Mulheim Computer System for Analytical Instrumentation

INSTRUMENTATION

Advisory Panel Jonathan W. Amy Glenn L. Booman Robert L. Bowman

Jack W. Frazer G. Phillip Hicks Donald R. Johnson

Howard V. Malmstadt Marvin Margoshes William F. Ulrich

Mulheim Computer System for Analytical Instrumentation Engelbert Ziegler, Dieter Henneberg, and Gerhard Schomburg Max-Planck-lnstitut fur Kohlenforschung, Mulheim/Ruhr, Germany

The close connection of an analytical on-line system to a large computational system will certainly stimulate the application of advanced analytical methods

THE PAST few years a number of different approaches in the computerization of analytical instruments have been described. Most commonly the instruments are connected to small "dedicated" computers. Another approach consists of a medium-sized computer system {e.g., IBM 1800) servicing several not too dissimilar instruments simultaneously {1,2). A different solution has been developed at the Max-Planck-Institut fur Kohlenforschung in Mulheim, Germany {3, 4). This institute is a research institute for organometallic chemistry and radiation chemistry with extended analytical, physical, and physicochemical laboratories. A large time-sharing computer (PDP 10) has been installed to meet the computational requirements for both general off-line computations and realtime acquisition and analysis of data from a variety of on-line analytical instruments. This paper describes the hardware configuration of the Mulheim computer system and the basic structure of the analytical on-line system incorporated into the interactive, conversational P D P 10 timesharing mode. TOURING

Computational Requirements

There are two distinct areas of computer applications at the Mulheim institute: (1) Off-line computations for X-ray diffractometry Molecular orbital calculations Chemical kinetics Spectra simulations and iterations Documentation and search of spectra Documentation of literature Administration (2) Real-time data acquisition and analysis for (a) "Slow" instruments (data rates ^ 20 Hz) 20-30 Gas chromatographs 1 Mass spectrometer 2-3 Nmr instruments 1 Ir-spectrometer 1 Raman spectrometer 1 Esr instrument 1 Spectropolarimeter (b) "Fast" instruments (data rates between 1.25 and 20 kHz) 2 Low-resolution, fast-scan mass spectrometers 1 Pulsed nmr instrument Hardware Configuration (Figure 1)

The hardware of the P D P 10 central processing unit includes re-

Figure 1. Hardware configuration of the Mulheim Computer System Dashed lines indicate the main expansions scheduled for 1970

ANALYTICAL CHEMISTRY, VOL. 42, NO. 9, AUGUST 1970

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Instrumentation

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and protection registers, and bit-handling instructions and seven levels of pri ority-nested interrupts. Core memory consists of 32K words of 36 bits (1 jixsec cycle time) and is connected through a fast data channel to a fixed-head disk with 17 msec of average access time, 13 /xsec transfer time per word and a capacity of 500K words. User pro grams are temporarily transferred from core memory to this disk (swapping), whenever core space becomes too small for all of the concurrently running programs. But p a r t of the disk is also used for data storage and for system programs such as compilers, as semblers, and text editors. The present set of peripheral de vices includes a line printer, card reader, plotter, magnetic tape units, paper tape units, and 14 teletype terminals. Several special devices are inter faced to the P D P 10 for the real time data acquisition. There is one A / D converter (analog-to-digital) to service up to 32 slow, simultane ously running instruments con nected through a multiplexer. This A D C provides 13 bits of resolution within a useful dynamic range of about 10 e subdivided into 11 differ ent gain ranges. T h e maximum over-all data rate of this device is 8 k H z with programmed selection of gain ranges and 3.3 k H z with automatic range selection. Auto

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matic (hardware) selection is slower because the range for the full conversion is determined by an additional preceding conversion cycle. For fast instruments, fastscan mass spectrometers, another A / D converter is used, capable of d a t a rates between 1.25 and 20 kHz. This A D C provides 10 bits of resolution within a dynamic range of 2.5 Χ 10 5 subdivided into three gain ranges. A multiplexer connects eight data lines to this ADC. But, to avoid conflicts with the general time-sharing system, only one fast instrument is allowed to transmit d a t a at any given time. Because of the very short time periods—typically 2 or 3 sec— when such a fast instrument will be active, this restriction is not a serious one. T h e timing for the real-time d a t a acquisition is provided by a real time clock, operating with 20 kHz pulses and a preset counter for each A / D converter, loaded by program. A contact scanner and a line driver are able to control 72 ex ternal relay contacts each. W i t h these devices, the operating system services start and stop requests, as wyell as certain instrument control functions. The capability of the contact scanner to interrupt the processor allows discontinuously scanning instruments, such as in frared spectrometers, to request an A / D conversion by closing the as sociated external relay.

