n e t to the IBM 360/50, which i n turn t r a n s f e r s the data to the IBM 370 system v i a the macronetwork f o r p r o c e s s i n g . The output from the IBM 370 -LA0C00N III program i s transmitted back to the m u l t i channel analyzer v i a a reversed sequence and i s p l o t t e d on the A56/60 recorder under the spectrogram. Because we do not operate the TI980A computer under an executive program, we must gain i t s a t t e n t i o n and monitor the i n i t i a l t r a n s f e r of d a t a . Entry to the Mininet a l s o requires a telephone a l e r t at the present time. While the f u l l t r a n s f e r operation seems cumbersome, i n p r a c t i c e the steps are simple and convenient. F u r t h e r , some processing can be done i n house at the option of the user. A complete s p e c t r a l a n a l y s i s requires 380K words o f core but o n l y about 4 to 6K words of core are needed f o r most k i n e t i c s t u d i e s . In f a c t some intermediate stages such as i n t e g r a t i o n can be accomplished on the multichannel analyzer i f the base l i n e i s linear. If n o t , base l i n e adjustment i s accomplished using the program, BLINE. We plan to l o c a t e a remote ASR 733 module i n the p h y s i c a l chemistry l a b o r a t o r y f o r use i n a short course i n l a b o r a t o r y computing. Presently a Wang 362 c a l c u l a t o r serves that purpose but does not accommodate the range of c a l c u l a t i o n s required during the two-semester course, f o r c i n g the c l a s s to use the TS0 l i n k s to the IBM 370 at Columbia. We also plan to acquire a computer graphics u n i t f o r attachment to the TI980A, which w i l l be used to introduce molecular o r b i t a l concepts i n the p h y s i c a l chemistry l a b o r a t o r y . Research a p p l i c a t i o n s are planned a l s o . In January 1973, the Chemical Engineering Department purchased a Data General Nova 800 computer system to support data a c q u i s i t i o n and control a c t i v i t i e s w i t h i n the department.
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The computer and p e r i p h e r a l s were bought as a system with Data General taking the r e s p o n s i b i l i t y f o r i n t e g r a t i n g components from a number of manufacturers. The system included a f u l l complement of computer and process I/O equipment and a f i x e d head d i s k f o r mass s t o r a g e . Subsequent purchases, i n c l u d i n g a c a r t r i d g e d i s k d r i v e , a d d i t i o n a l c o r e , and a CRT t e r m i n a l , r e s u l t e d i n a very f l e x i b l e system (Figure 6 ) . The Nova 800 computer s e l e c t e d i s a 1 6 - b i t word machine organized around f o u r accumulators. Options i n c l u d e d are hardware m u l t i p l y and d i v i d e , r e a l time c l o c k , power monitor/auto r e s t a r t , and automatic program l o a d . The o r i g i n a l 16K words o f memory has s i n c e been expanded to 24K. Equipment purchased f o r computer I/O c o n s i s t s of an ASR-33 t e l e t y p e , punched card r e a d e r , and 30 character per second, portable t e r m i n a l . An alphanumeric CRT terminal has since been added and i s now used as the primary computer c o n s o l e . Process I/O equipment was s e l e c t e d to provide f l e x i b i l i t y i n i n t e r f a c i n g with a v a r i e t y o f l a b o r a t o r y i n s t r u m e n t a t i o n . A wide-range a n a l o g - t o - d i g i t a l (A/D) system can accept up to 16 d i f f e r e n t i a l inputs with f u l l s c a l e ranges o f ± 2.54 mv to ± 10.24 ν i n 13 programmable steps at a r a t e of 200 samples per second. A high l e v e l , 4 channel A/D system can take up to 50,000 samples per second and d e p o s i t the data d i r e c t l y i n t o computer memory through a data channel. A d d i t i o n a l process 1/0 c o n s i s t s of 6 d i g i t a l to analog (D/A) channels, 16 d i g i t a l inputs and 16 d i g i t a l outputs. Present mass storage c o n s i s t s o f a r a p i d a c c e s s , f i x e d head d i s k and a removable c a r t r i d g e d i s k . With 256 Κ words of s t o r a g e , the f i x e d head d i s k provides f a s t , temporary storage of data and programs. The several 1.25 m i l l i o n word, removable d i s k c a r t r i d g e s give users permanent storage space f o r programs, d a t a , and computer d i s k operating systems. Vendor s u p p l i e d software f o r the Nova includes a r e a l time disk operating system and r e a l time F o r t r a n . This software, along with u t i l i t y programs f o r e d i t i n g and f i l e maintenance, provided a s t a r t i n g p o i n t f o r development of programs f o r data a c q u i s i t i o n and c o n t r o l . Fortran c a l l a b l e , assembly language programs were w r i t t e n at UMR to support A/D, D/A, and d i g i t a l 1/0. T h e r e f o r e , the m a j o r i t y of users can w r i t e a p p l i c a t i o n programs i n Fortran with no need to l e a r n assembly language programming. Perhaps the g r e a t e s t i n c e n t i v e f o r purchasing the Nova system f o r Chemical Engineering was the existence of several Novas i n other departments at UMR. The commonality of equipment and system software allows two people to handle a l l maintenance and m o d i f i c a t i o n of hardware and development of system software. Interfaces designed f o r one Nova are immediately a p p l i c a b l e f o r a l l Novas a t UMR. These have been important f a c t o r s i n the development o f the M i n i n e t .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch008
BEISTEL E T A L .
Networking
at UMR
graphics
Figure 5. Projected development of TI980A local network
Analog Front End 16 4 6 16 16
Channel, Wide Range A/D Channel, High Speed A/D Channel D/A D i g i t a l Inputs D i g i t a l Outputs
D i g i t a l Computer Computer I/O Punched Card Reader] CRT Terminal Execuport Terminal
Mininet Data General Nova 800 Interface Real Time Clock Power Monitor/Auto Restart^ 8 B i t , S e r i a l Asynchronous | Hardware Multiply/Divide Interface Auto Program Load 24 Κ Memory
Mass Storage 256 Κ Word, Fixed Head Disk 1.25 M i l l i o n Word, Removable Cartridge Disk
Figure 6.
Chemical Engineering Computer System
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I n i t i a l a p p l i c a t i o n s of the Chemical Engineering Nova have been as a stand alone system. G e n e r a l l y , one user a t a time w i l l use the system f o r data a c q u i s i t i o n and c o n t r o l . However, simple data a c q u i s i t i o n tasks may be executed i n a foreground p a r t i t i o n while program development or complicated c o n t r o l programs are conducted i n background. The f o l l o w i n g i n d i c a t e s present a p p l i c a t i o n s o f the Nova — both as a stand-alone system and as a part o f the m i n i n e t . The Nova system has been a p p l i e d to data a c q u i s i t i o n i n mixing s t u d i e s . A 0-10 v o l t signal output from the l a s e r doppler anemometer i s sampled by the high speed A/D system at a r a t e of 50,000 samples per second. Data i s stored d i r e c t l y i n t o memory u n t i l space i s exhausted. During the data a c q u i s i t i o n , the computer begins t r a n s f e r r i n g data to the f i x e d head d i s k . A f t e r a l l the data stored i n memory has been t r a n s f e r r e d to d i s k the sampling process c o n t i n u e s . In approximately f i v e seconds space i s exhausted on the f i x e d head d i s k and the experimental run i s complete. Disk data i s r e t a i n e d f o r processing on the Nova as a batch j o b . Using the M i n i n e t , t h i s data can be t r a n s f e r r e d d i r e c t l y from memory to the IBM 360/50 f o r high l e v e l a n a l y s i s and p l o t t i n g of r e s u l t s . The i n t e r f a c e with the mininet i s a 8 b i t s e r i a l , asynchronous, f u l l duplex i n t e r f a c e . The i n t e r f a c e can transmit data a t four d i f f e r e n t rates — 9 . 6 , 19.2, 38.4, and 76.8 Κ band — under program c o n t r o l . In the area of d i g i t a l computer process c o n t r o l , the Nova has been used to a u t o m a t i c a l l y control two experimental processes i n the process c o n t r o l l a b o r a t o r y . One process i s a simple l i q u i d l e v e l - f l o w system (Figure 7) used to demonstrate feedback c o n t r o l p r i n c i p l e s and evaluate d i g i t a l control a l g o r i t h m s . A second process mixes hot and c o l d water to produce a combined stream of c o n t r o l l e d temperature and flow r a t e . T h i s apparatus i s used to demonstrate cascade, r a t i o , and feedforward c o n t r o l and to design and evaluate n o n - i n t e r a c t i n g , m u l t i v a r i a b l e control s t r a t e g i e s . These s e t s o f equipment use conventional i n d u s t r i a l type s e n s o r s , control v a l v e s , and transducers to provide computer compatible s i g n a l s . Input s i g n a l s are accepted i n t o the computer v i a the wide-range A/D system. The D/A system provides control s i g n a l s to valves while computer s e t d i g i t a l outputs are used to s t a r t and stop pumps. These process control a p p l i c a t i o n s u t i l i z e m u l t i p l e task programs f o r a c q u i s i t i o n , c o n t r o l , a l a r m i n g , s t a r t u p , and emergency shutdown. Up t i l l now, t h i s work has been develop mental so that during operation the user r e q u i r e s e d i t i n g and compiling c a p a b i l i t i e s . Future a p p l i c a t i o n s i n c o n t r o l w i l l u t i l i z e the mininet f o r p e r i o d i c o p t i m i z a t i o n or e v a l u a t i o n o f complicated computer models o f l a b processes. Plans are to l i n k continuous
BEiSTEL E T A L .
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Figure 7. Liquid level-flow process used for computer control studies
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distillation equipment in the unit operations lab with the Nova for data acquisition and control. Large simulation programs on the IBM 360/50 will use the lab data as a comparison for evaluation of steady-state and dynamic characteristics. In kinetic studies of enzyme catalysis, data may be acquired by the computer during lengthy experimental runs. A 0-10 volt output from the mass spectrophotometer is sampled at relatively slow rates and for long periods of time. To allow continued program development during these times, the sampling is done by a foreground program, stored on disk, and analyzed at a later time. Future applications in this area will involve much faster reactions. Data will be sent to the IBM 360/50 via the mi ninet for regression analysis. The results will be returned to a terminal in the kinetics lab to guide subsequent experimental runs. Abstract The University of Missouri has two levels of computer net working in operation, a macronetwork to the central IBM 370 system at UMC and subnetworks at UMC and UMR. The subnetwork at UMR is a mininetwork of seven Data General Nova 800's and one Texas Instru ments 980A, tied by direct 19.2 KB data lines to a Data General Nova 800 link to the IBM 360/50. The TI980A (Chemistry) facility can be dedicated to on-line data acquisition with a JE01 D-100 mass spectrometer or act as a stand-alone terminal with plotter. The Data General Nova 800 (Chemical Engineering) is a stand-alone unit equipped for a variety of multiplexed, data acquisition appli cations. Hardware and software development for the Nova 800 is in advanced stages because of advanced applications such as computer graphics in other departments, while the TI980A link requires a variety of innovative developments to act as a functional link in a Nova network. The details of hardware and software development are discussed in the context of applications to chemical problems. 1. 2. 3. 4.
Literature Cited Beistel, D. W., J. Chem. Ed., (1973), 50, 145. Bothner-By, Α. Α., and Castellano, S., "LA0CN3", Mellon Institute, Pittsburgh. Lusebrink, T. R., Ph.D. Thesis, University of California at Berkeley, August 1965. Tracey, J. H., and Pottinger, H. J., Proc. IEEE, (August 1975), in press.
9
Computer Assembled Testing in a Large Network:
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch009
T h e S O C R A T E S System WILLIAM V. WILLIS Chemistry Department, California State University, Fullerton, Calif. 92634 OLIVER J. SEELY, JR. Chemistry Department, California State College, Dominguez Hills, Calif. 90747 The use of computers in the formal educational process is increasing in diversity and extent. As scientists, chemists have often used computer techniques to solve a wide variety of problems. As educators, we are beginning to use computers as a resource and tool to develop more effectively and efficiently the knowledge and s k i l l s of our students. Much of this use has been by individual instructors, and therefore has been developed with highly specialized goals in mind for a small number of users. For example, on-campus CAI type instruction in the analysis of NMR spectra, or solving stoichiometry problems etc. This paper describes the formulation and implementation of a large general purpose program called SOCRATES (Student Oriented Classroom Analysis and Test Evaluation System) designed for operation in a 19 campus computer network serving 290,000 students and 16,000 faculty in the California State University and Colleges. SOCRATES is a data management system designed to produce and process exercises (tests, tutorials, homework, etc.) as directed from collections of questions, or data banks, in thirteen fields: chemistry, physics, mathematics, psychology, economics, US history, accounting, FCC review, biology, testing and measurement, counseling and guidance, p o l i t i c a l science and data processing. The concept of generating tests by selecting prepared questions from a collection is certainly not novel. Instructors have traditionally maintained in personal collections f i l e cards which are searched and given to a typist for suitable duplication. On a larger scale, commerical testing services have maintained computerized files for approximately twenty years, and presently more than one hundred educational institutions in the USA and Canada have 129
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c o l l e c t i o n s s t o r e d on magnetic t a p e . Usage o f t h e l a t t e r has not been g r e a t f o r a v a r i e t y o f r e a s o n s , i n c l u d i n g poor communications, l i m i t e d a c c e s s i b i l i t y , and t e a c h e r a t t i t u d e s , One SOCRATES c r i t i c summed up t h e s e a t t i t u d e s i n the remark "You a r e j u s t automati n g what we a l l do." We w i l l attempt i n t h e f o l l o w i n g paragraphs t o d e s c r i b e t h i s v e r y automation, and the r e a c t i o n s o f e d u c a t o r s , s t u d e n t s , and o t h e r s which l e a d us t o b e l i e v e t h a t i t w i l l produce a p r o f o u n d change i n c e r t a i n a s p e c t s of the e d u c a t i o n a l p r o c e s s ; i n d e e d , t h e l a r g e s c a l e a p p l i c a t i o n o f computer t e c h nology t o e d u c a t i o n t h r u d a t a banks and networking i s f e a s i b l e , e c o n o m i c a l , and p e d a g o g i c a l l y sound.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch009
The
SOCRATES R e t r i e v a l System
Our d a t a banks were d e v e l o p e d i n i t i a l l y f o r use i n a r e t r i e v a l s y s t e m d e s c r i b e d by L i p p e y , e t a l . (_1) . I t was i m p o s s i b l e f o r a l l campuses i n t h e network t o a c c e s s the d a t a banks d i r e c t l y due t o hardware and management c o n s t r a i n t s . The system was r e d e s i g n e d and r e w r i t t e n i n ANSI COBOL t o o p e r a t i o n on a CDC 3300 c e n t r a l computer. Formal i n s t i t u t i o n a l s u p p o r t f o r t h e system has been a v a i l a b l e f o r the p a s t two y e a r s , d u r i n g which time t h e c h e m i s t r y d a t a bank has grown from 2,000 t o 10,000 i t e m s . The r e t r i e v a l system a l l o w s t h e u s e r t o s e l e c t items from the bank employing a v a r i e t y o f parameters, e i t h e r s i n g l y on i n c o n c e r t , t o execute the s e a r c h . These parameters i n c l u d e a c a t e g o r y number (see below), l e v e l o f d i f f i c u l t y , a b e h a v i o r l e v e l ( r e q u i r ing e i t h e r the d e m o n s t r a t i o n of knowledge o r t h e a p p l i c a t i o n of knowledge), key words, i t e m s o u r c e i d e n t i f i c a t i o n , and a s p e c i a l i z e d s e a r c h parameter whose f u n c t i o n v a r i e s from bank t o bank. Two o t h e r g e n e r a l s e a r c h parameters a r e a v a i l a b l e which a l l o w b l o c k s o f i n t e r r e l a t e d q u e s t i o n s (macro items) and items which r e q u i r e m a t e r i a l s not i n t h e d a t a bank, such as s l i d e s , a u d i o o r TV c a s s e t t e s and f i g u r e s , (enhanced items) t o be s e l e c t e d o r s u p p r e s s e d from selection. Each e x e r c i s e can c o n t a i n up t o 150 i t e m s , and may be e d i t e d by the u s e r t o d e l e t e o r add i t e m s . Up t o n i n e v e r s i o n s o f the same e x e r c i s e may be r e q u e s t e d w i t h d i f f e r e n t o r d e r s of p r e s e n t a t i o n of the c o n t e n t s , and t h e e x e r c i s e can be produced by l i n e p r i n t e r on e i t h e r c o n s o l e paper o r c o n t i n u o u s form r e p r o d u c t i o n m a s t e r s a t the u s e r s r e q u e s t . Obj e c t i v e items i n the e x e r c i s e s ( m u l t i p l e c h o i c e , t r u e f a l s e ) can be computer s c o r e d ; i n d i v i d u a l s t u d e n t performance may be then compared w i t h r e c o r d s o f
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a v e r a g e s f o r p a s t r e s p o n s e s m a i n t a i n e d by SOCRATES. The SOCRATES system c a n be used e i t h e r i n a b a t c h mode o r a t i m e s h a r i n g mode. No knowledge o f computer programming i s n e c e s s a r y t o use t h e system's e d u c a t i o n a l f e a t u r e s . The c o n t e n t , g e n e r a t i o n , admini s t r a t i o n , and g r a d i n g o f SOCRATES e x e r c i s e s i s cont r o l l e d by t h e u s e r . T y p i c a l l y , a request submitted by t e l e p h o n e w i l l r e s u l t i n t h e o v e r n i g h t p r o d u c t i o n o f t h e e x e r c i s e , and d e l i v e r y t h e f o l l o w i n g day. The most i m p o r t a n t f e a t u r e i n t h e d e s i g n f o r u s e r a c c e s s t o each d a t a bank i s t h e s u b j e c t m a t t e r c l a s s i f i c a t i o n system. The SOCRATES system u s e s t e n major c a t e g o r i e s which a r e a r r a y e d i n a h e i a r c h y f o r s e a r c h ing. T a b l e I shows t h e main s u b j e c t c l a s s i f i c a t i o n s f o r t h e c h e m i s t r y bank. Table I Major C a t e g o r i e s i n t h e SOCRATES C h e m i s t r y Bank 00000 I. Reserved (non-standard items) 10000 I I . I n t r o d u c t o r y Chemistry 20000 I I I . Atomic Theory and S t r u c t u r e s 30000 IV. Chemical P e r i o d i c i t y 40000 V. S t o i c h i o m e t r y and The Mole Concept 50000 V I . K i n e t i c and E q u i l i b r i u m 60000 V I I . S o l u t i o n Chemistry 70000 VIII.Bonding 8 0000 IX. Thermodynamics 90000 X. Topics W i t h i n each major c a t e g o r y , sub c a t e g o r i e s a r e e s t a b l i s h e d , as shown i n T a b l e I I which shows a p o r t i o n o f the d e t a i l e d c l a s s i f i c a t i o n system f o r s o l u t i o n chemistry. Table I I P a r t i a l SOCRATES C a t e g o r y L i s t i n g f o r S o l u t i o n Chemistry 60000 V I I . S o l u t i o n C h e m i s t r y 62000 62100 62140 62141 62142
B. A c i d s , Bases, and S a l t s 1. G e n e r a l P r o p e r t i e s (D) A c i d s and Bases (1) S t r o n g A c i d s ( i n c l u d i n g oxidizing properties) (2) Weak A c i d s
The e x e r c i s e g e n e r a t i o n program would, upon r e q u e s t f o r s o l u t i o n c h e m i s t r y i t e m s , s e a r c h a l l items between t h e l i m i t s 60000 and 69999; i f i n s t r u c t e d t o s e a r c h f o r items d e a l i n g w i t h a c i d s , bases, and s a l t s , c a t e g o r i e s 62000 t h r u 62999 would be s e a r c h e d , and so on. I n t h i s manner, a 10,000 i t e m bank c a n be s e a r c h -
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ed t o produce a 100 i t e m t e s t i n 1.07 minutes t o t a l time, i n c l u d i n g I/O, a t a c o s t o f $3.46. The u s e r i s p r o v i d e d a copy o f the t e s t w i t h a l l q u e s t i o n s s e q u e n t i a l l y numbered, a c o v e r i d e n t i f i c a t i o n page which a l s o has a t e l l t a l e t o i n s u r e p r i v a c y of t h e e x e r c i s e , a t e s t r e q u e s t page showing the r e q u e s t s u b m i t t e d , and an i t e m s t a t i s t i c s page which l i s t s c o r r e c t answers, i t e m s o u r c e s and o t h e r i n f o r m a t i o n . The c o n t e n t and c l a s s i f i c a t i o n system o f the d a t a banks i s c o n t r o l l e d by the d a t a bank c o o r d i n a t o r s and the SOCRATES d i r e c t o r . Their personal viewpoints w i l l be r e f l e c t e d t o some degree i n the c l a s s i f i c a t i o n system. The C h e m i s t r y bank f o l l o w s a g e n e r a l i z e d p a t t e r n d e r i v e d from the format of i n t r o d u c t o r y t e x t s , s i n c e the p r i n c i p a l use o f the bank i s e n v i s i o n e d to be f o r i n t r o d u c t o r y c o u r s e s w i t h l a r g e e n r o l l m e n t s . As an example o f another approach the U.S. h i s t o r y bank i s a r r a n g e d c h r o n o l o g i c a l l y . I r r e s p e c t i v e of t h e c l a s s i f i c a t i o n used w i t h i n the r e q u i r e d h e i r a r c h y , a l l banks a r e b e i n g d e v e l o p e d so as t o p e r m i t the g r e a t e s t f l e x i b i l i t y and promote u s e r a c c e p t a n c e . Thus items which f a v o r p a r t i c u l a r p e d g o g i c a l t e c h n i q u e s , such as programmed l e a r n i n g , a r e d i s c o u r a g e d . T e s t g e n e r a t i o n i s but one f u n c t i o n o f SOCRATES F i g u r e 1 shows a b l o c k diagram o f the c o n t r o l p o i n t s and s o f t w a r e modules. The b a t c h t e s t g e n e r a t o r has been d e s c r i b e d above. The i n t e r a c t i v e t e s t g e n e r a t o r (ITG) and s c o r i n g modules can o p e r a t e i n two modes. The f i r s t mode a l l o w s the t e a c h e r t o d e v i s e an e x e r c i s e i n t e r a c t i v e l y from a remote c o n s o l e u s i n g the same s e a r c h parameters as p r o v i d e d i n the b a t c h mode.
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A = Content and s c o r i n g determined by teacher. Β = Content and s c o r i n g determined by student. * = Module under development. Figure 1.
Principal SOCRATES modules and control points
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A f t e r e d i t i n g o u t p u t can be p r o v i d e d a t the j o b i n i t i a t i o n s i t e (hard c o p y ) , o r by l i n e p r i n t e r from the Los A n g e l e s d a t a p r o c e s s i n g c e n t e r . The second mode a l l o w s the s t u d e n t t o choose items from a group s e l e c t e d by t h e t e a c h e r , and t o answer them f o r c r e d i t . The s t u d e n t has o p t i o n s as t o t h e d i f f i c u l t y (hence p o i n t v a l u e ) and the c o n t e n t (the q u e s t i o n p r e s e n t e d may be r e f u s e d ) o f the e x e r c i s e . The ITG module does not p r o v i d e CAI o r programmed l e a r n i n g i n the sense t h a t s o l u t i o n h i n t s a r e not p r o v i d e d , and the c o n t e n t of subsequent q u e s t i o n s i s not n e c e s s a r i l y c o n t i n g e n t on s t u d e n t r e s p o n s e . ITG s c o r i n g i s p r o v i d e d by a s e p a r a t e module. The i n t e g r a t e d media module (IM) w i l l be developed t o use t y p e s of enhanced items i n the d a t a bank which r e q u i r e the use of i n f o r m a t i o n o r d e v i c e s m a i n t a i n e d o u t s i d e the SOCRATES d a t a bank, and t h e r e f o r e not d i r e c t l y under c o n t r o l o f the s o f t w a r e . P r e s e n t l y a l l enhanced items i n each bank a r e keyed t o r e s o u r c e f i g u r e f i l e s , c o p i e s o f which a r e p r o v i d e d f o r each SOCRATES u s e r on r e q u e s t . These a r e t y p i c a l l y l i n e drawings s p e c i f i c a l l y p r e p a r e d f o r ease o f d u p l i c a t i o n by Xerox o r s p i r i t p r o c e s s masters. The IM module would a l l o w u s e r s t o i n c l u d e q u e s t i o n s based on l o c a l r e s o u r c e s such as TV t a p e s , s l i d e s , f i l m l o o p s , e t c , t h i s i s , m a t e r i a l s which would not n o r m a l l y be d u p l i c a t e d and g i v e n t o s t u d e n t s i n d i v i d u a l l y i n o r d e r f o r them t o complete t h e e x e r c i s e (e.g., p e r i o d i c t a b l e s ) . Computing Hardware i n the C a l i f o r n i a S t a t e U n i v e r s i t y and C o l l e g e s CSUC The hardware c u r r e n t l y i n use i s shown i n T a b l e I I I . Networking i s l i m i t e d f o r data processing to computers and the S t a t e U n i v e r s i t y i n Los A n g e l e s .
i n t h e CSUC system i n t h e u s u a l y sense l i n t e between l o c a l Data C e n t e r (SUDC)
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T a b l e I I I . Computer Hardware i n t h e C a l i f o r n i a U n i v e r s i t y and C o l l e g e s System Time Enrollment Sharing Other CDC Campus (Fall, 1974) Ports* Long Beach 3150 11 31, 228 IBM 360/40 30, 564 12 San Diego 3300 26, 829 7 San Jose 3170 11 Northridge 25, 377 3150 23, 679 Los Angeles 7 12 3150 San Francisco 20, 855 Fullerton 7 3150 20, 053 8 3150 Sacramento 19, 662 8 3150 Fresno 15, 331 IBM 360/40 7 San Luis Obispo 14, 434 3150 Chico 6 12, 680 3150 Hayward 8 11, 711 3150 Pomona 6 11, 099 3150 3 Humbolt 7,290 NCR 200 Sonoma 2 5,798 Honeywell Dcminguez H i l l s 2 5,747 Honeywell 2 San Bernardino 3,501 Honeywell Bakersfield 1 2,897 Honeywell 2 Stanislaus 2,800 3300, State University 3300 Data Center Totals
291, 916
112
14
State
20/20 20/20 20/20 20/20
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*A11 t i m e s h a r i n g o p e r a t i o n s use t h e CDC 3170 memory and c e n t r a l p r o c e s s o r a t t h e N o r t h r i d g e Campus; p o r t s may have t e l e t y p e , CRT, o r b o t h t y p e s o f t e r m i n a l s ; a c c e s s i s c o n t r o l l e d by t h e SUDC CDC 3300 executive.
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Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch009
Data f i l e s i n o t h e r computers may be a c c e s s e d i n d i r e c t l y t h r o u g h the e x e c u t i v e CDC 3300 a t SUDC by p r e arrangement. The demand f o r memory o r c o m p u t a t i o n a l speed t o d a t e has been met by t h i s c o m b i n a t i o n , so t h a t d i r e c t l i n k between campus computers has not been needed. However, t h e demand f o r t i m e s h a r i n g o p e r a t i o n s has f a r exceeded c a p a c i t y , p a r t i a l l y because o f the low t r a n s m i s s i o n r a t e s (110 baud) d i c t a t e d by t h e e x i s t i n g equipment which must span some 1200 km (maximum) between t e r m i n a l s . To meet t h i s need, H e w l e t t P a c k a r d 2000 computers w i l l be i n s t a l l ed l o c a l l y f o r hard w i r e d t i m e s h a r i n g a t h i g h e r d a t a t r a n s m i s s i o n r a t e s . The impact o f t h e s e f a c t o r s on SOCRATES use and networking w i l l be d i s c u s s e d i n a following section. The
Chemistry
Data Bank
The c h e m i s t r y d a t a bank was f i r s t c o m p i l e d i n 1972-73 u s i n g items donated by the E d u c a t i o n a l T e s t i n g S e r v i c e and the Monmouth, Oregon C i t y S c h o o l s . The m o d i f i c a t i o n of t h e s e e x i s t i n g q u e s t i o n s a l l o w e d us t o q u i c k l y d e v e l o p t h e bank t o a u s e f u l s i z e . The p r o j e c t was supported by an I n n o v a t i v e Funds G r a n t from the O f f i c e o f t h e C h a n c e l l o r , C a l i f o r n i a S t a t e U n i v e r s i t y and C o l l e g e s . The i n i t i a l i n t e n t was t o d e v e l o p items c o v e r i n g the f i r s t y e a r o f c o l l e g e l e v e l chemistry. A t t h e p r o j e c t t e r m i n a t i o n d a t e , the bank c o n t a i n e d 4000 s e p a r a t e q u e s t i o n s , p r i m a r i l y of the m a c h i n e - g r a d a b l e m u l t i p l e c h o i c e t y p e . The manpower r e q u i r e d f o r p r o d u c t i o n was as f o l l o w s : 1/2 manyear f o r c l a s s i f y i n g and p r o o f r e a d i n g keypunched items; 1/2 manyear o f keypunch time; 1/2 man y e a r f o r c o o r d i n a t i o n o f t h e s e e f f o r t s and d a t a p r o c e s s i n g . (The SOCRATES s o f t w a r e system i t s e l f has r e q u i r e d some 5 manyears f o r development t o d a t e ) . In t h e p a s t y e a r the bank has been expanded t o 10,000 i t e m s . Itemë have been donated by E a s t e r n M i c h i g a n U n i v e r s i t y , M i c h i g a n S t a t e U n i v e r s i t y , and t h e U n i v e r s i t y o f P i t t s b u r g . T h i s e x p a n s i o n has r e q u i r e d approxi m a t e l y 3 manyears o f e f f o r t . The bank i s now b e i n g used by f i v e p e r c e n t of the r e g i s t e r e d u s e r s each day t o produce q u i z z e s , homework a s s i g n m e n t s , t u t o r i a l s , d i a g n o s t i c t e s t s , c h a l l e n g e e x a m i n a t i o n s , and f i n a l e x a m i n a t i o n s . Other bank uses (over twenty have been r e p o r t e d ) i n c l u d e p r o d u c t i o n o f c o p i e s o f the e n t i r e bank on paper on m i c r o f i c h e f o r s t u d e n t r e v i e w i n l i b r a r i e s o r l e a r n i n g c e n t e r , and p r o d u c t i o n o f b l o c k s o f " u n s u i t a b l e " q u e s t i o n s which a r e g i v e n t o s t u d e n t s t o
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch009
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AND
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c r i t i q u e and improve. A p o p u l a r f e a t u r e i s the p r o d u c t i o n o f a g e n e r a l c h e m i s t r y placement examin a t i o n which i s r e g u l a r l y a d m i n i s t e r e d t o a l l f i r s t time c h e m i s t r y s t u d e n t s a t f o u r campuses. T h i s has g r e a t l y f a c i l i t a t e d comparisons o f s t u d e n t p o p u l a t i o n s , and has l e d t o a study o f the p o t e n t i a l o f the placement t e s t as a c o u n s e l i n g t o o l f o r incoming freshmen. One c h r o n i c problem c r e a t e d by the d i v e r s i t y of hardware w i t h i n the system and the language r e q u i r e ments of c h e m i s t r y , p h y s i c s , and mathematics has r e v o l v e d around use o f s t a n d a r d b u s i n e s s p r i n t c h a i n s on l i n e p r i n t e r s . Many commonly used s c i e n i t i c symbols a r e not a v a i l a b l e , most i m p o r t a n t l y sub and s u p e r s c r i p t s and lower c a s e l e t t e r s . We have d e v e l o p e d a s e t o f c o n v e r s i o n s which i s s e r v i c e a b l e , and meets the f o l l o w i n g c r i t e r i a : (1) easy t o l e a r n ; (2) uses s t a n d a r d b u s i n e s s p r i n t c h a i n s ; (3) r e a d i l y i n t e r c o n v e r t i b l e t o y i e l d s i m i l a r o u t p u t by l o c a l computer s o f t w a r e ; (4) w i l l r e q u i r e m i n i m a l r e f o r mating as a p p r o p r i a t e p r i n t c h a i n s a r e a c q u i r e d . The c o n v e n t i o n s which have been used a r e perhaps d i s c o n c e r t i n g a t f i r s t g l a n c e t o t h e u s e r who has a l o n g - s t a n d i n g f a m i l i a r i t y w i t h commonly a c c e p t e d c h e m i c a l r e p r e s e n t a t i o n s , but students r e a d i l y l e a r n these conventions. A few h i g h l i g h t s f o l l o w as examples. E l e m e n t a l symbols ( t w o - l e t t e r ) a r e under l i n e d : thus c o b a l t i s w r i t t e n as CO which d i s t i n g u i s h e s i t from c a r b o n monoxide. S u b s c r i p t s a r e s h i f t e d a l i n e down, and s u p e r s c r i p t s a l i n e up: 238 H 50 ; ΤΗ . E q u i l i b r i u m i s r e p r e s e n t e d by <Ε===Ξ> , 2 4 resonance by < >, and r e a c t i o n by > . Questions u s i n g e l e c t r o n d o t f o r m u l a s o r Kekule s t r u c t u r e s a r e b e t e n o i r e o f the s t a n d a r d p r i n t c h a i n c h a r a c t e r s e t , and have g e n e r a l y been s u p p l i e d s e p a r a t e l y as enhanced items w i t h p r e p a r e d f i g u r e s . 1
Usage o f the C h e m i s t r y
Data Bank
Most t e s t r e q u e s t s a r e made v i a v o i c e t e l e p h o n e d i r e c t l y t o SUDC, w i t h a s m a l l e r p e r c e n t a g e i n i t i a t e d by remote b a t c h . S i n c e a t y p i c a l e x e r c i s e may c o n t a i n 1000 l i n e s , most u s e r s e l e c t t h e s e o p t i o n s r a t h e r t h a n i n t e r a c t i v e t e s t g e n e r a t i o n which must p r o c e e d a t 110 baud. The a c t u a l amount of t e a c h e r time i n v o l v e d i s perhaps s l i g h t l y l e s s than t h a t r e q u i r e d by t r a d i t i o n a l methods, but the f o l l o w i n g advantages ar«crueby SOCRATES usage: (1) t h e t e s t may be
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch009
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c o n v e n i e n t l y e d i t e d any number o f t i m e s ; (2) t h e t e s t i s produced neat and e r r o r - f r e e on r e p r o d u c t i o n m a s t e r s ready f o r p r o c e s s i n g (thus r e d u c i n g t h e amount o f p r o o f r e a d i n g and t y p i n g n e c e s s a r y ) ; (3) t h e t e s t i s machine graded; (4) s t a t i s t i c s a r e p r o v i d e d on s t u d e n t performance. The n e t r e s u l t i s t h a t t e a c h e r s spend t h e i r time i n two o f t h e t a s k s most d e s e r v i n g o f t h e i r a t t e n t i o n and e x p e r t i s e , namely s e l e c t i n g the c o n t e n t o f t h e e x e r c i s e and e v a l u a t i n g s t u d e n t p e r f o r m a n c e . T h i s s h o u l d p r o v i d e more time f o r t h e t e a c h e r t o spend i n s c h o l a r l y and academic endeavor, and o t h e r w i s e b e n e f i t the student. However, a c c e p t a n c e o f SOCRATES, i f demonstrated by i n c r e a s i n g usage, i s slow t o come. O b v i o u s l y p r o f e s s o r s do n o t have t h e same degree o f f a m i l i a r i t y w i t h e d u c a t i o n a l computer usage as w i t h r e s e a r c h o r i e n t e d usage, o r w i t h computer produced o u t p u t as w i t h m a t e r i a l s produced by s e c r e t a r i a l s t a f f . Complete, hands-on, immediate c o n t r o l o f a l l phases o f e x e r c i s e g e n e r a t i o n by t h e i n d i v i d u a l i s a s t r o n g h a b i t . How d e e p l y t h i s p r o c e s s i s i n g r a i n e d i n us i s amply demonstrated by some f a c u l t y who r e q u e s t t e s t s , perhaps e d i t once t o add and/or d e l e t e q u e s t i o n s , o b t a i n t h e f i n a l o u t p u t on r e p r o d u c t i o n m a s t e r s , then have t h e s e c r e t a r y r e t y p e t h e e n t i r e e x e r c i s e w i t h minor wording changes. Others p r e f e r t o examine a l i s t i n g o f t h e e n t i r e bank cont e n t s , s e l e c t i t e m s , and have a s e c r e t a r y type t h e e x e r c i s e d i r e c t l y from t h e l i s t i n g . Our e x p e r i e n c e has shown t h a t s c i e n c e t e a c h e r s , as opposed t o l i b e r a l a r t s t e a c h e r s , a r e more r e c e p t i v e t o t h e i d e a o f "computerized" t e s t i n g . This i s due t o two f a c t o r s : t h e s c i e n t i s t o f times has a c l o s e r a c q u a i n t e n c e w i t h t h e c a p a b i l i t i e s , modes, and l i m i t s o f computer usage; t h e n a t u r e o f s c i e n t i f i c study which l e n d s i t s e l f more r e a d i l y t o a q u a n t i t a t i v e approach t o t h e s u b j e c t , which f a c i l i t a t e s development and use o f i t e m banks s u i t a b l e f o r computer a d m i n i s t r a t i o n . The c h a l l e n g e t h e r e f o r e l i e s i n d e v e l o p i n g q u e s t i o n s which a r e b o t h p e d a g o g i c a l l y e f f e c t i v e and computer managable (e.g., machine g r a d a b l e ) . We have encountered a wide spectrum o f r e a c t i o n s t o SOCRATES machine g r a d a b l e q u e s t i o n format among e d u c a t o r s . Many t e s t i n g and c o u n s e l l i n g o f f i c e r s and community c o l l e g e t e a c h e r s a r e e x t r e m e l y enthusiastic. P r a c t i c a l l y a l l o f t h e c h e m i s t s we have t a l k e d t o f e e l t h a t our i t e m bank, i f n o t t h e e n t i r e SOCRATES system, i s a v a l u a b l e r e s o u r c e f o r t r a i n i n g t h e i r s t u d e n t s . O f t e n times t h e most
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch009
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WILLIS
A N D SEELY
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Testing
e n t h u s i a s t i c s u p p o r t e r s a r e those t e a c h e r s who have a l r e a d y d e v e l o p e d t h e i r own p e r s o n a l i t e m banks. Although o c c a s i o n a l o b j e c t i o n s are r a i s e d t o question phrasing or p r i n t e r conventions, people a c t i v e l y usi n g t h e banks items havfe found t h e i r s t u d e n t s have l i t t l e d i f f i c u l t y i n a d a p t i n g t o computer produced materials. A p o p u l a r f e a t u r e o f f e r e d by SOCRATES i s t h e m u l t i p l e v e r s i o n o p t i o n . Up t o n i n e v e r s i o n s o f t h e same e x e r c i s e c a n be g e n e r a t e d , e d i t e d , and s c o r e d as e a s i l y as one. The l a r g e s i z e o f t h e c h e m i s t r y bank p e r m i t s m u l t i p l e exams t o be d e v e l o p e d on t h e same s u b j e c t m a t t e r f o r use by c o u r s e s e c t i o n s meeting at d i f f e r e n t times. One c r i t i c i s m o f SOCRATES i s r a i s e d a t u s e r workshops and i n f o r m a t i o n a l meetings which d e s e r v e s some comment, as i t a l s o r e f l e c t s h a b i t u a t i o n t o t h e t r a d i t i o n a l t e s t i n g p r o c e s s as w e l l as a p h i l o s o p h i c a l viewpoint. Concern i s e x p r e s s e d about t h e e f f e c t i v e ness o f o b j e c t i v e m u l t i p l e c h o i c e q u e s t i o n s as t e a c h i n g and e v a l u a t i o n t o o l s i n s u b j e c t a r e a s such as c h e m i s t r y where g r e a t emphasis i s p l a c e d on d e v e l o p i n g t h e s t u d e n t s a b s t r a c t r e a s o i n g and conceptualizing s k i l l s . Many o f us have v e r y d e f i n i t e g o a l s f o r t h e c o n t e n t , p h i l o s o p h y , and a p p r o p r i a t e language f o r q u e s t i o n s . These f r e q u e n t l y i n v o l v e a d e m o n s t r a t i o n by t h e s t u d e n t o f some l o g i c a l s e t of o p e r a t i o n s which r e l a t e t o t h e s c i e n t i f i c p r i n c i p l e we a r e a s k i n g about. The a b i l i t y o f m u l t i p l e c h o i c e q u e s t i o n s t o meet t h e s e g o a l s depends on t h e i r d e s i g n , r a t h e r than t h e i r i n h e r e n t approach. By c a r e f u l c h o i c e o f o p t i o n s , i n c o r r e c t r e s p o n s e s c a n be made t o p i n p o i n t s p e c i f i c e r r o r s i n s t u d e n t s reasoni n g o r approach t o a problem, a t any l e v e l . Thus an e x a m i n a t i o n o f t h e i t e m s t a t i s t i c s ( s t u d e n t responses) to an e x e r c i s e c a n t e l l n o t o n l y g e n e r a l s t u d e n t performance, b u t i d e n t i f y i n d i v i d u a l déficiences a s well. T h i s i s not t o say t h a t m u l t i p l e c h o i c e quest i o n s w i l l s u p p l a n t t r a d i t i o n a l s u b j e c t i v e items such as e s s a y s , e t c . Indeed, t h e r e s e r v e d c a t e g o r y i n t h e c l a s s i f i c a t i o n system ( 0 0 0 0 0 ) i n c l u d e s t h e s e . However, o u r e x p e r i e n c e i s t h a t they a r e an e f f e c t i v e t e a c h i n g t o o l , as demonstrated by t h e f a c t t h a t s t u d e n t s from SOCRATES a i d e d p r e r e q u i s t e c l a s s e s p e r f o r m as w e l l i n subsequent c l a s s e s as o t h e r students. We a r e n o t d i s c o u r a g e d by t h e slow a c c e p t a n c e o f the u t i l i t y o f i t e m banks. They h o l d g r e a t promise f o r a l l o w i n g us t o do what we a l r e a d y do by a u t o mating c e r t a i n non c r u c i a l s t e p s . As t e a c h e r s we 1
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can thus r e a c h more s t u d e n t s , more r a p i d l y , more i n e x p e n s i v e l y , w i t h fewer e r r o r s , and a t many v a r i o u s levels. We view SOCRATES as a t o o l t o a l l o w us t o r e t u r n t o t h e i n d i v i d u a l s t u d e n t and h i s problems i n t h i s day of mass e d u c a t i o n .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch009
The
F u t u r e o f SOCRATES-Type Programs i n Networks
S i n c e SOCRATES i s b a s i c a l l y a d a t a management system u s i n g a m o d e r a t e l y s i z e d d a t a base, the main advantages of networking l i e i n p r o v i d i n g r a p i d s e r v i c e to a large geographical area. T h i s c o u l d be extended g l o b a l l y v i a s a t e l l i t e u s i n g the EDUCOM, CYBERNET, TYMSHARE, o r s i m i l a r f a c i l i t i e s . Phone l i n k s have a l r e a d y been used t o demonstrate SOCRATES i n P e n n s y l v a n i a , I l l i n o i s , and Texas; s a t e l l i t e r e l a y d e m o n s t r a t i o n s a r e planned i n F r a n c e and Mexico. The q u e s t i o n t h e r e f o r e i s not one o f t e c h n o l o g y , but o f u s e r demand. The c u r r e n t n a t i o n a l t r e n d i s f o r p a r a l l e l independent development o f i t e m banks. We have honored a number o f r e q u e s t s f o r c o n s o l e paper o r magnetic tape l i s t i n g s o f t h e c h e m i s t r y bank, and encourage the f r e e exchange o f i t e m s . However, such exchanges a r e a t times troublesome due t o i n t e r s c h o o l hardware and/or s o f t w a r e d i s p a r i t i e s . The problem o f s t a n d a r d i z a t i o n t o f a c i l i t a t e t r a n s f e r a b i l i t y has been r e c o g n i z e d and i s b e i n g a d d r e s s e d by groups such as CONDUIT. S u f f i c e i t t o say here t h a t good p l a n n i n g and communication i s needed t o p r e p a r e independent banks and s o f t w a r e f o r an easy merge as the need a r i s e s . In the immediate f u t u r e t o t a l d u p l i c a t i o n and t r a n s f e r of items banks w i l l be the r u l e , s i n c e most e d u c a t i o n a l i n s t i t u t i o n s p r e f e r t o s u p p o r t t h e i r own independent o p e r a t i o n s . The need f o r networking t o f a c i l i t a t e t i m e s h a r i n g o p e r a t i o n s such as t h e SOCRATES ITG module, o r g e n e r a l computer a s s i s t e d i n s t r u c t i o n (CAI) i s quest i o n a b l e f o r the near f u t u r e , p r i m a r i l y due t o hardware c o s t s o f p r o v i d i n g p o r t s and t e r m i n a l s f o r even modest c l a s s s i z e s . Typical installations in t h e CSUC system have one t o t h r e e t e r m i n a l s a t each port. P o r t s a r e l o c a t e d i n a c c e s s i b l e p l a c e s so t h a t s t u d e n t s may use t i m e s h a r i n g d u r i n g t h e i r f r e e p e r i o d s , and i n s t r u c t i o n a l use i s planned on t h a t b a s i s . Since system t i m e s h a r i n g use i s heavy (15,000 hr/month average connect time f o r the F a l l 1974 semester, 22,000 hr/month peak) minicomputers a r e b e i n g i n s t a l l ed on each campus f o r l o c a l i z e d t i m e s h a r i n g . Language and a c t i v e s t o r a g e r e s o u r c e s w i l l be l i m i t e d , so SOCRATES cannot be l o c a l l y implemented. It is felt
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that a l l SOCRATES banks could be implemented using the disc space released after transfer of certain operations to the local minicomputers. We envision that SOCRATES operations w i l l evolve primarily using RJE (remote job entry via local computer to the SUDC CDC 3300 executive) and either local line printers for remote areas, or a central line printer at SUDC and twice daily courier service for the Los Angeles service area. As with any evolving system, new uses w i l l be added as the demand for them arises. Management features such as preparing class grade l i s t s and some format options have already been discussed. Users may elect to write their own programs using the item banks as a resource, but the lessons learned from PLATO experience should be obvious: from 50 to 200 hours of programming effort are required to produce one hour of interactive program. Perhaps an observation by Marshall McLuhan w i l l also appropriately reflect the coming state of both the SOCRATES effort, and educational computer networking for information retrieval: "In the age of Xerox, every man is a publisher". With the advent of large accessible data bases, teachers can readily publish a wide variety of truly educational aids according to the dictates of their personal standards. Literature Cited 1. Lippey, G . , Toggenburger, F., and Brown, C.D., Assoc. for Educ. Data Syst. Journal (1971), March, p. 75.