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Instrumentation Time-Sharing Organization

The present system allows up to 15 concurrently running jobs (each job may run one program), which are initiated and controlled by the various teletype terminals distributed all over the institute. The hardware protection of the central processor provides the possibility of keeping several jobs in core separated, without interference, by allowing only "legal" memory references. Jobs may be shuffled in core or swapped out to the disk and located into different core areas when brought in again, because memory references are displaced by adding the contents of the relocation register during execution. Commands from the teletype terminals are interpreted by the operating system "monitor." The monitor also determines the job which is actually run by the central processor, and controls the allocation of the system resources to the various jobs. Whenever a running job becomes unrunnable—for instance, when starting input or output activities via one of the seven interrupt levels—or after certain time slices, the monitor looks for another job to run. Because of this time-sharing capability, the system is flexible enough to handle simultaneously many analytical instruments requiring different data acquisition and different data analysis methods. Software Organization

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The analytical instrumentation software is of course different for the slow and the fast instruments. These two software packages are each subdivided into (1) Code within the monitor (2) Data acquisition programs (3) Basic-analysis programs (4) Refined-analysis programs (5) Miscellaneous auxiliary programs (e.g., data plotting and testing programs) Software for Slow Instruments

Within the monitor a special routine looks at start or stop requests of any instruments every 20 msec. Every 50 msec (thus limiting the maximum data rate for a single instrument to 20/sec), a list of slow instruments is created, for which a

Instrumentation

conversion has to be started. When a conversion is completed, the data word from the A D C is brought in on interrupt level and stored into buffers of the d a t a acquisition job. This d a t a job ( G C D I R ) is started at system-setup time and put into a deactivated status. Whenever one of the data buffers has been filled with A D C data, this program is activated by the monitor to empty the accumulated data into files on the disk. I t is important t h a t no reduction or analysis of A D C data is performed at this stage. Because A D C data are generated continuously, the data job m a y not be swapped but has to stay resident in core. In this aspect, this job differs from normal time-sharing jobs. There is only one data job to service all of the slow instruments, but various different analysis programs m a y be started by the analyst in the laboratories a t any time. The basic-analysis programs process the files of unreduced A D C d a t a after an instrument run has been stopped. These programs may be initiated as to check at certain time periods automatically for any finished runs and they m a y control a large number of instruments which are using the same analysis methods, such as a group of gas chromatographs. The flexibility of this kind of software organization can be illustrated by gas chromatography. But the procedure with spectroscopic methods is quite similar. If a technician wants to run a gas chromatogram, he first starts a parameter - t y p e - in program ( P A R A M ) from the teletype in his laboratory. If no parameters are specified, those of the previous chromatogram on the same channel are t a k e n for the new run. The conversational parameter program asks him for the channel number, the d a t a rate, the run time, and for report headings. Then he m a y inject his sample and start the acquisition of d a t a by pressing the start button of the proper channel. The run is stopped either by the technician's pressing the corresponding stop button or if the specified run time has elapsed. If the channel is under automatic control of a basic analysis program Circle No. 97 on Readers Service Card

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( G C A N ) , then this program will print an analysis report on the teletype and on to the disk. This report consists of a list of peaks with peak positions, intensities, normalized area percentages, peak half widths, and information about peak overlapping and shoulders. If the analyst is not satisfied with this basic analysis, he m a y request a more sophisticated one by starting one of the so-called refined analysis programs. For instance, he m a y wish to apply any special standardization, such as a determination of Kovats indices ( I N D E X ) , or he m a y want to discard several regions of the chromatogram, or he m a y want to start the analysis on the tail of a large peak to determine the areas of small peaks on the tail with better accuracy. All this refined analysis is performed without requiring a rerun of the chromatogram, because all the unreduced A D C data, as well as the report of the basic-analysis program, remain on the disk until the end of the next run on the same channel. This type of operation (analyzing the different chromatograms individually with a set of programs dependent on the result of the basic analysis) is especially suited for a laboratory in a research and development environment with a variety of different problems. In the case of industry-type routine chromatography, some standard steps of the refined analysis would be incorporated into the basic-analysis program. A detailed description of the gas chromatography system and its performance and results will be given in a further paper. Software for Fast Instruments