10
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Impact o f a C o m p u t e r N e t w o r k o n College
Chemistry Departments—The Iowa Regional Network
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch010
WARREN T. ZEMKE Department of Chemistry, Wartburg College, Waverly, Ia. 50677 On the surface, the two main purposes for the existence of a regional computer network are (i) to provide large-scale computing capabilities for medium-sized institutions and (ii) to share in developing the use of instructional computing (1). The purpose of this paper is to examine the impact of these network goals from the perspective of the user (the remote institution or the "fingers of the hand") rather than the provider (the central computer facility or "palm of the hand"). Attention will be focused on the perspective of Departments of Chemistry at twelve of the thirteen remote institutions making up the Iowa Regional Network (officially entitled the Regional Computer Center, or RCC). There are numerous literature sources available for a broad, non-academic discipline approach to the many facets of networking such as financial considerations, hardware and data transmission considerations, network organization and cooperation, etc. (1-6). Two papers in this category which examine the Iowa Regional Network consider the mutual impact both on the central facility and the remote institutions; the author has used these papers as important background sources for this article (1,2). To bring our topic clearly into focus, let us couch i t in terms of two questions. To what extent can a network meet the needs of a Department of Chemistry of a remote institution? To what extent has the RCC met the needs of the Departments of Chemistry of its member institutions? After a brief resume of the RCC the paper will examine these needs. They will be divided into two parts, one dealing with the impact of increased hardware flexibility and user-services, and the other dealing with the past, present and future level of computing in the chemistry curriculum. The Regional Computer Center Iowa networking began in 1967 when the University of Iowa Computer Center established a telephone line link with two other neighboring institutions. In 1968, with substantial NSF support, the network expanded to eleven institutions: one junior college, 142
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nine four-year c o l l e g e s , and a government i n s t a l l a t i o n . Although three of these o r i g i n a l i n s t i t u t i o n s l e f t the network, the t o t a l today stands at t h i r t e e n as l i s t e d i n Table I. This t a b l e summar i z e s general i n f o r m a t i o n about each of the RCC s c h o o l s . A comp l e t e d e s c r i p t i o n of the IBM 360/65 c o n f i g u r a t i o n , the palm of the hand l o c a t e d at the U n i v e r s i t y of Iowa at Iowa C i t y , can be found elsewhere (1). The RCC from the s t a r t has been more than j u s t an organizat i o n c o n s i s t i n g of f a c u l t y and students from the v a r i o u s i n s t i t u t i o n s , computer p r o f e s s i o n a l s r e s i d i n g at Iowa C i t y , and computer hardware/software and communications equipment. I t i s a dynamic e n t i t y wherein i t s members a s s i s t each other with t h e i r primary e f f o r t d i r e c t e d towards i n s t r u c t i o n . The RCC c e n t r a l s t a f f i n t e r faces with a campus Computer Coordinator at each i n s t i t u t i o n . The l o c a l Coordinator acts as manager of the l o c a l t e r m i n a l , o f f e r s short courses i n programming, provides in-house e x p e r t i s e on the use of the c e n t r a l f a c i l i t y and i t s d i v e r s e compilers, e t c . Of no l e s s s i g n i f i c a n c e , he a l s o dons the r o l e of "sparkplug" to e x c i t e l o c a l f a c u l t y and students to make f u r t h e r use of the whole computer f a c i l i t y and s e r v i c e s . The U n i v e r s i t y of Iowa Computer Center s t a f f maintains the hardware and systems on the IBM 360/65. The RCC c e n t r a l s t a f f l i n k s the c e n t r a l f a c i l i t y with the user i n s t i t u t i o n s to achieve maximum e f f e c t i v e n e s s i n u t i l i z a t i o n . Beyond the communications equipment t h i s means r e g u l a r "update" meetings with frequent ons i t e v i s i t s by the " c i r c u i t r i d e r s " to each i n s t i t u t i o n to respond more d i r e c t l y to p a r t i c u l a r i n s t i t u t i o n a l and f a c u l t y needs, and r e g u l a r network-wide workshops f o r the f a c u l t y of member i n s t i t u t i o n s . A v a i l a b l e to each member i n s t i t u t i o n i s access to a l l the languages and l i b r a r y program packages a v a i l a b l e l o c a l l y at Iowa City. In a d d i t i o n to FORTRAN, PL/I, COBOL, and ALGOL, these i n c l u d e the super-batch, i n - c o r e compilers WATFIV, WATBOL, PL/C, ASSEMBLER-G, and SPITBOL which are very f a s t and inexpensive to run. Notable i s the SPSS package and the P o l i t i c a l Science Department's S o c i a l Science Data A r c h i v e s . Also notable i s the s u b s t a n t i a l number of computer-based, c e r t i f i e d teaching modules i n the d i s c i p l i n e s of Business, Chemistry, Economics, Mathematics, P h y s i c s , and S o c i a l Science, a l l because of U n i v e r s i t y of Iowa p a r t i c i p a t i o n i n the CONDUIT experiment (7). A Smart Terminal or A Dumb Terminal? Table I i n c l u d e s a l i s t of the a c t u a l t e r m i n a l hardware as w e l l as i n s t i t u t i o n a l data. The Mason C i t y School D i s t r i c t w i l l be excluded from a l l f u r t h e r c o n s i d e r a t i o n i n t h i s study because i t concerns a h i g h school r a t h e r than a c o l l e g e system. Most of the schools have a "dumb" t e r m i n a l (one which can f u n c t i o n only as a t e r m i n a l to the c e n t r a l computer f a c i l i t y , such as an IBM 3780), but s e v e r a l have a "smart" terminal (one with stand-alone academic as w e l l as remote batch c a p a b i l i t y , such as an IBM 1130). For
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Table I. The Iowa Regional Network Schools
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch010
School
a
Augustana College Rock I s l a n d , IL C e n t r a l College P e l l a , IA Clarke College Dubuque, IA G r i n n e l l College G r i n n e l l , IA Iowa Wesleyan College Mt. Pleasant, IA Loras College Dubuque, IA Marycrest College Davenport, IA Mason C i t y School D i s t . Mason C i t y , IA Monmouth College Monmouth, IL Quincy College Quincy, IL St. Ambrose College Davenport, IL Univ. o f Northern Iowa Cedar F a l l s , IA Wartburg College Waverly, IA a
Enrollment (Staff)
Terminal
Type
2100 (6)
IBM 360/20
Dumb
1300 (3)
IBM 1130
Smart
600 (3)
IBM 1130
Smart
1200 (5)
PDP 11/45
j Dumb
DATA 100-70
Dumb
1500 (4)
IBM 3780
Dumb
1000 (2)
DATA 100-70
Dumb
HP 2000F
Smart
IBM 3780
Dumb
1300 (3)
DCT 132
Dumb
1300 (3)
DATA 100-88
Dumb
8700 (10)
SPC 16
Dumb
1200 (4)
IBM 3780
Dumb
b
600 (2)
e 700 (4)
c
a
A l l o f the schools l i s t e d are p r i v a t e l i b e r a l a r t s c o l l e g e s except the Mason C i t y p u b l i c school d i s t r i c t and the U n i v e r s i t y of Northern Iowa, a p u b l i c u n i v e r s i t y , k The number i n s i d e the parentheses i s the number o f s t a f f i n the Department o f Chemistry. Although i t might serve as a smart t e r m i n a l , f o r e s s e n t i a l l y a l l academic use Augustana has used i t s computer as a dumb t e r m i n a l . P r i o r to January 1975, G r i n n e l l had only an IBM 3780. Thus f o r the p e r i o d p e r t i n e n t to t h i s study, G r i n n e l l has only had a dumb t e r m i n a l . The Mason C i t y School D i s t r i c t w i l l be excluded from any a n a l y s i s s i n c e i t i s a high school r a t h e r than c o l l e g e system. The SPC 16 can emulate the IBM 360/20; to date i t has only been used as a dumb t e r m i n a l . c
d
e
f
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reasons given i n the footnotes of the t a b l e , a l l but two of the twelve schools i n t h i s study are considered to have dumb t e r m i n a l s . This c l a s s i f i c a t i o n assumes the reference p o i n t of usage to be academic years 1973-74 and 1974-75. Three sources of i n f o r m a t i o n were used to o b t a i n a measure of "chemistry computer a c t i v i t i e s " at the RCC s c h o o l s . F i r s t , RCC u s e r - s t a t i s t i c s from J u l y 1973 through A p r i l 1975 were a v a i l a b l e from the RCC f o r each month of the year f o r each s c h o o l . These s t a t i s t i c s were c a t e g o r i z e d according to number and c l a s s type of jobs f o r each d i s c i p l i n e , chemistry i n our case. Second, i n a d d i t i o n to the q u a n t i t a t i v e RCC u s e r - s t a t i s t i c s , a survey of the RCC Coordinators from each school was taken to a s c e r t a i n chemistry department usage, user a t t i t u d e s , coordinator-department cooperat i o n , hardware c o n s i d e r a t i o n s , e t c . T h i r d , a more d e t a i l e d survey was taken of each chemistry department to a s c e r t a i n curriculum o f f e r i n g s i n which the computer was used, the s p e c i f i c type of use, the l e v e l of use, the number of a c t i v e users on each departmental s t a f f , the sources of chemistry computer programs, e t c . A d d i t i o n a l reference to t h i s chemistry q u e s t i o n n a i r e w i l l be made i n the next s e c t i o n . One of the options f a c i n g a c o l l e g e i n Iowa and western I l l i n o i s i s whether or not to a f f i l i a t e with the RCC or to go the route of a s m a l l stand-alone computer. From the p e r s p e c t i v e of chemistry users i n the Iowa Network, no c l e a r preference arose f o r or against a stand-alone computer. To the question "Could a s m a l l stand-alone computer with no Iowa C i t y terminal c a p a b i l i t i e s more than adequately serve your present t o t a l needs?," the response was almost evenly d i v i d e d . Reasons f a v o r a b l e to a t e r m i n a l f a c i l i t y v a r i e d with the a v a i l a b l e p e r i p h e r a l equipment at Iowa C i t y (e.g. d i s k storage, calcomp p l o t t e r output), the a v a i l a b i l i t y of a s s i s t a n c e from computer experts at Iowa C i t y , and the resources at the U n i v e r s i t y of Iowa a v a i l a b l e to RCC Chemistry F a c u l t y (e.g. Chemical T i t l e s f i l e s , E.R.I.C. f i l e s ) . Not i n s i g n i f i c a n t l y , s e v e r a l chemistry users opposed a s m a l l stand-alone computer because they needed a s o p h i s t i c a t e d , l a r g e - c o r e computer l i k e the IBM 360/65 f o r t h e i r research a c t i v i t i e s . Reasons f a v o r a b l e to a stand-alone computer o b v i o u s l y r e s t i n each chemistry user's p e r c e p t i o n of "needs" to the above q u e s t i o n . For s e v e r a l departmental s t a f f s where only one member used the computer and only then o c c a s i o n a l l y , classroom usage was commonly l i m i t e d to s e v e r a l canned programs. Not s u r p r i s i n g l y t h i s s o r t of user sees no broader i m p l i c a t i o n s or usage f o r h i s students or h i m s e l f i n the resources a v a i l a b l e through the RCC. For example, the use of the computer i n a modern chemical l i t e r a t u r e course has probably never r e c e i v e d s e r i o u s c o n s i d e r a t i o n . Then there i s another s i t u a t i o n where a stand-alone f a c i l i t y i s s a t i s f a c t o r y under present departmental budget l i m i t a t i o n s . I f most of the d e s i r e d classroom/laboratory a p p l i c a t i o n s can be accomplished on the in-house ("free") f a c i l i t y , why use the open-ended ("not free")
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t e r m i n a l and s t r a i n the budget? An astute and dedicated Coordin a t o r can r e a d i l y convince users and administrators that in-house use of elementary computer programs i n a number of academic d i s c i p l i n e s can be more c o s t - e f f e c t i v e than t e r m i n a l use. C l e a r l y there are many f a c t o r s i n v o l v e d i n any i n s t i t u t i o n a l d e c i s i o n concerning a stand-alone versus a t e r m i n a l f a c i l i t y and i t i s not the purpose of t h i s paper to consider them i n d e t a i l . But one very i n t e r e s t i n g trend has c l e a r l y emerged from the RCC user-statistics. The r e l a t i v e academic versus a d m i n i s t r a t i v e use has decreased s i g n i f i c a n t l y i n over h a l f of the RCC schools. This increased a d m i n i s t r a t i v e a c t i v i t y i s due to the r a p i d and i n t e n t i o n a l development i n A d m i n i s t r a t i v e Data Processing (ADP) systems by the RCC s t a f f . C u r r e n t l y over h a l f the RCC schools use the Registration-Grade Reporting and P a y r o l l systems; member s c h o o l i n t e r e s t i n the use of the Alumni and Business O f f i c e systems i s growing. I t appears at t h i s p o i n t that newer and b e t t e r ADP a p p l i c a t i o n s v i a the terminal to Iowa C i t y w i l l d i c t a t e increased r a t h e r than decreased support of the terminal f o r most of the RCC schools. What about the needs of a Department of Chemistry whose p r i n c i p a l concern i s l i m i t e d to the baccalaureate degree? Based on the responses to the chemistry q u e s t i o n n a i r e , the RCC chemists do not view the p r o v i s i o n of l a r g e - s c a l e computing c a p a b i l i t y as primary, except i n very few circumstances. Nor do many of them care very much about e x t r a computer and chemistry s e r v i c e s a v a i l able through the Iowa Network arrangement. For many of them a s m a l l stand-alone computer w i l l serve j u s t f i n e i n t h e i r classroom s i t u a t i o n . Yet, i n l i g h t of the apparent increased t o t a l i n s t i t u t i o n a l support of a terminal arrangement, the o l d question of a remote t e r m i n a l versus a stand-alone computer no longer seems a p p r o p r i a t e . Rather the question now seems to be one of whether to s e l e c t a smart or dumb t e r m i n a l . A smart t e r m i n a l c o n f i g u r a t i o n would seem to provide the best of both worlds f o r a l l d i s c i p l i n e s s i n c e the d e s i r a b l e a d m i n i s t r a t i v e and academic a p p l i c a t i o n s of a normal remote job entry t e r m i n a l are s t i l l p o s s i b l e while the c o s t - e f f e c t i v e n e s s of running many small academic canned programs l o c a l l y i s maintained. Because o f p a r t i c u l a r circumstances and personnel at C e n t r a l and Clarke Colleges (the only RCC c o l l e g e s possessing smart terminals used a c a d e m i c a l l y ) , i t i s i n a p p r o p r i a t e to use t h e i r chemistry usage as i n d i c a t i v e of the norm. Yet i s i t not s u r p r i s i n g to f i n d l i t t l e chemistry terminal usage f o r e i t h e r c o l l e g e and a l s o a n o t i c e a b l e increase i n t e r m i n a l ADP type of usage f o r one of them. One other very important trend surfaces from both the Coordin a t o r survey and the chemistry q u e s t i o n n a i r e : there i s broad i n t e r e s t i n time-sharing among chemistry users. Even those users who could l i v e with a stand-alone, batch-mode computer were i n t e r ested i n time-sharing! As i n d i c a t e d i n Table I, G r i n n e l l College i s already i n t o time-sharing with the purchase of t h e i r PDP 11/45; by f a l l the f a c i l i t y i s expected to be f u l l y o p e r a t i o n a l f o r
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classroom use. The U n i v e r s i t y o f N o r t h e r n Iowa h a s p u r c h a s e d an HP 2000F w i t h d e l i v e r y t i m e t h i s summer. Other i n d i v i d u a l schools have made d e c i s i o n s t o go i n t o t i m e - s h a r i n g and a w a i t o n l y t h e c o n c e r t e d f i n a n c i a l campaign n e c e s s a r y t o s e c u r e f u n d s f o r s u c h a facility. Much o f t h i s t i m e - s h a r i n g i n t e r e s t i s due t o t h e e f f o r t o f t h e RCC s t a f f t o i n v o l v e t h e n e t w o r k i n an e f f o r t t o p u r c h a s e a computer l i k e t h e HP 2 0 0 0 F , w i t h t h e c p u l o c a t e d a t Iowa C i t y and the t e r m i n a l s at the p a r t i c i p a t i n g network i n s t i t u t i o n s . Included i n t h e p l a n was a p r o v i s i o n f o r RCC f a c u l t y t o l o c a t e / w r i t e s o f t w a r e f o r s e l e c t e d d i s c i p l i n e s (one o f w h i c h was c h e m i s t r y ) t o a s s u r e an i m m e d i a t e and f r u i t f u l e v a l u a t i o n o f t i m e - s h a r i n g on a network-wide b a s i s . I n t h e hope o f p r o p o s i n g a m o d e l c o n f i g u r a t i o n b e s t s a t i s f y i n g t h e many and d i v e r s e n e e d s o f a " t y p i c a l " s m a l l e r D e p a r t m e n t o f C h e m i s t r y , f r o m t h e e x p e r i e n c e o f t h e Iowa N e t w o r k i t a p p e a r s t h a t a smart t e r m i n a l arrangement where t i m e - s h a r i n g i s a p a r t o f t h e c o n f i g u r a t i o n w o u l d be t h e i d e a l m o d e l , one s i m i l a r t o t h e f a c i l i t y at G r i n n e l l . H o w e v e r , f i n a n c i a l r e s o u r c e s do n o t a l l o w many ( i f n o t m o s t ) m e d i u m - s i z e d i n s t i t u t i o n s a t t h i s p o i n t i n t i m e t o s e r i o u s l y c o n t e m p l a t e s u c h an a r r a n g e m e n t . P r o g r a m A v a i l a b i l i t y and L e v e l o f Use i n t h e C h e m i s t r y C u r r i c u l u m From t h e d i s c u s s i o n i n t h e p r e v i o u s s e c t i o n , t h e RCC has h a d l i t t l e o r no i m p a c t on t h e member i n s t i t u t i o n s , a t l e a s t so f a r as h a r d w a r e and " c o m p u t e p o w e r " i n t h e d i s c i p l i n e o f c h e m i s t r y a r e concerned. A l t h o u g h the use o f c h e m i s t r y s e r v i c e s a t p r e s e n t i s l i m i t e d , more and more RCC u s e r s a r e b e c o m i n g i n t e r e s t e d i n C h e m i c a l A b s t r a c t s , C h e m i c a l T i t l e s , and E . R . I . C . f i l e s . And t h e r e i s a d e f i n i t e and b r o a d s u r g e o f i n t e r e s t i n t i m e - s h a r i n g , much o f w h i c h i s due t o RCC s t a f f e f f o r t s i n c o n v i n c i n g u s e r s t h a t RCC t i m e - s h a r i n g c a p a b i l i t y b e l o n g s t o t h e " r e a l m o f t h e p o s s i b l e . " Y e t t h e s e areas have been the l e a s t c r i t i c a l t o c h e m i s t r y u s e r s and i f we a r e t o f u l l y measure t h e i m p a c t o f t h e RCC on t h e n e t w o r k D e p a r t m e n t s o f C h e m i s t r y we must l o o k e l s e w h e r e . It is i n the a r e a of p r o v i d i n g programs f o r use i n the c h e m i s t r y c u r r i c u l u m t h a t t h e Iowa N e t w o r k h a s made i t s b i g g e s t i m p a c t on c h e m i s t r y u s e r s , and a l s o w h e r e t h e r e s t i l l r e m a i n s t h e g r e a t e s t p o t e n t i a l . I t i s o b v i o u s t h a t t h e r e i s no way t o b e n e f i t f r o m c o m p u t e r based m a t e r i a l s i n the c l a s s r o o m u n l e s s the m a t e r i a l s are r e a d i l y available. A l t h o u g h t h e c h e m i s t r y u s e r s i n t h e Iowa N e t w o r k a r e n o t t h e w o r s t o f t h e l o t c l a s s i f i e d by J o e Denk (8) as " s o f t w a r e s t a r v e d l i t t l e p e o p l e , " t h e d i f f i c u l t i e s i n o b t a i n i n g good p r o g r a m s f o r c l a s s r o o m use a r e s t i l l common t o a l l o f us i n t h e network. I n t h e l a s t two y e a r s t h i n g s h a v e i m p r o v e d c o n s i d e r a b l y . T y p i c a l l y t h e u s e r h a d two s o u r c e s f o r o b t a i n i n g c h e m i s t r y c o m p u t e r p r o g r a m s , w r i t e h i s own a n d / o r l o c a t e them v i a t h e l i t e r ature. A l m o s t a l l o f t h e a c t i v e u s e r s c o n t i n u e t o do b o t h , b u t due t o U n i v e r s i t y o f Iowa p a r t i c i p a t i o n i n t h e c o o p e r a t i v e n a t i o n a l CONDUIT e x p e r i m e n t i n t h e t r a n s p o r t a b i l i t y o f c o m p u t e r - b a s e d
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u n d e r g r a d u a t e c u r r i c u l u m m a t e r i a l s , t h e u s e r s o f t h e n e t w o r k now a l s o h a v e a v a i l a b l e CONDUIT as a s o u r c e o f p r o g r a m s . A q u i c k g l a n c e a t t h e c h e m i s t r y q u e s t i o n n a i r e and t h e t y p e s o f l i t e r a t u r e s o u r c e s e m p l o y e d by t h e RCC c h e m i s t r y u s e r s i n d i c a t e s t h a t t h e J o u r n a l o f C h e m i c a l E d u c a t i o n and CONDUIT a r e t h e most common s o u r c e s o f c h e m i s t r y p r o g r a m s ( 9 ) . Although r e a d i l y a v a i l a b l e o n t h e d i s k a t Iowa C i t y , CONDUIT c h e m i s t r y p r o g r a m s h a v e s u f f e r e d i n t h e p a s t f r o m o c c a s i o n a l bugs and i n c o m p l e t e o r inappropriate documentation. On t h e o t h e r h a n d , anyone who o b t a i n s a p r o g r a m d i r e c t l y f r o m an a u t h o r n o t e d i n t h e l i t e r a t u r e does n o t have t h e CONDUIT r e v i e w / c e r t i f i c a t i o n p r o c e s s t o r e l y u p o n . M o r e o v e r , he must o f t e n m o d i f y t h e p r o g r a m t o f i t h i s p a r t i c u l a r computer s y s t e m . A d d i t i o n a l programs have been o b t a i n e d f r o m t h e t e x t b o o k s b y W i b e r g ( 1 0 ) , D i c k s o n (11) , DeTar ( 1 2 ) , and I s e n h o u r and J u r s ( 1 3 ) ; f r o m CCUC (14) ; f r o m t h e Quantum C h e m i s t r y P r o g r a m E x c h a n g e a t I n d i a n a U n i v e r s i t y ; and f r o m Oak R i d g e and A r g o n n e N a t i o n a l L a b o r a t o r i e s t h r o u g h t h e U n i v e r s i t y o f Iowa Department of Chemistry ( 1 5 , 1 6 ) . A c c o r d i n g to the twelve Departments of Chemistry of t h i s s t u d y , t h e use o f t h e c o m p u t e r o c c u r r e d most o f t e n i n t h e p h y s i c a l c h e m i s t r y c u r r i c u l u m ( e i g h t u s e r s i n d i c a t e d r e g u l a r use on t h e a v e r a g e o f a t l e a s t once a m o n t h ) . Computer usage i n a n a l y t i c a l c h e m i s t r y was n e x t most f r e q u e n t ( o n l y t h r e e u s e r s i n d i c a t e d no u s e a t a l l ) , f o l l o w e d c l o s e l y b y f r e s h m a n c h e m i s t r y and t h e n o r g a n i c c h e m i s t r y ( s i x u s e r s i n d i c a t e d no use a t a l l ) . Other c u r r i c u l u m o f f e r i n g s i n w h i c h t h e c o m p u t e r was u s e d r a n g e d f r o m c o u r s e s i n t h e I d e n t i f i c a t i o n o f O r g a n i c Compounds and B i o c h e m i s t r y t o t h o s e i n R e s e a r c h and I n d e p e n d e n t S t u d y and one i n Computer A p p l i c a t i o n s i n C h e m i s t r y . Types o f p r o g r a m s v a r y f r o m l e a s t s q u a r e s a n a l y s i s and o t h e r d a t a r e d u c t i o n r o u t i n e s t o p l o t t i n g and o t h e r s i m u l a t i o n p r o g r a m s . A few o f t h e s p e c i f i c a p p l i c a t i o n s i n c l u d e k i n e t i c s s t u d i e s , quantum m e c h a n i c a l c a l c u l a t i o n s , n u m e r i c a l i n t e g r a t i o n s , a t o m i c and m o l e c u l a r o r b i t a l c a l c u l a t i o n s , I R and NMR r o u t i n e s , and s e v e r a l t i t r a t i o n a p p l i c a t i o n s ( f r o m s i m u l a t i o n to endpoint determination). I n a d d i t i o n to the i n c r e a s e d base o f programs a v a i l a b l e f o r f u t u r e use i n t h e c h e m i s t r y c u r r i c u l u m , a n o t h e r i m p o r t a n t b e n e f i t from network a f f i l i a t i o n i s the h o l d i n g of network-wide workshops and m e e t i n g s . The i n t e n t o f s u c h w o r k s h o p s h a s b e e n t o f o s t e r i n t e r a c t i o n b e t w e e n members o f remote i n s t i t u t i o n s and s t i m u l a t e new i d e a s and a p p l i c a t i o n s i n t h e c l a s s r o o m . As a p o i n t o f r e f e r e n c e , t h e l a s t c h e m i s t r y w o r k s h o p was h e l p i n September 1 9 7 3 . A b o u t t h i r t y p a r t i c i p a n t s ( c h e m i s t r y f a c u l t y and s t u d e n t s and some C o o r d i n a t o r s ) a t t e n d e d f r o m e l e v e n o f t h e RCC i n s t i t u t i o n s and a l s o f r o m t h r e e o t h e r Iowa c o l l e g e s and u n i v e r s i t i e s . Over t w o - t h i r d s o f t h o s e s c h o o l s w h i c h w e r e b o t h a t t h e w o r k s h o p and are a l s o a p a r t o f t h i s s t u d y c l a i m e d t h a t the workshop i n c r e a s e d b o t h f a c u l t y i n t e r e s t i n new c o m p u t e r p r o g r a m s and u s a g e o f t h e computer. The u s e r - s t a t i s t i c s i n d i c a t e d a s u r g e o f c h e m i s t r y u s e i n t h e s e v e r a l months i m m e d i a t e l y f o l l o w i n g t h e w o r k s h o p .
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And o f the twelve schools i n t h i s study, a l l but one wanted at l e a s t o c c a s i o n a l chemistry workshops, with n e a r l y one-half wanting annual workshops! From e a r l i e r d i s c u s s i o n i t should be c l e a r that the RCC has functioned more as a " u s e r - s e r v i c e s " network than a " t r a n s m i s s i o n " or " f a c i l i t a t i n g " network ( 4 ) . The f i n g e r s and the palm of the RCC hand seem more and more to r e a l i z e t h e i r mutual interdependency. I t i s the author's f e e l i n g that there i s a growing change i n a t t i t u d e among chemistry users. In t h e i r eyes the RCC has always e x i s t e d to provide a f a c i l i t y f o r accomplishing s p e c i f i c computational tasks. But with workshops by and f o r chemical educators i n which pedagogical use of the computer becomes an important i n g r e d i e n t , the network becomes more than j u s t an agent to p a r c e l out b i g g e r and b e t t e r canned programs. Such workshops can e l i c i t i n t e r e s t from the u n i n i t i a t e d as w e l l as serve as a s o r t of f u e l i n g s t a t i o n f o r the more knowledgeable users. In a d d i t i o n to p r o v i d i n g new and u s e f u l knowledge about p a r t i c u l a r r o u t i n e s , the i n t e r p e r s o n a l contacts of the workshop more o f t e n than not serve to k i n d l e f u r t h e r a c t i v i t y i n the p a r t i c i p a n t s . As a case i n p o i n t , the frequent workshops h e l d by the North C a r o l i n a E d u c a t i o n a l Computing S e r v i c e have played a key r o l e i n the high r a t e of growth i n the use o f the computer i n the North C a r o l i n a Network (17). To be sure there are s t i l l chemistry users who are not i n t e r e s t e d i n network s h a r i n g i n the Iowa Network and who would r a t h e r "do i t alone." Another type of response to our network, the "do i t f o r me" a t t i t u d e , i s a l s o s t i l l too common. Yet the author detects a trend away from these responses and i n s t e a d a "do i t with me" response p r e v a i l i n g i n more and more chemistry users. The i n c l u s i o n of more frequent f a c u l t y t r a i n i n g workshops as an i n t e g r a l p a r t of the o v e r a l l RCC implementation s t r a t e g y at present appears to be one of the most e f f e c t i v e ways to c a p i t a l i z e on t h i s f a v o r a b l e response. In t u r n , the i n c r e a s e d l e v e l o f usage would b e n e f i t both f i n g e r s and palm s i g n i f i c a n t l y . Conclusions The computer i s f a s t becoming a t o o l v i t a l to the whole of modern-day chemistry. I t i s causing a r e v o l u t i o n i n the f r o n t i e r s of chemical education! The a c t i v i t y of the ACS D i v i s i o n s of Computers i n Chemistry and Chemical Education ( p a r t i c u l a r l y i t s Committee on the Role of Computing i n Chemical Education) at recent Regional ACS Meetings and N a t i o n a l ACS Meetings ( i n c l u d i n g t h i s one) i s not going unnoticed by the chemists at the RCC member institutions. Although i n the recent past the chemistry users have not taken advantage of computing c a p a b i l i t y and chemistry s e r v i c e s a f f o r d e d through the RCC, they are beginning to recognize them as probable future needs o f a modern Department of Chemistry. The present f i n a n c i a l s i t u a t i o n at most of the RCC schools precludes immediate and extensive use of these f e a t u r e s , but the chemistry users do seem to recognize the p o t e n t i a l that e x i s t s .
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Increased availability of computer programs for use in the chemistry curriculum and network-wide chemistry workshops have had a strong impact on the chemistry users of the RCC institutions. Regular chemistry workshops for and by chemical educators are clearly recognized as valuable and highly desired by almost all the member institutions Departments of Chemistry. The RCC has generated a wholesome demand for network cooperation and with extra effort towards filling this demand, such as more frequent workshops, it is in a position of seeing a significant increase in the level of computing by the chemists of the Iowa Network. Finally, there is a growing nationwide interest in the use of computer-assisted test construction (CATC), with the discipline of chemistry taking an active leadership position (18). Moreover, the CONDUIT Chemistry Advisory Committee is examining the possibility of providing a transportable CATC item pool and question retrieval program (19). Because of these circumstances and the close-to-home fact that the Department of Chemistry at the University of Iowa has just completed a CATC program in freshman chemistry (20), it is but a matter of time before Iowa chemistry users will have to face the decision of CATC on a network-level cooperative basis, or on an individual institutional basis, or not at all! Because of the considerable effort involved to construct and maintain a large data pool of chemistry questions acceptable to even a few users and because of the size of the computer necessary for even a modest CATC system, a cooperative CATC venture would be a natural next step for a network like the RCC. Although CATC is still off on the horizon, so far as most RCC chemistry users are concerned, a network-wide effort in this area of instructional computing could prove very beneficial to each of the RCC Departments of Chemistry. It should hold a key position in future institutional and network deliberations.
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1
Acknowle dgemen ts It is a pleasure to acknowledge Chuck Shomper, Director of the Regional Computer Center, and Pete Trotter, Manager of Network Academic Services of the RCC. Without their help this study would have been impossible. Willing assistance from the chemistry users and Coordinators of the RCC member institutions is also gratefully acknowledged. Literature Cited 1. Weeg, G.P., and Shomper, C.R., EDUCOM Bulletin (Spring 1974), 9, 14. 2. Weingarten, F.W., Nielsen, N.R., Whiteley, J.R., and Weeg, G.P., "A Study of Regional Computer Networks," University of Iowa, Iowa City, IA, 1973. 3. See, for example, "Networks and Disciplines" (Proceedings of the EDUCOM Fall 1972 Conference), EDUCOM, Princeton, NJ, 1972.
10. ZEMKE 4. 5. 6. 7.
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8. 9.
10. 11. 12. 13. 14.
15. 16.
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Greenberger, Μ., Aronofsky, J., McKenney, J . L . , and Massy, W.F., Science (1973), 182, 29. Luehrmann, A.W., and Nevison, J.M., Science (1974), 184, 957. Chambers, J.A., and Poore, R.V., Communications of the ACM (1975), 18, 193. CONDUIT stands for Computers at Oregon State University, North Carolina Educational Computing Service, Dartmouth College, and the Universities of Iowa and Texas (Austin). Sponsored by the National Science Foundation, this consortium of regional computer networks was organized in January 1972 to study and evaluate the transportability and dissemination of computer -based curriculum materials for use on the undergraduate level of instruction. Denk, J.R., Proceedings of the Conference on Computers in the Undergraduate Curricula (1972), 3, 547. The Journal of Chemical Education is a very common source of computer programs for all sorts of applications in the chem istry curriculum. See, for example, the "Selected Biblio graphy of Computer Programs in Chemical Education" submitted by the author for publication in J. Chem. Educ. This biblio graphy lists 168 digital computer programs noted in J. Chem. Educ. for the eight years 1967-74; computer language and machine and a brief statement about the program usage are given. Wiberg, K.B., "Computer Programming for Chemists," W. A. Ben jamin, Inc., New York, 1965. Dickson, T.R., "The Computer and Chemistry," W. H. Freeman and Co., San Francisco, 1968. DeTar, D.F., "Computer Programs for Chemistry," W. A. Benja min, Inc., New York, 1968(I), 1970(II). Isenhour, T.L., and Jurs, P.C., "Introduction to Computer Pro gramming for Chemists," Allyn and Bacon, Inc., Boston, 1972. CCUC stands for Conference on Computers in the Undergraduate Curricula. Below are dates and places of the annual confer ence. CCUC/1, Iowa City, IA June 1970 CCUC/2, Hanover, NH June 1971 CCUC/3, Atlanta, GA June 1972 CCUC/4, Claremont, CA June 1973 CCUC/5, Pullman, WA June 1974 CCUC/6, Fort Worth, TX June 1975 Copies of the Proceedings for any of these conferences can be purchased from Ted Sjoerdsma, Lindquist Center, University of Iowa, Iowa City, IA, 52242. Johnson, C.K., "ORTEP (Oak Ridge Thermal Ellipsoid Plot Pro gram)," Oak Ridge National Laboratory Report 3794, 1965. Wahl, A.C., Bertoncini, P.J., Kaiser, Κ., and Land, R.H., "BISON, A Fortran Computer System for the Calculation of Ana lytic SCF Wavefunctions, Properties, and Charge Densities for Diatomic Molecules," Argonne National Laboratory Report 7271,
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1968. 17. Joe Denk, private communication. 18. See, for example, "The Computer Assisted Test Construction Conference" held at San Diego, October 1974. 19. Private communication. 20. Kenneth Sando, private communication.
11 A Case History in Computer Resource Sharing:
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ab initio Calculations via a Remote Control* D. G. HOPPER,† P. J. FORTUNE, and A. C. WAHL Chemistry Division, Argonne National Laboratory, Argonne, Ill. 60439 T. O. TIERNAN†† Chemistry Research Laboratory, Aerospace Research Laboratories, Air Force Systems Command, Wright-Patterson Air Force Base, Ohio 45433 In this paper we discuss the experience that we have had in performing large scale molecular structure calculations remotely using the CDC6600 computers at Wright-Patterson Air Force Base. Certain elements of this effort are general and can be expected to be encountered by other researchers. Before proceeding with a discussion of this computational research project we w i l l give a brief history of the development of the Wright-Patterson AFB Aeronautical Systems Division (ASD) computer center, which played a historic and central role in the development of modern computational chemistry. Computational chemistry has become a pervasive tool contributing to the solution of problems in the biological, inorganic, organic, and physical subfields of chemistry. And it w i l l undoubtedly become an even more important tool in years to come. Such growth is due to the fact that in many areas of computational chemistry, the methods used yield results which meet experimental accuracy, allowing quantitative prediction and interpretation to be made (1-3). Methods of performing e.g. accurate quantum mechanical calculations are now available in computer codes which can be obtained from code exchanges (3) and from individual research groups. It is proper to refer to these codes and the hardware associated with their application as instruments for chemical research, in the same sense as an *Work performed under the auspices of the USERDA and Air Force Contract No. F33615-72-M-5015. †ARL-NRC Research Associate 1972-1974. ††Present address: Department of Chemistry, Wright State University, Dayton, Ohio 45431.
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e q u a l l y s o p h i s t i c a t e d e x p e r i m e n t a l " a p p a r a t u s " (£) . Remote usage o f t h e s e l a r g e c o m p u t a t i o n a l systems i s becoming i n c r e a s i n g l y more common. The r e a s o n s f o r t h i s i n c r e a s e d remote usage a r e : (a) t r u e p o r t a b i l i t y i s d i f f i c u l t t o a c h i e v e i n a l a r g e s o f t w a r e system, (b) the maintenance, r e l i a b i l i t y , and c o n t i n u i n g d e v e l o p ment o f t h e s e codes r e q u i r e s more e f f o r t and e x p e r t i s e than c a n be m a r s h a l l e d by i n d i v i d u a l c h e m i c a l r e s e a r c h e r s and (c) remote use i s p o s s i b l e , c o n v e n i e n t , and economically competitive with on-site v i s i t s . I ti s r e a s o n a b l e t o e x p e c t t h a t an even more s u b s t a n t i a l p o r t i o n o f c h e m i c a l c a l c u l a t i o n s w i l l be performed remote l y from i n t e r a c t i v e ( t i m e - s h a r i n g ) and b a t c h t e r m i n a l s (.5) , p a r t i c u l a r l y as computer networks (£, Ί_, £, 9) become more w i d e l y a c c e s s i b l e . In t h i s r e p o r t we r e v i e w our s p e c i f i c e x p e r i e n c e w i t h remote i n t e r a c t i v e t e r m i n a l a c c e s s . We d i s c u s s the f e a s i b i l i t y o f p e r f o r m i n g m o d e r a t e l y e x t e n s i v e ab i n i t i o p r o d u c t i o n c a l c u l a t i o n s w i t h no more than a t e l e t y p e a t t h e remote s i t e . The e n t i r e p r o c e d u r e i s s t r a i g h t - f o r w a r d and, a l t h o u g h t e d i o u s , c a n be g r e a t l y f a c i l i t a t e d by a p p r o p r i a t e code m o d i f i c a t i o n s and code developments. The f o l l o w i n g d i s c u s s i o n i s broken down i n t o the s i x s e c t i o n s : nature o f the c a l c u l a t i o n s b e i n g performed, equipment a v a i l a b l e , communication l i n k s , i n s t a l l a t i o n and maintenance o f codes, i n p u t and o u t p u t o f j o b s , and a summary and i n d i c a t i o n o f f u t u r e plans. F o r t h e purpose o f g a i n i n g p e r s p e c t i v e on t h i s e f f o r t we b e g i n by r e v i e w i n g t h e r o l e p l a y e d by t h e ASD Computer C e n t e r a t W r i g h t - P a t t e r s o n AFB i n computer r e s o u r c e s h a r i n g i n quantum c h e m i s t r y c o m p u t a t i o n s . H i s t o r y o f Computer Resource A i r F o r c e Base
Sharing a t Wright-Patterson
The h i s t o r i c a l e v o l u t i o n o f o u r remote usage has p a r a l l e l e d t h e development o f t h e computer c e n t e r a t W r i g h t - P a t t e r s o n A i r F o r c e Base. I t was t h e s h a r i n g o f computer r e s o u r c e s by W r i g h t - P a t t e r s o n i n t h e l a t e 1950's t h a t e n a b l e d one o f t h e f i r s t i n t e g r a l programs t o be d e v e l o p e d and r u n . T h i s e v o l u t i o n i n t h e use o f the W r i g h t - P a t t e r s o n c o m p u t a t i o n a l f a c i l i t y by o f f - s i t e p e r s o n n e l , a c c o m p l i s h e d e n t i r e l y by s i t e v i s i t s i n about 1958, t o t h e p r e s e n t s t a g e o f e x t e n s i v e remote o p e r a t i o n s p r o v i d e s , t h e r e f o r e , a v i v i d example o f com p u t e r r e s o u r c e a v a i l a b i l i t y and s h a r i n g . T h i s example i s i l l u s t r a t i v e o f a r e s e a r c h a r e a — c o m p u t a t i o n a l chem i s t r y — w h i c h w i l l be markedly advanced by t h e d e v e l o p ment o f computer networks.
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Background on t h e ASP Computer C e n t e r . There has been a computer o r g a n i z a t i o n as a p a r t o f t h e W r i g h t P a t t e r s o n A r e a Β l a b o r a t o r y complex s i n c e 1949 (10). A t t h a t time the C o m p u t a t i o n a l Branch o f t h e Research D i v i s i o n , O f f i c e o f A i r Research, was e s t a b l i s h e d . T h i s group began w i t h an e a r l y v i n t a g e MIT a n a l o g computer which was soon r e p l a c e d w i t h t h e f i r s t c o m m e r c i a l l y a v a i l a b l e a n a l o g computer, t h e REAC S e r i e s 100. The d i g i t a l e f f o r t began i n 1951 w i t h t h e d e l i v e r y o f an IBM C a r d Programmed C a l c u l a t o r . To p u t t h e s e e v e n t s i n p e r s p e c t i v e , the d i g i t a l computer was i n v e n t e d by H a r o l d A i k e n o n l y i n 1944; the a n a l o g computer, by Vannevar Bush i n 1930 (11). The f i r s t r e a l s t o r e d program d i g i t a l computer was the OARAC ( O f f i c e o f A i r R e s e a r c h A u t o m a t i c Computer) i n s t a l l e d i n 1953. T h i s computer was a " o n e - o f - a - k i n d " b u i l t s p e c i f i c a l l y by G e n e r a l E l e c t r i c f o r t h e A e r o n a u t i c a l Systems D i v i s i o n . I t was v e r y slow, had l i m i t e d I/O c a p a b i l i t y , and was u n r e l i a b l e . In 1956 i t was r e p l a c e d by a s c i e n t i f i c a l l y - o r i e n t e d U n i v a c 1103. I n 1957 t h e 1103 was upgraded t o an 1103A and assembly language programming became a v a i l a b l e . It i s t h i s computer t h a t p l a y e d an i m p o r t a n t r o l l , as d e s c r i b e d i n t h e n e x t s e c t i o n , i n the development o f ab i n i t i o quantum c h e m i s t r y . The f i r s t e x t e n s i v e use o f a s o u r c e language d i d n ' t o c c u r u n t i l 1961 when the 1103A was r e p l a c e d by an IBM 7090 which a l l o w e d programming i n FORTRAN I I . Open shop was formed a t about t h i s t i m e . The IBM 7090 was t h e f i r s t r e a l b a t c h computer a t ASD; i t used two IBM 1401 computers f o r c o n v e r t i n g c a r d s t o tape i n p u t f o r the 7090 and 7090 tape o u t p u t t o punch and p r i n t e d form. In 1963 the 7090 was upgraded t o a 7094 and t h e n r e p l a c e d i n l a t e 1964 by an IBM 7044/7094 Mod ΓΙ D i r e c t 7044 t o m o n i t o r I/O, j o b f l o w , and d i s k s t o r a g e a l l o c a t i o n f o r the 7094 program e x e c u t i o n . T h i s system had one IBM 1440 remote b a t c h t e r m i n a l i n the Aero P r o p u l sion Laboratory. In 1966 a second, somewhat slower IBM 7040/7090 D i r e c t Coupled System was added; i t had a remote b a t c h t e r m i n a l i n the F l i g h t Dynamics L a b o r a t o r y . Both D i r e c t Coupled systems were r e p l a c e d by a CDC6600 w i t h 31 t e l e t y p e s and 9 remote b a t c h t e r m i n a l s i n January 1971. In December 1973 a CDC CYBER73 was i n s t a l l e d w i t h t h e b a t c h t e r m i n a l s r e a l l o c a t e d among the two systems. * The t e l e t y p e t e r m i n a l s (HOB) were c o n v e r t e d t o o p e r a t e t h r o u g h a d i a l - u p system i n March 1973 and some 300B l i n e s were s i m u l t a n e o u s l y added. There a r e now 32 110/300B l i n e s i n t o each system, t h e CDC6600 and t h e CYBER73. One l i n e o p e r a t i n g a t 2 K/B was added i n •Notation —
Β = Baud
= b i t - p e r - s e c o n d . 1K/B
= 1000B.
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A p r i l 1974 and a second o p e r a t i n g a t 4.8 K/B, i n F e b r u ary 1975. The ASD Computer C e n t e r became a node on the ARPA network (ARPANET) i n October 1973 w i t h t h e i n s t a l l a t i o n of a t e r m i n a l i n t e r f a c e processor (TIP). F u t u r e developments p l a n n e d f o r t h e ASD and o t h e r A i r F o r c e System Command computer c e n t e r s w i l l be d i s c u s s e d below. F o r now we t u r n t o a d i s c u s s i o n o f the r o l e p l a y e d by t h e 1103 and 1103A i n the e v o l u t i o n o f quantum c h e m i s t r y . Development o f Master I n t e g r a l s and SCF Codes. D u r i n g the p e r i o d 1955-1962 the master SCF m o l e c u l e program was d e v e l o p e d f o r l i n e a r systems by the L a b o r a t o r y o f M o l e c u l a r S t r u c t u r e and S p e c t r a o f t h e U n i v e r s i t y o f C h i c a g o as a p a r t o f i t s o v e r a l l e f f o r t i n m o l e c u l a r computations (12,13). The m o l e c u l a r i n t e g r a l s package was d e v e l o p e d and r u n on the U n i v a c 1103 and 1103A a t W r i g h t - P a t t e r s o n A i r F o r c e Base under a con t r a c t w i t h the U n i v e r s i t y . The SCF package was combined w i t h the STO i n t e g r a l package t o form the f i r s t master i n t e g r a l s - S C F code. I t was i n t h i s p e r i o d o f c a l c u l a t i o n s on the 1103 and 1103A t h a t many o f t h e f i r s t m o l e c u l a r H a r t r e e - F o c k c a l c u l a t i o n s w i t h good b a s i s s e t s were c a r r i e d o u t by McLean, Weiss, and Yoshimine (14), K o l o s and Roothaan (15,16), R a n s i l (12,13), and R i c h a r d s o n (Γ7) , e t c . Indeed one f i n d s t h a t the A p r i l 1960 i s s u e o f Reviews o f Modern P h y s i c s — a c o l l e c t i o n of p a p e r s g i v e n a t t h e C o n f e r e n c e on M o l e c u l a r Quantum Mechanics h e l d a t B o u l d e r , C o l o r a d o June 21-27, 1959 — c o n t a i n s no fewer than t w e l v e p a p e r s t h a t acknowledge the use o f t h e 1103 a t the then Wright A i r Development C e n t e r a t W r i g h t - P a t t e r s o n AFB (12-23). These p a p e r s i n c l u d e c o n t r i b u t i o n s by K o l o s , Roothaan, and Sach (18) on t h e ground s t a t e o f H3, Roothaan (19) i n h i s c l a s s i c work on t h e t h e o r y o f open s h e l l s o f e l e c t r o n i c systems, K o l o s and Roothaan {20) on c o r r e l a t e d o r b i t a l s f o r He, F r a g a and M u l l i k e n (21) on t h e r o l e o f Coulomb energy i n v a l e n c e bond t h e o r y , Frôman (22) on r e l a t i v i s t i c c o r r e c t i o n s , and Lowdin (23) on e x p a n s i o n t h e orems f o r t h e t o t a l w a v e f u n c t i o n and extended H a r t r e e Fock schemes. Many o t h e r i n d i v i d u a l s p a r t i c i p a t e d i n this c a l c u l a t i v e e f f o r t at Wright-Patterson—Bagus, C l e m e n t i , Ehrenson, Huo, Lykos, M a l l i , P h i l l i p s o n , and Wahl t o mention a few. S. Huzinaga w r i t e s i n a l e t t e r to Dr. R. Euwema o f the t h e o r e t i c a l s o l i d - s t a t e group a t W r i g h t - P a t t e r s o n d a t e d F e b r u a r y 7, 1975: "WrightP a t t e r s o n i s one o f my f o n d e s t memories d u r i n g my s t a y i n U.S.A. some 15 y e a r s ago. I had a c c e s s t o a b i g computer (UNIVAC 1103?) f o r t h e f i r s t time i n my l i f e . "
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The 1103 and 1103A p r o v i d e d a c o m p u t a t i o n a l t e s t ground f o r many i d e a s i n t h e o r e t i c a l c h e m i s t r y and a p l a c e where the seeds o f f u t u r e developments i n the I 9 6 0 s were sowed. I t was h e r e , f o r example, where newer i d e a s on how t o code d i a t o m i c i n t e g r a l s were e v a l u a t e d and the o n e - e l e c t r o n i n t e g r a l s coded and t e s t e d (24). The c h o r e s o f c o d i n g and e x e c u t i o n o f computations on the 1103A were markedly d i f f e r e n t from the p r e s e n t day h i g h - l e v e l language and b a t c h j o b i n p u t o p e r a t i o n s , as one o f us (A.C.W.) v i v i d l y r e c a l l s . Coding was p e r formed d i r e c t l y i n o c t a l machine language, t o o p t i m i z e the use o f computer memory. A c c u r a t e f l o a t i n g - p o i n t operations required a user-supplied subroutine. Job s u b m i s s i o n was an e x t r a o r d i n a r y e x e r c i s e i n p r e p a r a t i o n and p a t i e n c e . The computer r e s i d e d on a l o v e l y , b l u e l i t d i a s and the u s e r w a i t e d i n a "ready room" u n t i l h i s name was c a l l e d . He would t h e n r u s h i n w i t h h i s paper t a p e s f o r a 2-3 minute s h o t a t g e t t i n g h i s j o b on the machine. I f he f a i l e d t o g e t i t g o i n g i n t h a t l e n g t h o f time he l o s t h i s t u r n and had t o go t o the end o f the queue. A n o t h e r t u r n would come i n two hours t o two days, depending upon demand. The use o f the 1103 and 1103A by the C h i c a g o group was a m i l e s t o n e i n the e a r l y s h a r i n g o f computer r e sources. In t h i s case c o m p u t a t i o n a l c h e m i s t s o b t a i n e d a c c e s s t o a s u f f i c i e n t l y p o w e r f u l computer f o r t h e i r purposes - a computer u n a v a i l a b l e t o them i n C h i c a g o by making s i t e v i s i t s t o W r i g h t - P a t t e r s o n .
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1
Ab I n i t i o Quantum C a l c u l a t i o n s from 1961-1975 a t W r i g h t - P a t t e r s o n AFB. D u r i n g the p e r i o d 1961-1972 the ab i n i t i o work i n quantum c h e m i s t r y a t W r i g h t - P a t t e r s o n AFB was much more l i m i t e d than the 1956-1961 p e r i o d . The r e a s o n was the a v a i l a b i l i t y o f e q u i v a l e n t o r b e t t e r computers a t o r v e r y near the i n s t i t u t i o n s i n C h i c a g o and elsewhere a t which t h e quantum c h e m i s t s r e s i d e d . However, d u r i n g much o f t h i s p e r i o d and c o n t i n u i n g on u n t i l 1975 t h e r e has been a s t r o n g t h e o r e t i c a l s o l i d s t a t e group a t the A e r o s p a c e Research L a b o r a t o r i e s . T h i s group has been d e v e l o p i n g methods and v e r y h i g h l y s o p h i s t i c a t e d codes f o r p e r f o r m i n g r i g o r o u s ab i n i t i o H a r t r e e - F o c k c a l c u l a t i o n s o v e r the y e a r s on the IBM 7094 and, c u r r e n t l y , the CDC6600. The p e r i o d 1972-1975 saw an upsurge i n ab i n i t i o quantum c h e m i c a l c a l c u l a t i o n s . A few group l e a d e r s i n the C h e m i s t r y R e s e a r c h L a b o r a t o r y o f the A e r o s p a c e Research L a b o r a t o r i e s brought i n t h e o r e t i c a l p e r s o n n e l on a temporary b a s i s t o e x e c u t e c o m p u t a t i o n a l r e s e a r c h p r o j e c t s r e l a t e d t o on-going, in-house e x p e r i m e n t a l
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programs. The Aerospace R e s e a r c h L a b o r a t o r i e s , t h r o u g h a program i n i t i a t e d by one o f t h e p r e s e n t a u t h o r s (T.O. T.), a l s o c o n t r a c t e d out-of-house t h e o r e t i c a l c a l c u l a t i o n s r e l e v a n t to A i r Force i n t e r e s t s . One such cont r a c t i n v o l v e d t h e c o m p u t a t i o n a l c h e m i s t r y groups a t Argonne N a t i o n a l L a b o r a t o r y and the N a t i o n a l Bureau o f Standards who undertook a c o n c e r t e d l i t e r a t u r e e v a l u a t i o n and i n i t i a t e d a s t a t e - o f - t h e - a r t c o m p u t a t i o n a l p r o j e c t t o o b t a i n i n f o r m a t i o n on the v e r t i c a l e x c i t a t i o n s p e c t r a and p o t e n t i a l energy h y p e r s u r f a c e s o f t h e e l e c t r o n i c s t a t e s o f t h e f i f t e e n m o l e c u l e s and i o n s H 0 , N20* , C 0 , N0 , 0 , m = +1, 0, -1 (24-31). The work r e p o r t e d i n t h i s paper i s a development o f t h a t computational p r o j e c t . I t i s i n the context of t h i s program t h a t we w i l l d i s c u s s remote usage. m
1
m
m
m
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2
Nature
o f P r o j e c t and C a l c u l a t i o n s B e i n g
Performed.
F o r about t h r e e y e a r s our r e s e a r c h groups, i n conc e r t w i t h those o f M. Krauss a t t h e N a t i o n a l Bureau o f Standards (NBS) and J . Simons a t the U n i v e r s i t y o f Utah (Utah) have c o o p e r a t e d i n c o m p u t a t i o n a l c h e m i s t r y p r o jects. In t h e s e j o i n t i n v e s t i g a t i o n s the group a t the Aerospace Research L a b o r a t o r i e s (ARL) c o l l a b o r a t e d i n the development o f o b j e c t i v e s , m o n i t o r e d p r o g r e s s , and p r o v i d e d computer r e s o u r c e s . The group ab Argonne N a t i o n a l L a b o r a t o r y (ANL) c o n s t r u c t e d CDC6600 v e r s i o n s o f i t s BISON, BISONMC, DASCI, and POLYINT codes and made them o p e r a t i v e a t W r i g h t - P a t t e r s o n AFB (24-28). The group at t h e U n i v e r s i t y o f Utah implemented codes f o r i t s e q u a t i o n s - o f - m o t i o n method f o r computing i o n i z a t i o n p o t e n t i a l s and e l e c t r o n a f f i n i t i e s from SCF wavefunct i o n s (32). Our remote i n t e r a c t i v e t e r m i n a l set-up i s d e p i c t e d s c h e m a t i c a l l y i n F i g u r e 1. These r e s e a r c h groups then proceeded t o pursue program o b j e c t i v e s u t i l i z i n g t h e s e common r e s o u r c e s . The ARL-ANL-NBS p r o j e c t i s d e s i g n e d t o c a t a l o g what i s p r e s e n t l y known from b o t h t h e o r y and experiment about the dominant a t m o s p h e r i c m o l e c u l e s H2O, N0 / CO2, O3, N 0 and t h e i r p o s i t i v e and n e g a t i v e i o n s , t o c r i t i c a l l y r e v i e w t h i s i n f o r m a t i o n , and t o supplement t h a t information i n a systematic computational f a s h i o n with theoretical calculations. T h i s new t h e o r e t i c a l knowl e d g e can then be used t o advance the e x p e r i m e n t a l •* T h i s s e t o f codes p r o v i d e s f o r the ab i n i t i o computat i o n o f p o l y a t o m i c w a v e f u n c t i o n s , p r o p e r t i e s , and potent i a l s u r f a c e s by t h e o p t i m i z e d v a l e n c e c o n f i g u r a t i o n s (OVC) multiconfiguration self-consistent-field (MCSCF) c o n f i g u r a t i o n - i n t e r a c t i o n (CI) t e c h n i q u e . 2
2
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a n a l y s i s by p a r t i c i p a t i n g i n a feedback p r o c e s s which h i s t o r i c a l l y has proven t o be i m p o r t a n t i n u n d e r s t a n d i n g the phenomena i n v o l v e d . A c r i t i c a l review of the l i t e r a t u r e has been completed i n which e x t e n s i v e use i s made of s t a t e a d i a b a t i c c o r r e l a t i o n diagrams t o summarize p o t e n t i a l energy s u r f a c e c h a r a c t e r i s t i c s (33). The v e r t i c a l s p e c t r a o f the above f i f t e e n m o l e c u l e s and m o l e c u l a r i o n s have been computed a t the SCF l e v e l and, f o r some, a t the OVC-MCSCF-CI* l e v e l (34). Potential surf-aces f o r v a r i o u s s t a t e s o f Η 2 θ , H2O, N2O"", Ν 2 θ , Ν 0 ~ and NO2 have a l s o been examined (34) . F u r t h e r s t u d i e s w i t h t h e OVC-MCSCF-CI t e c h n i q u e a r e c u r r e n t l y underway. +
1
2
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Equipment
In the e a r l y s t a g e s o f t h i s p r o j e c t a l l a c t i v i t y proceeded by s i t e v i s i t s t o W r i g h t - P a t t e r s o n A i r F o r c e Base (WPAFB). A f t e r about one y e a r , d i a l - u p i n t e r a c t i v e t e r m i n a l c o n n e c t i o n s became a v a i l a b l e a t WPAFB and we were a b l e t o p e r f o r m much o f the maintenance and produc t i o n work r e m o t e l y from 110R and, somewhat l a t e r , from 300B i n t e r a c t i v e t e r m i n a l s . Most o f our e f f o r t was w i t h s i m p l e HOB t e l e t y p e s l o c a t e d a t ANL, NBS, Utah, and WPAFB. A 30OB CRT t e r m i n a l was a v a i l a b l e f o r code maintenance o n - s i t e a t W r i g h t - P a t t e r s o n on the same d i a l - u p b a s i s as the HOB and 300B o f f - s i t e t e r m i n a l s . The r e q u i r e m e n t s imposed upon the c h o i c e o f a r e mote t e r m i n a l and upon the t a c t i c s o f o p e r a t i o n i n an e f f o r t such as o u r s are e s s e n t i a l l y t h o s e o f any l a r g e s c i e n t i f i c c o m p u t a t i o n a l p r o j e c t . One needs the c a p a c i t y t o f o r m u l a t e and t r a n s m i t numerous p r o d u c t i o n j o b s t o the h o s t computer b a t c h i n p u t queue and t o r e c e i v e and examine o u t p u t . I t i s then n e c e s s a r y t o be a b l e t o m a n i p u l a t e f i l e s on the h o s t computer v i a some s o r t o f an i n t e r a c t i v e o p t i o n (e.g. CDC INTERCOM, IBM TSO). However, t h e r e a r e some c h a r a c t e r i s t i c s o f ab i n i t i o quantum c h e m i c a l c a l c u l a t i o n s which r e q u i r e s p e c i a l attention. W h i l e i t might be p o s s i b l e , f o r i n s t a n c e , f o r us t o e s t a b l i s h p r o d u c t i o n l o a d modules p e r i o d i c a l l y , i t i s n e c e s s a r y t o m a i n t a i n and c o n t i n u a l l y upgrade each o f f i v e , 4000-7000 c a r d , s o u r c e codes r e s i d e n t on the h o s t computer. A CRT t e r m i n a l component and a means o f o b t a i n i n g updated line-numbered, 80-80 s o u r c e l i s t i n g s worked w e l l f o r us. T h i s p r o c e d u r e r e q u i r e d ons i t e personnel. Some m o d i f i c a t i o n s were a c c o m p l i s h e d * See
footnote
on p r e v i o u s
page.
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c o m p l e t e l y r e m o t e l y w i t h a t e l e t y p e from e i t h e r Argonne or Utah. Furthermore, t h e i n p u t decks f o r p r o d u c t i o n runs a r e q u i t e l a r g e (200-400 c a r d s ) and o f t e n change v e r y s u b s t a n t i a l l y from one r u n t o t h e n e x t . For t h i s reason i t i s not expedient t o c o n s t r u c t these input decks s o l e l y v i a t h e keyboard. I n s t e a d , we found i t u s e f u l t o m a i n t a i n a l i b r a r y o f model i n p u t decks on the h o s t computer mass s t o r a g e media o r on remote s i t e media such as paper tape o r magnetic tape c a s s e t t e s . A model i n p u t deck c a n c o n s i s t o f t h e "punched" o u t p u t from a p r e v i o u s r u n and may be s t o r e d w i t h t h e j o b cont r o l cards attendent t o i t s execution i n p l a c e . Input decks on t h e above-mentioned remote s i t e media c a n be c o n s t r u c t e d l o c a l l y from punched c a r d s i f a b a t c h computer f a c i l i t y i s a v a i l a b l e . The t e x t e d i t o r o f t h e i n t e r a c t i v e s o f t w a r e system o f t h e h o s t computer c a n then be used t o c o n s t r u c t t h e d e s i r e d i n p u t deck from these sources. Another c h a r a c t e r i s t i c o f t h e type o f c a l c u l a t i o n s w i t h which we a r e c o n c e r n e d i s t h e l a r g e s i z e o f t h e output f i l e s . F o r such f i l e s as t h e s e — f i l e s o f t e n i n e x c e s s o f 4000 l i n e s — complete p r i n t i n g a t a r e mote i n t e r a c t i v e t e r m i n a l o p e r a t i n g a t 110-1200B i s n o t practical. Even a remote b a t c h t e r m i n a l o p e r a t i n g a t 2000-4800B would r e q u i r e p r o h i b i t i v e t r a n s m i s s i o n times. To remedy t h i s problem we have m o d i f i e d o u r codes t o produce p r i n t e d o u t p u t f i l e s i n a summary, as w e l l as the d e t a i l e d s t a n d a r d , form. For production c a l c u l a t i o n s w i t h o u r BISONMC code some 100 70-column l i n e s s u f f i c e t o c o n t a i n the important i n f o r m a t i o n . A t e l e type has s e r v e d , i n o u r p r o j e c t , t o e n a b l e t h e p r o d u c t i o n o f such p r i n t e d summaries a t each remote s i t e . The s t a n d a r d o u t p u t f i l e s were p r i n t e d a t t h e h o s t comp u t e r and m a i l e d t o t h e r e s p e c t i v e u s e r as needed. T a b l e I i s a comparative d i s p l a y o f t h e c h a r a c t e r i s t i c s o f t h e i n t e r a c t i v e t e r m i n a l s we have used r e m o t e l y — u n i t s 1 and 2 — and would l i k e t o — unit 3. Some d e s i r a b l e b a t c h t e r m i n a l c h a r a c t e r i s t i c s a r e i n c l u d e d i n T a b l e I f o r completeness; d i s c u s s i o n o f these i s d e f e r r e d t o a l a t e r s e c t i o n . F o r o u r type o f a p p l i c a t i o n , o p t i o n s such as d i s k packs, p l o t t e r s , and tape d r i v e s , w h i l e c o s t l y t o a c q u i r e and m a i n t a i n , p r o v i d e no s e r v i c e n o t a l r e a d y a v a i l a b l e v i a t h e h o s t computer. F o r t h i s r e a s o n t h e y have been o m i t t e d from T a b l e I . Of c o u r s e , i f some o f t h e s e components a r e a l r e a d y a v a i l a b l e , t h e y c a n be used t o advantage. AISQ a remote s i t e t e x t e d i t i n g c a p a b i l i t y c a n be h e l p f u l t o our t y p e o f a p p l i c a t i o n . Examples o f t h e l a t t e r i n c l u d e a d u a l tape c a s s e t t e u n i t and t h e i n t e r a c t i v e s o f t w a r e o f a computer l o c a l t o t h e remote s i t e .
11.
HOPPER E T A L .
Calculations
via Remote
Terminal
161
U n i t 1, t h e t e l e t y p e o r e q u i v a l e n t d e v i c e , i s p r o m i n e n t l y numbered i n T a b l e I t o s t r e s s t h e f a c t s (a) t h a t i t i s i n our experience capable o f e n a b l i n g , a t m i n i m a l c o s t , a modest r a t e o f p r o d u c t i o n c o m p u t a t i o n and (b) t h a t i t i s a l r e a d y w i d e l y a v a i l a b l e . F o r i n d i v i d u a l s e v a l u a t i n g equipment f o r a remote t e r m i n a l ( i n t e r a c t i v e o r batch) we note t h a t a v e r y d e t a i l e d compendium o f i n f o r m a t i o n about t e r m i n a l s , modems, d a t a communications, e t c . i s a v a i l a b l e (35.) as w e l l as o t h e r background i n f o r m a t i o n (_36) .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch011
Communication L i n k s . The most common communication l i n k between remote t e r m i n a l s and computers i s a phone l i n e . While the s i m p l e s t and an o f t e n r e l i a b l e way t o use a phone l i n e i s t o d i r e c t - d i a l o v e r t h e p u b l i c network, t h i s i s n o t always p o s s i b l e . Thus, i t i s o f t e n n e c e s s a r y t o go t h r o u g h e x t r a l a y e r s o f e f f o r t on each c a l l — i . e . i n s t i t u t i o n a l exchanges — and t o p u t up w i t h t h e n o i s y l i n e s o f p r i v a t e phone networks. The h i g h e r t r a n s m i s s i o n f a i l u r e r a t e s on n o i s y l i n e s c a n l i m i t an i n t e r a c t i v e t e r m i n a l / h o s t computer c o m b i n a t i o n c a p a b l e o f 1200B o r 300B t o H O B . Regular voice-grade p u b l i c t e l e p h o n e l i n e s a r e c a p a b l e o f t r a n s m i s s i o n r a t e s up t o 4800B ( 3 5 ) . P u t a n o t h e r way, t h e u n d e t e c t e d e r r o r r a t e on p u b l i c l i n e s i s one i n Ι Ο ^ - Ι Ο b i t s a t most, g i v e n the c u r r e n t t e c h n o l o g y f o r s i g n a l t r a n s m i s s i o n o v e r an audio w i r e . Leased l i n e s a r e much more e x p e n s i v e b u t can s u p p o r t up t o 9600B (3j>) . I n t e r a c t i v e t e r m i n a l s and h o s t computers a r e commonly c a p a b l e o f s u p p o r t i n g 110, 300, and 1200B o p e r a t i o n . Remote b a t c h t e r m i n a l s and h o s t computers a r e commonly c a p a b l e o f s u p p o r t i n g 2000 and 4800B o p e r a t i o n . However, i t i s c l e a r t h a t one s h o u l d n o t p u r c h a s e a t e r m i n a l and modem c a p a b l e o f more than 110 o r 300B i f i t i s n o t p o s s i b l e t o e s t a b l i s h t h a t t h e r e m o t e - t o - h o s t phone c o n n e c t i o n c a n support the higher t r a n s m i s s i o n r a t e . When o u r p r o j e c t began we were l i m i t e d t o 110B t r a n s m i s s i o n by our i n t e r a c t i v e t e r m i n a l — a Model 33 T e l e t y p e — and we employed d i r e c t - d i a l i n g o f t h e W r i g h t - P a t t e r s o n AFB computer from Argonne. L a t e r we upgraded o u r i n t e r a c t i v e t e r m i n a l c a p a c i t y t o 300B b u t were s t i l l l i m i t e d t o H O B by a r e q u i r e m e n t t h a t we employ FTS l i n e s , which we found t o be r a t h e r n o i s y . T h i s problem was compounded by t h e f a c t t h a t FTS c a l l s t o t h e computer a t W r i g h t - P a t t e r s o n had t o go t h r o u g h the base s w i t c h b o a r d and were, t h e r e f o r e , l i m i t e d t o about f i v e minutes d u r i n g b u s i n e s s h o u r s . Future s o l u t i o n s t o t h e communication l i n k problem ( c o s t and 7
162
Table I.
Unit
1
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch011
2
3
4
COMPUTER
NETWORKING
Renote Terminal Choices for Computational
Baud Rate Cap.
110
110 300 1200
110 300 1200 2400 4800
2000 4800 9600
Equipment
AND CHEMISTRY
Chemistry.
0
Type In
Usage Stor. Out
Cost
^$
teletype keyboard 70 c o l . printer (impact) paper tape
-
X
-
X
X
X
X
X
electronic keyboard 80 c o l . printer (thermal) dual tape cassettes electronic keyboard 132 c o l . printer dual tape cassettes card reader card punch CRT batch terminal keyboard 132 char, printer card reacher card punch
900
^$ 3600
-
X
-
X
X
X
X
X
^$ 9000
X
-
X X
-
X
X
-
X —
X
-
X
X
X
-
X
X X
-
-
-
^$30000
-
X
X
X
X
Obtention of an appropriate modem i s assumed (35). t r a n s m i s s i o n r a t e ) and a l t e r n a t i v e s t o phone l i n e s w i l l be d i s c u s s e d below. From our e x p e r i e n c e on communicat i o n l i n k s the phone c o n n e c t i o n i s the major d i f f i c u l t y o f remote d a t a p r o c e s s i n g .
* I n s t a l l a t i o n and Maintenance
o f Codes
In our work t h e computer programs (codes)^have been i n s t a l l e d o n l y by s i t e v i s i t s . Maintenance of Maintenance o f codes i s , i n the p r e s e n t c o n t e x t , t a k e n t o i n c l u d e n o t o n l y t h e maintenance o f o p e r a t i v e l o a d modules and s o u r c e decks on the h o s t computer p u b l i c d i s k and tape l i b r a r i e s , b u t a l s o t h e u p d a t i n g o f codes t o accomodate changes i n the o p e r a t i n g system, t o improve performance, and t o i n c o r p o r a t e new f e a t u r e s .
11.
HOPPER E T
AL.
Calculations
via
Remote
Terminal
163
the f o u r ANL codes ( 2 4 - 2 7 ) was a l s o performed o n - s i t e f o r the most p a r t , m a i n l y by the use o f a CRT i n t e r active terminal. The l a t t e r was g r e a t l y f a c i l i t a t e d by the g e n e r a t i o n o f an updated s o u r c e l i s t i n g , l i n e numb e r e d i n the same s t y l e as i n the e d i t f i l e , a f t e r each code m o d i f i c a t i o n s e s s i o n a t the t e r m i n a l . However, a s i g n i f i c a n t p o r t i o n o f the code maintenance was performed v i a t e l e t y p e from e i t h e r Argonne o r Utah. I t was v e r y h e l p f u l , t h e r e f o r e , t o keep a c u r r e n t and d e t a i l e d s e t o f manuals f o r the h o s t comp u t e r a t each remote s i t e (Argonne and Utah) from which code maintenance a c t i v i t y was u n d e r t a k e n .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch011
Input and
Output
Job I n p u t . The t r a d i t i o n a l way o f j o b i n p u t i s by p h y s i c a l c a r d decks v i a a c a r d r e a d e r . A cardr e a d e r can be o b t a i n e d as an add-on o p t i o n t o many i n t e r a c t i v e t e r m i n a l s on the market and i s a s t a n d a r d component o f b a t c h t e r m i n a l s . However, as d i s c u s s e d e a r l i e r a c a r d r e a d e r i s not i n d i s p e n s i b l e t o an i n t e r active terminal operation. The power o f the h o s t comp u t e r i n t e r a c t i v e s o f t w a r e (e.g. INTERCOM on CDC and TSO on IBM machines) can be b r o u g h t t o bear on j o b a s sembly; and d u a l tape c a s s e t t e s can make i t p o s s i b l e t o p e r f o r m many o f the same j o b c o n s t r u c t i o n t a s k s o f f line. I t i s h e l p f u l t o m o d i f y codes t o a c c e p t f o r m a t f r e e i n p u t as o u r s have been ( 2 4 - 2 7 ) . In a d d i t i o n , s m a l l programs f o r , (a) d a t a s e t c o n s t r u c t i o n - b y i n t e r a c t i v e - t e r m i n a l - i n t e r v i e w , and (b) d a t a s e t v e r i f i c a t i o n , are q u i t e u s e f u l . We have w r i t t e n such s m a l l , r a p i d t u r n - a r o u n d programs f o r use i n c o n j u n c t i o n w i t h our BISON and BISONMC codes (24,2J5) . Such u s e r s o f t ware m o d i f i c a t i o n , development, and u t i l i z a t i o n measures make i t p o s s i b l e t o o p e r a t e e f f i c i e n t l y w i t h o u t p h y s i c a l card decks. In the p r e s e n t l y r e p o r t e d work j o b s were e s t a b l i s h e d i n the e d i t f i l e under the EDITOR mode o f CDC INTERCOM and t h e n saved and b a t c h e d i n t o the i n p u t queue. The e d i t f i l e was e s t a b l i s h e d by (a) k e y - i n , (b) r e a d - i n o f a paper t a p e , o r (c) l o a d - i n o f a f i l e s t o r e d on a h o s t computer d i s k , f o l l o w e d by a p p r o p r i a t e modifications. A t Argonne, a u t i l i t y program was w r i t t e n t o run on the C h e m i s t r y D i v i s i o n SIGMA 5 computer t o c o n v e r t a punched-card i n p u t deck f o r the CDC6600 i n t o a paper t a p e . T h i s paper tape was then r e a d i n o v e r the t e l e t y p e . Back-up o f i n p u t j o b s was on paper tape o r h o s t d i s k f i l e .
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch011
164
COMPUTER
NETWORKING
AND
CHEMISTRY
Output — G e n e r a l Comments. Output f i l e s a r e generated f o r s e v e r a l reasons: the p e r u s u a l of r e s u l t s from a r u n , t h e c o n s t r u c t i o n o f i n p u t d e c k s , and t h e archiving of r e s u l t s . As w i t h t h e i n p u t o f j o b s , o u t p u t has t r a d i t i o n a l l y been h a r d copy — print-outs and punched c a r d d e c k s . Again, both of these are usuall y a v a i l a b l e from a b a t c h t e r m i n a l . A l t e r n a t i v e l y , one can t a k e advantage o f the h o s t computer i n t e r a c t i v e s o f t w a r e and c o d i n g i n n o v a t i o n s t o handle t h e n e c e s s a r y o u t p u t m a n i p u l a t i o n s from an i n t e r a c t i v e t e r m i n a l . T h i s i s e s p e c i a l l y advantageous f o r l o n g p r i n t - f i l e s , f o r l a r g e numbers o f p r i n t f i l e s , and f o r punch f i l e s . Any p o r t i o n o f a f i l e can be l i s t e d a t w i l l , so t h a t t h e r e i s l e s s need t o p r i n t f u l l o u t p u t f i l e s . An o u t p u t m a i l - b a c k p r o c e d u r e must s t i l l be m a i n t a i n e d , however, f o r t h o s e c a s e s where a l e n g t h y p r i n t - o u t (on paper o r m i c r o f i c h e ) o r r e a l punched o u t p u t i s n e c e s s a r y . The p e r u s a l f u n c t i o n can be s a t i s f a c t o r i l y performed w i t h a CRT o u t p u t d i s p l a y o r a low-speed p r i n t e r . The a r c h i v a l f u n c t i o n r e q u i r e s some type o f s t o r a g e d e v i c e on the h o s t computer o r a t the remote s i t e . File s t o r a g e and m a n i p u l a t i o n a r e d i s c u s s e d under o t h e r subheadings. In our c a s e a l l remote o u t p u t has been by t e l e t y p e or t e l e t y p e - l i k e d e v i c e s . I t was n e c e s s a r y t o s t o r e the punch f i l e as a c a t a l o g u e d d i s k o r magnetic tape f i l e d u r i n g e x e c u t i o n o f a r e m o t e - e n t r y j o b on the WPAFB CDC6600; o t h e r w i s e i t was l o s t t o t h e remote u s e r . A l s o , o u t p u t p r i n t and punch f i l e s had t o be backed up on h o s t computer tape b e f o r e r u n t e r m i n a t i o n i f we were t o a v o i d s u f f e r i n g from the o c c a s i o n a l l o s s of u n a r c h i v e d and o f temporary d i s k f i l e s . We p r o t e c ted o u r s e l v e s from l o s i n g a r u n c o m p l e t e l y , due t o , (a) abnormal program t e r m i n a t i o n o r (b) an o p e r a t o r drop (e.g. "SORRY — MUST DROP TO RUN CLASSIFIED") by making the punched as w e l l as the p r i n t e d o u t p u t summary f i l e dynamic i n t h a t i t was updated a f t e r each i t e r a t i o n t o the l a t e s t o r b i t a l s , e n e r g i e s , and configuration coefficients. Output — 70 C h a r a c t e r / L i n e O p t i o n . Because n a r row c a r r i a g e p r i n t e r s and CRT s c r e e n s a r e so common f o r i n t e r a c t i v e t e r m i n a l s , we have m o d i f i e d our codes POLYINT, BISONMC, and DASCI t o p r o v i d e an o p t i o n by which the u s e r may s p e c i f y t h a t a l l p r i n t e d o u t p u t f i l e s be i n a 70 c h a r a c t e r / l i n e format. These We chose 70 c h a r a c t e r s / l i n e because we found i t t o be the maximum s u i t a b l e f o r a model 35 t t y .