The organization of the software for fast instruments differs in some aspects from t h a t described for the slow instruments. For each fast instrument on-line an extra d a t a acquisition program is used, whereas all slow lines are handled by a single data job. As soon as a run of a fast instrument, such as a fast-scan mass spectrometer, is requested by closing one of the contacts controlled by the contact scanner, the data job associated with the requesting instrument is brought into core to accept all the d a t a

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Instrumentation

from the A D C and stays in core as long as the instrument runs—just for a few seconds. During this period, no other start requests from fast instruments are accepted, because only one fast line is allowed to be active at any given moment. The data acquisition of the simultaneously running slow instruments, of course, continues as well as timesharing response, for other jobs and service of computational programs are still guaranteed. This is possible because all input and output activities occur on different hardware interrupt levels and are accomplished within short periods of time. The normal data rate for fast-scan mass-spectrometer runs is 5 kHz. Thus, every 200 ,usec, a data word from the A D C is transferred. But the transfer itself takes only 6 ynsec, leaving the remaining 194 jusec available for other tasks. Up to now, one fast-scan, lowresolution mass spectrometer (MAT CH4) and a spin-echo nmr setup are connected on-line. For the latter, the data job just transfers the A D C data without any reduction to the disk. A time-averaging program or a Fourier transform program then reads the data from there. For the mass spectrometer, the associated data job performs a data reduction and writes these reduced data on the disk. Similar to the organization of the slow instruments, the analysis program is running in parallel to the data job waiting for any finished runs. A considerable amount of work has been put into the development of programs for the fast-scan lowresolution mass spectrometer. 1. D a t a reduction program (MSDAT) By preliminary peak-search, the 10,000 samples of a low resolution mass spectrum are reduced to 50—1000 intensities and positions of potential peaks, depending on intensity and mass range of the spectrum 2. Calibration of mass scale (MASCAL) Out of the reduced data of a polyfluoro kerosine mass spectrum, a list of positions of masses 1—1000 is created automatically 3. Evaluation of spectra out of reduced data (MACO)


Masses and intensities of sharp peaks and metastables are determined peak intensities with a dynamic range of 3.10 4 4. Spectra are printed out in a normalized form as table on the line printer (REMAS) Presently a Varian-Statos recorder is interfaced to the system to provide fast output of spectra in the form of bargraphs in two different intensity scales simultaneously 5. A set of programs has been developed to test and to analyze unreduced A D C data and to check the performance of analysis algorithms. The operational procedures and the algorithms used for analysis and calibration purposes will be described later. The most difficult application incorporated into the Mulheim System is the automatic operation of a G C / M S combination. In this setup, high-resolution capillary-gas chromatography is applied, causing fast narrow peaks within the chromatogram. Therefore the system response time is a very critical p a rameter for this application. When a start of the mass spectrometer is necessary, the corresponding data job to receive the A D C data from the spectrometer normally resides on the swapping area of the disk. Some time is lost until this job is brought back into core memory. To achieve the required response times of less than 1 sec, special modifications of the time-sharing monitor were necessary. In the present implementation, the monitor checks at certain time intervals for beginning and end of peaks within the signal from the total ion current (representing the chromatogram) which is recorded via one line of the slow A D C system. Between the beginning and end of a peak, the monitor starts successive mass spectra. Up to now, this application is the only case in which, not only a real-time data acquisition, but also a realtime data analysis is performed. However, this mode of operation will be changed as soon as the core memory of the system is expanded. Then during the entire experiment, successive mass spectra will be started every 5 sec with cycling magnetic field (2-sec duration of

Instrumentation

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Figure 2. " S y s t e m s n a p s h o t " illustrating t h e variety of simultaneously active t i m e sharing jobs: GCDIR (job 1) is the data acquisition program for " s l o w " on-line instru m e n t s ; TRADAT (job 3) transfers data f r o m t h e f a s t ADC to the disk ( u s e d for p u l s e d n m r ) ; MSDAT (job 6) transfers reduced mass spectra to t h e d i s k ; GCAN (job 13) a n d REMAS (job 7) are analysis programs for gas c h r o m a t o g r a p h y and mass s p e c t r o m e t r y ; INDEX (job 4) is a refined analysis program for gc; PARAM (job 14) a parameter-spec ification p r o g r a m for runs of slow i n s t r u m e n t s

t h e active d a t a transfer), but only valuable spectra are transferred to the disk by the d a t a acquisition and reduction program (MSDAT). During the remaining 3 sec, another mass spectrometer or fast instru ment m a y be started. The G C / M S combination is not yet running in a routine fashion, because some work on the analysis methods, especially for the intensity corrections of mass peaks with the total ion current, has still t o be done. Present System Performance