Calculations
HOPPER E T A L .
via Remote
Terminal
UTAH TTY-33
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch011
Figure 1. Interactive terminal connections to Wright-Patterson AFB from Argonne National Laboratory, The National Bureau of Standards, and the University of Utah
PAINT — ANL MODIFICATION OF THE PA300 POLYAT CM PROGRAM. INTEGRALS ARE GENERATED I N CANONICAL L I S T S FOR INTERFACE WITH THE ANL COOES OVC, KR A S AND O A S C I . BY H.BASCH, BELL LABORATORIES PA300/CDC6600 BV C.J.HORNBACK, NYU. ANL CANONICAL VERSION BY A.HINOS, A N L . ANL VERSION INPLENENTEO ON COC6600 BY R.P.HOSTENY, A N L . ANL VERSION/COC66I0 MODIFICATIONS BY O.G.HOPPER, ANL. TNIS IS THE MPAFB COC6600 CANONICAL VERSION OF A P R I L , 1 9 7 5 FOR INFORMATION OR THE LATEST WRITE-UP CONTACT O.G.HOPPER, ANL, X A R L / L J , MPAFB ,OH. * 5 * 3 3 , P H i l J - 2 5 5 - * 8 6 9 . t
DATE —
OS/07/75
TIME — 1 7 . 3 1 . 1 2 .
RUN TITLE NNO B
•COOROINANTS-2.13198906 0.00000000 2.23781372
GAUSSIAN FUNCTION SPECIFICATIONS NUMBER OF PRIMITIVE GAUSSIANS = 7 2 NUMBER OF BASIS FUNCTIONS » 39 BASIS SET fSYMMETRY) BLOCKING = 21 GAUS FUNC COMP CENT TYPE Nl S 1 Nl S 2 Nl S 3 Nl S Nl S 5 Nl S 6 Nl S 7 Nl S Nl S 9 Nl 10 Nl 11 Nl 12 Nl 13 Nl 1* N2 15 N2 16 N2 17 N2 18 N2 19 N2 20 N2 21 N2 IB 22 N2 23 11 N2 12 N2 25 12
k
β
Zh
0.00300000 0.00000Û00 0.00000000
CHARGE 7. 7. β.
18
EXPONENT COi : F F I C I E N T , 00200*0 5909.**00000 ,0153100 887.*510000 • 07*2930 20*.7*90000 ,25336*0 39.8376000 ,6005760 19.9981000 .2*51110 2.6860000 7 . 1 9 2 7 0 0 0 1 , 0000000 . 7 0 0 0 0 0 0 1 , 0000090 . 2 1 3 3 0 0 0 1 .0000000 ,0382**0 26.7860000 .2*38*60 5. 956*000 .8171930 1.7071*000 . 5 3 1 * 0 0 0 1 .0000000 .165*000 1 . 0000000 .00200*0 C P O 5909.**00000 .0153100 C P O 887.*510000 ,07*2930 C P O 20*.7*90000 ,25336*0 C P O 59.8376000 .6005760 C P O 19.9981000 ,2*51110 C P O 2.6860000 7 . 1 9 2 7 0 0 0 1 .0000000 C P O . 7 0 0 0 0 0 0 1 .OOObOQO C P O . 2 1 3 3 0 0 0 1 .0000000 C P O .0382**0 C P O 26.7860000 .2*38*60 C P O 5.956*000
FROM FROM FROM FROM FROM FROM FROM FROM FROM FROM FROM
Figure 2(a). Examples of 70-column output formatting for teletype and teletype emulating terminal devices. Only partial listings are shown, (a) PAINT: an unoverUyed CDC6600 version of the ANL code POLYINT.
166
COMPUTER NETWORKING AND CHEMISTRY
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch011
OVC-1
A COMPUTING SYSTEM FOR MCSCF C A L C U L A T I O N OF O P T I M I Z E D V A L E N C E C O N F I G U R A T I O N H A V E F U N C T I O N S FOR P O L Y A T O M I C M O L E C U L E S 8Y G . O A S A . H I N D S ANO A . C . W A H L , CHEM* O I V . ARGONNE N A T I O N A L L A 7 0 R A T O S Y IMPLEMENTED ON THE C O C 6 6 0 0 3Y R · P # H O S T L N Y » ARGONNE N A T I O N A L LABORATORY MODIFIED ΘΥ O . G . H O P P E R ANO P . J . F O R T U N E » ARGONNE N A T I O N A L L A R C n A T O ^ Y T H I S IS THE C A N O N I C A L V E R S I O N OF A P R I L . 1 9 7 5 . FOR T H £ L A T : S T K R I T > U » CONTACT D . G . H O P P E R , X A R L / L J , MPAFB.OH*5<*33, PH->13-255-<*809.
OATE RUN
—
05/08/75
TIME
—
DATA
19.pQ.2i·.
SET
f
1.
TITLE NNO 1 S I *
PROGRAM IOPEN* IPRCTs INFLG=
B<*3
CONTROL F L A G S 0 IVECT= 0 0 ISCFs 0 0 ISAVE= 1
Pill
IPRINT= ICH= IOVC=
0 0 1
KFLAG* »• IPUNCH* - 7 NORBPB = 6
DOCUMENTATION OF I N T E G R A L G E N E R A T I O N FROM ZB 60.823 ZA 1.000 1 . 0 0 0 0 BCHRS INTERNUCLEAR DISTANCE 1 . 0 0 0 0 BOHRS I N T E G R A T I O N T R U N C . AT NOUN 0 NO.NEUMANN I T E R A T I O N S 0 MASS OF C E N T E R A 775.0000 VECTOR C O E F . D I A G . T H S . 1.000E+00 C O U L O M B - H Y B R I Û CONV.THS. 1.000E+03
JFLAG= I J E BUG
2
e i S O M STO B A S I S F U N C T I C N S XNUCL 60.8223803200 A.U. NO.GAUSS P O I N T S ON XI 30 NO.GAUSS P O I N T S ON E T A 30 MOUMF 0 N O . S I M P S O N S POINTS 0 MASS OF C E N T E R 9. 111.3000 B I A S FOR O N E - - L E C . G R I D 0 PRIOR I T E R A T I O N S 0
I N T E G R A L S O B T A I N E D FROM S A V E T A P E = UNIT <*3 JSUPMX I N T E G R A L S C O P I E O FROM UNIT *»3 TO E S T A B L I S H KSUPNXS I N T E G R A L S C O P I E O FROM UNIT <*3 TO E S T A B L I S H UTS I N T E G R A L S C O P I E O FROM U N I T <*3 TO E S T A B L I S H
DISK DISK OISK
UATA S L T DATA S E T OATA S L T
<*0
Figure 2(b). OV1-1: the CDC6600 version of the ANL code; this code is referred to as BISONMC in the text. The basis function documentation is the default; in actuality the integrals were computed from a contracted Gaussian basis with program PAINT.
11.
HOPPER ET
AL.
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Remote
Terminal
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m o d i f i c a t i o n s e n a b l e the p r i n t i n g o f our .output i n a n e a t , e a s i l y r e a d f o r m a t on narrow l i n e d e v i c e s . There a r e a l s o the a d d i t i o n a l advantages t h a t the average number o f c h a r a c t e r s p e r l i n e i s i n c r e a s e d (decreasing the p r i n t i n g time) and t h a t the narrow-width p r i n t - o u t s can be f i l e d i n l e t t e r - s i z e d f o l d e r s t o document the run. Examples a r e d i s p l a y e d i n F i g u r e s 2a, 2b, and 3a. F i g u r e 3b i l l u s t r a t e s a 132 c h a r a c t e r / l i n e format l a i d out such t h a t i f i t had been p r i n t e d on a t e l e t y p e , f o r i n s t a n c e , the r e s u l t would have s t i l l been a n e a t , c o n c i s e p r i n t - o u t w i t h the r i g h t - h a n d columns v e r t i c a l l y a l i g n e d , but i n t e r l e a v e d w i t h the c o n f i g u r a t i o n s on the left. Output—Summary F i l e s . There are two r e a s o n s f o r c r e a t i n g an o u t p u t summary f i l e . The f i r s t i s t o m i n i mize t h e amount o f time r e q u i r e d t o p r i n t e s s e n t i a l i n f o r m a t i o n from a r u n . The second i s t o reduce the cumu l a t i v e volume o f the p r i n t - o u t s t h a t one must s t o r e t o document the c a l c u l a t i o n s . The c a p a b i l i t y t o produce summary f i l e s has been i n t r o d u c e d i n t o the W r i g h t P a t t e r s o n AFB CDC6600 v e r s i o n s o f POLYINT, BISONMC, and DASCI. An example f o r BISONMC i s d i s p l a y e d i n F i g u r e 3a. The o u t p u t summary f o r the W r i g h t - P a t t e r s o n v e r s i o n o f BISONMC i s dynamic i n t h a t , j u s t as f o r the punch f i l e and e x c e p t i n the e v e n t o f a t e r m i n a t i o n by the o p e r a t o r o r a system c r a s h , i t i s always p r o d u c e d , and c o n t a i n s the o r b i t a l s a t the l a s t completed i t e r a tion. Program g e n e r a t e d e r r o r messages a r e d e l i v e r e d t o the o u t p u t summary f i l e i n a condensed manner. Storage. There a r e many forms o f s t o r a g e a v a i l a b l e t o the remote t e r m i n a l u s e r . F i r s t and f o r e m o s t among t h e s e forms a r e the tape and d i s k l i b r a r i e s o f the h o s t computer. P o s s i b l e s t o r a g e media a t the remote t e r m i n a l i n c l u d e paper t a p e , magnetic tape c a s s e t t e s , d i s k s ( s t a n d a r d and f l e x i b l e ) , p r i n t - o u t s ( t e l e t y p e l i k e and s t a n d a r d ) and c a r d s . None o f t h e s e , e x c e p t for a very l i m i t e d p r i n t e r c a p a c i t y , i s i n d i s p e n s i b l e t o a remote t e r m i n a l f o r our t y p e o f c o m p u t a t i o n a l problem. S t o r a g e i n the form o f the t r a d i t i o n a l f u l l p r i n t - o u t s and c a r d decks can be employed i f o p e r a t i o n i s from a b a t c h t e r m i n a l , o r i f t h e r e i s someone a t the h o s t s i t e t o m a i l o u t p u t (perhaps on m i c r o f i c h e , i f a v a i l a b l e ) i f o p e r a t i o n i s from an i n t e r a c t i v e t e r m i n a l . C a t a l o g u e d P r o c e d u r e s and JCCRGEN. The CDC j o b c o n t r o l language i s r e l a t i v e l y easy t o use - e s p e c i a l l y for routine tasks. I t does s u f f e r from the f a u l t t h a t a c a t a l o g u e d p r o c e d u r e cannot be m o d i f i e d a t e x e c u t i o n
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OVC OUTPUT SUMMARY —
05/08/73
ΐ*·'ΰ·2*· —
09C-I . MPAFB CDC660D CANONICAL \/_«Slo'l NNO 1SI* 8*3 P i l l 10 PARAMETERS 0 NCINPT PARAMtTtRS 0.0 0 1.0.1-0·. ITERATION 2 ORBITALS. --- SLOCK C(l) 2(2) BP TYPc ζετΑ CENT* .003*3 A •00506 1 18 0 5 9 0 9 · * * 0 0 •Oils? A .00686 7.1327 2 10 0 A -.01985 - . 0 J J - 3 • 7000 S 10 0 A -.0102-) -•uobyi • 2133 % 10 0 A -.001*9 -.0103* S 10 0 2 6 . 7 9 6 0 A -.00110 -.00878 . 5 3 1 * 0 «7 10 • 00 Jo* A .00290 .165* 10 0 0 5 9 0 9 . * * 0 0 A • 00*39 . 5 9 * * 1 Β 10 A .00593 .*>J32 7.1927 9 10 0 A -.01*08 -.03712 • 7000 I f 10 0 A -•00718 - . 0 2 * 1 - » • 2133 11 10 0 .01182 A •0038? 12 10 0 26.7060 .01316 A •00249 .531* 13 IB 0 .00589 A •00310 • 165% 1% 10 0 A -•54*76 - . 3 0 3 Ô O 19 10 0 7 8 1 6 . 5 * 0 1 A -•*o70Q - . 0 0 7 - 0 9.5322 IB 10 0 •03200 A .0190* • 9398 17 10 0 •030C5 A •01*81 .20*6 IB 10 0 •007b* A •00760 19 10 0 3 5 . 1 8 3 2 •0100* A •00399 • 7171 Ν 10 0 A • 0 0*69 . 0 0 5 9 1 • 2137 21 10 0
Figure 3(a). Output summary and further examples of 70-column output format ting, (a) OVC output summary for a 19configuration MCSCF calculation for the X*V state of N 0 at its experimental equi librium geometry with the Dunning (see Ref. 30) (4s3p)/ [9s5p] contracted Gaussian basis set. The exponent of the first member of each contracted Gaussian is listed under the heading Zeta. 2
11.
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E T AL.
Calculations
169
via Remote Terminal
Is s»
ii to
Is
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-s s M l
> 8 § O Q S to ^•S »
l e i
•I S § s &g 8o§-S
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s .s 3g
1-5
11 co *s
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time by parameters e n t e r e d on the c o n t r o l c a r d which c a l l s i t into execution. Nonetheless, i t i s p o s s i b l e t o run a s i n g l e program w i t h o n l y a few, simple j o b c o n t r o l statements. I n i t i a l l y we d i d so. Later i t became n e c e s s a r y t o use even more c o m p l i c a t e d j o b c o n t r o l c a r d r e c o r d s (JCCR's) t o s o l v e the problems i n volved i n executing m u l t i p l e job steps. When the c a p a c i t y t o c a t a l o g t h e s e p r o c e d u r e s became a v a i l a b l e , i t was used t o reduce i n p u t j o b f o r m u l a t i o n e r r o r s and t o m i n i m i z e the knowledge o f the CDC j o b c o n t r o l language r e q u i r e d i n the c o n s t r u c t i o n o f an i n p u t deck. Figure 6b i s an example o f one such c a t a l o g u e d p r o c e d u r e . Now we have gone one s t e p f u r t h e r . We have w r i t t e n a program, JCCRGEN, i n FORTRAN IV t o p e r f o r m the t a s k o f s u b s t i t u t i n g the p r o p e r CDC c o n t r o l c a r d s e quences f o r each o f a l i m i t e d number o f r u n - s p e c i f y i n g commands. These commands a r e e n t e r e d by the u s e r a t the head of the j o b i n r e c o r d two. T h i s program i s keyed t o our immediate needs, but i t can e a s i l y be expanded t o h a n d l e o t h e r codes and f i l e m a n i p u l a t i o n tasks. The r o l e t h a t t h i s program p e r f o r m s on the CDC system i s , i n e s s e n c e , a v a i l a b l e i m p l i c i t y i n IBM j o b c o n t r o l language v i a the c a p a b i l i t y one has t h e r e t o w r i t e c a t a l o g u e d p r o c e d u r e s w h i c h can be m o d i f i e d a t each e x e c u t i o n by means o f parameters e n t e r e d on t h e EXEC c a r d . Our j o b c o n t r o l c a r d r e c o r d g e n e r a t i o n (JCCRGEN) program i s i n v o k e d by the use o f a j o b deck s e t - u p as shown i n F i g u r e 4. The commands a r e d i s p l a y e d i n F i g u r e 5. F i g u r e 6a shows how simple the overhead i s i n the a p p l i c a t i o n o f JCCRGEN t o the t a s k o f t h e cons t r u c t i o n o f the j o b c o n t r o l c a r d r e c o r d (JCCR) shown i n F i g u r e 6b. F i g u r e 7 d i s p l a y s a simple j o b t h a t one might run t o r e t r i e v e a f i l e from an a r c h i v e tape on the h o s t computer and p l a c e a copy o f i t on a d i s k f i l e f o r subsequent use i n c o n s t r u c t i n g a new j o b o r f o r p e r u s a l purposes. Batch Terminals. We have had no d i r e c t e x p e r i e n c e g o i n g i n t o WPAFB w i t h remote b a t c h t e r m i n a l s . However, t h e r e a r e , o f c o u r s e , i n d i v i d u a l s who have s u c c e s s i v e l y employed them f o r ab i n i t i o c a l c u l a t i o n s . T h e i r advantage o v e r remote i n t e r a c t i v e t e r m i n a l s i s t h a t they p e r m i t one t o o p e r a t e from c a r d s and w i t h punched and p r i n t e d o u t p u t much as i f he were " o n - s i t e " . T h i s l a t t e r i s p a r t i c u l a r l y t r u e i f the t r a n s m i s s i o n r a t e i s 4.8 K/B o r h i g h e r . T h e i r d i s a d v a n t a g e , as can be seen from T a b l e I , i s t h a t t h e i r p u r c h a s e p r i c e i s many times t h a t of a t e l e t y p e or other i n t e r a c t i v e t e r m i n a l .
HOPPER E T A L .
Calculations
via
Remote
Terminal
JOB CARD ATTACH, JCCRGEN. JCCRGEN. CCLINK, JCCR. *EOR COMMANDS FOR JCCRGEN SEPARATED BY ONE OR MORE SPACES *EOR INPUT DATA SETS NOT MADE AVAILABLE BY THE JCCRGEN COMMANDS IN THE HIERARCHIAL SEQUENCE BISON OR PAINT BEFORE BISONMC BEFORE DASCI. SEPARATE THE DATA SETS WITH AN END-OF-RECORD (*EOR,LEFT-JUSTIFIED).
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch011
Figure 4. General form of a remote interactive terminal input job that uses JCCRGEN via CDC INTERCOM. For a remote batch terminal a card with a column 1 multi-punch 7/8/9 replaces the *EOR; a column 1 multi-punch 6/7/8/9 replaces the ==.
TERMINAL DESIGNATION—INTERACTIVE OR BATCH. MUST BE FIRST COMMAND INTERTERM (IT) BATCHTERM (BT)
T h i s i s the d e f a u l t .
CODE RETRIEVAL AND EXECUTION COMMANDS. BISON BISONMC DASCI PAINT
(or (or (or (or
BI) MC o r OVC) CI) PA)
FORM:
COMMAND, OPTIONS.
BIMC PAMC PAMCCI MCCI (or OVCCI)
INTEGRAL STORAGE OPTION TAPE,file label,tape # DISK,pf l a b l e , c y c l e # , f i l e # TAPE,tape # , f i l e #
BISON PAINT
INTEGRAL RETRIEVAL COMMAND INTEGRALS_TAPE,file l a b e l , t a p e # (or INT) DISK,pf l a b e l , c y c l e # , f i l e # OUTPUT FILE STORAGE COMMANDS AND COMMAND OPTIONS BASIC FORM:
PRINTSAVE INDECKSAVE OUTDECKSAVE MCPUSAVE
COMMAND=TAPE,file l a b e l , t a p e # DISK,pf l a b e l , c y c l e # , f i l e # (or PRS) (or IDS) (or ODS) (or MCPUS)
COMMAND=TAPE,file l a b e l , t a p e # DISK,pf l a b e l , c y c l e # , f i l e #
(or PAIN) (or MCIN) (or CIIN)
BIINPUT TAPETODISK DISKTOTAPE
(or BUN) (or TTD) (or DDT)
COMMENTS " l a b e l " i s 1-17 alphanumeric c h a r a c t e r s f o r tape, 1-40 f o r disk. " f i l e #" need not be g i v e n i f i t i s 1. Figure 5.
Commands for
JCCRGEN
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6(a) DHACS,CM225000,T1500,IO1000,MT1. R750825,HOPPER,ARL/LJ,54869. ATTACH,JCCRGEN. JCCRGEN. CCLINK,JCCR. *EOR INT=TAPE,NNOB43P111,L00001 OVC,MCPUS=TAPE,NNOB43P111X1SIP,L00002 C I , CIIN=TAPE, XISIPCONFIGS,L 0 0 0 0 3 PRS=TAPE NNOB43PlllXlSIPPR,L00004 EPRS=TAPE,NNOEXITSAVE,L= 0 0 0 0 5 EDS=DISK,NNOEXITSAVE,6 *EOR i n p u t d a t a s e t f o r BISONMC f
Figure 6(a). JCCRGEN Example 1. (a) Depiction of an input job formulated in the EDITOR mode of CDC6600 INTERCOM which uses JCCRGEN commands to (1) retrieve a stored integral set from tape, (2) perform an MCSCF calculation, (3) archive the converged orbitals on tape in the format of a BISONMC input deck, (4) formulate an input data set for the DASCI program from the final orbitals from the BISONMC run and an archived CI configuration list, (5) execute a DASCI run, (6) augment the printed output file with an 80-80 listing of the entire input job deck and with a copy of the output summary file (TAPE57), (7) archive a copy of the augmented printed output file on tape, and, (8) in the event of the encounter of an abnormal run termination condition, archive a copy of the output file on tape and create and store on disk a completed input job deck equivalent in all detail to the original except that the orbitals contained are those from the last successfully completed MCSCF iteration. Job control passes to the file JCCR upon encounter of the command CCLINKJCCR.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch011
The job control card record (JCCR) file generated by the JCCRGEN mands in Figure 6a
com
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Summary and F u t u r e
COMPUTER
NETWORKING AND
CHEMISTRY
Plans
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Summary. We have demonstrated t h a t i t i s p o s s i b l e t o execute s t a t e - o f - t h e - a r t ab i n i t i o quantum m o l e c u l a r c a l c u l a t i o n s r e m o t e l y w i t h an i n t e r a c t i v e t e r m i n a l (37). P a r t i c i p a n t s i n our c o m p u t a t i o n a l c h e m i s t r y p r o j e c t have used t e l e t y p e s t o p e r f o r m OVC-MCSCF c a l c u l a t i o n s a t W r i g h t - P a t t e r s o n A i r F o r c e Base, Ohio, from Argonne, I l l i n o i s , and Washington, D. C , and e q u a t i o n s - o f - m o t i o n c a l c u l a t i o n s from S a l t Lake C i t y , Utah. I t has been p o s s i b l e t o s u s t a i n a moderate p r o d u c t i o n r a t e i n t h i s manner. We have a l s o demonstrated t h a t i t i s p o s s i b l e t o m a i n t a i n and update major computer codes from such a s i m p l e remote t e r m i n a l . F u t u r e P l a n s — To Ease Remote O p e r a t i o n s . There a r e s e v e r a l t h i n g s t h a t we hope t o do t o ease remote o p e r a t i o n s on our p r o j e c t . One i s the use o f a remote b a t c h t e r m i n a l . More i m p o r t a n t l y , i t may soon be p o s s i b l e t o use network c o n n e c t i o n s t o reduce the problems a s s o c i a t e d w i t h the communication l i n k — s p e e d and c o s t . Most networks now e x t a n t o p e r a t e a t 4800-50,000B, comp a r e d t o our 110-300B t e l e t y p e t r a n s m i s s i o n r a t e (35.) . In our p a r t i c u l a r case t h e c a l l t o WPAFB from ANL c o u l d go o v e r the ARPANET a t 50 K/B i n about a y e a r from t h i s w r i t i n g , when the computer c e n t e r s a t b o t h s i t e s have become f u l l y o p e r a t i o n a l nodes on t h i s network. See F i g u r e 8. I t i s i m p o r t a n t t o note t h a t , so f a r as our p r o j e c t i s concerned, the communication c o s t s w i l l be n e g l i g i b l e s i n c e the phone c a l l would be t o a network node w i t h i n a l o c a l c a l l r a d i u s . A n o t h e r p o s s i b l e f u t u r e s o l u t i o n t o the communicat i o n speed problem would be t o engage the s e r v i c e s o f one o f t h e commercial companies now g o i n g i n t o the s o l e b u s i n e s s o f e s t a b l i s h i n g and p r o v i d i n g h i g h speed (50, 230, 1300 K/B), low u n d e t e c t e d e r r o r r a t e (1 i n 1 0 b i t s ) , d a t a t r a n s m i s s i o n c o n d u i t s over s p e c i a l ground l i n e s and by microwave and s a t e l l i t e t r a n s m i s s i o n (35.) · The e x p a n s i o n o f networks and the i n c r e a s e d a v a i l a b i l i t y o f h i g h speed d a t a communication s e r v i c e s o v e r the n e x t few y e a r s s h o u l d combine t o i n c r e a s e the speed w h i l e d e c r e a s i n g t h e c o s t . The l i m i t t o the maximum u s a b l e t r a n s m i s s i o n r a t e w i l l then become the t e r m i n a l and t e r m i n a l - t o - n o d e t r a n s m i s s i o n speed r a t h e r t h a n t h e c a p a c i t y and q u a l i t y o f the l o n g d i s t a n c e t r a n s m i s s i o n link. I t i s , t h u s , a p p r o p r i a t e t o a n t i c i p a t e the development o f h i g h - s p e e d r a d i o - t e r m i n a l s t o complete the s o l u t i o n t o t h e p r e s e n t day d a t a communication b o t t l e n e c k t o our t y p e o f d a t a p r o c e s s i n g a p p l i c a t i o n . 1 2
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch011
Figure 7(a). JCCRGEN—Example 2. (a) Depiction of an input job, formulated on an interactive terminal using the EDITOR mode of CDC6600 INTERCOM, which employs JCCRGEN commands to retrieve an archived file from tape and produce a copy on disk. The latter is then available for perusal or editing to produce an input deck via the EDITOR mode.
PAUSE. THIS JOB IS FROM A REMOTE TERMINAL (E.G.TTY). PAUSE. PLEASE GET MY TAPES FROM THE LIBRARY. REQUEST,MFN1,MF,VSN=L 00002,NORING. LABEL,TAPE,R,L=NNOB4 3P111X1SIP. REQUEST,DISK,*PF. COPYBF,TAPE,DISK. CATALOG,DISK,DHWORKFILE,CY=1,RP=9 9 9. Figure 7(b).
Figure 8. ARPA network and the proposed "piggy-back" AFSC test network.
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The f u t u r e i n s t a l l a t i o n and maintenance o f codes a t WPAFB on t h i s p r o j e c t might be performed e n t i r e l y remotely. There a r e two ways we a n t i c i p a t e t h a t we might go about t h i s : (a) w i t h a remote t e r m i n a l e q u i p ped w i t h a c a r d r e a d e r and an i n i t i a l s o u r c e deck on p h y s i c a l c a r d s , o r (b) w i t h an i n t e r a c t i v e t e r m i n a l equipped w i t h , e.g., tape c a s s e t t e s and an i n i t i a l r e c o r d i n g (over perhaps s e v e r a l c a s s e t t e s ) o f the p r o gram.* I t i s p e r t i n e n t i n t h i s r e g a r d t o note t h a t 120,000-240,000 c h a r a c t e r s may be c o n t a i n e d on one tape c a s s e t t e , depending on t h e r e c o r d i n g mode. Thus, the e n t i r e BISONMC s o u r c e code c o u l d be c o n t a i n e d on s i x o r t h r e e c a s s e t t e s , a g a i n depending on the r e c o r d i n g mode. F u t u r e P l a n s — A i r F o r c e Systems Command Network. The development o f the ASD Computer C e n t e r a t W r i g h t P a t t e r s o n AFB i s , o f c o u r s e , c o n t i n u i n g , i n o r d e r t o e s t a b l i s h c a p a b i l i t i e s beyond t h o s e a l r e a d y d e s c r i b e d . D u r i n g the p a s t two y e a r s , the A i r F o r c e Systems Command has been c o n s i d e r i n g p r o c e d u r e s t o l i n k the comp u t e r s a t i t s v a r i o u s t e c h n i c a l c e n t e r s l o c a t e d throughout the c o u n t r y . The major m o t i v a t i o n i s t o p e r m i t r e s o u r c e s h a r i n g between e q u i v a l e n t computers. Several s t u d i e s o f the b e s t methods t o e f f e c t t h i s l i n k i n g were commissioned by SADPR-85 (the Support o f A i r F o r c e A u t o m a t i c D i g i t a l P r o c e s s i n g Requirements M i s s i o n A n a l y s i s f o r 1985). In December 1974, i t was proposed t h a t a t e s t network (AFSCNET), c o n s i s t i n g o f the comput e r c e n t e r s a t E g l i n , K i r t l a n d , and W r i g h t - P a t t e r s o n A i r F o r c e Bases be s e t up t o r i d e p i g g y - b a c k on the ARPA network (ARPANET). See F i g u r e 8. The ARPA network was d e v e l o p e d by the Bolt-BaranekNewman Co. under a c o n t r a c t from the Advanced R e s e a r c h P r o j e c t s Agency m o n i t o r e d by the A i r F o r c e Systems Command (6, 8, 9, 38-41). From the f i r s t f o u r nodes (U.C. - S a n t a B a r b a r a , U n i v e r s i t y o f Utah, S t a n d f o r d R e s e a r c h I n s t . , UCLA) i n about 1968-9 the network has expanded r a p i d l y so t h a t by 1973-4 about 47-48 u n i v e r s i t y and *The ANL-WPAFB l o n g d i s t a n c e phone b i l l f o r a 5000 c a r d source deck would be on the o r d e r o f $10 a t 2400B o r $5 a t 4800B, b u t p r o h i b i t i v e a t lower speeds. A c a l l on the ARPANET would be l o c a l and t e r m i n a l - l i m i t e d i n speed. **A " P h i l i p s - t y p e " c a s s e t t e which c o n t a i n s 300 f e e t o f 0.15-inch-wide magnetic tape w i t h s e r i a l d a t a r e c o r d i n g a t 47 c h a r a c t e r s / i n c h and i n t e r - r e c o r d gaps o f 2.2 i n c h e s has a s t o r a g e c a p a c i t y o f 483 256-character r e c o r d s f o r a t o t a l o f 123,648 c h a r a c t e r s (35.)· Twot r a c k r e c o r d i n g a l l o w s 246,296 c h a r a c t e r s / c a s s e t t e .
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government s i t e s were i n t e r c o n n e c t e d . See F i g u r e 8. The ARPANET was e s t a b l i s h e d as an e x p e r i m e n t a l , n o t an o p e r a t i o n a l , network. However, w i t h i t s t r a n s i t i o n from ARPA s u p p o r t , i t seems t o be becoming more o p e r a t i o n a l l y o r i e n t e d . The proposed AFSCNET i s an example. Each node on the proposed AFSCNET c u r r e n t l y p o s s e s s e s a p a i r o f CDC6600's o r e q u i v a l e n t machines ( i . e . CYBER73). The p l a n i s t o employ a PDP-11 t o cont r o l the f l o w o f j o b s between the network and the ons i t e computers on the one hand, and between the h a r d w i r e d b a t c h t e r m i n a l s (CDC1700's) and the o n - s i t e comp u t e r s o r the network on the o t h e r . See F i g u r e 9. It i s e x p e c t e d t h a t an IBM 370 can be i n c l u d e d by d i r e c t c o u p l i n g t o the CDC6600 as w e l l as t o the PDP11. The a c q u i s i t i o n o f an IBM 370/155 i s c u r r e n t l y under s t u d y . I n t e r a c t i v e t e r m i n a l a c c e s s a t 110, 300, and 1200B i s t o be p r o v i d e d t o a l l o n - s i t e computers and t o remote u s e r s through the network. Remote b a t c h t e r m i n a l s o p e r a t i n g a t 2 K/B and 4.8 K/B a r e e x p e c t e d t o have a c c e s s t o a CDC6600 and t h r o u g h i t t o o t h e r computers o n - s i t e and on AFSCNET. In about one y e a r enough components o f the system s h o u l d be completed t o e n a b l e s h a r i n g o f work-load o v e r f l o w among the CDC6600's a t the t h r e e A i r F o r c e bases i n the t e s t network. By t h a t time t o o , Argonne N a t i o n a l L a b o r a t o r y w i l l be i n o p e r a t i o n on the ARPANET so t h a t i t might be — a t l e a s t i n t h e o r y — p o s s i b l e t o p e r f o r m c a l c u l a t i o n s on the W r i g h t - P a t t e r s o n comput e r s by complete remote o p e r a t i o n from Argonne. Few s i t e v i s i t s s h o u l d then be r e q u i r e d and t h i s c o u l d l e a d t o the e s t a b l i s h m e n t o f a network i n c o m p u t a t i o n a l c h e m i s t r y o f enormous power and v e r s a t i l i t y . C o n c l u d i n g Remark. I t i s r e a l i s t i c , we t h i n k , t o e x p e c t t h a t the now-developing e x p e r t i s e i n the remote e x e c u t i o n o f p r o d u c t i o n runs o f s o p h i s t i c a t e d codes w i l l make t h i s a c t i v i t y common p l a c e . Much work remains t o be done, but i t seems l i k e l y t h a t t h i s development c o u l d be h i g h l y u s e f u l t o the r e s e a r c h e r who may o n l y upon o c c a s i o n need t o execute a s e t o f quantum-chemical, s c a t t e r i n g , k i n e t i c , o r other type of c a l c u l a t i o n s i n c o n n e c t i o n w i t h h i s major r e s e a r c h a c t i v i t i e s . This development w i l l make t h e s o p h i s t i c a t e d i n s t r u m e n t s o f c o m p u t a t i o n a l c h e m i s t r y a c c e s s i b l e t o the average l a b o r a t o r y o r o f f i c e and t o the f i n g e r - t i p s o f v i r t u a l l y every chemist.
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Figure 9. Example diagram for the proposed AFSC network test sites at Eglin, Kirtland, and Wright-Patterson Air Force Base.
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Acknowledgements We thank Mr. Demetrius C. Zonars of the Aeronautical Systems Division Computer Center, Air Force Systems Command, Wright-Patterson Air Force Base, for providing us with the cronology of computational equipment and contractor usage. Dr. Paul Nicolai of the Mathematical Research Laboratory, Aerospace Research Laboratory, Air Force Systems Command, Wright-Patterson Air Force Base, provided the information on the Wright-Patterson role in the ARPANET and the plans for an AFSC network. Dr. Paul Messina of the Applied Mathematics Division, Argonne National Laboratory, provided the information concerning Argonne s participation in the ARPANET. Dr. Nicolai and the open shop personnel at the ASD Computer Center, Mr. Jim Bittle and Mr. Jim Hudson in particular, have aided our remote usage effort tremendously in discussion of the details of implementing our IBM codes on the CDC6600 and in obtaining solutions to routine operating problems. Much of the preliminary work in establishing our remote usage procedures was performed by Dr. Richard P. Hosteny. Dr. Richard J . Blint aided in the establishment of the Utah connection. We thank Dr. Bob Euwema of the theoretical solid-state group, Aerospace Research Laboratories, Air Force Systems Command, Wright-Patterson AFB, for permitting us to quote from his letter from Dr. S. Huzinaga of the University of Alberta, Canada and for answering our numerous questions about running sophisticated codes on the CDC6600.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch011
1
Abstract A historical perspective of quantum chemical c a l culations, starting with the master integrals-SCF codes constructed and extensively employed on-site at Wright-Patterson AFB on the Univac 1103 during the approximate period 1956-1961 and evolving to our current remote usage, is sketched. These two decades of experience at Wright-Patterson provide a currently developing example of computer resource sharing directly related to chemistry. Procedures have been devised for the execution of ab i n i t i o quantum mechanical computations from a remote interactive terminal. Most of the procedural and software tactics apply to the execution of such calculations from a remote batch terminal as well. While the optimun - and most expensive - situation is to have both interactive and batch terminals available along with a high speed data link to a computer, a simple teletype u t i l i z i n g regular phone lines is quite sufficient to
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engage i n t h i s a c t i v i t y if the user i s properly organ ized on the host computer. Our experience with such remote usage i s discussed. L i t e r a t u r e Cited
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1.
Karo, Α . , Krauss, Μ., and Wahl, A. C., Int. J. Quantum Chem. (1973) 75, 143. 2. Schaefer, H. F., "The E l e c t r o n i c Structure of Atoms and Molecules; A Survey of Rigorous Quantum Mechanical Results," Addison-Wesley, Reading, Mass., 1972. 3. For example, the Quantum Chemistry Program Ex change, U n i v e r s i t y of Indiana, Bloomington, Indiana, now has broaden its scope to the c o l l e c t i o n and d i s t r i b u t i o n of computer codes i n all areas of com putational chemistry. QCPE i s beginning to perform some service c a l c u l a t i o n s as w e l l . 4. H a l l , G. G., Chem. Soc. Rev. (1973) 2, 21. 5. The term "interactive" (or, equivalent, "time -sharing") terminal i s taken to mean asynchronous transmission at 110B, 300B, 1200B, e t c . The term "batch terminal" i s taken here to mean a terminal capable of synchronous transmission at 2 K/B or 4.8 K/B over normal voice grade phone l i n e s . The ad j e c t i v e "remote" i s taken to imply access from off - s i t e throughout t h i s paper. The "host computer" i s understood to be o f f the premises of the user's institution. 6. Peterson, J. J. and V e i t , S. Α . , "Survey of Compu ter Networks," The MITRE C o r p . , September, 1971. A v a i l a b l e from the National Technical Information Service, U. S. Department of Commerce, S p r i n g f i e l d , V i r g i n i a 22151. 7. Greenberger, Μ., Aronofsky, J., McKenney, J. L., and Massy, W. F., "Networks for Research and Edu cation - Sharing Computer and Information Resources Nationwide," MIT Press, Cambridge, Mass., 1974. 8. Bouknight, W. J., Grossman, G. R . , and Grothe, D. Μ., "The ARPA Network Terminal System - A New Approach to Network Access," Proc. Data Communica tions '73, Nov. 1973. 9. Sher, M. S . , "A Case Study i n Networking", Datama t i o n (1974) March, 56-59. 10. This h i s t o r y i s constructed mainly from the "Intro duction to ASD Computer Center", Wright-Patterson A i r Force Base, Ohio, May, 1974 and from material furnished by Mr. D. Zonars and Dr. P. N i c o l a i at Wright-Patterson.
11.HOPPERETAL.Calculations via Remote Terminal 11. 12. 13. 14. 15. 16. 17. 18. Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch011
19. 20. 21. 22. 23. 24.
25.
26. 27.
28. 29.
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Readers Digest 1975 Almanac and Yearbook, The Reader's Digest Association, Inc., Pleasantville, New York, 1975. Ransil, B. J., Revs. Mod. Phys. (1960) 32, 239. Ransil, B. J., Revs. Mod. Phys. (1960) 32, 245. McLean, A. D . , Weiss, Α . , and Yoshimine, Μ., Revs. Mod. Phys. (1960) 32, 211. Kolos, W. and Roothaan, C. C. J., Revs. Mod. Phys. (1960) 32, 219. Kolos, W. and Roothaan, C. C. J., Revs. Mod. Phys. (1960) 32, 219. Richardson, J. W., Revs. Mod. Phys. (1960) 32, 461. Kolos, W., Roothaan, C. C. J., and Sack, R. A. Revs. Mod. Phys. (1960) 32, 178. Roothaan, C. C. J., Revs. Mod. Phys. (1960) 32, 179. Roothaan, C. C. J., and Weiss, A. W., Revs. Mod. Phys. (1960) 32, 194. Fraga, S. and Mulliken, R. S., Revs. Mod. Phys. (1960) 32, 254. Fröman, Α . , Revs. Mod. Phys. (1960) 32, 317. Löwdin, P. O., Revs. Mod. Phys. (1960) 32, 328. Wahl, A. C., Bertoncini, P . , Kaiser, Κ., and Land, R. H . , "BISON - A Fortran Computer System for the Calculation of Analytic Self-Consistent-Field Wavefunctions, Properties, and Charge Densities for Diatomic Molecules: Part 1. User's Manual and General Program Description," Argonne National Laboratory Report ANL-7271 (January, 1968). For availability see Ref. 6. Das, G. and Wahl, A. C., "BISON-MC: A FORTRAN Computing System for Multiconfigurational Self -Consistent-Field (MCSCF) Calculations on Atoms, Diatoms, and Polyatoms," Argonne National Labora tory Report ANL-7955 (July, 1972). For avail a b i l i t y see Ref. 6. DASCI is a small (100) configuration interaction program written by G. Das, Argonne National Labor atory for use with BISON-MC. Neuman, D . , et al., "POLYATOM (Version 2)," Bell Labs. Rep.; PA300 was modified and linked to BISON -MC by A. Hinds, Argonne National Laboratory; we refer to this modified version, which generates canonical l i s t s of integrals and no labels, as POLYINT. Das, G. and Wahl, A. C., J. Chem. Phys. (1972) 56, 1769. See also Ref. 1. Hosteny, R. P . , Hinds, A. R., Wahl, A. C., and Krauss, Μ., Chem. Phys. Letters (1973) 23, 9.
182 30. 31.
32. 33.
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34.
35. 36. 37.
38.
39. 40.
41.
COMPUTER NETWORKING AND CHEMISTRY Hopper, D. G . , Chem. Phys. Letters (1975) 31, 446. Fortune, P. J., Rosenberg, B. J., Das, G . , and Wahl, A. C . , Abstracts of the Eighth Midwest Theoretical Chemistry Conference, University of Wisconsin, Madison (May 1975) 8, 26. See, e.g., Smith, W. D., Chen, T. T . , and Simons, J., J. Chem. Phys. (1974) 61, 2670. Krauss, Μ., Hopper, D. G . , Hosteny, R. P . , Fortune, P. J., Wahl, A. C . , and Tiernan, Τ. Ο., "Potential Energy Surfaces for Atmospheric Triatomic Mole cules. I. Literature Review," ARL Tech. Rep., June, 1975. For availability see Ref. 6. Fortune, P. J., Hopper, D. G . , Rosenberg, B. J., England, W. Β . , Gillespie, G . , Hosteny, R. P . , Das, G . , Wahl, A. C . , and Tiernan, T. O., "Poten tial Energy Surfaces of Atmospheric Triatomic Molecules. II. Results of SCF and Preliminary OVC-MCSCF-CI Calculations," ARL Tech. Rep., June 1975, and references therein. Availability -- Ref. 6. "Datapro 70, the EDP Buyer's Bible," Datapro Research Corporation, Morris Town, N. J., 1972, and updates through 1975. Carter, C . , "Guide to Reference Sources in the Computer Sciences," MacMillan Information, MacMillan Publishing Co., Ν. Y . , 1974. Harris, F. Ε. and Ault, R. H . , "Abstracts of the 169th ACS National Meeting," paper COMP30, Amer. Chem. Soc., Washington, 1975, have discussed, for another type of computer, software ideas similar to some of ours. Heart, F. E., Kahn, R. E., Ornstein, S. Μ., and Crowther, W. R. and Walden, D. C . , Proc. SJCC '70 (1970), 551. Description of the ARPANET IMP (Interface Message Processor). McQuillan, J. Μ., Crowther, W. R., Cosell, B. P . , Walden, D. C . , and Heart, F. E., Proc. FJCC '72 (1972), 741. ARPA improvements. Ornstein, S. Μ., Heart, F. Ε . , Crowther, W. R., Rising, H. K . , Russell, S. Β . , and Michel, Α . , Proc. SJCC '72 (1972), 243. Description of the ARPANET TIP - terminal IMP. McKenzie, Α. Α . , Cosell, B. P . , McQuillan, J. Μ., and Thorpe, M. J., Proc. ICCC '72 (1972), 185. Description of an ARPANET control center.
12
C o m p u t e r Identification a n d I n t e r p r e t a t i o n o f U n k n o w n M a s s Spectra U t i l i z i n g a C o m p u t e r N e t w o r k System
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch012
R. VENKATARAGHAVAN, GAIL M. PESYNA, and F. W. McLAFFERTY Department of Chemistry, Cornell University, Ithaca, Ν. Y. 14850 Mass spectrometry/computer systems in routine use in many research laboratories are capable of producing a complete mass spectrum (unit resolution) every few seconds (1, 2). The unique applicability of mass spectrometry to nanogram samples, and the ability to obtain spectra directly on components of com plex mixtures separated by a gas (3) or liquid chromatograph (4) have tremendously increased the number of spectra taken for the purpose of compound identification. These capabilities have provided unique solutions to research and control problems in a wide variety of fields, including environmental pollution, metabo lism studies, medical diagnoses, insect pheromones, forensic analyses, military detection systems, and conversion of coal or shale to liquid fuels. The importance of these applications has motivated a large increase in basic research in organic mass spectrometry, greatly expanding our knowledge of mass spectral fragmentation behavior. Unfortunately, the quantity (and quality) of chemists trained in the interpretation of mass spectra has not increased as rapidly, and thus the interpretation process is becoming an in creasingly serious bottleneck in proper utilization of this tech nique. The modern computer is an obvious possibility to alleviate these problems, and a number of computer systems for identifica tion and interpretation have been proposed (i, 2, 5-13). If a reference mass spectrum of the unknown compound is in the data file, computer matching programs can be used for its retrieval. Although such retrieval is relatively efficient, the present mass spectral reference file (14/15) of 30/000 different compounds represents a very small fraction of the possible organic com pounds, so that interpretation is required whenever a poor match is obtained. Thus both "retrieval" and "interpretive" systems are necessary to solve problems in most important areas. These systems have been reviewed in detail recently 2, 5); here we will only describe the Cornell systems which are now available over a computer networking system (TYMNET). 183
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P B M . A " P r o b a b i l i t y B a s e d M a t c h i n g " s y s t e m for the r e t r i e v a l of unknown mass s p e c t r a has r e c e n t l y b e e n d e s c r i b e d (12, 13). R e s e a r c h i n the area of document and information r e t r i e v a l has f i r m l y e s t a b l i s h e d that s y s t e m e f f i c i e n c y i s i n c r e a s e d by the proper w e i g h t i n g of the r e l a t i v e importance of items u s e d for i d e n t i f y i n g e a c h member of a l i b r a r y (16). For P B M the m/e v a l u e s of the p e a k s are w e i g h t e d a c c o r d i n g to t h e i r u n i q u e n e s s i n the f i l e , and the abundance v a l u e s are w e i g h t e d a c c o r d i n g to a l o g normal d i s t r i b u t i o n (17). The u s e of t h e s e v a l u e s i s b a s e d u p o n the " G e n e r a l Rule of M u l t i p l i c a t i o n " of p r o b a b i l i t y theory; thus i f p e a k s w i t h m a s s e s m^ and rn_2 h a v i n g i n t e n s i t i e s j . ^ and_i2 o c c u r i n mass s p e c t r a w i t h p r o b a b i l i t i e s χ>ι and £2 / p r o b a b i l i t y that both o c c u r at random i n an unknown spectrum i s ρ χ times P2 · product i s s m a l l , i t i s much more l i k e l y that the p r e s e n c e of p e a k s m i and rn_2 i s due to the i d e n t i t y of the unknown spectrum and the compared reference spectrum i n w h i c h both o c c u r w i t h the i n t e n s i t i e s J.j a n d j . ^ . The low v a l u e of t h i s p r o b a b i l i t y p r o v i d e s a c o n f i d e n c e that this i d e n t i f i c a t i o n i s c o r r e c t , w h i c h i s measured b y a " c o n f i d e n c e v a l u e , K " . This m e a s u r e , as w e l l as a l l the i n d i v i d u a l p r o b a b i l i t i e s , i s e x p r e s s e d as the c o r r e s p o n d i n g b a s e two logarithm for c o n v e n i e n c e of c a l c u l a t i o n ; i n v e r s e p r o b a b i l i t i e s are a l s o u s e d to s i m p l i f y the c a l c u l a t i o n s and to produce a f i n a l r e s u l t w h i c h i s a d i r e c t measure of " c o n f i d e n c e . " In t h i s r e v e r s e s e a r c h , there i s computed for e a c h reference spectrum matched a g a i n s t the unknown a c o n f i d e n c e v a l u e , " K " , e q u a l to the sum of the i n d i v i d u a l Kj v a l u e s c a l c u l a t e d for e a c h peak i n the u n known w h o s e i n t e n s i t y agrees w i t h i n a predetermined range to that of the c o r r e s p o n d i n g peak i n the reference s p e c t r u m . K. c o m b i n e s four t e r m s , t
n
e
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I f
t
n
i
s
K. = U . + A. + W . - D 3 J 3 3 where U i s the c o n t r i b u t i o n to the p r o b a b i l i t y of the " u n i q u e n e s s " of the m/e v a l u e of the peak; A i s the c o n t r i b u t i o n to the p r o b a b i l i t y of the abundance v a l u e of the peak as i t appears i n the reference spectrum; W , the " w i n d o w f a c t o r " , i s a measure of the agreement required between the abundance of the peak i n the r e f erence and i n the unknown; and D , the " d i l u t i o n f a c t o r " for m i x ture s p e c t r a , i s a measure of the o v e r a l l r e d u c t i o n of peak i n t e n s i t i e s i n the unknown due to the p r e s e n c e of other components (if the unknown spectrum i s of a pure c o m p o u n d , D = 0). The s y s t e m i s d e s c r i b e d i n d e t a i l e l s e w h e r e (13). E x t e n s i v e s t a t i s t i c a l s t u d i e s have shown (13) that the p r e c i s i o n / r e c a l l performance of the s y s t e m i s s u b s t a n t i a l l y better than others w h i c h employ no or l i m i t e d w e i g h t i n g . The " r e v e r s e s e a r c h " feature i s e s p e c i a l l y v a l u a b l e w i t h m i x t u r e s , as i l l u s trated by r e s u l t s from the m a s s spectrum of a mixture shown i n Table I. The mixture c o n t a i n e d amobarbital ( 5 - e t h y l - 5 - i s o a m y l -
5 -ethyl-5 - i s o a m y l barbituric a c i d (amobarbital, amytal)
b
a
C o m p o u n d s s e l e c t e d of h i g h e s t Κ v a l u e s from a data b a s e of 3 5 , 8 2 8 s p e c t r a . M u l t i p l e v a l u e s represent different s p e c t r a of the same compound; the a s t e r i s k s i n d i c a t e the number of " f l a g g e d " p e a k s (see text) omitted i n c a l c u l a t i n g that Κ v a l u e , and the p l u s s i g n i n d i c a t e s that the m o l e c u l a r i o n of the reference w a s found i n the unknown and u s e d i n the Κ c a l c u l a t i o n .
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barbituric a c i d ) , hexobarbital ( 5 - c y c l o h e x e n y l - l , 5 - d i m e t h y l b a r b i t u r i c a c i d ) , and n i c o t i n e . P B M has s u c c e s s f u l l y retrieved a r e l a t i v e l y large number of s p e c t r a of the c o r r e c t c o m p o u n d s , measured under a w i d e v a r i e t y of c o n d i t i o n s , without r e t r i e v i n g a s i n g l e i n c o r r e c t compound of comparable Κ v a l u e . The m a s s spectrum of p e n t o b a r b i t a l , the s e c - a m y l i s o m e r of the f i r s t c o m p o u n d , i s c l o s e l y s i m i l a r to that of a m o b a r b i t a l , so that the s e l e c t i v i t y e x h i b i t e d by P B M i n this c a s e , d e s p i t e the p r e s e n c e of a s e c o n d b a r b i t u r a t e , i s g r a t i f y i n g . STIRS. F o r the " S e l f - T r a i n i n g Interpretive and R e t r i e v a l S y s t e m " (11) a number of c l a s s e s of mass s p e c t r a l data known to h a v e h i g h structural s i g n i f i c a n c e , s u c h as c h a r a c t e r i s t i c i o n s , s e r i e s of i o n s , and m a s s e s of neutrals l o s t , are i d e n t i f i e d ; for e a c h c l a s s the computer m a t c h e s the data of the unknown m a s s spectrum a g a i n s t the c o r r e s p o n d i n g data of a l l reference s p e c t r a . In e a c h data c l a s s the reference compounds w h o s e s p e c t r a have the h i g h e s t " m a t c h - f a c t o r " (MF) v a l u e s are examined by the c h e m i s t for any common structural f e a t u r e s , w i t h a h i g h f r e q u e n c y of o c c u r r e n c e i n d i c a t i n g a h i g h p r o b a b i l i t y that the structural feature i s present i n the u n k n o w n . In a recent m o d i f i c a t i o n (18) the 15 s e l e c t e d compounds of h i g h e s t M F v a l u e are examined i n s t e a d by the computer for the p r e s e n c e of s p e c i f i c s u b s t r u c t u r a l groups to p r o v i d e a s t a t i s t i c a l e v a l u a t i o n of the p r o b a b i l i t y of the p r e s e n c e of e a c h group i n the unknown c o m p o u n d . At present STIRS i s a b l e to p r e d i c t the p r e s e n c e of 179 substructures at the 98 percent c o n f i d e n c e l e v e l w i t h an a v e r a g e r e c a l l of 49 percent ( i . e . , u s i n g c r i t e r i a i n w h i c h STIRS i s wrong o n l y o n c e i n 50 t i m e s , the substructure c a n be i d e n t i f i e d i n h a l f of the compounds i n w h i c h it i s a c t u a l l y p r e s e n t ) . B e c a u s e of the nature of mass s p e c t r a we do not have STIRS attempt to p r e d i c t the a b s e n c e of a substructure; the i n f l u e n c e of a p a r t i c u l a r substructure o n the m a s s s p e c t r a l b e h a v i o r c a n be greatly r e d u c e d by the p r e s e n c e i n the m o l e c u l e of another substructure w h i c h more strongly d i r e c t s the f r a g m e n t a t i o n . Structural data for a l l compounds i n the reference f i l e have b e e n c o d e d i n W i s w e s s e r L i n e N o t a t i o n ( W L N ) , w h i c h i s a l i n e a r r e p r e s e n t a t i o n of the c o m p o u n d ' s structure r e q u i r i n g a r e l a t i v e l y s m a l l v o l u m e of computer s t o r a g e . In W L N , s y m b o l s s u c h as 1, R, Μ , Ζ , V are u s e d to represent i n d i v i d u a l c h e m i c a l units s u c h as - C H - , C 6 H 5 , ^ N H , -NH2, g respectivesc o n n e c t i o n transfers are u s e d to show breaks from l i n e a r r e p r e s e n t a t i o n , ring units to show the p r e s e n c e of rings i n the s t r u c t u r e , and ring f u s i o n u n i t s to show ring i n t e r r e l a t i o n s i n a m u l t i c y c l i c s y s t e m . In c o m p a r i s o n to other modes of structure r e p r e s e n t a t i o n , W L N has s e v e r a l s p e c i a l advantages for the interpretation of m a s s s p e c t r a l d a t a . In an a c y c l i c s y s t e m the l i n e a r notation i s u s e f u l i n i d e n t i f y i n g fragmentations r e s u l t i n g from s i m p l e c l e a v a g e s , the c h e m i c a l units of W L N often b e i n g d i r e c t l y related to m a s s e s and mass d i f f e r e n c e s i n the s p e c t r u m . 2
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The p r e s e n c e of c e r t a i n c h e m i c a l units s u c h as V (carbonyl) and Ζ (primary amino) c a n exert a strong i n f l u e n c e on the f r a g m e n t a t i o n b e h a v i o r of the m o l e c u l e and c a n thus be r e a d i l y u s e d for the i d e n t i f i c a t i o n and a s s i g n m e n t of e l e m e n t a l c o m p o s i t i o n s to different i o n s . D e v i a t i o n s from structural l i n e a r i t y are d e s i g n a t e d c l e a r l y i n the notation by c o n n e c t i o n t r a n s f e r s , and c a n thus be r e c o g n i z e d by the computer s y s t e m to relate p o i n t s of b r a n c h i n g and s u b s t i t u t i o n i n a m o l e c u l e to m a s s s p e c t r a l c l e a v a g e s c o m monly triggered by s u c h structural f e a t u r e s . Complex c y c l i c m o l e c u l e s are among the most d i f f i c u l t types of structures for mass s p e c t r a l interpretation; the a b i l i t y of W L N to represent the r e l a t i o n s h i p s of different rings and s u b s t i t u e n t s w i t h i n the s t r u c ture often makes it p o s s i b l e for the computer to r e c o g n i z e major fragmentations and to d e v e l o p s p e c t r a - s t r u c t u r e c o r r e l a t i o n s . As an example (11), running the spectrum of c h o l e s t e r o l as an " u n k n o w n " , STIRS for match f a c t o r 5 s e l e c t e d neutral l o s s e s of 18, 0 ( M t ) 33, 15, 17, and 61; the s i x compounds found w i t h the h i g h e s t M F 5 v a l u e s are the s t e r o i d a l d e r i v a t i v e s a l l o p r e g n a n o l 3 a - o n e - 2 0 , pregnenolone a l c o h o l , p r e g n e n o l o n e , 7 β - h y d r o x y c h o l e s t a n y l 3 p - a c e t a t e , 1 6 a - m e t h y l p r e g n e n o l o n e (a large number of of other oxygenated c a r b o c y c l i c compounds are present i n the data b a s e ) . Although the l o s s of t h e s e s i m p l e neutral s p e c i e s from c h o l e s t e r o l i s quite c o n s i s t e n t w i t h present k n o w l e d g e of the m a s s s p e c t r a l b e h a v i o r of s u c h m o l e c u l e s , i t i s doubtful that t h e s e l o s s e s were known to be c h a r a c t e r i s t i c of s u c h m o l e c u l e s . /
The " A r t i f i c i a l I n t e l l i g e n c e " (9) method u s e s the computer to a p p l y human m a s s s p e c t r a l k n o w l e d g e to p r e d i c t s p e c t r a of i s o m e r i c p o s s i b i l i t i e s . As far as p o s s i b l e a l l of the known m a s s s p e c t r a l fragmentation b e h a v i o r i s programmed into the computer, and then the mass s p e c t r a of f e a s i b l e i s o m e r s (the p o s s i b i l i t i e s are generated by the D E N D R A L algorithm) are p r e d i c t e d and c o m pared to the unknown m a s s s p e c t r u m . This demands that the unknown compound be i n the rather narrow c l a s s for w h i c h the program i s written and that its e l e m e n t a l c o m p o s i t i o n has b e e n e s t a b l i s h e d . A n A r t i f i c i a l I n t e l l i g e n c e program for estrogens (10) appears to be the o n l y one that has b e e n t e s t e d e x t e n s i v e l y o n true u n k n o w n s . STIRS i s complementary to the " A r t i f i c a l I n t e l l i g e n c e " t e c h n i q u e i n that it c a n be a p p l i e d to the s p e c t r a of total unknowns (such as p o l l u t a n t s , i n s e c t s e c r e t i o n s , and abnormal urinary constituents) to o b t a i n p a r t i a l structural i n f o r m a t i o n . For e x a m p l e , STIRS i n g e n e r a l c a n e a s i l y i d e n t i f y estrogens and often some of the substitutents t h e r e o n , but the A r t i f i c i a l I n t e l l i g e n c e method i s s u p e r i o r for properly p l a c i n g the s u b s t i t u e n t s and e l u c i d a t i n g other structural d e t a i l s . STIRS u t i l i z e s d i r e c t l y the information of a l l a v a i l a b l e reference s p e c t r a without prior s p e c t r a - s t r u c t u r e c o r r e l a t i o n , " t r a i n i n g " i t s e l f s e p a r a t e l y for e a c h submitted unknown spectrum; thus the o n l y s p e c i a l p r e p a r a t i o n n e c e s s a r y to make STIRS s e n s i t i v e for estrogens i s to make sure that there are r e p r e s e n t a t i v e m a s s s p e c t r a of e s t r o g e n s i n the reference data b a s e .
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C h e m i s t s sometimes forget the p o t e n t i a l c o m p l e x i t y of the problem of determining the e x a c t m o l e c u l a r structure of a new compound of a m o l e c u l a r weight of e v e n a f e w h u n d r e d . Although a r e l a t i v e l y s m a l l amount of information u s u a l l y c a n greatly reduce the m i l l i o n s of p o s s i b i l i t i e s ( b i l l i o n s i f l e s s common elements are i n c l u d e d ) , the effort required to narrow the p o s s i b i l i t i e s further u s u a l l y i n c r e a s e s e x p o n e n t i a l l y . Thus s c i e n c e c a n o n l y afford the luxury of determining the e x a c t m o l e c u l a r structure of a new unknown compound for s p e c i a l c a s e s . Knowledge of e v e n a f e w of the g r o s s structural features o f t e n i s enough to t e l l the s c i e n t i s t that the compound i s not germane to h i s i n v e s t i g a t i o n — f o r e x a m p l e , that i t i s p r o b a b l y n o n - t o x i c , s h o u l d not show the d e s i r e d p h a r m a c o l o g i c a l a c t i v i t y , or i s not a l o g i c a l metabolite of the drug u s e d . O u t s i d e U s e of STIRS and P B M . STIRS h a s b e e n a v a i l a b l e free to o u t s i d e u s e r s s i n c e January 1974 through a p h o n e l i n e l i n k to our laboratory P D P - 1 1 / 4 5 , and has b e e n u s e d at a rate of ~100 unknown s p e c t r a per month for a s u b s t a n t i a l part of t h i s t i m e . This i n d i c a t e d that STIRS w a s u n i q u e l y meeting a r e a l s c i e n t i f i c n e e d , but a l s o showed that a v e r y s u b s t a n t i a l proportion of the unknowns s h o u l d have been examined f i r s t b y a r e t r i e v a l s y s t e m . This l e d to implementing both P B M and STIRS o n the C o r n e l l I B M 370/168 to make them a v a i l a b l e i n t e r n a t i o n a l l y o v e r the T Y M N E T computer network s y s t e m . This s y s t e m has the further advantage that i t employ s a data b a s e that currently h a s approximately 4 0 , 0 0 0 m a s s spectra of 3 0 , 0 0 0 d i f f e r e n t compounds (15) w h i c h , to our k n o w l e d g e , i s larger than any other a v a i l a b l e c o l l e c t i o n . The C o r n e l l PBM/STIRS s y s t e m became o p e r a t i o n a l o n T Y M N E T i n M a y 1975 and the i n i t i a l r e s p o n s e h a s b e e n e n c o u r a g ing. The programs appear to be u s e d i n a complementary f a s h i o n ; if P B M cannot i d e n t i f y the unknown m a s s spectrum as a compound a l r e a d y i n the reference f i l e at a s a t i s f a c t o r y c o n f i d e n c e l e v e l , STIRS u s u a l l y e l u c i d a t e s at l e a s t p a r t i a l structural information c o n c e r n i n g the u n k n o w n . N o t s u r p r i s i n g l y , e s p e c i a l l y h i g h e n t h u s i a s m has b e e n e x p r e s s e d b y t h o s e l a b o r a t o r i e s w i t h r e l a t i v e l y l i t t l e e x p e r i e n c e i n m a s s s p e c t r a l i n t e r p r e t a t i o n . Although h i g h l y automated g a s chromatograph/mass spectrometer/computer s y s t e m s are common i n many s e r v i c e l a b o r a t o r i e s , s u c h as f o r drug i d e n t i f i c a t i o n , f o r e n s i c a n a l y s i s , and c l i n i c a l a s s a y s , the s p e c t r a l r e t r i e v a l s y s t e m s a v a i l a b l e w i t h t h e s e are r e l a t i v e l y p r i m i t i v e , u s u a l l y b a s e d o n a l i m i t e d number of p e a k s , and u t i l i z i n g o n l y s m a l l s p e c i a l i z e d data b a s e s . More experienced m a s s spectrometry l a b o r a t o r i e s seem to be u s i n g the C o r n e l l system mainly for " d i f f i c u l t " spectra, finding P B M valuable b e c a u s e of our more c o m p r e h e n s i v e data b a s e , a n d STIRS of s p e c i a l u s e for those types of compounds w i t h w h i c h the l a b o r a tory i s not p a r t i c u l a r l y f a m i l i a r . The H e l l e r / N I H " C o n v e r s a t i o n a l M a s s Spectral S e a r c h S y s t e m " (19) h a s been a v a i l a b l e for p h o n e - l i n e u s e s i n c e 1971,
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and s i n c e 1973 o v e r the G E i n t e r n a t i o n a l computer n e t w o r k . The p r e s e n t l i s t of o v e r 200 u s e r s attests to the need as w e l l as the u s e f u l n e s s of t h i s s y s t e m . At the time of t h i s w r i t i n g , the s y s t e m u t i l i z e d o n l y approximately 1 3 , 0 0 0 reference s p e c t r a , but e n largement of the data b a s e to 3 5 , 0 0 0 s p e c t r a i s p l a n n e d f o r the immediate f u t u r e . This i n t e r a c t i v e s y s t e m c a n be u s e d for both r e t r i e v a l and interpretive p u r p o s e s , interrogating the reference f i l e c o n c e r n i n g the p r e s e n c e of p a r t i c u l a r p e a k s on an i n d i v i d u a l b a s i s . Although this s y s t e m i s not s u i t a b l e for automatic m a t c h ing of complete unknown mass s p e c t r a , s u c h as i s P B M , a d e t a i l e d c o m p a r i s o n of the advantages and d i s a d v a n t a g e s of this c o n v e r s a t i o n a l s y s t e m v e r s u s the PBM/STIRS s y s t e m has not b e e n made. A p p l i c a b i l i t y of a Computer N e t w o r k i n g S y s t e m to A n a l y s i s of Unknown S p e c t r a . O u r e x p e r i e n c e to date d o e s g i v e us some i n d i c a t i o n of the types of problems w h i c h are b e s t examined by s u c h computer s y s t e m s . It seems l o g i c a l that the b e s t way to implement a r e t r i e v a l s y s t e m i s as part of the computer data a c q u i s i t i o n and r e d u c t i o n s y s t e m of the m a s s spectrometer. Here the p r a c t i c a l l i m i t a t i o n s of computer s p e e d , p o w e r , and reference data storage c a p a c i t y w i l l prevent s u c h a s y s t e m from b e i n g u s e d i n p a r t i c u l a r a p p l i c a t i o n s . H o w e v e r the a p p l i c a t i o n of P B M i n a G C / M S s y s t e m c o n t r o l l e d by a d e d i c a t e d microcomputer (12) shows that this i s c e r t a i n l y the method of c h o i c e under the proper circumstances. F u r t h e r , i f s u c h a s y s t e m w i l l produce answers q u i c k l y and a c c u r a t e l y i n a s u b s t a n t i a l proportion of c a s e s , the remainder c a n then o b v i o u s l y be examined i n the more s o p h i s t i c a t e d PBM/STIRS s y s t e m a v a i l a b l e on the network. It d o e s appear that the ready a c c e s s i b i l i t y to most l a b o r a tories w h i c h w i l l on o c c a s i o n require s u c h a s e r v i c e i s an i m portant k e y to the s u c c e s s of s u c h a c e n t r a l i z e d s y s t e m for m a s s s p e c t r a l r e t r i e v a l and i n t e r p r e t a t i o n . It i s v e r y d i f f i c u l t for most l a b o r a t o r i e s to m a i n t a i n a growing m a s s s p e c t r a l data b a s e of high accuracy. Further, s y s t e m s s u c h as P B M and STIRS are undergoing rapid r e s e a r c h improvements and o b v i o u s l y there must be a large time l a g i n i n c o r p o r a t i o n of s u c h c h a n g e s u n l e s s there i s a c l o s e c o n n e c t i o n w i t h the r e s e a r c h laboratory i n v o l v e d . The proper method of funding s u c h a c e n t r a l i z e d r e s o u r c e has not b e e n r e s o l v e d ; at present the f i n a n c i a l support of the C o r n e l l P B M / STIRS s y s t e m i s e n t i r e l y b a s e d on computer u s e c h a r g e s , w i t h further r e s e a r c h and d e v e l o p m e n t of the s y s t e m s supported through F e d e r a l g r a n t s . A number of u s e r s have e x p r e s s e d strong o p i n i o n s that the w h o l e o p e r a t i o n s h o u l d be funded by the F e d e r a l G o v e r n m e n t , w i t h at l e a s t a c a d e m i c and governmental u s e r s p a y i n g at most a s m a l l s e r v i c e charge for the networking o p e r a tion. Acknowledgment. The authors are d e e p l y indebted to the N a t i o n a l Institutes of H e a l t h , the N a t i o n a l S c i e n c e F o u n d a t i o n , and the Environmental P r o t e c t i o n A g e n c y for generous f i n a n c i a l support of the r e s e a r c h programs o n P B M and STIRS. The P B M
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system was developed in cooperation with Dr. R. H. Hertel and R. D. Villwock of the Universal Monitor Corporation, Pasadena, California. Implementation of PBM and STIRS on the network system would have not have been possible without the close cooperation of J. W. Rudan; J. Aikin, R. Cogger, and B. A. Meyer of the Office of Computer Services, Cornell University.
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Literature Cited 1. Ridley, R. G., in Waller, G. R., Ed., "Biochemi cal Applications of Mass Spectrometry," p 177, John Wiley, New York City, 1972. 2. Fennessey, P. V . , in Milne, G. W. Α., Ed., "Mass Spectrometry: Techniques and Applications," p 77, John Wiley, New York City, 1971. 3. Fenselau, C., Appl. Spectr., (1974), 28, 305. 4. Arpino, P. J., Dawkins, B. G., and McLafferty, F. W., J. Chrom. Sci., (1974), 12, 574. 5. Pesyna, G. Μ . , and McLafferty, F. W . , "Determina tion of Organic Structures by Physical Methods," Volume 6, Nachod, F. C., Zuckerman, J. J., and Randall, E. W . , Academic Press, New York City, 1975. 6. Crawford, L. R., and Morrison, J. D . , Anal. Chem., (1968), 40, 1464. 7. Jurs, P. C., Kowalski, B. R., and Isenhour, T. L., Anal. Chem., (1969), 41, 21. 8. Isenhour, T. L., and Jurs, P. C., Anal. Chem., (1971), 43, 21A. 9. Buchs, Α . , Delfino, A. B., Duffield, Α. Μ . , Djerassi, C., Buchanan, B. G., Feigenbaum, Ε. Α . , and Lederberg, J., Helv. Chim. Acta, (1970), 53, 1394. 10. Smith, D. Η . , Buchanan, B. G., Engelmore, R. S., Duffield, Α. Μ . , Yeo, Α . , Feigenbaum, Ε. A . , Lederberg, J., and Djerassi, C., J. Am. Chem. Soc., (1972), 94, 5962. 11. Kwok, K.-S., Venkataraghavan, R., and McLafferty, F. W . , J. Am. Chem. Soc., (1973), 95, 4185. 12. McLafferty, F. W . , Hertel, R. Η . , and Villwock, R. D . , Org. Mass Spectrom., (1974), 9, 690. 13. Pesyna, G. Μ . , McLafferty, F. W., Venkataraghavan, R., and Dayringer, Η. Ε . , Anal. Chem., submitted. 14. Stenhagen, Ε . , Abrahamsson, S., and McLafferty, F. W., "Registry of Mass Spectral Data," Wiley-Interscience, New York City, 1974. 15. Mass Spectral Data Collection, Cornell University and the Environmental Protection Agency. 16. Salton, G., "Automatic Information, Organization, and Retrieval," McGraw-Hill, New York City, 1968. 17. Pesyna, G. Μ . , McLafferty, F. W . , and Venkatarag havan, R., Anal. Chem., June, (1975).
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18. Dayringer, H. E., Pesyna, G. Μ., Venkataraghavan, R., and McLafferty, F. W . , Anal. Chem., submitted. 19. Heller, S. R., Koniver, D. Α., Fales, Η. Μ . , and Milne, G. W. Α., Anal. Chem., (1974), 46, 947.
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N e t w o r k i n g and a Collaborative Research Community:
a Case Study Using the D E N D R A L
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch013
Programs RAYMOND E. CARHART, SUZANNE M. JOHNSON, DENNIS H. SMITH, BRUCE G. BUCHANAN, R. GEOFFREY DROMEY, and JOSHUA LEDERBERG Departments of Computer Science, Genetics, and Chemistry, Stanford University, Stanford, Calif. 94305 Computer Science is one of the newest, but also one of the least "cumulative" of the sciences. Gordon (1) has recently pointed out the upsetting disparity between the number of potentially sharable programs in existence and the number which are easily accessible to a given researcher. Although some mechanisms exist for the systematic exchange of program resources, for example the World List of Crystallographic Computer Programs (2), a great deal of programming effort i s duplicated among different research groups with common interests. The reasons for this are understandable: these groups are separated by geography, by incompatibilities in computer facilities and by a lack of a means to keep abreast of a rapidly changing field. The emergence of more economical technologies for data communications provides, in principle, a method for lowering these geographical and operational barriers; for creating, through computer networking, remote sites at which functionally specialized capabilities are concentrated. The SUMEX-AIM (Stanford University Medical Experimental computer - A r t i f i c i a l Intelligence in Medicine) project is an experiment in reducing this principle to practice, in the specific area of a r t i f i c i a l intelligence research applied to health sciences. The SUMEX-AIM computer facility (3) is a National Shared Computing Resource being developed and operated by Stanford University, in partnership with and with financial support from the Biotechnology Resources Branch of the Division of Research Resources, National Institutes of Health. It is national in scope in that a major portion of its computing capacity is being made available to authorized research groups throughout the country by means of communications networks. Aside from demonstrating, on managerial, administrative and technical levels, that such a national computing resource is a viable concept, the primary objective of SUMEX-AIM is the building of a collaborative research community. The aim is to encourage individual participants not only to investigate applications of a r t i f i c i a l intelligence in health science, but also to share their 192
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programs and d i s c u s s t h e i r ideas w i t h other r e s e a r c h e r s . T h i s places a r e s p o n s i b i l i t y upon SUMEX-AIM to develop e f f e c t i v e means of communication among community members and among the programs they w r i t e . I t a l s o places r e s p o n s i b i l i t y upon those members to design and document programs that r e a d i l y can be used and understood by others. Another aspect of the SUMEX f a c i l i t y i s p r o v i d i n g s e r v i c e to i n d i v i d u a l s whose i n t e r e s t i s i n u s i n g , r a t h e r then developing, the a v a i l a b l e computer programs. Although t h i s i s not a primary c o n s i d e r a t i o n , i t i s an e s s e n t i a l p a r t of the growth of these programs. Most of the SUMEX-AIM p r o j e c t s have formed, or are forming, t h e i r own user communities which provide v a l u a b l e " r e a l world" experience. F i g u r e 1 d e p i c t s the t y p i c a l i n t e r a c t i o n of such a p r o j e c t with i t s user community, and w i t h other p r o j e c t s . The p a r t i c i p a t i o n by users i n program development i s not j u s t r e s t r i c ted to suggestions, but can a l s o i n c l u d e software created by comp u t e r - o r i e n t e d users to s a t i s f y s p e c i a l needs. In some p r o j e c t s , methods are being considered to f u r t h e r promote t h i s k i n d of participation. The purposes of t h i s paper are t h r e e f o l d : f i r s t , to i n d i c a t e the range of research p r o j e c t s c u r r e n t l y a c t i v e at SUMEX; second, to d e s c r i b e i n d e t a i l one of these p r o j e c t s , DENDRAL, which i s of p a r t i c u l a r i n t e r e s t to chemists; and t h i r d , to d i s c u s s some problems and p o s s i b l e s o l u t i o n s r e l a t e d to networking and communitybuilding. I.
RESEARCH ACTIVITIES AT SUMEX-AIM
The community of p a r t i c i p a n t s i n -SUMEX-AIM can be d i v i d e d g e o g r a p h i c a l l y i n t o l o c a l (i._e., Stanford-based) p r o j e c t s and remote p r o j e c t s , and below i s given a b r i e f d e s c r i p t i o n of the major r e p r e s e n t a t i v e s of each. Communication with the remote proj e c t s i s accomplished through one or both of the communications networks shown i n F i g u r e 2 . In most cases, connection with SUMEXAIM from these remote s i t e s i n v o l v e s only a l o c a l telephone c a l l to the nearest network "node". The SUMEX-AIM system i s i t s e l f undergoing constant improvement which deserves to be c a l l e d research, and thus a t h i r d s e c t i o n i s i n c l u d e d here to represent system development. Remote P r o j e c t s The Rutgers P r o j e c t . O r i g i n a t i n g from Rutgers U n i v e r s i t y are s e v e r a l research e f f o r t s designed t o introduce advanced methods i n computer s c i e n c e - p a r t i c u l a r l y i n a r t i f i c i a l i n t e l l i g e n c e and i n t e r a c t i v e data base systems - i n t o s p e c i f i c areas of biomedical research. One such e f f o r t i n v o l v e s the development of computerbased c o n s u l t a t i o n systems f o r diseases of the eye, s p e c i f i c a l l y the establishment of a n a t i o n a l network of c o l l a b o r a t o r s f o r d i a g n o s i s and recommendations f o r treatment of glaucoma by computer.
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Figure 1.
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Total ion current vs. spectrum number in a GC/LRMS run
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Another p r o j e c t concerns the BELIEVER program, which represents a theory of how people a r r i v e at an i n t e r p r e t a t i o n of the s o c i a l a c t i o n s of others. SUMEX-AIM provides an e x c e l l e n t medium f o r c o l l a b o r a t i o n i n the development and t e s t i n g of t h i s theory. The Rutgers p r o j e c t i n c l u d e s , i n a d d i t i o n , s e v e r a l fundamental s t u d i e s i n a r t i f i c i a l i n t e l l i g e n c e and system design, which provide much of the support needed f o r the development of such complex systems. The DIALOG P r o j e c t . The DIAgnostic LOGic p r o j e c t , based at the U n i v e r s i t y of P i t t s b u r g h , i s a l a r g e s c a l e , computerized medic a l d i a g n o s t i c system that makes use of the methods and s t r u c t u r e s of a r t i f i c i a l i n t e l l i g e n c e . U n l i k e most other computer d i a g n o s t i c programs, which are o r i e n t e d to d i f f e r e n t i a l diagnosis i n a rather l i m i t e d area, the DIALOG system has been designed to d e a l with the general problem of diagnosis i n i n t e r n a l medicine and c u r r e n t l y accesses a medical data base which encompasses approximately f i f t y percent of the major diseases i n i n t e r n a l medicine. The MISL P r o j e c t . The Medical Information Systems Laboratory at the U n i v e r s i t y of I l l i n o i s (Chicago C i r c l e campus) has been e s t a b l i s h e d to explore i n f e r e n t i a l r e l a t i o n s h i p s between a n a l y t i c data and the n a t u r a l h i s t o r y of s e l e c t e d eye diseases, both i n t r e a t e d and untreated forms. This p r o j e c t w i l l u t i l i z e the SUMEXAIM resource to b u i l d a data base which could then be used as a t e s t bed f o r the development of c l i n i c a l d e c i s i o n support algorithms. D i s t r i b u t e d Data-Base System f o r Chronic Diseases. This p r o j e c t , based at the U n i v e r s i t y of Hawaii, seeks to use the SUMEXAIM f a c i l i t y to e s t a b l i s h a resource sharing p r o j e c t f o r the development of computer systems f o r c o n s u l t a t i o n and research, and to make these systems a v a i l a b l e to c l i n i c a l f a c i l i t i e s from a set of d i s t r i b u t e d data bases. The r a d i o and s a t e l l i t e l i n k s which compose the communication network known as the AL0HANET, i n conj u n c t i o n with the ARPANET, w i l l make these programs a v a i l a b l e to other Hawaiian i s l a n d s and to remote areas of the P a c i f i c b a s i n . This p r o j e c t could w e l l have a s i g n i f i c a n t l y b e n e f i c i a l e f f e c t on the q u a l i t y of h e a l t h care d e l i v e r y i n these l o c a t i o n s . Modelling of Higher Mental Functions. A p r o j e c t at the U n i v e r s i t y of C a l i f o r n i a at Los Angeles i s using the SUMEX-AIM f a c i l i t y to c o n s t r u c t , t e s t , and v a l i d a t e an improved v e r s i o n of the computer s i m u l a t i o n of paranoid processes which has been developed. These simulations have c l i n i c a l i m p l i c a t i o n s f o r the understanding, treatment, and prevention of paranoid d i s o r d e r s . The current i n t e r a c t i v e v e r s i o n (PARRY) has been running on SUMEXAIM and has provided a b a s i s f o r improvement of the f u t u r e v e r sion's language c a p a b i l i t y .