As the data acquisition is inde pendent of the spectroscopic method, any instrument m a y be connected to the system, which de livers voltage signals between —10 and + 1 0 V and runs either with d a t a rates of 20 Hz and less or with rates between 1.25 and 20 k H z . Up to now, one fast-scan, low-reso lution mass spectrometer and one pulsed-nmr instrument are con nected to the "fast" A D C , whereas 10 gas chromatographs (the elec tronic cleanup of the other gas chro matographs is not yet accom plished), 1-nmr, 1-ir spectrometer, and 1 spectropolarimeter are on-line via the slow A D C . The reliability of the system is improving after some difficulties in the beginning (mostly hardware


failures of the special real-time de vices and a few, but nevertheless, disturbing monitor malfunctions). As an average the system has one hardware breakdown every three weeks and about three software "crashes" every week. As shown by the null time in the system snapshot (Figure 2 ) , the central processor is far from being used to its full capacity. But nevertheless there are two bottle necks in the present system causing difficulties under heavy system load: (1) As the installation is not only used for the real-time applications, the present core memory is too small for the number of simultane ous users. The time-sharing moni tor including the real-time code re sides in 16K of core. T o allow up to 32 simultaneously running slow on-line instruments, the associated d a t a job needs 3K of core perma nently. Temporary restriction to 20 simultaneously active lines saves IK. But the remaining 14K of core is not sufficient for 15 concurrent jobs (even, if larger computational programs are run during the nights with a very small monitor), because too much processor time is wasted by swapping actions, and time-shar ing response is decreased consider ably, especially for programs with many i n p u t / o u t p u t actions {e.g.,

Instrumentation

Fortran compilations). Therefore the system is now being expanded by 32K of core. As swapping does not need CPU time, even during swap periods, the processor is available to other programs which are in core. But if core memory is too limited no other programs will fit into the remaining core when large programs are being swapped. (2) The capacity (500K words) of the disk is too small for extensive data storage for all the users and especially for extensive storage of real-time data. Furthermore the future development of documentation systems for molecular spectra will need a large bulk of backup storage. Therefore the system will be expanded by the addition of disk packs. Discussion of System Layout

When we consider the system economics, we should keep in mind that the Mulheim system had been designed to handle both off-line and on-line applications in theoretical and analytical chemistry. The purchase price of the system without the special devices for the realtime applications totals $450,000. This system would have been necessary for the off-line applications anyhow. The costs of the additional real-time hardware are about $65,000. The availability of resources such as a line printer, plotter, magnetic tapes, and disk, as well as the high computing power of a large computer system, proved to be extremely useful in the development of the analytical instrumentation software. The use of high-level languages, such as Fortran, text editors, and debugging aids facilitate the writing, testing, and modifying of programs. To find suitable algorithms for the analysis programs, a close look at the unreduced ADC data is necessary. This can be accomplished by especially developed test programs. The fact that all this program development could be done within the interactive time-sharing mode, thus avoiding long turn-around times of batch systems or tedious loading and testing procedures on small computers, has, without doubt, accelerated the development of programs. It seems to be obvious that there

will be an increasing need in the future for large computational programs in the field of analytical chemistry (e.g., extensive spectra iterations, spectra identification by documentation systems, "artificial intelligence" programs), which will use the output data from on-line systems for input. The close connection of the analytical on-line system to a large computational system will certainly stimulate the application of advanced analytical methods. As far as the special hardware for the real-time data acquisition is concerned, some improvements to the Mulheim system are possible. In the present layout, all ADC data are handled by the CPU of the P D P 10, which has to perform all the bookkeeping and sorting of these data. Connecting the slow ADC and its multiplexer to a small satellite computer as a data concentrator would decrease the load on the P D P 10 processor. The satellite could overtake most of this bookkeeping and data formatting and transfer the ADC data blockwise to the P D P 10 (5). The Mulheim system will most certainly be modified in this way, if by increasing computational requirements the CPU time of the P D P 10 should be used to a much higher degree than it is now. Small satellites could also become desirable if the need for more realtime experimental control arises. It is difficult to incorporate extensive real-time functions into the timesharing monitor, and modifications to this code are tedious. Therefore small satellites are suited more for this type of application. References (1) Sederholm, C. H., Friedl, P . J., and Lusbrink, T. R., Pittsburgh Conference on Analytical Chemistry and Applied Spectroscopy, March 1968. (2) Sederholm, C. H., 21st ACS Annual Summer