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The P r o t e i n C r y s t a l l o g r a p h y P r o j e c t . The P r o t e i n C r y s t a l l o g r a p h y p r o j e c t i n v o l v e s s c i e n t i s t s a t two d i f f e r e n t u n i v e r s i t i e s (Stanford and the U n i v e r s i t y of C a l i f o r n i a a t San Diego), p o o l i n g t h e i r r e s p e c t i v e t a l e n t s i n p r o t e i n c r y s t a l l o g r a p h y and computer s c i e n c e , and u s i n g the SUMEX-AIM f a c i l i t y as the c e n t r a l r e p o s i t o r y f o r programs, data and other i n f o r m a t i o n of common i n t e r e s t . The general o b j e c t i v e of the p r o j e c t i s to apply problem s o l v i n g techniques, which have emerged from a r t i f i c i a l i n t e l l i g e n c e research, to the w e l l known "phase problem" of x-ray c r y s t a l l o g r a p h y , i n order to determine the three-dimensional s t r u c tures of p r o t e i n s . The work i s intended t o be of p r a c t i c a l as w e l l as t h e o r e t i c a l value to both computer s c i e n c e ( p a r t i c u l a r l y a r t i f i c i a l i n t e l l i g e n c e research) and p r o t e i n c r y s t a l l o g r a p h y . The MYCIN P r o j e c t . MYCIN i s an e v o l v i n g program that has been developed to a s s i s t p h y s i c i a n n o n s p e c i a l i s t s w i t h the s e l e c t i o n of therapy f o r p a t i e n t s w i t h b a c t e r i a l i n f e c t i o n s . The proj e c t has i n v o l v e d both p h y s i c i a n s , with e x p e r t i s e i n the c l i n i c a l pharmacology of b a c t e r i a l i n f e c t i o n s , and computer s c i e n t i s t s , with i n t e r e s t s i n a r t i f i c i a l i n t e l l i g e n c e and medical computing. The MYCIN program attempts to model the d e c i s i o n processes of the medical experts. I t c o n s i s t s of three c l o s e l y i n t e g r a t e d components: the C o n s u l t a t i o n System asks questions, makes c o n c l u s i o n s , and gives advice; the E x p l a n a t i o n System answers questions from the user to j u s t i f y the program's advice and e x p l a i n i t s methods; and the R u l e - A c q u i s i t i o n System permits the user to teach the s y s tem new d e c i s i o n r u l e s , or to a l t e r p r e - e x i s t i n g r u l e s that a r e judged to be inadequate or i n c o r r e c t . The DENDRAL P r o j e c t . T h i s p r o j e c t , being of p a r t i c u l a r chemical i n t e r e s t , i s d e s c r i b e d i n d e t a i l i n S e c t i o n I I . Through the SUMEX-AIM f a c i l i t y DENDRAL has gained a growing community of p r o d u c t i o n - l e v e l users whose experience with the programs i s a v a l u a b l e guide to f u r t h e r development. Although t e c h n i c a l l y u s e r s , some members of t h i s community might b e t t e r be d e s c r i b e d as c o l l a b o r a t o r s because they have provided SUMEX-AIM w i t h v a r i o u s special-purpose programs which a r e of i n t e r e s t to other chemists and which extend the usefulness of the DENDRAL programs. SUMEX-AIM System Development Current research a c t i v i t i e s a t SUMEX-AIM are developing along s e v e r a l l i n e s . On a system development l e v e l there are ongoing p r o j e c t s designed to make the system more user o r i e n t e d . Curr e n t l y , the system can be expected to provide help to the user who i s confused about what i s expected i n response to a c e r t a i n prompt. A " ? " typed by the user, w i l l , i n most cases, provide a l i s t of p o s s i b l e responses from which to choose. A l s o a v a i l a b l e
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i n response to t y p i n g "HELP" to the monitor i s a general help d e s c r i p t i o n c o n t a i n i n g p o i n t e r s to f i l e s l i k e l y to be of i n t e r e s t to a new user. In an e f f o r t to f a c i l i t a t e communication between c o l l a b o r a t o r s , a program c a l l e d CONFER has been developed to prov i d e an o r d e r l y method f o r m u l t i p l e p a r t i c i p a n t t e l e t y p e "conference c a l l s " . B a s i c a l l y , the program a c t s as a character processor f o r a l l the terminals l i n k e d i n the conference, a c c e p t i n g input from only one at a time, and passing i t out to the remaining t e r minals. In t h i s way, the conference, i n e f f e c t , has a "moderat o r " t e r m i n a l , thus a l l o w i n g f o r a more o r d e r l y t r a n s f e r of ideas and i n f o r m a t i o n . SUMEX-AIM i s a l s o aware of the n e c e s s i t y of making i t s f a c i l i t i e s a v a i l a b l e f o r t r i a l use by p o t e n t i a l users and c o l l a b o r a t o r s . To t h i s end, a GUEST mechanism has been e s t a b l i s h e d f o r persons who wish to have b r i e f , t r i a l access to c e r t a i n programs they f e e l may be of value to them, and about which they would l i k e to o b t a i n more knowledge. T h i s provides a convenient mechanism whereby persons, who have been given an a p p r o p r i a t e phone number and LOGIN procedure, can d i a l up SUMEX-AIM and r e c e i v e a c t u a l experience u s i n g a program they may only have heard about. Another area of system development c u r r e n t l y being explored at SUMEX-AIM i s that of c r e a t i n g a comprehensive " b u l l e t i n board" f a c i l i t y where users can f i l e " b u l l e t i n s " , that i s , messages of i n t e r e s t to the SUMEX-AIM community. The f a c i l i t y w i l l a l s o a l e r t users to new b u l l e t i n s which are l i k e l y to be of i n t e r e s t to them, as determined by i n d i v i d u a l u s e r - i n t e r e s t p r o f i l e . I I . DENDRAL - CHEMICAL APPLICATIONS OF INTERACTIVE COMPUTING IN A NETWORK ENVIRONMENT The major research i n t e r e s t of the DENDRAL P r o j e c t at Stanford U n i v e r s i t y i s a p p l i c a t i o n of a r t i f i c i a l i n t e l l i g e n c e techniques f o r chemical i n f e r e n c e , f o c u s i n g i n p a r t i c u l a r on molecular s t r u c t u r e e l u c i d a t i o n . P o r t i o n s of our research are i n the area of combined gas chromatography/high r e s o l u t i o n mass spectrometry and i n c l u d e instrumentation and data a c q u i s i t i o n hardware and software development. T h i s area i s beyond the scope of t h i s r e p o r t ; we focus i n s t e a d on the concurrent development of programs to a s s i s t chemists i n v a r i o u s phases of s t r u c t u r e e l u c i d a t i o n beyond the p o i n t of i n i t i a l data c o l l e c t i o n . SUMEX-AIM provides the computer support f o r development and a p p l i c a t i o n of these programs. Another aspect of our research i s our commitment to share developments among a wider community. We f e e l that s e v e r a l of our programs are advanced enough to be u s e f u l to chemists engaged i n r e l a t e d work i n mass spectrometry and s t r u c t u r e e l u c i d a t i o n i n general. These programs are w r i t t e n p r i m a r i l y i n the programming language INTERLISP, and thus are not e a s i l y exportable (exceptions are i n d i c a t e d subsequently). SUMEX-AIM provides a mechanism f o r
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a l l o w i n g others access to the programs without the requirement f o r any s p e c i a l programming or computer system e x p e r t i s e . The a v a i l a b i l i t y of the SUMEX f a c i l i t y over nationwide networks allows remote users to access the programs, i n many instances v i a a l o c a l telephone c a l l . Much of the f o l l o w i n g d i s c u s s i o n i s p r e l i m i n a r y because our programs have only r e c e n t l y been r e l e a s e d f o r outside use. Some announcement of t h e i r a v a i l a b i l i t y has been made, and other announcements w i l l occur i n the near f u t u r e , through t a l k s , p u b l i c a t i o n s i n press, demonstrations and i n f o r m a l d i s c u s s i o n s . Although most of our experience has been with l o c a l users, they have been good models of remote users i n that t h e i r previous exposure to the a c t u a l programs and computer systems i s minimal. T h e i r experience has been extremely u s e f u l i n h e l p i n g us to smooth out clumsy i n t e r a c t i o n s with programs and to l o c a t e and f i x program bugs. Such p o l i s h i n g i s important f o r programs which may be u t i l i z e d by users from widely d i f f e r i n g backgrounds with respect to computers, networks and time sharing systems. We are i n the processes of b u i l d i n g a community of remote users. We a c t i v e l y encourage such use f o r two reasons: 1) we f e e l the programs a r e capable of a s s i s t i n g others i n s o l v i n g c e r t a i n molecular s t r u c t u r e problems, and 2) such experience with outside users w i l l be a tremendous a s s i s t a n c e i n i n c r e a s i n g the power of our programs as the programs a r e forced to confront new real-world problems. The remainder of t h i s s e c t i o n o u t l i n e s the programs which a r e a v a i l a b l e v i a SUMEX, the u t i l i z a t i o n of these programs i n h e l p i n g to solve s t r u c t u r e e l u c i d a t i o n problems and the l i m i t a t i o n s we see to t h e i r use. We d i s c u s s current a p p l i c a t i o n s of the programs to our research and the research of other users to i l l u s t r a t e b e t t e r the v a r i e t y of p o t e n t i a l a p p l i c a t i o n s and to stimulate an i n t e r change of ideas. Where a p p r o p r i a t e , we p o i n t out current d i f f i c u l t i e s with the use both of our programs and of SUMEX. New a p p l i c a t i o n s and wider use w i l l c e r t a i n l y change the nature of these problems; we s t r i v e t o s o l v e current problems, but new ones w i l l always a r i s e t o take t h e i r p l a c e . DENDRAL Programs We have s e v e r a l programs which we employ i n d e a l i n g with v a r i o u s aspects of problems i n v o l v i n g unknown s t r u c t u r e s . Some of these programs a r e exportable, w h i l e the remainder are a v a i l a b l e at SUMEX. The a v a i l a b i l i t y o f each program i s discussed below. Our i n i t i a l emphasis i n studying a p p l i c a t i o n s of a r t i f i c i a l i n t e l l i g e n c e f o r chemical i n f e r e n c e was i n the area of mass spectrometry (4-6). This emphasis remains because many of our problems r e q u i r e mass spectrometry as the a n a l y t i c a l t o o l of choice i n p r o v i d i n g s t r u c t u r a l information on small q u a n t i t i e s of sample. More r e c e n t l y , we have been developing a program (C0NGEN, below) d i r e c t e d a t more general aspects of s t r u c t u r e e l u c i d a t i o n . This has extended the scope of problems f o r which we can provide
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computer a s s i s t a n c e . We w i l l begin, however, with d i s c u s s i o n of the mass spectrometry programs. The examples used i n the d i s c u s s i o n are c h a r a c t e r i s t i c of our c u r r e n t research problems, although we have focused on r e l a t i v e l y simple problems to keep the p r e s e n t a t i o n b r i e f . We t r a c e , i n what might be c h r o n o l o g i c a l terms, the a p p l i c a t i o n of the programs to v a r i o u s phases of a s t r u c t u r e problem. In t h i s way we hope to i l l u s t r a t e the p l a c e of each program i n the a n a l y s i s . We begin by d i s c u s s i n g preprocessing of mass s p e c t r a l data (CLEANUP and MOLION). Subsequent a n a l y s i s of such data i n terms of s t r u c t u r e i s then covered (PLANNER). The use of CONGEN i s discussed f o r problems which cannot be handled by the previous programs. F i n a l l y , we d i s c u s s e f f o r t s to d i s c o v e r , with the use of the computer, systematics i n the behavior of known substances i n the mass spectrometer as a means of extending the knowledge of the system f o r a p p l i c a t i o n s i n new areas (INTSUM and RULEGEN). Programs f o r Molecular S t r u c t u r e Problems The f i r s t three programs, CLEANUP, the l i b r a r y - s e a r c h program and MOLION are i n a sense u t i l i t y programs, but a l l three p l a y a c r i t i c a l r o l e i n p r o c e s s i n g mass s p e c t r a l data. Subsequent a p p l i c a t i o n s of programs (e.£., PLANNER) f o r more d e t a i l e d s p e c t r a l a n a l y s i s i n terms of s t r u c t u r e depend on the s u c c e s s f u l treatment of the data by CLEANUP and MOLION, w h i l e the l i b r a r y search program f i l t e r s out common s p e c t r a which need not undergo a f u l l a n a l y s i s . The examples used are drawn from our c o l l a b o r a t i o n w i t h persons i n the Genetics Research Center a t Stanford H o s p i t a l . The experimental data which are c o l l e c t e d are the r e s u l t s of combined gas chromatographic/low r e s o l u t i o n mass s p e c t r a l (GC/LRMS) analys i s of organic components (chemically f r a c t i o n a t e d and d e r i v a t i z e d where necessary) of body f l u i d s , blood, u r i n e . A t y p i c a l experiment c o n s i s t s of 500-600 i n d i v i d u a l mass s p e c t r a f o r each f r a c t i o n , taken s e q u e n t i a l l y over time as the v a r i o u s components, l a r g e l y separated from one another, e l u t e from the gas chromatograph and pass i n t o the mass spectrometer. Each mass spectrum c o n s i s t s of the mass analyzed fragment ions of the component(s) i n the mass spectrometer a t the time the spectrum was taken. Such s p e c t r a are r e l a t e d , i n d i r e c t l y , to the molecular s t r u c t u r e of the component(s). CLEANUP(7). The i n d i v i d u a l mass s p e c t r a obtained from f r a c t i o n a t e d GC/LRMS a n a l y s i s are q u i t e o f t e n poor r e p r e s e n t a t i o n s of corresponding s p e c t r a taken from pure compounds. They can be contaminated by the presence of a d d i t i o n a l peaks and/or d i s t o r t i o n s of the i n t e n s i t i e s of e x i s t i n g peaks i n the spectrum. Fragment ions from e i t h e r the l i q u i d phase of the GC column or from components incompletely separated by the gas chromatograph are r e s p o n s i b l e f o r the contamination. We have developed a program, r e f e r r e d to here as CLEANUP, which examines a l l mass s p e c t r a i n a
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GC/LRMS run, s e l e c t s those s p e c t r a which contain ions other than background i m p u r i t i e s , and removes c o n t r i b u t i o n s from background and overlapping components. A spectrum r e s u l t s which compares f a v o r a b l y with the spectrum of a pure component. B i l l e r and Biemann (8) have developed a s i m i l a r but l e s s powerful program. For example, the CLEANUP program detected components at p o i n t s marked with a v e r t i c a l bar i n the ( p a r t i a l ) p l o t of t o t a l i o n current v s . scan number (time), F i g u r e 3. Note that o v e r l a p ping components were detected under the envelopes of the GC peaks i n the r e g i o n of scans 485-488, 525-529 and 539-552. We focus our a t t e n t i o n on the spectrum recorded at scan 492. The raw data, p r i o r to cleanup, are presented i n F i g u r e 4 (top). The spectrum r e s u l t i n g from CLEANUP i s presented i n Figure 4 (bottom). Note that the l a r g e ions (e.g., m/e 207, 221 and 315) from background i m p u r i t i e s are removed, and that the i n t e n s i t y r a t i o s of peaks at lower masses (e.g., 51 and 77) have been adjusted to r e f l e c t t h e i r true i n t e n s i t i e s i n the spectrum. The CLEANUP program i s capable of d e t e c t i o n of q u i t e l o w - l e v e l components i n complex mixtures as i n d i c a t e d by some of the areas of the t o t a l i o n current p l o t (Figure 3) where components were detected. I t i s completely general because nothing i n the program code i s s e n s i t i v e to the types of compounds analyzed or the c h a r a c t e r i s t i c s of p o s s i b l e i m p u r i t i e s a s s o c i a t e d with the compounds or from the GC column. I t s major l i m i t a t i o n i s that mass s p e c t r a must be taken r e p e t i t i v e l y during the course of a GC/MS run. I t s performance i s enhanced when such s p e c t r a are measured c l o s e l y i n time. The program i s o f f e r e d v i a SUMEX as an adjunct to use of our other programs; i t i s not o f f e r e d as a r o u t i n e s e r v i c e . Because the program i s w r i t t e n i n FORTRAN, we r o u t i n e l y use i t on our data a c q u i s i t i o n computer system so as not to burden SUMEX with tasks b e t t e r done elsewhere. S i m i l a r l y , we would a s s i s t other frequent users to mount the program on t h e i r own systems. L i b r a r y Search. With a s e t of " c l e a n " mass s p e c t r a a v a i l a b l e , the next problem i s i d e n t i f i c a t i o n of the v a r i o u s components. Over the course of s e v e r a l years, l i b r a r i e s of mass s p e c t r a l data have been assembled (9). These l i b r a r i e s can be very u s e f u l i n weeding out from a group of s p e c t r a those which represent known compounds (10). C l e a r l y , one should spend time on s o l v i n g the s t r u c t u r e s of unknown compounds, not on r e d i s c o v e r i n g o l d ones. The CLEANUP program provides mass s p e c t r a which are of s u f f i c i e n t q u a l i t y to expect that known compounds would be i d e n t i f i e d e a s i l y from such l i b r a r i e s . The s p e c t r a detected by CLEANUP i n the r e g i o n of scans 480 to 580 (Figure 3) were matched against the l i b r a r y of b i o m e d i c a l l y r e l e v a n t s p e c t r a compiled by S. Markey (National I n s t i t u t e s of Health) and our extensions to that l i b r a r y (we wish to thank S. Grotch, J e t P r o p u l s i o n Laboratory, Pasadena, Ca. f o r p r o v i d i n g some of the l i b r a r y matchings). E x c e l l e n t matches with the
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l i b r a r y were obtained f o r scans 492, 496, 509, 519, 529 and 548. The components are i n d o l e a c e t i c a c i d methyl e s t e r , d i - n - b u t l y phthalate, c a f f e i n e , s a l i c y l u r i c a c i d methyl e s t e r , methoxyh i p p u r i c a c i d methyl e s t e r and n-C24 hydrocarbon r e s p e c t i v e l y ( s t r u c t u r e s given i n Figures 3 and 4). Spectra scans at 485, 487, 525, 530, 536, 539, 554 and 576 d i d not match w e l l w i t h any spectrum i n the l i b r a r y and thus must be examined f u r t h e r f o r s t r u c t u r i n g information. The n e c e s s i t y f o r preprocessing the data using CLEANUP p r i o r to l i b r a r y matching i s i l l u s t r a t e d from i n d o l e a c e t i c a c i d methyl e s t e r (scan 492). The " c l e a n " spectrum (Figure 4, bottom) was matched to the l i b r a r y spectrum of t h i s compound much b e t t e r than to that of any other compound. The raw spectrum (Figure 4, top), when compared to the l i b r a r y r e s u l t e d i n eleven other compounds which matched more c l o s e l y that the c o r r e c t one. This b r i e f example i l l u s t r a t e s the obvious v a l u e and l i m i t a t i o n s of l i b r a r y searching. The most i n t e r e s t i n g compounds f o r subsequent a n a l y s i s are those which are unknown. The f r a c t i o n s of u r i n e e x t r a c t s are r e p l e t e with u n i d e n t i f i e d compounds because of the inadequacy of current l i b r a r y compilations. As new compounds are i d e n t i f i e d they are, of course, added to the l i b r a r y so that f u t u r e analyses need not r e i n v e s t i g a t e the same m a t e r i a l . We c u r r e n t l y perform l i b r a r y searching on our data a c q u i s i t i o n and r e d u c t i o n computer systems. We can, i f necessary, o f f e r l i m i t e d l i b r a r y search f a c i l i t i e s v i a SUMEX. However, because commercial f a c i l i t i e s are a v a i l a b l e (e.&., over the GE network), r o u t i n e l i b r a r y search s e r v i c e i s not a v a i l a b l e on SUMEX. MOLION(ll). At t h i s stage we are l e f t with a c o l l e c t i o n of mass spectra of unknown compounds. The l i b r a r y search r e s u l t s may have provided some clues as to the type of compound present, je.j£., compound c l a s s . Structure e l u c i d a t i o n now begins i n earnest. The key elements i n problems of s t r u c t u r e e l u c i d a t i o n are the molecul a r weight and e m p i r i c a l formula of a compound. Without these e s s e n t i a l data, the s t r u c t u r a l p o s s i b i l i t i e s are u s u a l l y too immense to proceed f u r t h e r . Mass spectrometry i s f r e q u e n t l y used to determine molecular weights and formulae, but there i s no guarantee that the mass spectrum of a compound d i s p l a y s an i o n c o r r e s ponding to the i n t a c t molecule. For example, many of the d e r i v a t i v e s of the amino a c i d f r a c t i o n s of u r i n e d i s p l a y no molecular i o n s . When we are given only the mass spectrum (and f o r GC/MS a n a l y s i s a mass spectrum may be a l l that i s a v a i l a b l e ) we must somehow p r e d i c t l i k e l y molecular i o n candidates, The program MOLION performs t h i s task. Given a mass spectrum, i t p r e d i c t s and ranks l i k e l y molecular i o n candidates independent of the presence or absence of an i o n i n the spectrum corresponding to the i n t a c t molecule. The published manuscript (11) provides many examples of the performance of the program.
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The mass spectrum of an example, unknown X, (which we w i l l pursue i n more d e t a i l below) i s given i n F i g u r e 5. The r e s u l t s obtained from MOLION are summarized i n Table I . The observed i o n at m/e 263 i s ranked as the most l i k e l y candidate.
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Figure 5. Low-resolution mass spectrum of unknown X. The indicated superatoms were deduced from the spectrum and the chemical history of the sample. Based on these and other constraints, CONGEN obtains the indicated result.
Table I .
Results of Molecular Ion Determination f o r the Unknown Compound, X, whose Mass Spectrum i s Presented i n F i g u r e 5. CANDIDATE 263.0 307.0 299.0 295.0 281.0
RANKING INDEX 100 41 38 34 25
The MOLION program i s w r i t t e n to operate on e i t h e r low o r high r e s o l u t i o n mass s p e c t r a . The program has c e r t a i n l i m i t a t i o n s which have been summarized i n d e t a i l p r e v i o u s l y (11). MOLION i s a v a i l a b l e on SUMEX. A FORTRAN v e r s i o n , i n i t i a l l y f o r low r e s o l u t i o n mass s p e c t r a , i s being w r i t t e n so that the pro gram can be run on smaller computers and exported to o t h e r s . How ever, i t w i l l continue to be a v a i l a b l e v i a SUMEX so that others can access i t e a s i l y . MOLION i s contained w i t h i n PLANNER as one of the a v a i l a b l e methods f o r d e t e c t i n g candidate molecular i o n s .
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PLANNER(12). The PLANNER program i s designed to analyze the mass spectrum of a compound or of a mixture of r e l a t e d compounds. Because there i s no ab i n i t i o way of r e l a t i n g a mass spectrum of a complex organic molecule to the s t r u c t u r e of that molecule, PLANNER r e q u i r e s fragmentation r u l e s f o r the c l a s s of compounds to which the unknown belongs. T h i s i s i t s major l i m i t a t i o n . For our example the c l a s s was unknown, f o r c i n g us to r e s o r t to other means of a s s i s t a n c e . A p p l i c a t i o n s and l i m i t a t i o n s of PLANNER have been discussed e x t e n s i v e l y (12,13). The program i s very powerful i n instances where mass spectrometry r u l e s are strong (i.e.., g e n e r a l , w i t h few e x c e p t i o n s ) . In instances where r u l e s are weak or nonexistent, a d d i t i o n a l work on known s t r u c t u r e s and s p e c t r a may y i e l d u s e f u l r u l e s to make PLANNER a p p l i c a b l e (see INTSUM and RULEGEN, below) . One important f e a t u r e of PLANNER i s i t s a b i l i t y to analyze the s p e c t r a of mixtures i n a systematic and thorough way. Thus, i t can be a p p l i e d to s p e c t r a obtained as mixtures when GC/MS data are u n a v a i l a b l e or impossible to o b t a i n . PLANNER i s a v a i l a b l e i n an i n t e r a c t i v e v e r s i o n over SUMEX, r e q u i r i n g three kinds of informat i o n as i n p u t : the h i g h or low r e s o l u t i o n mass spectrum^ the c h a r a c t e r i s t i c s k e l e t a l s t r u c t u r e f o r molecules i n the s p e c i f i c compound c l a s s , and the fragmentation r u l e s f o r the c l a s s . Addit i o n a l knowledge about the unknown can be used by the program to c o n s t r a i n the s t r u c t u r a l p o s s i b i l i t i e s . C0NGEN(14,15). S t r u c t u r e problems are u s u a l l y not solved with mass spectrometry alone. Even when sample s i z e i s too l i m i t e d f o r o b t a i n i n g other s p e c t r o s c o p i c data, knowledge of chemical i s o l a t i o n and r e s u l t s of d e r i v a t i z a t i o n procedures f r e quently a c t as powerful c o n s t r a i n t s on s t r u c t u r a l p o s s i b i l i t i e s . Larger amounts of sample permit determination of other s p e c t r o s c o p i c data. Taken together, t h i s i n f o r m a t i o n allows determinat i o n of s t r u c t u r a l f e a t u r e s (substructures) of the molecule and c o n s t r a i n t s on the p l a u s i b i l i t y of ways i n which the substructures may be assembled. The CONGEN program i s capable of prov i d i n g a s s i s t a n c e i n s o l u t i o n of such problems. CONGEN performs the task of c o n s t r u c t i o n , or generation, of s t r u c t u r a l isomers under c o n s t r a i n t s . The program accepts as input known s t r u c t u r a l fragments of the molecule ("superatoms") and any remaining atoms (C,N,0,P,...), together w i t h c o n s t r a i n t s on how they may be assembled. I t i s based on the exhaustive s t r u c t u r e generator (16,17) and extensions (18) which permit a stepwise assembly of s t r u c t u r e s . In an i n t e r a c t i v e s e s s i o n with the program, a user s u p p l i e s s t r u c t u r a l i n f o r m a t i o n determined by h i s own a n a l y s i s of the data (perhaps w i t h the help of the above programs), together w i t h whatever other c o n s t r a i n t s are a v a i l a b l e concerning d e s i r e d and undes i r e d s t r u c t u r a l f e a t u r e s , r i n g s i z e s and so f o r t h . The program b u i l d s s t r u c t u r e s i n a s e r i e s of s t e p s , during which a user can i n t e r a c t f u r t h e r w i t h the procedure, f o r example, to add new
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c o n s t r a i n t s . Although very much a developing program, i t s a b i l i t y to accept u s e r - i n f e r r e d c o n s t r a i n t s from many data sources makes CONGEN a general t o o l f o r s t r u c t u r e e l u c i d a t i o n which we are mak i n g a v a i l a b l e v i a SUMEX-AIM i n i t s c u r r e n t form. For the unknown X, the observed fragment ions from the molecular i o n (M) a t m/e 263 (Figure 5) suggest s e v e r a l s t r u c t u r a l features when coupled w i t h the knowledge of the chemical d e r i v a t i z a t i o n procedures used on t h i s f r a c t i o n of the u r i n e e x t r a c t . The i o n at m/e 194 represents l o s s of 69 amu, probably CF3, from f r a g mentation of a t r i f l u o r o a c e t y l d e r i v a t i v e of an amine. T h i s sug gests the p a r t i a l s t r u c t u r e 2, F i g u r e 5. The ions a t m/e 190 (M-74 amu) and m/e 162 (M-101 amu) suggest the c h a r a c t e r i s t i c fragmentation of an η-butyl e s t e r r e s u l t i n g from the second d e r i v a t i z a t i o n procedure, formation of the η-butyl e s t e r s of f r e e c a r b o x y l i c a c i d f u n c t i o n s . This suggests the p a r t i a l s t r u c t u r e _1, F i g u r e 5. Taken together, a l l the above i n f o r m a t i o n i m p l i e s ( i f no other elements are present) that the e m p i r i c a l formula contains an odd number of n i t r o g e n atoms, at l e a s t three oxygen atoms, three f l u o r i n e atoms and at l e a s t seven carbon atoms. I n t e r e s t i n g l y , there i s only one p l a u s i b l e e m p i r i c a l formula under these c o n s t r a i n t s , C11H12N03F3. S t r u c t u r a l fragments ("superatoms") _1 and 2 were s u p p l i e d to CONGEN, together with the remaining four carbon atoms and three degrees of u n s a t u r a t i o n (that i s , r i n g s p l u s m u l t i p l e bonds). With no a d d i t i o n a l c o n s t r a i n t s , 155 s t r u c t u r e s r e s u l t . The i n c l u s i o n of other p l a u s i b l e c o n s t r a i n t s (e._g., no aliènes, a c e t y l e n e s , cyclopropenes, cyclobutenes) reduces the number of s t r u c t u r a l cand i d a t e s to j u s t the two isomeric forms of _2, F i g u r e 5. This problem represents a simple example of a l a r g e c l a s s of such problems. Although a chemist could probably reach the same c o n c l u s i o n s q u i c k l y i n t h i s case, i n the general case, p i e c i n g together p o t e n t i a l s o l u t i o n s i s not a t r i v i a l task. Although s t i l l a developing program, CONGEN i s capable of considerable a s s i s t a n c e i n a wide v a r i e t y of s t r u c t u r e problems. Some areas of current a p p l i c a t i o n are summarized i n the subsequent s e c t i o n . I t i s already proving i t s v a l u e i n s t r u c t u r e e l u c i d a t i o n problems by suggesting s o l u t i o n s w i t h a guarantee that no p l a u s i b l e a l t e r n a t i v e s have been overlooked. The program has a great d e a l of f l e x i b i l i t y . Many of the types of c o n s t r a i n t s normally brought to bear on s t r u c t u r e e l u c i d a t i o n problems can be expressed. However, some types of cons t r a i n t s cannot be e a s i l y expressed (e.g., d i s j u n c t i o n s of f e a t u r e s and s t e r e o - c o n s t r a i n t s ) . Recent work by our group and Wipke's (19) w i l l make i t p o s s i b l e to add c o n s i d e r a t i o n s of stereoisomerism r e l a t i v e l y e a s i l y (a good example of c o l l a b o r a t i o n v i a SUMEX). We are depending on a broad user community to help us guide f u r t h e r development of CONGEN.
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Programs f o r Knowledge A c q u i s i t i o n INTSUM(20) and RULEGEN(21). When the mass spectrometry r u l e s f o r a given c l a s s of compounds are not known, the INTSUM and RULEGEN programs can help a chemist formulate those r u l e s . Essent i a l l y , these programs c a t e g o r i z e the p l a u s i b l e fragmentations f o r a c l a s s of compounds by l o o k i n g a t the mass s p e c t r a of s e v e r a l molecules i n the c l a s s . A l l molecules a r e assumed to belong to one c l a s s whose s k e l e t a l s t r u c t u r e must be s p e c i f i e d . A l s o , the mass s p e c t r a and the s t r u c t u r e s of a l l the molecules must be given to the program. INTSUM c o l l e c t s evidence f o r a l l p o s s i b l e fragmentations (within u s e r - s p e c i f i e d c o n s t r a i n t s ) and summarizes the r e s u l t s . For example, a user may be i n t e r e s t e d i n a l l fragmentations i n v o l v i n g one or two bonds, but not three; aromatic r i n g s may be known to be unfragmented; and the user may be i n t e r e s t e d only i n fragmentations r e s u l t i n g i n an i o n c o n t a i n i n g a heteroatom. Under these c o n s t r a i n t s , the program c o r r e l a t e s a l l peaks i n the mass s p e c t r a with a l l p o s s i b l e fragmentations. The summary of r e s u l t s shows the molecules whose s p e c t r a d i s p l a y evidence f o r each p a r t i c u l a r fragmentation, along w i t h the t o t a l (and average) i o n current a s s o c i a t e d with the fragmentation. The RULEGEN program attempts to e x p l a i n the r e g u l a r i t i e s found by INTSUM i n terms of the u n d e r l y i n g s t r u c t u r a l f e a t u r e s around the bonds i n question that seem to " d i r e c t " the fragmentat i o n s . For example, INTSUM w i l l n o t i c e s i g n i f i c a n t fragmentation of the two d i f f e r e n t bonds alpha to the carbonyl group i n a l i p h a t i c ketones. I t i s l e f t to RULEGEN to d i s c o v e r that these a r e both instances of the same fundamental alpha-cleavage process that can be p r e d i c t e d any time a bond i s alpha to a carbonyl group. These programs are p a r t of the s o - c a l l e d Meta-DENDRAL e f f o r t , whose general goal i s to understand r u l e formation a c t i v i t i e s . Both INTSUM and RULEGEN a r e a v a i l a b l e as i n t e r a c t i v e programs on SUMEX, the former being much more h i g h l y developed that the l a t t e r ; Although these programs can be very u s e f u l to chemists i n t e r e s t e d i n f i n d i n g new mass spectrometry r u l e s , they r e q u i r e having the c o l l e c t i o n of mass s p e c t r a and molecular s t r u c t u r e d e s c r i p t i o n s a v a i l a b l e i n one computer f i l e . Because of t h i s , they have been used mostly by chemists a t Stanford. A p p l i c a t i o n s and Resource
Sharing
The DENDRAL programs are being developed t o serve a broad community of chemists with s t r u c t u r e e l u c i d a t i o n problems. Our experience i s admittedly l i m i t e d . In t h i s s e c t i o n we d i s c u s s some of the a p p l i c a t i o n s , both l o c a l and from remote s i t e s , where these programs have proven u s e f u l . CLEANUP and MOLION. These programs are i n r o u t i n e use as p a r t of the Genetics Research Center's GC/LRMS e f f o r t s . In
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a d d i t i o n , MOLION has been incorporated as part of PLANNER. T h e i r g e n e r a l i t y has proven very u s e f u l i n a p p l i c a t i o n s to a v a r i e t y of GC/MS problems i n v o l v i n g s t r u c t u r a l s t u d i e s of u r i n a r y metabolites.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch013
PLANNER. The planning program has been used to i n f e r p l a u s i b l e placement of s u b s t i t u e n t s around a s k e l e t a l s t r u c t u r e f o r numerous t e s t problems i n which the c l a s s of the sample was known and the fragmentation r u l e s f o r the c l a s s were known. Those t e s t s have r e s u l t e d i n a program that we b e l i e v e i s general. We have a p p l i e d t h i s program to unknown mixtures of estrogenic s t e r i o d s (13). We are preparing to use PLANNER f o r screening mass spectra of marine s t e r o l s to i d e n t i f y q u i c k l y those spectra of known compounds and to suggest s t r u c t u r e s f o r spectra of new compounds. CONGEN. CONGEN i s being used l o c a l l y and from remote s i t e s i n a wide v a r i e t y of a p p l i c a t i o n s . We have used i t f o r construct i o n of r i n g systems under c o n s t r a i n t s (22) and f o r generation of s t r u c t u r e s of chlorocarbons (23). We have i n v e s t i g a t e d s e v e r a l monoterpenoid and sesquiterpenoid s t r u c t u r e problems to suggest s o l u t i o n s and to ensure that a l l a l t e r n a t i v e s had been considered. We are c u r r e n t l y i n v e s t i g a t i n g the scope of terpenoid isomerism. Two problems r e l a t i n g to unknown photochemical r e a c t i o n products have been analyzed and r e s u l t s used to suggest f u r t h e r e x p e r i ments. In most cases we do not know the p r e c i s e problems under study by remote users, only that they are using the program. CONGEN w i l l perhaps be the most widely used (by remote users) program of those mentioned above as a c c e s s i b l e through SUMEX. This i s p r i m a r i l y a r e s u l t of the wider scope of problems which might b e n e f i t from use of the program. However, the need f o r remote users to have t h e i r mass s p e c t r a l data a v a i l a b l e at SUMEX f o r a n a l y s i s present a s i g n i f i c a n t energy b a r r i e r to use of the programs which r e q u i r e these data. INTSUM and RULEGEN. INTSUM i s e s s e n t i a l l y a production program now, and i s being used as such i n a v a r i e t y of a p p l i c a t i o n s i n v o l v i n g c o r r e l a t i o n s of molecular s t r u c t u r e s with t h e i r respective spectra. Recent or current a p p l i c a t i o n s i n c l u d e analys i s of the mass spectra of progestérones and r e l a t e d s t e r o i d s , androstanes, macrolide a n t i b i o t i c s , i n s e c t j u v e n i l e hormones and phytoecdysones. These s t u d i e s serve to develop fragmentation r u l e s which, i f of s u f f i c i e n t g e n e r a l i t y , can i n turn be used i n PLANNER i n the study of unknown compounds. III.
PROBLEMS RELATED TO NETWORKING
During t h i s f i r s t year of operation, the SUMEX-AIM f a c i l i t y has encountered a v a r i e t y of problems a r i s i n g from i t s network availability. In most cases, there has been no c l e a r precedent
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f o r the handling of these s i t u a t i o n s , i n f a c t , many problem-areas s t i l l r e f l e c t the i n f l u e n c e s of a yet-developing p o l i c y . The hope i s that t h i s p r e s e n t a t i o n and d i s c u s s i o n of problems and t h e i r s o l u t i o n s may give f o r e s i g h t t o others who contemplate networking or network use. The problems to be discussed can be l o o s e l y a s s o c i a t e d i n t o three c l a s s e s ; those r e l a t e d t o the management of the f a c i l i t y , those p e r t a i n i n g to research a c t i v i t i e s on the s y s tem, and those i n v o l v i n g p s y c h o l o g i c a l b a r r i e r s to network use.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch013
Managerial
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"Gatekeeping". The most general problem faced by the organizers of the SUMEX-AIM f a c i l i t y i s the question of "gatekeeping." In order t o i n s u r e a high q u a l i t y of p e r t i n e n t research, some k i n d of r e f e r e e i n g system i s needed to assess the value of proposed new p r o j e c t s . The o r g a n i z e r s of the f a c i l i t y would seem to be the best source of such judgements; y e t , because we are both organizers and members of the SUMEX community, there i s a danger that our d e c i s i o n s would u n f a i r l y favor l o c a l p r i o r i t i e s . In order to e s t a b l i s h c r e d i b i l i t y i n SUMEX-AIM as a t r u l y n a t i o n a l resource, a management system has been i n s t i t u t e d that a l l o c a t e s a defined f r a c t i o n ( i n i t i a l l y 50%) of the SUMEX resource to e x t e r n a l users, under the j u r i s d i c t i o n of an independent n a t i o n a l committee (the AIM advisory group). The remaining 50%, a l l o c a t e d f o r l o c a l use, contains a p o r t i o n f o r f l e x i b l e experiments outside of l o c a l p r o j e c t s , but on our own r e s p o n s i b i l i t y . Choice of computer and operating system. A second management l e v e l problem i s the choice of a computer and operating system which optimize the usefulness of the f a c i l i t y f o r a m a j o r i t y of users, and which encourage intercommunication between remote c o l l a b o r a t o r s . Because SUMEX-AIM i s intended to be used p r i m a r i l y f o r a p p l i c a t i o n s of a r t i f i c i a l i n t e l l i g e n c e , and because i n t e r a c t i v e LISP (24) i s a primary language i n t h i s type of work, the choice of TENEX (25) as an operating system was d i c t a t e d somewhat by n e c e s s i t y . TENEX incorporates m u l t i p l e address spaces, thereby a l l o w i n g m u l t i p l e " f o r k " s t r u c t u r e and paging, a design which i s necessary to c r e a t e the l a r g e memory v i r t u a l machine r e q u i r e d by INTERLISP. The PDP-10 i s a popular machine f o r i n t e r a c t i v e computing of a l l s o r t s i n u n i v e r s i t y research environments, and thus an added b e n e f i t of t h i s choice was expected - the p o s s i b i l i t y of e a s i l y t r a n s f e r r i n g to SUMEX programs developed a t other s i t e s . Many of these programs were w r i t t e n not under TENEX but under the 10/50 monitor s u p p l i e d by the manufacturer. Because a l a r g e and u s e f u l program l i b r a r y was already a v a i l a b l e under the 10/50 monitor, one of the design c r i t e r i a of TENEX was c o m p a t i b i l i t y with such programs; when a 10/50 program i s run under TENEX, a s p e c i a l "compati b i l i t y package" of r o u t i n e s i s invoked to t r a n s l a t e 10/50 monitor c a l l s i n t o equivalent TENEX monitor c a l l s . Although the concept
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch013
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i s sound, we have found that i n p r a c t i c e very few programs w r i t t e n f o r the 10/50 monitor are able t o run under TENEX without extensive m o d i f i c a t i o n . Other problems with TENEX i n c l u d e weaknesses i n the support of p e r i p h e r a l devices and the l a c k of a d e f a u l t l i n e - e d i t o r . The l a t t e r has caused a p r o l i f e r a t i o n of e d i t i n g programs, and some confusion has r e s u l t e d because e d i t o r conventions vary from program t o program. These d i f f i c u l t i e s have dampened somewhat our i n i t i a l enthusiasm f o r the TENEX system. Nonetheless, TENEX provides some f e a t u r e s which a r e c r u c i a l to a comfortable network environment. The standard support programs i n c l u d e d with t h i s system f a c i l i t a t e both the sending of messages to other users ( e i t h e r a t the same s i t e or a t other s i t e s on the ARPA network) and the t r a n s f e r of data and programs from s i t e t o s i t e on that network; a l s o the a b i l i t y to " l i n k " two or more terminals allows users t o communicate e a s i l y and immediately. Both the l i n k i n g and message f a c i l i t y have been found to be i n v a l u a b l e a i d s i n inter-group communications and i n such problems as i n t e r a c t i v e program debugging. When two t e r m i n a l s are l i n k e d , t h e i r output streams are merged, thus a l l o w i n g each t e r m i n a l to d i s p l a y everything typed a t the other t e r m i n a l . Since only the output stream i s a f f e c t e d under these circumstances, i t i s s t i l l p o s s i b l e f o r each t e r m i n a l to be used to provide input to separate programs, i n a d d i t i o n to being used i n a c o n v e r s a t i o n a l mode. Resource a l l o c a t i o n . As noted above, the computational resources of the SUMEX-AIM f a c i l i t y a r e apportioned by the AIM advisory group and SUMEX management. Some extensions to the b a s i c TENEX system have been made to r e f l e c t t h i s a p p o r t i o n i n g i n the a c t u a l use of the f a c i l i t y . B a s i c a l l y , i t was recognized that users of the f a c i l i t y are members o f groups working on s p e c i f i c p r o j e c t s , and i t i s among these p r o j e c t s that the f a c i l i t y i s apportioned. Disk space and cpu c y c l e s a r e now d i s t r i b u t e d among groups i n s t e a d of among i n d i v i d u a l u s e r s . For example, a user may exceed h i s i n d i v i d u a l d i s k a l l o c a t i o n somewhat without any i l l e f f e c t , so long as the t o t a l a l l o c a t i o n of h i s group remains w i t h i n the l i m i t s . S i m i l a r l y , a Reserve A l l o c a t i o n Scheduler has been added to TENEX which t r i e s to match the a d m i n i s t r a t i v e c y c l e d i s t r i b u t i o n over a n i n e t y second time frame. Thus a p a r t i c u l a r group cannot dominate the machine i f a l o t of i t s members are logged i n a t one time. I t i s t y p i c a l f o r usage of a f a c i l i t y to peak through the middle hours of the day. Indeed, one of the advantages of having users from around the country i s the spreading of the load caused by the d i f f e r e n c e i n time zones. Even so, the f a c i l i t y could o f f e r b e t t e r s e r v i c e i f more people would s h i f t t h e i r main usage hours toward e i t h e r end of the day. To encourage " s o f t - s c h e d u l i n g " w i t h i n groups on the system, SUMEX-AIM p u b l i s h e s a weekly p l o t of d i u r n a l l o a d i n g . T h i s p l o t shows the t o t a l number of jobs on the system as w e l l as the number of LISP j o b s , s i n c e these jobs seem to make the b i g g e s t demands of system resources. The r e s u l t
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has been an Increased awareness by users of system l o a d i n g and a n o t i c e a b l e i n c r e a s e i n the number of users at a l l hours of the n i g h t and e a r l y morning. P r o t e c t i o n and system s e c u r i t y . P r o t e c t i o n f o r a computer system covers a range of i d e a s . I t means the a b i l i t y to maintain secrecy - f o r example, to guarantee the p r i v a c y of p a t i e n t records. I t a l s o guarantees i n t e g r i t y by a s s u r i n g that programs and data are not modified by an unauthorized p a r t y . Questions of p r o t e c t i o n g e n e r a l l y become more i n t e r e s t i n g and complex as more s h a r i n g i s i n v o l v e d . Consider the example of a p r o p r i e t o r y program which generates l a y o u t s given a user's c i r c u i t data. The program owner demands assurance that he w i l l be p a i d whenever h i s program i s used and that copies of the program cannot be made. The user wants guarantees that h i s data s e t s cannot be destroyed or copied f o r a competitor. Yet the user must have access to the program and the program must have access to the d a t a Unable to support such complicated examples of p r o t e c t i o n , SUMEXAIM assumes that s h a r i n g takes p l a c e between f r i e n d l y u s e r s . T h i s i s not to imply that i s s u e s of p r o t e c t i o n and s h a r i n g have not appeared. For example, i n an e f f o r t to improve the human e n g i n e e r i n g of programs f o r p u b l i c use, the c a p a b i l i t y of r e c o r d i n g a s e s s i o n has been b u i l t i n t o s e v e r a l of the programs. Studied by the programs' designers to p i n p o i n t confusing aspects of programs, these recordings serve to improve program design. Since the i s s u e of v i o l a t i o n of p r i v a c y has been r a i s e d , some of these programs now request permission to r e c o r d a s e s s i o n b e f o r d doing so. At t h i s time, any guarantee of p r i v a c y must be provided by the program designer because TENEX i t s e l f does not have the a b i l i t y to render p r o t e c t i o n . The general design f o r systems o f f e r i n g " s t a t e of the a r t " p r o t e c t i o n i n v o l v e s a t o l e r a n c e f o r f a i l u r e ; that i s , i f a potent i a l offender succeeds i n breaking through some of the defenses, he s t i l l does not p l a c e the e n t i r e computer system at h i s mercy. Encrypting of data f i l e s provides an a d d i t i o n a l l i n e of defense. This method i s used by at l e a s t two calendar or appointment programs on the computer. At t h i s time, however, there are no general e n c r y p t i n g f a c i l i t i e s a v a i l a b l e and users must do t h i s f o r themselves as needed. TENEX provides the u s u a l keyword p r o t e c t i o n at l o g i n time and a measure of f i l e p r o t e c t i o n . Owners of a f i l e may a s s i g n a prot e c t i o n number which s p e c i f i e s some combination of READ, WRITE, EXECUTE, or APPEND access to a f i l e f o r owners, members of a group, or other users. T h i s l e v e l of p r o t e c t i o n i s b a s i c a l l y enough to prevent a c c i d e n t s and most m i s c h i e f . System programmer's around the country are aware of a number of TENEX bugs which permit t h i s access to be v i o l a t e d . One user of our system found a way to p l a c e h i m s e l f i n a mode where he could modify any f i l e on the system. To date, we have no examples of such a c t i v i t y a c t u a l l y having a d e l e t e r i o u s e f f e c t on SUMEX-AIM.
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To make the use of SUMEX-AIM programs easy, on a t r i a l b a s i s f o r p r o s p e c t i v e users, a 'guest account system has been established. Since t h i s makes l o g g i n g i n t o SUMEX-AIM so easy, i t has i n v i t e d some misuse by people using t h i s account to p l a y computer games. A proposed extension to the system now being implemented i s a s p e c i a l "guest EXEC" which would extend the p r o t e c t i o n of the TENEX monitor by a l l o w i n g guest accounts access to only a more r e s t r i c t e d set of programs.
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1
F i l e backup. In order to assure the user maximum p r o t e c t i o n against l o s s of v a l u a b l e work, SUMEX operates a m u l t i - l e v e l f i l e backup system. In a d d i t i o n to a r o u t i n e f i l e backup system, there are f a c i l i t i e s to enable the user to s e l e c t i v e l y a r c h i v e h i s or her d i s k f i l e s . By i s s u i n g a simple command to the TENEX execut i v e , the user can transmit a message to the operator to copy s p e c i f i e d f i l e s to magnetic tape. Each such f i l e i s copied to two magnetic tapes w i t h i n 24 hours of i s s u i n g the a r c h i v e command. F i l e r e t r i e v a l i s a f f e c t e d by a s i m i l a r process. The user a l s o has the a l t e r n a t i v e o p t i o n of being able to lodge f i l e s i n a s p e c i a l backup d i r e c t o r y . F i l e s are h e l d i n t h i s d i r e c t o r y u n t i l the next e x c l u s i v e f i l e dump (see below) a t which time they are d e l e t e d . In t h i s way the user can remove f i l e s from h i s d i r e c t o r y at h i s own choosing knowing they w i l l be a r c h i v e d by the e x c l u s i v e dump. On a system l e v e l , an e f f o r t i s made to maintain f i l e backups such that the maximum p o s s i b l e l o s s , i n the event of a crash f a t a l to the f i l e system, would amount to no more that one day's work. Once each day a l l f i l e s that have been read or w r i t ten w i t h i n the l a s t 48 hours are dumped onto magnetic tape. F i l e s that e x i s t f o r 48 hours are thus h e l d on two separate tapes. The r o t a t i o n p e r i o d f o r f i l e s dumped i n t h i s way i s 60 days. Once each week a f u l l f i l e dump i s made to separate d i s k storage. Each such dump i s kept f o r two weeks a t which time i t i s r e p l a c e d by a new f i l e dump. Each month there i s a f u l l system dump from d i s k to magnetic tape. F i l e s can be recovered from the system backup by sending a message to the operator s p e c i f y i n g the f i l e name(s) and when the f i l e was l a s t read or w r i t t e n ( i f such i n f o r m a t i o n is available). Excessive demand f o r p r o d u c t i o n programs. One of the concepts behind the c r e a t i o n of a shared resource i s e l i m i n a t i o n of the problems which a r i s e when l a r g e , complex computer programs are exported. Since, i n theory, e x p o r t a b i l i t y i s no longer a problem, there i s greater l a t i t u d e i n choice of a language i n which program development can take p l a c e . In the case of some of the DENDRAL programs, i t was thought that program development should take p l a c e i n INTERLISP, a language that lends i t s e l f w e l l to the a r t i f i c i a l i n t e l l i g e n c e nature of these programs, but does not l e a d to p a r t i c u l a r l y e f f i c i e n t run-time code.
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In order to a s c e r t a i n the u s e f u l n e s s of these programs and to determine what areas remain i n need of work, chemist c o l l a b o r a t o r s are being sought. As these users i n c r e a s e i n number and begin to use the programs more f r e q u e n t l y , i t i s almost c e r t a i n that the inherent slowness of the predominately LISP code w i l l a f f e c t the whole system as w e l l as handicap the e f f i c i e n t use of the DENDRAL programs. A d d i t i o n a l l y , some of the chemist-users who are f i n d i n g the programs most u s e f u l and who are most e n t h u s i a s t i c about t h e i r p o t e n t i a l use, are persons working i n i n d u s t r y . Although, i n one sense, t h i s i n t e r e s t from i n d u s t r y could be i n t e r p r e t e d as an i n d i c a t i o n of the " r e a l - w o r l d " u s e f u l n e s s of the programs, i t came as r a t h e r a s u r p r i s e to both SUMEX and DENDRAL personnel. The f a c t that SUMEX-AIM i s funded by NIH as a n a t i o n a l resource p r o h i b i t s the f a c i l i t y from p r o v i d i n g a s e r v i c e , at taxpayer's expense, to a p r i v a t e i n d u s t r y . Although there i s precedent f o r a s i t e funded v i a government grant to charge a fee f o r s e r v i c e , such an arrangement leads to h i g h l y complicated bookkeeping, and i s contrary to the e s s e n t i a l purpose of SUMEX-AIM; to be a r e s e a r c h - o r i e n t e d r a t h e r than a s e r v i c e - o r i e n t e d f a c i l i t y . This leaves the i n d u s t r i a l users i n the p o s i t i o n of being more than w i l l i n g to pay f o r the use of the programs, but of having no mechanism whereby they can be charged. Furthermore, the f a c t that the programs are coded i n LISP f o r a h i g h l y s p e c i a l i z e d environment, almost guarantees the i m p o s s i b i l i t y of export, except to an almost i d e n t i c a l computer system. An intermediate s o l u t i o n that w i l l help to s o l v e the problem of i n d u s t r i a l users on SUMEX and w i l l help to a l l e v i a t e the system l o a d i n g r e s u l t i n g from heavy usage of LISP coded p r o d u c t i o n programs, i s to mount CONGEN on a c l o s e l y r e l a t e d computer which i s operated on a fee f o r s e r v i c e b a s i s . However, i n order to make t h i s program a v a i l a b l e at a reasonable f e e , i t has become evident that i t w i l l be necessary to recode the LISP s e c t i o n s of the p r o gram i n t o a more e f f i c i e n t and e a s i l y exportable language. Research-oriented
Problems
Community mindedness. Those i n v o l v e d i n computer s c i e n c e research at SUMEX face a general problem which i s absent or g r e a t l y lessened at non-network s i t e s ; the problem of community mindedness. The network provides a l a r g e and v a r i e d s e t of other researchers and users who have an i n t e r e s t i n t h e i r work. Although the network-TENEX combination provides new forms of communication w i t h these remote p a r t i e s , the t r a d i t i o n a l means of f u l l y d e s c r i b i n g the use and s t r u c t u r e of a complex program, a d e t a i l e d personto-person d i s c u s s i o n , i s not convenient. Comprehensive documentat i o n gains importance i n such a s i t u a t i o n , and w i t h i n the DENDRAL p r o j e c t a great d e a l of time has been needed i n the development of program d e s c r i p t i o n s which are adequate f o r a d i v e r s e audience. A l s o , i n both DENDRAL and MYCIN, e f f o r t has been and i s being d i r e c t e d toward "human e n g i n e e r i n g " i n program design; to p r o v i d e
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the user with commands which a s s i s t him i n using the programs, i n understanding the l o g i c by which the programs reach c e r t a i n d e c i sions and i n communicating questions or comments on the programs' operation to those r e s p o n s i b l e f o r development. Such "housekeeping" tasks can o f t e n be neglected, y e t are q u i t e important i n smoothing i n t e r a c t i o n with the community. Choice of programming language. High l e v e l programming languages which are designed f o r ease of program development are f r e q u e n t l y poor as p r o d u c t i o n - l e v e l languages. This i s because developmental languages f r e e the researcher from a r a f t of programming d e t a i l s , thus a l l o w i n g him to concentrate upon the c e n t r a l l o g i c a l i s s u e s of the problem, but the automatic handling of these d e t a i l s i s seldom optimal. A l s o , because such languages tend to be s p e c i a l i z e d f o r c e r t a i n computers and operating systems, the e x p o r t a t i o n of programs can be a s e r i o u s problem. One s o l u t i o n to these problems i s the recoding of r e s e a r c h - l e v e l programs i n t o more e f f i c i e n t language when f a s t and exportable v e r s i o n s are needed. Networking g r e a t l y eases the problem of e x p o r t a b i l i t y , but can a l s o aggrevate the problem of e f f i c i e n c y . As mentioned i n the previous s e c t i o n , DENDRAL programs, which are undergoing constant development, found a s u b s t a n t i a l number of p r o d u c t i o n - l e v e l u s e r s . Because of the i n e f f i c i e n c i e s of INTERLISP (a 50- to 100-fold improvement i n running time i s not uncommon when an INTERLISP program i s t r a n s l a t e d i n t o FORTRAN), t h i s use adversely impacted the e n t i r e system. Because the DENDRAL programs are q u i t e l a r g e and complex, t h e i r t r a n s l a t i o n i n t o other languages i s i m p r a c t i c a l l y tedious. A p a r t i a l s o l u t i o n to t h i s problem i s provided by the TENEX operating system, which allows some i n t e r f a c e between programs w r i t t e n i n d i f f e r e n t languages. With such intercommunicat i o n , time-consuming segments of an INTERLISP program which are not undergoing a c t i v e development can be reprogrammed i n another more e f f i c i e n t language. The developmental p a r t s of the program are l e f t i n INTERLISP, where m o d i f i c a t i o n s can e a s i l y be made and t e s t e d . The CONGEN program uses three languages; INTERLISP, FORTRAN and SAIL (26). The SAIL segment was added when a new f e a t u r e , whose implementation was f a i r l y s t r a i g h t f o r w a r d , was included i n CONGEN. Since then, the SAIL p o r t i o n g r a d u a l l y has been taking over some of the more time-consuming tasks. T h i s method allows a balance i n the t r a d e o f f between ease of program development and e f f i c i e n c y of the f i n a l program. Accumulation of expert knowledge i n knowledge-based programs. Just as s t a t i s t i c s - b a s e d programs need to worry about accumulation of l a r g e data bases, knowledge-based programs need to worry about the accumulation of l a r g e amounts of e x p e r t i s e . The performance of these programs i s t i e d d i r e c t l y to the amount of knowledge they have about the task domain — i n a phrase, knowledge i s power. Therefore, one of the goals of a r t i f i c i a l i n t e l l i g e n c e research i s
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to b u i l d systems that not only perform as w e l l as an expert but that a l s o can accumulate knowledge from s e v e r a l experts. Simple a c c r e t i o n of knowledge i s p o s s i b l e only when the " f a c t s " , or i n f e r e n c e r u l e s , that are being added to the program are e n t i r e l y separate from one another. I t i s unreasonable to expect a body of knowledge to be so w e l l organized that the f a c t s or r u l e s do not o v e r l a p . ( I f i s were so w e l l organized, i t i s u n l i k e l y that an a r t i f i c i a l i n t e l l i g e n c e program would be the best encoding of the problem s o l v e r . ) One way of d e a l i n g with the overlap i s to examine the new r u l e s on an i n d i v i d u a l b a s i s , as they are added to the system i n order to remove the o v e r l a p . T h i s was the s t r a t e g y f o r developing the e a r l y DENDRAL programs. However, i t i s very i n e f f i c i e n t and becomes i n c r e a s i n g l y more d i f f i c u l t as the body of knowledge grows. The problem of removing c o n f l i c t s , or p o t e n t i a l c o n f l i c t s , from o v e r l a p p i n g r u l e s becomes more acute when more that one expert adds new r u l e s to the knowledge base. Of course, the advantages of a l l o w i n g s e v e r a l experts to "teach" the system are enormous — not only i s the program's breadth of knowledge p o t e n t i a l l y greater than that of a s i n g l e expert, but the r u l e s are more apt to be r e f i n e d when looked at by s e v e r a l experts. On the other hand, one can expect not only a greater volume of new r u l e s but a higher percentage of c o n f l i c t s when s e v e r a l experts are adding r u l e s . Having a computer program that can accumulate knowledge presupposes having an o r g a n i z a t i o n of the program and i t s knowledge base that allows accumulation. I f the knowledge i s b u i l t i n t o the program as sequences of l o w - l e v e l program statements — as o f t e n happens — then changing the program becomes impossible. Thus, current a r t i f i c i a l i n t e l l i g e n c e research s t r e s s e s the importance of s e p a r a t i n g problem-solving knowledge from the c o n t r o l s t r u c t u r e of the program that uses that knowledge. Another problem, at a p o l i t i c a l r a t h e r than a programming l e v e l , becomes apparent with one accumulation process: how does the program d i s t i n g u i s h an expert from a novice? In the MYCIN p r o gram we have circumvented the problem by having the program ask the current user f o r a keyword that would i d e n t i f y him as an expert. I t i s then a b u r e a u c r a t i c d e c i s i o n as to which users are given that keyword. There i s nothing s u b t l e i n t h i s s o l u t i o n , and one can imagine f a r b e t t e r schemes f o r accomplishing the same t h i n g . The p o i n t here i s that not every user should have the p r i v i l e g e of changing r u l e s that experts have added to the system, and that some safeguards must be implemented. "Human nature" b a r r i e r s to SUMEX use Countering d i s b e l i e f . There i s sometimes a tendency among those u n f a m i l i a r with the c a p a b i l i t i e s and l i m i t a t i o n s of computers and computer programs to express d i s b e l i e f . T h i s i s not d i s b e l i e f i n the sense of worrying that the programs have e r r o r s and produce erroneous r e s u l t s . Indeed, the f a c t that a problem i s being done
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by a computer seems to generate some f a i t h that i t might be r i g h t , or a t l e a s t s i g n i f i c a n t l y reduces questions about c o r r e c t n e s s . The d i s b e l i e f i s that programs, which are designed to model, or to emulate, human problem s o l v i n g w i l l not be capable of u s e f u l performance. T h i s , of course, i s the c l a s s i c argument a g a i n s t a r t i f i c i a l i n t e l l i g e n c e - we t h i n k i n mysterious ways and have such a complex b r a i n that a computer program must be i n f e r i o r . In some cases, authors of a r t i f i c i a l i n t e l l i g e n c e programs have brought such c r i t i c i s m upon themselves by not s t r e s s i n g l i m i t a t i o n s , or by making extravagant c l a i m s . In the DENDRAL p r o j e c t , we have t r i e d to counter t h i s type of d i s b e l i e f i n a number of ways. We have t r i e d to s t r e s s that our programs are designed to a s s i s t , not r e p l a c e chemists. We have always d i s c u s s e d l i m i t a t i o n s to give a reasonable p e r s p e c t i v e on c a p a b i l i t i e s v s . l i m i t a t i o n s of a program. Most importantly however, we have focused on those aspects of problems which are amenable to systematic a n a l y s i s , j i . e . , those problems which can be done manually, but only with d i f f i c u l t y and w i t h the consumption of a great d e a l of time which a chemist could b e t t e r spend on more productive p u r s u i t s . Examples of t h i s would i n c l u d e the a p p l i c a t i o n of PLANNER to mixtures where a l l fragmentations may have to be considered as p o s s i b l e fragments of every molecular i o n , the systematic a n a l y s i s by INTSUM of p o s s i b l e fragmentation processes, the c o n s i d e r a t i o n by MOLION of a l l p l a u s i b l e p o s s i b i l i t i e s , and the s t r u c t u r e generation c a p a b i l i t i e s of CONGEN. We have a l s o t r i e d to reduce chemists' d i s b e l i e f by b l u r r i n g the " o u t s i d e r - i n s i d e r " d i s t i n c t i o n , i n p a r t i c u l a r by having t r a i n e d chemists work on the programs and make them u s e f u l to themselves first. F u r t h e r , when " o u t s i d e " chemists are f i r s t introduced to the programs, the i n t r o d u c t i o n i s done by another chemist who has already thought through and can r e a d i l y e x p l a i n many of the c h e m i s t r y - r e l a t e d problems. The u l t i m a t e way to counter d i s b e l i e f , however, i s to i l l u s t r a t e h i g h l e v e l s of performance. I f a p o t e n t i a l user i s aware of the goals ( i n t e n t ) of a program and i t s l i m i t a t i o n s , a few examples of r e s u l t s which would be extremely d i f f i c u l t to o b t a i n without the program are very c o n v i n c i n g . The " s e c u r i t y " of a l o c a l f a c i l i t y . Networking i s s t i l l a r e l a t i v e l y new concept to many people, and there i s a r e s i s t a n c e to departing from the " t r a d i t i o n a l " modes of computing. There i s a sense of s e c u r i t y i n having a l o c a l computing f a c i l i t y w i t h knowledgeable c o n s u l t a n t s w i t h i n walking d i s t a n c e , and i n having "hard" forms of input (e^j*., boxes of computer cards) and output (e.£., voluminous l i s t i n g s ) . These props are d i f f i c u l t to simul a t e over a network connection - i n most cases a user ' s i n t e r a c t i o n with the remote s i t e takes p l a c e e x c l u s i v e l y through a computer terminal - yet the q u a l i t y of s e r v i c e can match or exceed that of a l o c a l f a c i l i t y ; programs and l a r g e data s e t s can be entered and stored on secondary storage as can l a r g e output f i l e s ; a l l types
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of program and data e d i t i n g can be done w i t h i n t e r a c t i v e e d i t i n g programs; programs can be w r i t t e n i n an i n t e r a c t i v e mode so that small amounts of c o n t r o l i n f o r m a t i o n can be input and key r e s u l t s output i n " r e a l time" over the t e r m i n a l ; and as noted i n a p r e vious s e c t i o n , c o n s u l t a t i o n can be s i g n i f i c a n t l y more productive p r o v i d i n g that the remote operating systems supports the a p p r o p r i ate types of communication p o s s i b i l i t i e s . There can, of course, be no denying that there are problems i n l e a r n i n g to use a d i s t a n t computer system, be i t f o r program development or f o r the use of c e r t a i n programs. Whether or not overcoming these problems to gain access to the s p e c i a l resources which are a v a i l a b l e , i s worth the e f f o r t , i s a question answerable only by the i n d i v i d u a l s i n v o l v e d . F o r t u n a t e l y , there w i l l always be those persons who have a p r e s s i n g problem i n need of s o l u t i o n and who are w i l l i n g to t r y a new approach; r e g a r d l e s s of whether or not they have had p r i o r network experience. IV.
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The SUMEX-AIM computer f a c i l i t y c o n s i s t s of a D i g i t a l Equipment Corporation model KI-10 c e n t r a l processor o p e r a t i n g under the TENEX time s h a r i n g monitor. I t i s l o c a t e d at Stanford U n i v e r s i t y Medical Center, Stanford, C a l i f o r n i a . The system has 256K words (36 b i t ) of high speed memory; 1.6 m i l l i o n words of swapping storage; 70 m i l l i o n words of d i s k s t o r age; two 9-track, 800 b p i i n d u s t r y tape u n i t s ; one dual DEC-tape u n i t ; a l i n e p r i n t e r ; and communications network i n t e r f a c e s providing user t e r m i n a l access v i a both TYMNET and ARPANET. Software support has evolved, and w i l l continue to evolve, based on user research goals and requirements. Major user l a n guages c u r r e n t l y i n c l u d e INTERLISP, SAIL, FORTRAN-10, BLISS-10, BASIC and MACRO-10. Major software packages a v a i l a b l e i n c l u d e OMNIGRAPH, f o r graphics support of m u l t i p l e t e r m i n a l types, and MLAB, f o r mathematical modelling. The SUMEX-AIM computer g e n e r a l l y i s l e f t w i t h no operator i n attendance; thereby h e l p i n g to e l i m i n a t e some overhead, but a l s o c r e a t i n g some problems. Users who wish to run jobs r e q u i r i n g tapes must make arrangements to mount t h e i r own tapes. Likewise, o b t a i n i n g l i s t i n g s from the l i n e p r i n t e r can be somewhat d i f f i c u l t s i n c e there i s no r e g u l a r schedule f o r d i s t r i b u t i o n of t h i s output. The s o l u t i o n to these two problems has been to make keys to the machine room a v a i l a b l e at s t r a t e g i c l o c a t i o n s , convenient to a l l groups of l o c a l u s e r s . T h i s experiment i n b a s i c "resource s h a r i n g " has not r e s u l t e d i n any of the major problems one might expect from having a f a i r l y l a r g e group of people with hands-on access to a computer.
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Acknowledgements The SUMEX-AIM facility is supported by the National Institutes of Health (grant number RR 00785-02), as is the DENDRAL project (grant number RR 00612-05A1). We wish to thank Robert Engelmore, Mark Stefik, Janice Aikens and Peter Friedland for their contributions to this report and Tom Rindfleisch and William White for valuable discussions.
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Literature Cited (1) Gordon, R. Μ., Datamation(1975), 21, (2), 127. (2) "World List of Crystallographic Computer Programs", Second Edition, D. P. Shoemaker, Ed., Bronder-Offset, Rotterdam, 1966. (3) Professor Joshua Lederberg, Principal Investigator. (4) Lederberg, J., Sutherland, G. L . , Buchanan, B. G., Feigenbaum, Ε. Α., Robertson, Α. V., Duffield, A. M. and Djerassi, C., J. Amer. Chem. Soc. (1969), 91, 2973. (5) Duffield, A. M., Robertson, Α. V., Djerassi, C., Buchanan, B. G., Sutherland, G. L . , Feigenbaum, E. A, and Lederberg, J., J. Amer. Chem. Soc. (1969), 91, 2977. (6) Buchanan, B. G., Duffield, A. M. and Robertson, Α. V., "Mass Spectrometry: Techniques and Applications," G. W. A. Milne, Ed., p. 121, John Wiley and Sons, New York, 1971. (7) Dromey, R. G., unpublished results, preprint available on request, Dept. of Computer Science, Serra House, Stanford University, Stanford, Calif. 94305. (8) Biller, J. E. and Biemann, Κ., Anal. Lett. (1974), 7, 515. (9) Several libraries of mass spectral data are available in various forms. The Aldermaston Data Centre (Mass Spectrometry Data Center, AWRE, Aldermaston, Reading RG7 4PR, England) can provide information on the availability of such libraries. (10) Hertz, H. S., Hites, R. A. and Biemann, K., Anal. Chem. (1971), 43, 681. (11) Dromey, R. G., Buchanan, B. G., Smith, D. H., Lederberg, J. and Djerassi, C., J. Org. Chem. (1975), 40, 770. (12) Smith, D. H., Buchanan, B. G., Engelmore, R. S., Duffield, A. M., Yeo, Α., Feigenbaum, Ε. Α., Lederberg, J. and Djerassi, C., J. Amer. Chem. Soc. (1972), 94, 5962. (13) Smith, D. H., Buchanan, B. G., Engelmore, R. S., Aldercreutz, H. and Djerassi, C., J. Amer. Chem. Soc. (1973), 95, 6078. (14) Smith, D. H. and Carhart, R. Ε., Abstracts, 169th Meeting of the American Chemical Society, Philadelphia, April 6-11, 1975. (15) Carhart, R. E . , Smith, D. H., Brown, H. and Djerassi, C., J. Amer. Chem. Soc., submitted for publication. (16) Masinter, L. M., Sridharan, N. S., Lederberg, J. and Smith, D. H., J. Amer. Chem. Soc. (1974). 96, 7702. (17) Masinter, L. M., Sridharan, N. S., Carhart, R. E . , and Smith, D. H., J. Amer. Chem. Soc. (1974), 96, 7714. (18) Brown, H., SIAM Journal on Computing, submitted for
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publication. (19) Wipke, W. T. and Dyott, T. M., J . Amer. Chem. Soc. (1974), 96, 4825. (20) Smith, D. H., Buchanan, B. G., White, W. C., Feigenbaum, E. Α., Lederberg, J. and Djerassi, C., Tetrahedron(1973), 29, 3117. (21) Buchanan, B. G., to appear in the Proceedings of the NATO Advanced Study Institute on Computer Oriented Learning Processes, 1974, Bonas, France. (22) Carhart, R. E . , Smith, D. H. and Brown, H., J. Chem. Inf. Comp. Sci., in press (May, 1975). (23) Smith, D. H., Anal. Chem., in press (May, 1975). (24) Teitelman, W., "INTERLISP Reference Manual," Xerox Corp. (Palo Alto Research Center), Palo Alto, Calif., 1974. (25) Bobrow, D. G., Burchfiel, J. D. and Tomlinson, R. S., Commun. ACM(1972), 15, (3), 135. (26) VanLehn, Κ. Α., "SAIL User Manual," Stanford Artificial Intelligence Laboratory, Stanford, Calif., 1973.
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Networks for Research Sharing
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JAMES C. EMERY Executive Director, Planning Council on Computing in Education and Research, Interuniversity Communications Council, Inc. (EDUCOM), P. O. Box 364, Princeton, N. J. 08540
The importance of the computer continues to grow in terms of the number of applications, number of users served, level of resources expended, and the increasingly crucial role i t plays in organizations and intellectual activities. An organization or professional worker denied access to the best computing resources w i l l suffer increased penalties as these trends continue. The explosive advances in computer technology and the diversity of applications make i t exceedingly d i f f i c u l t for any one person or organization to keep up with the computer f i e l d . Current budget pressures often severely limit the resources available for exploring ways in which the computer can increase an organization's efficiency or effectiveness. Faced with this situation, many organizations are looking to resource sharing as a means to take advantage of the f u l l range of the computer's power while also limiting their expenditures in trying to keep up with the march of technology. Benefits of Sharing The traditional argument for sharing computing power is the substantial economy of scale exhibited by computers. Grosch hypothesized in the late 1940 s that raw capacity increased in proportion to the square of cost, and this relationship has held reasonably well over the past 25 years. Very large compute-bound 1
This reasearch was supported in part by the Office of Naval Research under Contract #N0014-67-A-0216-0007.
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jobs w i l l c o n t i n u e to b e n e f i t from t h i s phenomenon, and so the s h a r i n g o f a l a r g e p r o c e s s o r among manyu s e r s w i l l c o n t i n u e to o f f e r a t t r a c t i v e economies. Other hardware economies are a l s o p o s s i b l e through s h a r i n g . S h a r i n g a l l o w s a u s e r w i t h l a r g e but i n t e r m i t t e n t demands to a v o i d the h i g h c o s t o f maint a i n i n g h i s own, l a r g e l y i d l e , c a p a c i t y . S h a r i n g many demands o f t h i s s o r t can r e s u l t i n a much h i g h e r capaci t y u t i l i z a t i o n than each u s e r c o u l d a c h i e v e on h i s own. T h i s same argument a p p l i e s to i n t e r m i t t e n t peak loads: by m a i n t a i n i n g o n l y the c a p a c i t y n e c e s s a r y to meet the minimum "base l o a d " demands and then u s i n g a shared computer to s a t i s f y peak demands, c a p a c i t y u t i l i z a t i o n can be i n c r e a s e d s u b s t a n t i a l l y . I f jobs are f r e e l y t r a n s p o r t a b l e among m u l t i p l e computers conn e c t e d through a network, g r e a t e r u t i l i z a t i o n can be a c h i e v e d by s h i f t i n g jobs from an o v e r l o a d e d computer to one h a v i n g i d l e c a p a c i t y . A l t h o u g h these economies s h o u l d not be i g n o r e d , they are becoming o f much l e s s importance than they were f o r m e r l y . Hardware c o s t s , and the d i r e c t c o s t s o f o p e r a t i n g a f a c i l i t y , c o n t i n u e to d e c l i n e as a f r a c t i o n of the o v e r a l l c o s t of computing. Other c o s t s -- d a t a c o l l e c t i o n , s t o r a g e , communications, remote t e r m i n a l s , and d e s i g n and maintenance of the system -- have become the dominant f a c t o r s i n most c u r r e n t systems. The c o s t of raw CPU power has become almost i r r e l e v a n t i n many c a s e s , and advances i n e l e c t r o n i c s w i l l continue t h i s trend. Does t h i s mean t h a t the s h a r i n g o f computing r e s o u r c e s has become i r r e l e v a n t ? Not at a l l . The s h a r i n g of s o f t w a r e and databases w i l l c o n t i n u e to o f f e r v e r y s u b s t a n t i a l b e n e f i t s . Indeed, the v e r y t e c h n i c a l advances t h a t have g i v e n us such low-cost p r o c e s s o r s now make i t e c o n o m i c a l l y f e a s i b l e to o p e r a t e a w i d e s p r e a d network f o r s h a r i n g programs and d a t a . The s h i f t i n c o s t s from hardware to o t h e r components w i l l i n c r e a s e the r e l a t i v e importance o f t h i s form o f sharing. Such s h a r i n g spreads the c o s t of d e v e l o p i n g , o p e r a t i n g , and m a i n t a i n i n g the programs and databases. I t a l s o a v o i d s problems of i n c o n s i s t e n c i e s and r e c o n c i l i a t i o n t h a t i n e v i t a b l y a r i s e i f r e s u l t s from separate programs or databases must be compared. In some cases a program or database may o f f e r unique c a p a b i l i t i e s t h a t can o n l y be a c c e s s e d through s h a r i n g . Ways of
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means. The t r a d i t i o n a l way of s h a r i n g software and d a t a i s by r e p l i c a t i n g the r e s o u r c e at the u s e r ' s own computer c e n t e r . A s t a t i s t i c a l package or a database c o n s i s t i n g o f c o r p o r a t e f i n a n c i a l d a t a , f o r example, might be r e c o r d e d on magnetic tape and t r a n s p o r t e d to each computer c e n t e r s e r v i n g u s e r s who want to access the shared r e s o u r c e . T h i s has proved extremely u s e f u l , but i t c e r t a i n l y has some s e r i o u s l i m i t a t i o n s . Incomp a t i b l e hardware or systems s o f t w a r e o f t e n make t r a n s p o r t a b i l i t y q u i t e d i f f i c u l t -- even among machines o f the same m a n u f a c t u r e r and model number. The maintenance of d u p l i c a t e programs i s u s u a l l y a n o n - t r i v i a l problem. P r o v i d i n g t r a i n i n g and o t h e r s e r v i c e s to remote u s e r s i s d i f f i c u l t and expensive -- and t h e r e f o r e u s u a l l y not done v e r y w e l l . With few e x c e p t i o n s , s u c c e s s f u l examples o f t r a n s p o r t e d r e s o u r c e s have been a c h i e v e d by an o r g a n i z a t i o n t h a t had a s t r o n g i n c e n t i v e to promote t r a n s p o r t a b i l i t y and was w i l l i n g to p r o v i d e the n e c e s s a r y e f f o r t and r e s o u r c e s to make i t happen. A network t h a t p r o v i d e s remote u s e r s access to a shared r e s o u r c e overcomes some (but by no means a l l ) of the l i m i t a t i o n s o f program and database t r a n s p o r t ability. I t a l s o p e r m i t s the s h a r i n g o f hardware r e s o u r c e s as w e l l as programs or d a t a . I f a u s e r wants to access a program or database, the computation norm a l l y takes p l a c e at the s i t e where the program or database i s m a i n t a i n e d , but i n some cases a u s e r might p r e f e r to t r a n s m i t the r e s o u r c e to h i s own l o c a l comp u t e r and p e r f o r m the computation t h e r e . Network o p e r a t i o n may be e i t h e r c e n t r a l i z e d or decentralized. A c e n t r a l i z e d network may c o n s i s t o f one or more computers* governed as a s i n g l e e n t i t y . Hardware and software are u s u a l l y s t a n d a r d i z e d , and a l l u s e r s must conform to the s t a n d a r d . In c o n t r a s t , a d e c e n t r a l i z e d network c o n s i s t s o f m u l t i p l e computers, each o f which i s governed i n d e p e n d e n t l y . C e n t r a l i z e d management o f the network encourages s t a n d a r d i z a t i o n and e f f i c i e n c y . A d e c i s i o n can be made on the b a s i s of i t s e f f e c t on the network as a whole, r a t h e r than on o n l y one p a r t of i t . For examp l e , the number and c o n f i g u r a t i o n o f computers i n the network, and the a l l o c a t i o n of t a s k s among them, can be determined on the b a s i s of the b e s t b a l a n c e between c o s t , r e l i a b i l i t y , response time, and the l i k e . A s i n g l e computer s e r v i n g remote t e r m i n a l s has been l a b e l e d a s t a r network, a l t h o u g h t h e r e i s some q u e s t i o n whether t h i s s h o u l d be r e g a r d e d as a network.
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What may appear advantageous i n p r i n c i p l e , howe v e r , may n o t always prove to be a t t r a c t i v e i n p r a c tice. O p t i m i z a t i o n o f a complex network i s an enormously complex t a s k , and the c e n t r a l i z e d d e c i s i o n p r o c e s s may n o t be a b l e t o cope w i t h i t . Managers o f a l a r g e , c e n t r a l i z e d network may become l e s s r e s p o n s i v e to u s e r needs than t o t h e i r own (perhaps l i m i t e d ) c r i t e r i a of efficiency. The o r g a n i z a t i o n s s e r v e d by the network may p r e f e r t o p a r t i c i p a t e i n i t s management i n s t e a d o f t u r n i n g over t h i s t a s k to a c e n t r a l i z e d group. These d i s a d v a n t a g e s have l a r g e l y r e s t r i c t e d the c e n t r a l i z e d approach t o networks e s t a b l i s h e d by a s i n g l e o r g a n i z a t i o n t o s e l l e x t e r n a l s e r v i c e s o r to s e r v e i t s own s u b u n i t s ; v e r y few independent o r g a n i z a t i o n s have banded t o g e t h e r t o form a c e n t r a l i z e d n e t work t o serve t h e i r combined needs. U n i v e r s i t i e s , i n p a r t i c u l a r , have seldom chosen t h i s p a t h except through the a p p l i c a t i o n o f e x t e r n a l i n c e n t i v e s or p r e s sure (by a S t a t e l e g i s l a t u r e , f o r example). In the summer o f 1974, e i g h t e e n u n i v e r s i t i e s (soon t o be twenty) agreed to form a P l a n n i n g C o u n c i l on Computing i n E d u c a t i o n and Research. Organized w i t h i n the c o r p o r a t e s t r u c t u r e o f EDUCOM, the C o u n c i l has e s t a b l i s h e d as i t s p r i m a r y g o a l the e x p l o r a t i o n and development o f ways t o improve the e f f i c i e n c y and e f f e c t i v e n e s s o f computing w i t h i n h i g h e r e d u c a t i o n . A network w i l l v e r y l i k e l y p l a y an important r o l e i n meeting t h i s o b j e c t i v e . Any such network w i l l undoubtedly c o n s i s t o f d e c e n t r a l i z e d computer c e n t e r s o p e r a t e d by independent u n i v e r s i t i e s and c o l l e g e s . Costs o f S h a r i n g S h a r i n g , though v e r y a t t r a c t i v e i n a number o f c i r c u m s t a n c e s , does n o t come f o r f r e e . When hardware i s shared among m u l t i p l e u s e r s , some means must e x i s t f o r a l l o c a t i n g r e s o u r c e s among j o b s . At the d e t a i l e d l e v e l , the computer's o p e r a t i n g system must a l l o c a t e CPU time, p r i m a r y and a u x i l i a r y s t o r a g e , i n p u t / o u t p u t f a c i l i t i e s , and the l i k e ; at a h i g h e r l e v e l , s h a r i n g e n t a i l s e x t r a e f f o r t t o determine the combined hardware and software needs o f u s e r s , e s t a b l i s h p r i c i n g p o l i c i e s t o a l l o c a t e c o s t s , d e f i n e j o b p r i o r i t i e s , and s i m i l a r matters concerned w i t h the j o i n t use o f a shared r e s o u r c e . S h a r i n g o f a computing r e s o u r c e can be expanded -w i t h the aim t o i n c r e a s e the economies o f s c a l e - - b y a t t r a c t i n g a broader group o f u s e r s . This necessarily i n c r e a s e s the g e n e r a l i t y o f the system, o f t e n a t a
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c o n s i d e r a b l e c o s t . For example, a computer t h a t comb i n e s s c i e n t i f i c computing w i t h d a t a p r o c e s s i n g might w e l l r e s u l t i n u s e f u l economies o f s c a l e ; the genera l i t y and c o m p l e x i t y of the combined system w i l l c e r t a i n l y be g r e a t e r than i f each group of u s e r s were s e r v e d by a s e p a r a t e machine. Generality in software -- f o r example, a s t a t i s t i c a l a n a l y s i s package t h a t o f f e r s a l a r g e number of o p t i o n s i n o r d e r to s e r v e a wide range of u s e r s -- f o s t e r s s h a r i n g . I t does t h i s , though, at a c o s t i n d e s i g n time, o p e r a t i n g e f f i c i e n c y , and c o m p l e x i t y . Rather than i n c r e a s i n g a s y s t e m s g e n e r a l i t y i n o r d e r t o a t t r a c t a wider c l a s s o f u s e r s , one might a l t e r n a t i v e l y r e q u i r e the u s e r s to adapt to a common s t a n d a r d as a way o f i n c r e a s i n g r e s o u r c e s h a r i n g . T h i s a v o i d s some c o s t s o f g e n e r a l i t y , but might impose on u s e r s an e x t r a c o s t o f changing to the new standa r d , l i v i n g w i t h a system t h a t does not meet t h e i r needs as w e l l as a more t a i l o r e d r e s o u r c e , or s i m p l y doing without a d e s i r a b l e s e r v i c e . In any case, the s t a n d a r d i z a t i o n i s not a c h i e v e d w i t h o u t c o s t . S h a r i n g can a l s o be expanded by i n c r e a s i n g the s i z e of the g e o g r a p h i c a l a r e a s e r v e d i n s t e a d of i n c r e a s i n g the i n t e n s i t y o f use w i t h i n a g i v e n a r e a . T h i s a l l o w s the use o f a r e l a t i v e l y s p e c i a l i z e d r e source -- and t h e r e b y g a i n i n g the economies o f spec i a l i z a t i o n (or a v o i d i n g the diseconomies of g e n e r a l i z a t i o n ) -- w h i l e at the same time p e r m i t t i n g a l a r g e enough l o a d to e x p l o i t some economies o f s c a l e . Thus, a n a t i o n w i d e or worldwide group of u s e r s h a v i n g a common i n t e r e s t might w e l l j u s t i f y d e v e l o p i n g t a i l o r e d hardware or s o f t w a r e to s e r v e t h a t s p e c i a l i z e d market. The c o s t of such s h a r i n g i s the c o s t o f communications over a w i d e l y d i s p e r s e d a r e a , as w e l l as the added c o s t o f p r o v i d i n g m a r k e t i n g and o t h e r s u p p o r t s e r v i c e s to a group o f remote u s e r s . A d m i n i s t r a t i o n of a network adds f u r t h e r to the c o s t o f r e s o u r c e s h a r i n g . C o n t r a c t u a l arrangements must be made w i t h u s e r s and s u p p l i e r s of s e r v i c e . A u t h o r i z a t i o n p r o c e d u r e s , which d e f i n e who has access t o what r e s o u r c e s , must be e s t a b l i s h e d and o p e r a t e d . I n f o r m a t i o n about a v a i l a b l e r e s o u r c e s must be c o l l e c t e d , m a i n t a i n e d , and d i s s e m i n a t e d . A p o t e n t i a l c o s t o f s h a r i n g i s the l o s s of autonomy and c o n t r o l brought about by j o i n t use o f a resource. S c h e d u l i n g problems and the need to adapt to a common s t a n d a r d o f t e n a t t e n d such s h a r i n g . S c h e d u l i n g d e l a y s and compromise s t a n d a r d s t h a t s e r v e no one group v e r y w e l l c o u l d i n some cases impose s e r i o u s c o s t s . These c o s t s can mount i f the network i s
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a d m i n i s t e r e d c e n t r a l l y w i t h a narrow view of " e f f i c i e n c y " and an i n s u f f i c i e n t m o t i v a t i o n to remain r e s p o n s i v e to u s e r needs (which can e a s i l y happen, f o r example, i f the network s e r v e s a c a p t u r e d audience h a v i n g no a l t e r n a t i v e source o f computing s e r v i c e s ) .
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Characteristics Education
o f a " F a c i l i t a t i n g " Network f o r H i g h e r
The d e s i g n o f a network must r e c o g n i z e the t r a d e o f f s among the c o s t s and b e n e f i t s o f r e s o u r c e sharing. Each s i t u a t i o n may c a l l f o r a unique s e t o f d e c i s i o n s r e g a r d i n g the u s e r s to be s e r v e d , s e r v i c e s o f f e r e d , a p p r o p r i a t e degree o f c e n t r a l i z a t i o n and s t a n d a r d i z a t i o n , and a d m i n i s t r a t i v e arrangements. These d e c i s i o n s are always s u b j e c t to change i n l i g h t of more d e t a i l e d d e s i g n work or o p e r a t i n g e x p e r i e n c e . The computing community w i t h i n h i g h e r e d u c a t i o n -s t u d e n t s , f a c u l t y members, r e s e a r c h e r s , and administ r a t o r s -- has a number o f s p e c i a l needs; a network d e s i g n e d to serve t h i s p o p u l a t i o n must r e c o g n i z e t h i s fact. Each i n s t i t u t i o n views i t s e l f as autonomous and i n s i s t s on remaining so. I n d i v i d u a l s w i t h i n each i n s t i t u t i o n are themselves o f t e n independent o f effective central control. Users range from the n a i v e to the s u p e r - s o p h i s t i c a t e d . A p p l i c a t i o n s c o v e r an extremely wide spectrum o f academic d i s c i p l i n e s , computing t e c h n i q u e s , and l e v e l of r e s o u r c e s r e q u i r e d . In view o f these s p e c i a l r e q u i r e m e n t s , one can o u t l i n e d e s i r a b l e c h a r a c t e r i s t i c s o f a network f o r higher education: • The network w i l l p r e s e r v e the autonomy of each i n s t i t u t i o n t h a t s u p p l i e s or purchases s e r v i c e s on the network. • Hardware, programs, and databases w i l l be d i s t r i b u t e d g e o g r a p h i c a l l y and a d m i n i s t e r e d decentrally. • The network w i l l not have a monopoly as a buyer or s e l l e r of s e r v i c e s -- i . e . , each buyer and s e l l e r w i l l be f r e e to d e a l w i t h o t h e r s o u t s i d e of the network ( a l t h o u g h v o l u n t a r y e x c l u s i v e c o n t r a c t s would not be precluded). • E n t r y and e x i t from the network w i l l be open to a l l i n s t i t u t i o n s . • A market mechanism w i l l be the p r i m a r y means of a l l o c a t i n g r e s o u r c e s of the network. • A wide v a r i e t y o f s p e c i a l i z e d and p r o p r i e t a r y s e r v i c e s w i l l be o f f e r e d over the network.
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Network a d m i n i s t r a t i v e f u n c t i o n s authorizat i o n o f u s e r s , b i l l i n g and r e p o r t i n g , d i s s e m i n a t i o n of i n f o r m a t i o n about a v a i l a b l e r e s o u r c e s , and s i m i l a r s e r v i c e s aimed a t f a c i l i t a t i n g r e l a t i o n s between buyers and s e l l e r s -- w i l l be a v a i l a b l e from a c e n t r a l network o r g a n i z a t i o n . Buyers and s e l l e r s w i l l a v a i l themselves of these f a c i l i t a t i n g s e r v i c e s o n l y to the e x t e n t t h a t i t s e r v e s t h e i r i n t e r e s t s to do so. The c o s t s o f o p e r a t i n g the network and p r o v i d i n g computing r e s o u r c e s must be borne by the u s e r s o f the network.
of a F a c i l i t a t i n g
Network
The a v a i l a b i l i t y of a n a t i o n a l f a c i l i t a t i n g n e t work w i l l open up important new o p p o r t u n i t i e s f o r c o l l e g e s and u n i v e r s i t i e s . Not a l l i n s t i t u t i o n s w i l l use the network i n the same way. Some i n s t i t u t i o n s might choose to become t o t a l l y dependent on the network f o r computing s e r v i c e s , doing away w i t h t h e i r own l o c a l computers (except f o r t e r m i n a l s w i t h v a r y i n g degrees o f " i n t e l l i g e n c e ) . Others may not buy s e r v i c e s to any s i g n i f i c a n t e x t e n t , but r a t h e r use the network to market t h e i r s e r v i c e s to e x t e r n a l u s e r s . And, i n d e e d , o t h e r i n s t i t u t i o n s w i l l d e c i d e to i g n o r e the network, c h o o s i n g to be n e i t h e r a buyer nor s e l l e r o f e x t e r n a l computing r e s o u r c e s . The t y p i c a l l a r g e i n s t i t u t i o n w i l l p r o b a b l y be both a buyer and a s e l l e r o f s e r v i c e . I t w i l l no doubt serve the b u l k of i t s u s e r s w i t h i t s own l o c a l computer. The emphasis i s l i k e l y to be p l a c e d on meeting the a s s u r e d "base l o a d " r e q u i r e m e n t s , and then meeting peak o v e r l o a d s from the network. Relatively s i m p l e , low c o s t a p p l i c a t i o n s -- such as r o u t i n e b a t c h p r o c e s s i n g and s m a l l i n t e r a c t i v e programs -- w i l l be handled l o c a l l y . The i n s t i t u t i o n can gear up to s a t i s f y these needs i n a v e r y c o s t - e f f e c t i v e manner -- f o r example, w i t h a purchased machine c o n f i g u r e d f o r e f f i c i e n t b a t c h p r o c e s s i n g and kept f u l l y loaded over a long l i f e t i m e , or by a minicomputer d e d i c a t e d to providing r e l a t i v e l y l i m i t e d time-sharing c a p a b i l i t i e s ( o n l y programs w r i t t e n i n BASIC, s a y ) . Most computer u s e r s on a campus c o u l d be s a t i s f i e d w i t h i n the l o c a l base l o a d c a p a c i t y , w h i l e r e l a t i v e l y few ( p r o b a b l y fewer than 20 p e r c e n t ) would have to r e s o r t to the network to o b t a i n more s p e c i a l i z e d s e r v i c e s . D e s p i t e the f a c t t h a t few u s e r s would r e q u i r e network s e r v i c e s , the a v a i l a b i l i t y of such s e r v i c e s 1 1
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would p e r m i t s u b s t a n t i a l economies. T r a d i t i o n a l l y , an i n s t i t u t i o n ' s computer c e n t e r has f e l t o b l i g e d to o f f e r a wide range of s e r v i c e s , because u s e r s had no o t h e r source. I f , however, the network a l t e r n a t i v e e x i s t s , the c h o i c e o f which s e r v i c e to o f f e r l o c a l l y can be r e s o l v e d l a r g e l y on t e c h n i c a l and economic grounds. S p e c i a l i z e d s e r v i c e s t h a t are r a r e l y r e q u i r e d t y p i c a l l y absorb a d i s p o r t i o n a t e share of c o s t s at most computer centers. I f these low-volume, h i g h - c o s t a p p l i c a t i o n s can be s e r v e d through the network, s u b s t a n t i a l reduct i o n s can be e f f e c t e d i n hardware, programming, and data c o l l e c t i o n costs. The s u p p l i e r o f a s p e c i a l i z e d s e r v i c e can combine the demands from many i n s t i t u t i o n s i n o r d e r to s p r e a d the h i g h c o s t of p r o v i d i n g the service. Not a l l s o p h i s t i c a t e d and s p e c i a l i z e d s e r v i c e s w i l l be o b t a i n e d from the network; most i n s t i t u t i o n s w i l l choose to o f f e r s e r v i c e s i n which they have a s p e c i a l i n t e r e s t or unique c a p a b i l i t i e s . Network s a l e s of these s e r v i c e s to e x t e r n a l u s e r s might o f t e n o f f s e t a u n i v e r s i t y ' s p u r c h a s e s o f o t h e r s e r v i c e s from o t h e r institutions. Thus, a u n i v e r s i t y c o u l d l i m i t i t s net e x t e r n a l purchases w h i l e at the same time p e r m i t t i n g i t s u s e r s to take advantage o f a v a s t l y expanded a r r a y of s e r v i c e s a v a i l a b l e from the network. S h a r i n g over a n a t i o n a l network would o f f e r to a l l i n s t i t u t i o n s the b e s t computing r e s o u r c e s a v a i l a b l e throughout the c o u n t r y . Even a m o d e s t - s i z e d c o l l e g e or u n i v e r s i t y might o b t a i n access to l a r g e - s c a l e computers or hardware d e s i g n e d f o r s p e c i a l i z e d a p p l i c a t i o n s . It c o u l d take advantage of an e x t e n s i v e l i b r a r y of programs f o r p e r f o r m i n g s t a n d a r d a n a l y s e s or s p e c i a l i z e d a p p l i c a t i o n s i n such d i v e r s e areas as f i n a n c i a l p l a n n i n g models f o r u n i v e r s i t y a d m i n i s t r a t o r s and computer-assisted instruction material. I t s f a c u l t y and s t u d e n t s c o u l d r e t r i e v e i n f o r m a t i o n from a wide range o f databases t h a t d e a l w i t h such matters as econom e t r i c and demographic d a t a , b i b l i o g r a p h i c r e f e r e n c e s , and p h y s i c a l c h a r a c t e r i s t i c s of m a t e r i a l s . Not even the l a r g e s t and most h e a v i l y endowed u n i v e r s i t i e s c o u l d hope to p r o v i d e such a wide range of r e s o u r c e s except through s h a r i n g . But s m a l l e r i n s t i t u t i o n s perhaps s t a n d to g a i n even more than l a r g e ones. The s h a r i n g of r e s o u r c e s p e r m i t s a s m a l l c o l l e g e to r e t a i n i t s i d e n t i t y and i n d i v i d u a l i t y w h i l e at the same time p e r m i t t i n g i t to o f f e r the same c o m p u t a t i o n a l r e s o u r c e s a v a i l a b l e at a l a r g e i n s t i t u t i o n . Without access to s h a r e d r e s o u r c e s , i t would be at a severe d i s a d v a n t a g e i n a t t r a c t i n g the b e s t f a c u l t y and students.
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Some r e g i o n a l and s t a t e w i d e networks have a l r e a d y been e s t a b l i s h e d as a means o f g a i n i n g the advantages of s h a r i n g . A l t h o u g h they have c e r t a i n l y expanded the s e r v i c e s a v a i l a b l e to u s e r s , they are s t i l l l i m i t e d i n their capabilities. Such networks thus become prime c a n d i d a t e s f o r l i n k i n g to a " d i s t r i b u t e d " network t h a t combines l o c a l , r e g i o n a l , and n a t i o n a l r e s o u r c e sharing.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch014
Problems to Overcome As c o m p e l l i n g as the argument i s f o r such sharing, the f a c t i s t h a t r e l a t i v e l y l i t t l e o f i t curr e n t l y takes p l a c e among e d u c a t i o n a l i n s t i t u t i o n s . To some e x t e n t , t h i s stems from the c r e a t i v e n a t u r e o f e d u c a t i o n a l and r e s e a r c h i n s t i t u t i o n s t h a t encourages s t u d e n t s and f a c u l t y to d i s c o v e r t h i n g s on t h e i r own. It i s easy to overemphasize such r e s i s t e n c e to shari n g , however; f a r more s e r i o u s have been the l i m i t a t i o n s o f e a r l i e r t e c h n o l o g y and a d m i n i s t r a t i v e impediments to e f f e c t i v e s h a r i n g . The t r a n s p o r t a b i l i t y of programs and d a t a has always p r o v e d more d i f f i c u l t than one might suppose. As a r e s u l t , i t i s o f t e n e a s i e r t o r e c r e a t e a program or database than i t i s to f i n d i t at some o t h e r l o c a t i o n and t r a n s p o r t i t to a l o c a l f a c i l i t y or use i t remotely. Because o f the l i m i t e d s h a r i n g t h a t c u r r e n t l y takes p l a c e , l i t t l e i n c e n t i v e e x i s t s f o r f a c u l t y members or t h e i r i n s t i t u t i o n s to e x e r t the e x t r a e f f o r t r e q u i r e d to make t h e i r r e s o u r c e s more t r a n s p o r t a b l e . In o r d e r f o r a program to be used e l s e w h e r e , i t must be c a r e f u l l y t e s t e d and debugged, e x h a u s t i v e l y documented, and f a i t h f u l l y m a i n t a i n e d and extended. The e d u c a t i o n of p o t e n t i a l u s e r s and even d i r e c t p e r s o n a l a s s i s t a n c e are o f t e n n e c e s s a r y . P r o p r i e t a r y f i r m s have been r e l a t i v e l y s u c c e s s f u l i n p r o v i d i n g s e r v i c e s to remote u s e r s , but o n l y because they have had the economic i n c e n t i v e s to do so; members of the academic community t y p i c a l l y have had n e i t h e r f i n a n c i a l nor p r o f e s s i o n a l i n c e n t i v e s to share c o m p u t a t i o n a l resources. It i s q u i t e c l e a r t h a t e x t e n s i v e s h a r i n g w i l l not take p l a c e u n t i l a b e t t e r mechanism e x i s t s to f o s t e r it. One of the important t e c h n i c a l r e q u i r e m e n t s i s a communications network t h a t l i n k s e d u c a t i o n a l i n s t i t u tions. The network must p e r m i t ready and t i m e l y access to a l l o f the a v a i l a b l e r e s o u r c e s at each o f the conn e c t e d computer c e n t e r s . A p r o s p e c t i v e u s e r must a l s o have access to i n f o r m a t i o n about what r e s o u r c e s are
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a v a i l a b l e and t h e i r p r i c e s . I f the u s e r runs i n t o d i f f i c u l t i e s i n u s i n g a remote r e s o u r c e , he s h o u l d be a b l e to o b t a i n a s s i s t a n c e and i n s t r u c t i o n s . The t e c h n o l o g y f o r d e v e l o p i n g such a network already l a r g e l y e x i s t s . Computer o p e r a t i n g systems have developed t o a p o i n t t h a t p e r m i t s widespread shari n g among many u s e r s and programs. Commercial "packet s w i t c h i n g " networks and o t h e r r e c e n t advances i n communications technology w i l l provide h i g h l y r e l i a b l e and r e l a t i v e l y 1 ow-cost d a t a t r a n s m i s s i o n . F u r t h e r more, the c o s t o f communications i n an advanced n e t work can be made l a r g e l y independent o f d i s t a n c e ; as a r e s u l t , g e o g r a p h i c a l s e p a r a t i o n w i l l cease to i n h i b i t s h a r i n g to the e x t e n t t h a t i t has i n the p a s t . The p r i n c i p a l problems t h a t remain a r e c h i e f l y a d m i n i s t r a t i v e and m o t i v a t i o n a l . In o r d e r f o r the network t o f u n c t i o n w i t h any hope o f s u c c e s s , a means must e x i s t to c o o r d i n a t e network a c t i v i t i e s , p r o v i d e communications s e r v i c e s , e s t a b l i s h p r i c e s , d i s s e m i n a t e i n f o r m a t i o n about a v a i l a b l e r e s o u r c e s , s i m p l i f y access procedures, provide i n c e n t i v e s to s u p p l i e r s o f r e s o u r c e s , c o n t r o l access t o the network, p r o v i d e s e c u r i t y and p r i v a c y , and handle the b i l l i n g f o r s e r v i c e s rendered. The network w i l l r e l y p r i m a r i l y on a market mechanism t o a l l o c a t e r e s o u r c e s and encourage s u p p l i e r s to remain r e s p o n s i v e t o u s e r needs. Conditions within the network -- many buyers and s e l l e r s and up-to-date i n f o r m a t i o n about the s e r v i c e s a v a i l a b l e and t h e i r p r i c e s (with perhaps a q u a l i t y r a t i n g as w e l l ) -approximate the e c o n o m i s t s d e f i n i t i o n of a perfectly c o m p e t i t i v e market w i t h i t s a t t e n d a n t e f f i c i e n c y i n a l l o c a t i n g resources. P r i c i n g o b v i o u s l y p l a y s a c r i t i c a l r o l e i n such a network. S u p p l i e r s would have an i n c e n t i v e t o s e t p r i c e s t h a t encourage e f f i c i e n t use o f t h e i r r e s o u r c e s . For example, p r i c e d i f f e r e n t i a l s s h o u l d m o t i v a t e some u s e r s t o s h i f t t h e i r demands from peak t o o f f - p e a k p e r i o d s i n o r d e r t o impose a more l e v e l l o a d on the system. The p r i c i n g s t r u c t u r e s h o u l d be f l e x i b l e enough t o p e r m i t buyers and s e l l e r s t o s a t i s f y t h e i r needs w i t h i n a l e v e l o f r i s k they are w i l l i n g t o assume. F o r example, l o n g term c o n t r a c t s s h o u l d be p e r m i t t e d t o reduce u n c e r t a i n t y r e g a r d i n g the a v a i l a b i l i t y o f s e r v i c e and the p r i c e s t h a t w i l l be charged. On the o t h e r hand, " s p o t " s a l e s at any p r i c e above m a r g i n a l c o s t s h o u l d a l s o be p e r m i t t e d to encourage the use o f excess c a p a c i t y ( a l t h o u g h t h i s opens up some v e r y d i f f i c u l t i s s u e s c o n c e r n i n g f u l l v e r s u s m a r g i n a l p r i c i n g and c o s t a c c o u n t i n g r e g u l a t i o n s o f the F e d e r a l government). 1
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Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch014
Conclusions Given the independent n a t u r e o f e d u c a t i o n a l i n s t i t u t i o n s , i t i s almost c e r t a i n t h a t a m o n o l i t h i c , c e n t r a l i z e d computing network would be n e i t h e r f e a s i b l e nor d e s i r a b l e . C o n n e c t i o n to the network, and the use or s u p p l y i n g o f network r e s o u r c e s , w i l l remain a matter governed by d e c e n t r a l i z e d d e c i s i o n s . Each i n s t i t u t i o n w i l l be g u i d e d by i t s own s e l f - i n t e r e s t . But i n p u r s u i n g i t s own i n t e r e s t s , an i n s t i t u t i o n w i l l have an i n c e n t i v e t o become a s u p p l i e r o f s e r v i c e s f o r which i t enjoys a comparative advantage and to purchase s e r v i c e s t h a t i t can o b t a i n more c h e a p l y , o r w i t h h i g h e r q u a l i t y , than d u p l i c a t i n g them l o c a l l y . Thus, the i n v i s i b l e hand o f Adam Smith, r a t h e r than the heavy hand o f a c e n t r a l i z e d b u r e a u c r a t , w i l l p r o v i d e the p r i m a r y means o f f o s t e r i n g the exchange o f s e r v i c e s . A " f a c i l i t a t i n g network" p r o v i d e s a l l o f the advantages o f d e c e n t r a l i z e d o p e r a t i o n , w h i l e a l s o c r e a t i n g v a s t o p p o r t u n i t i e s t h a t would o t h e r w i s e not exist. Not o n l y would i t g r e a t l y broaden the r e s o u r c e s a v a i l a b l e t o u s e r s o f computers and d a t a b a s e s , but i t c o u l d a l s o open e x c i t i n g p o s s i b i l i t i e s f o r p e r s o n s who have so f a r not b e n e f i t e d much from computer t e c h nology. As the c o s t o f t e r m i n a l s and communications goes down, i t i s not a t a l l i n c o n c e i v a b l e t h a t v i r t u a l l y e v e r y f a c u l t y member and s t u d e n t w i l l have access t o a network through h i s own t e r m i n a l . A w i d e s p r e a d network o f t h i s s o r t c o u l d be used to communicate among s c h o l a r s as w e l l as w i t h computers. Even the most c o n f i r m e d n o n - q u a n t i t a t i v e p e r s o n c o u l d take advantage o f some o f the network s e r v i c e s -- f o r example, an " e l e c t r o n i c m a i l b o x " t h a t a l l o w s him to communicate r a p i d l y and i n e x p e n s i v e l y w i t h remote c o l laborators. Each p e r s o n would thus have access t o both computer-based and human r e s o u r c e s t h r o u g h o u t the c o u n t r y and, i n d e e d , the w o r l d . The u s e f u l n e s s o f the s o - c a l l e d " i n v i s i b l e c o l l e g e , " the i n f o r m a l p e r s o n - t o p e r s o n network t h a t has proven so e f f e c t i v e i n the exchange o f i n f o r m a t i o n among s c h o l a r s , would be augmented immeasurably. The development o f a mature network w i l l come about through an extended and c a u t i o u s e v o l u t i o n a r y process. At each stage i n i t s development the system must prove i t s worth by s u s t a i n i n g i t s e l f f i n a n c i a l l y . Growth i n usage w i l l be g r a d u a l as i n s t i t u t i o n s accommodate themselves t o new o p p o r t u n i t i e s and make approp r i a t e adjustments i n t h e i r l o c a l computer c e n t e r s . There seems t o be l i t t l e doubt, however, t h a t a
230
COMPUTER NETWORKING AND CHEMISTRY
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ch014
w i d e s p r e a d network w i l l e v o l v e . The arguments f o r i t are c o m p e l l i n g , and we can see no i n s u p e r a b l e t e c h n i c a l , economic, or a d m i n i s t r a t i v e problems t h a t would p r e v e n t i t s development.
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ix001
INDEX A Acetylcholine 10 Adams-Bashforth 36 Adams-Bashforth predictor-corrector integration 39 Administrative data processing (ADP) 146 A D P , administrative data processing 146 Air Research Automatic Computer, O A R A C Office of 155 Allosteric effects 45 Analysis conformational 28 electrical system 46 Fourier 46 mechanical system 46 Angles, bond lengths and 30 Applications models of 41 of network conferencing, geologic 53 specific biomolecular 43 ARPA 53,58 ARPANET 9,42, 111, 156 Array processor, Floating Point Systems' 36 A S D Computer Center, background on the 154 Assembled testing in a large network, computer 129 ASSIGN 120 Assignment, core memory 104 Associative processing 24 Astrophysics 22 Atomic motion 22 Atomic positions 27 Β Barrel-roll discriminator 33,36 Bashforth, Adams36 Batch-processing, open-shop 93 BCM 87 Beam scattering, molecular 30 BINARY 75 BISON 163 BISONMC 163, 166 Bond lengths and angles 30 Bond strengths 30 Born-Oppenheimer 28 Box, twinkle 26 Brookhaven National Laboratory 4 BUILDER 3 Bus structure, memory 102
C CALCOMP 92 Calculation, maximum likelihood 24 Calculational Techniques 23 Calculations, quantum mechanical .... 28 CAMAC 37, 40,42, 48 Cambridge Crystal Data File 6 Cancer Research, Institute for 4 Capacity measurements, heat 100 Card records, job control 170 Carnegie-Mellon Multi-Mini Processor 25 Catalysis, enzyme 128 CATC 150 CD 30 CDC-CTBERNET 9 Central, network 68 Centralized/localized computing Ill Channel interface Ill Characteristics, network programming 73 Charge distributions 30 Chemical applications of interactive computing 197 kinetics 46 physics 20 reactions and evolution of molecular systems, dynamics 41 Chemistry data bank 136, 137 Chemistry, polymer 21 CHESS 120 C I M S , Courant Institute of Mathematical Science 11 City University of New York ( C U N Y ) 11 CLEANUP 199 C L E A N U P , spectrum output by 201 C.mnp 25 Code(s) hollerith 13 installation and maintenance of .... 162 reentrant 104 COGEODATA 63 Collaborative research community ... 192 Collisions, short-range 23 Communication ( s ) and control, user 89 dyadic 56,58 interprocessor 37 terminal 103 Complexity, particle 23 Computation, long-term 93 Computation, molecular dynamics .... 31
231
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ix001
232 Computational system 31 Computer(s) assembled testing in a large network 129 configuration 88 graphics, remote terminal 9 identification and interpretation of unknown mass spectra 183 network, hierarachical 36,42 network of real-time 67 network on college chemistry de partments, the impact of 142 paper tape based 73 resource sharing, history of 154 utility for interactive instrument control 85 Computing centralized/localized Ill C R Y S E T : A Network for Crystallographic 1 distributed 78 Concurrent user operations 91 CONDUIT 140, 142, 147, 148 Conferencing, geologic application of network 53 Conferencing system 53 Configuration computer 88 hardware 88 U - w i d e computer network 119 Conformation, protein 21 Conformational analysis 28 CONGEN 204,207 Connections, diagram of interactive terminal 165 Control card records, job 170 computer utility for interactive instrument 85 points, S O C R A T E S modules and .... 133 programs, custom designed 89 Core memory assignment 104 Coulomb 30 Courant Institute of Mathematical Sciences ( C I M S ) 11 CRT 26 C R Y S E T : A Network for Crystallo graphic Computing 1 C R Y S N E T Vector General 3 Crystal Data File, Cambridge 6 Crystallographic Computing, C R Y S N E T : A Network for 1 Crystallography 1 project, protein 196 x-ray 9 C U N Y , City University of New York 11 Current interfaced instruments 95 Current on-line experiments 94 Custom designed control programs .... 89 C Y B E R 70/76 1,2 CYBERNET 140
COMPUTER
NETWORKING AND
CHEMISTRY
D Data bank, chemistry 136 protein 6 usage of the chemistry 137 file, Cambridge crystal 6 flow 103 processing ( A D P ) , administrative 146 transfer 88 DECOMP 120 DENDRAL 187,192, 197, 215 programs 198 project 196 Depth, well 30 Description tables, program 104 Design, prosthetic device 46 Detection, nuclear particle 99 Detection systems, multi-particle 106 D-glucaro-3-lactone, space-filling model of 5 D I A L O G project 195 Differential equations, solution of coupled 24 Differential transmission scheme 122 Diffraction, x-ray 30 Diffractometer, neutron 96,106 Digital and hybrid graphics systems 26 Digital voltmeter ( D V M ) readings .... 99 Discriminator 34 Discriminator, barrel-roll 33,36 Disk sector, logical 90 Dispersion forces, London 30 Distance, internuclear 30 Distributed computing 78 Distribution of molecular parameters, statistics 43 Distributions, charge 30 D V M readings, digital voltmeter 99 Dyadic communication 56,58 Dynamics 18 chemical reactions and evolution of molecular systems 41 computation, molecular 31 molecular 9, 20, 22 particle 22 Ε EBCIDIC-ASCII EDUCOM Effects, allosteric Effects, scale of Electrical system analysis Electron-density map Electronic spectroscopy ELLIPS Empirical and semi-empirical energy functions E N D O R and E S R spectroscopy
104 140 45 23 46 6 30 2 28 98
233
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ix001
INDEX
Energy functions, empirical and semi-empirical Energy surface, potential Entry, intelligence remote job Enzyme catalysis Enzyme kinetics Equations, solution of coupled differential Equilibrium Equilibrium geometry Ergodic theorem Evolution of molecular systems, dynamics—chemical reactions and Examples, paper tape program Execution, non-resident program Expansion, incremental Experiment(s) interfaces current on-line with the U.S.G.S
28 20 11 128 46 24 22 30 43 41 74 90 94 103 94 58
Facilities, graphics 92 Feely, Touchy 26,33,44 Floating point array processors 36 Flow, data 103 Force(s) 18 functions 20,27 functions, interatomic potential or 29 interatomic 20 London dispersion 30 theoretical 29 FORTRAN IV-H 87,93 FORUM 53,54 system at U.S.G.S 59,60 system, current experiments with the 53 Fourier analysis 46 transformations 85 transform methods 23 Functions empirical and semi-empirical energy 28 force 20,27 interatomic potential (or force) ...20,29 protein 45 trigonometric 21
Geologic applications of network conferencing Geometry, equilibrium Graphics facilities molecular remote terminal computer systems, digital and hybrid
Identification and interpretation of unknown mass spectra, computer 183 Illiac IV 24 Incremental expansion 94 INFONET 58 Infrared and Raman spectroscopy, vibrational 30 Infrared spectroscopy, U V , visible and 100 Installation and maintenance of codes 162 Institute for Cancer Research 4 Instructions, general user 62 Instrument control, computer utility for interactive 85 Instruments, current interfaced 95 Integration, Adams-Bashforth predictor-corrector 39 Interaction complexity 23 Interaction, scale of 23 Interactive computing, chemical applications of 197 Interactive terminal connections, diagram of 165 Interatomic forces 20 potential (or force) functions 20,29 Interface channel Ill molecular manipulation—touch 33 molecular portrayal—visual 33 touch 26 visual 26 Interfaced instruments, current 95 Interfaces, experiment 103 Interfaces, visual and touch 36 Internal rotation, barriers to 30 International networking 63 Internuclear distance 30 Interpretation of unknown mass spectra, computer identification and 183
234
COMPUTER
Interpretive and Retrieval System, Self-Training Interprocessor communication INTSUM Isomerization I T G module, S O C R A T E S
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ix001
C C R G E N example CCR's EOL EOLJMS MS-D100 Job control card records entry, intelligence remote entry, R J E (remote) Johns Hopkins University
186 37 207 21 140
172, 175 170 121 121 121
Kinetics chemical enzymes stopped-flow
170 11 141 4
46 46 98
Laboratory methodology Langrangian L A O C O O N III Law, Newtons Second LDS Lengths and angles, bond Level-flow process, liquid Lincoln Wand system Line Notation, Wiswesser Liquid level-flow process LISTING Lockheed Differential Equation Processor Logical disk sector London dispersion forces Long-term computation L-phenylalanine cation, drawing of L-phenylalanine hydrochloride
M Macronetwork Magnetic resonance facility, repetitive scanning Magnetic resonance spectroscopy Maintenance of codes, installation and Manipulation—touch interface, molecular MANIPL M A N I P L , output of program Map, electron-density Mass memory operating system support
118 122 9 162 33 3 7 6 77
NETWORKING
AND
CHEMISTRY
Mass spectra, computer identification and interpretation of unknown .... 183 Master integrals and S C F codes, development of 156 Match factor 186 Maximum likelihood calculation 24 Measurements, heat capacity 100 Mechanical system analysis 46 Mechanics multiprocessor molecular 17 statistical 22 stellar and plasma 22 Medical Foundation of Buffalo 4 Medical Information Systems Laboratory 195 Membrane transport 45 Memory assignment, core 104 bus structure 102 operating system support, mass 77 protection 102 Meta-4 39,40 Methods, Fourier transform 23 Methodology, laboratory 112 MF 186 MHBOOT 121 Microde 33 Microphone, strip 26 Microwave spectroscopy, rotational.... 30 Minicomputer ( s ) interfacing support system (MISS) 109 network of real-time 67 support, hierarchical 108 Mininet, U M R 119 MIOP 89,90 MIPS 25 M I S L project 195 MISS, minicomputer interfacing support system 109 Modes of application 41 Molecular beam scattering 30 dynamics 9, 20-22 computation 31 graphics 2 manipulation—touch interface 33 mechanics, multiprocessor 17 parameters, statistics—-distribution of 43 portrayal—visual interface 33 statics 20 structure, statics 41 systems, dynamics—chemical reactions and evolution of 41 MOLION 202 Momentum 22 Motion, atomic 22 Multi-mini Processor, CarnegieMellon 25 Multi-particle detection systems 106
235
INDEX
Multiprocessor molecular mechanics Multiprocessor network M Y C I N project
17 33 196
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ix001
Ν
Network central 68 conferencing, geologic applications of 53 configuration 72 configuration, U-wide computer .... 119 hardware 69 hierarchical computer 36,42 multiprocessor 33 of real-time mini computers 67 programming characteristics 73 Networking at U M R , computer 118 Networking, international 63 Neutron diffractometer 96, 106 NEWTON 25, 30,33,36-43 macroscopic machine 17 Newtons Second L a w 27 NMR 30 spectrometer 106 Non-resident program execution 90 Notation, Wiswesser line 186 Nuclear magnetic resonance spectroscopy, pulsed 95 Nuclear particle detection 99 Nuclease, staphylococcal 6 Ο On-line experiments, current Open-shop batch-processing Operations, concurrent user Operations, vector Optical processing ORD ORFFE-3 ORFLS-3 ORTEP Output
94 93 91 21 24 30 97 97 10 164
Ρ PAINT Paper tape based computers Paper tape program examples Parallel Element Processing Ensemble ( P E P E ) Parameters, statistics—distribution of molecular PBM 184, Particle(s) complexity detection, nuclear dynamics of Pattern recognition Pen, sonic PEPE
165 73 74 25 43 188 23 99 22 24 26 25
Pharmacology-toxicology 46 Physics, chemical 20 Physics, plasma 22 PLANET 53 PLANET-1 56 PLANNER 204,207 Plasma 23 mechanics, stellar and 22 particle calculations 7 physics 22 Plate reading, spectroscopic 99 PLATO 141 Plotter, Versatec 4 Polarizabilities 30 Polymer chemistry 21 Polymers, biological 19 Portrayal—visual interface, molecular 33 Positions, atomic 27 Potential energy surface 20 Potential functions, interatomic 20 Predictor-corrector integration, Adams-Bashforth 39 PRJCTN 2,4 Probability based matching 184 Process, liquid level-flow 127 Processing associative 24 open-shop batch93 optical 24 signal 24 Processor(s) array 36 Carnegie-Mellon M u l t i - M i n i 25 floating point array 36 Floating Point Systems' array 36 hardware 26 Lockheed differential equation 24 supervisory 33 terminal interface 156 Program(s) custom designed control 89 DENDRAL 198 description tables 104 execution, non-resident 90 Programming characteristics, network 73 Project DENDRAL 196 DIALOG 195 MISL 195 MYCIN 196 protein crystallography 196 Proline ring 7 Prosthetic device design 46 Protection, memory 102 Protein(s) 20 conformation 21 crystallography project 196 data bank 6 function 45 structure 45
236
COMPUTER NETWORKING
Pulse radiolysis Pulsed nuclear magnetic resonance spectroscopy
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ix001
R RAD 90,93 Radiolysis, pulse 97 Raman spectroscopy, vibrational (infrared and) 30 Reactions and evolution of molecular systems, dynamics—chemical 41 Reading, spectroscopic plate 99 Readings, digital voltmeter ( D M V ) 99 Real-time mini computers, network of 67 Real-time response 89 Records, job control card 170 Recognition, pattern 24 Reentrant code 104 Regional computer center ( R C C ) 142 R C C , regional computer center 142 Remote job entry, R J E 141 terminal choices 162 terminal computer graphics 9 Research community, collaborative ... 192 Resource sharing, history of computer 154 Resource sharing, networks for 219 Response, real-time 89 Retrieval System, Self-Training Interpretive and 186 Retrieval system, S O C R A T E S 130 RJE (remote job entry) 141 Rotation, barriers to internal 30 Rotation (microwave) spectroscopy 30 RULEGEN 207 S Sample transcript 61,64 Scale of effects 22 Scale of interaction 23 Scanners 26 Scanning magnetic resonance facility, repetitive 122 Scattering, molecular beam 30 S C F codes, development of master integrals and 156 Scheduling 105 Scheme, differential transmission 122 Second Law, Newton's 27 Sector, logical disk 90 Self-Training Interpretive and Retrieval System 186 Semi-empirical energy functions, empirical and 28 Services, system 88
AND
CHEMISTRY
Sharing, history of computer resource 154 Sharing, networks for resource 219 Short-range collisions 24 Signal processing 24 Signal, ultrasonic 26 SOCRATES I T G module 140 modules and control points 133 retrieval system 130 system 129 Software 11,14 Solution of coupled differential equations 24 Sonic pen 26 Spectrometer, N M R 106 Spectroscopic plate reading 99 Spectroscopy 30,31 electronic 30 magnetic resonance 9 pulsed nuclear magnetic resonance 95 rotational (microwave) 30 U V , visible and infrared 100 Stanford University Medical Experimental computer 192 Staphylococcal nuclease 6,7 Statics 18 molecular 20,21 molecular structure 41 Statistical mechanics 22 Statistical thermodynamics 9 Statistics—distribution of molecular parameters 43 Stellar and plasma mechanics 22 STIPL 3,5 STIRS 186,187,188 Stopped-flow kinetics 98 Storage 167 Strengths, bond 30 Strip microphone 26 Structure dynamics-function 47 memory bus 102 protein 45 statics, molecular 41 SUMEX-AIM 192, 193, 216 access to 194 community, interactions in 194 Support, hierarchical minicomputer 108 Support, mass memory operating system 77 Supervisory processor 33 Surface, potential energy 20 SYMBOL 87 System(s) 26 analysis, electrical 46 analysis, mechanical 46 computational 31 conferencing 53 digital and hybrid graphics 26
237
INDEX
dynamics—chemical reactions and evolution of molecular Lincoln Wand multi-particle detection services support, mass memory operating ....
41 26 106 88 77
Publication Date: June 1, 1975 | doi: 10.1021/bk-1975-0019.ix001
Τ Tables, program description 104 Tape based computers, paper 73 Tape program examples, paper 74 Techniques, calculational 23 Tektronix 92 Tektronix 4010 storage tube display terminal 14 Teleconferencing 53 Teleprocessing 9 Terminal communications 103 connections, diagram of interactive 165 interface processor 156 Testing in a large network, computer assembled 129 Texas A & M University 4 Theorem, Ergodic 43 Theoretical, forces 29 Thermochemistry 30 Thermodynamics, statistical 9 Thymidine-3',5-diphosphate, stereoview of 7 TI980A 121, 125,128 Time-sharing 93 TIP 156 Touch interface 26 Touch interface, molecular manipulation— 33 Touch interfaces, visual and 36 Touchy Feely 26 Touchy Feely I 33,44 Touchy Feely II 33 Touchy Twisty 26 Touchy Twisty I 33 Toxicology, pharmacology 46 Transcript, sample 61,64 Transfer, data 88 Transformation, Fourier 85 Transmission scheme, differential 122
U Ultrasonic signal 26 U M R , computer networking at 118 U M R mininet 119 User communication and control 89 User instructions, general 62 U.S.G.S., experiments with the 58 U.S.G.S., F O R U M system at 59,60 Utility for interactive instrument control, computer 85 U V , visible, and infrared spectroscopy 100 U-wide computer network configuration 119
V Van der Waals Vector operations Vector general, C R Y S N E T Versatec plotter Vibrational (infrared and Raman) spectroscopy Vickers Wand Viscosity Visible, and infrared spectroscopy, U V Visual interface Visual interface, molecular portrayal— Visual and touch interfaces Voltmeter ( D V M ) readings
30 21 3 4 30 26 22 100 26 33 36 99
W Wand system, Lincoln Wand, Vickers Well depth WLN
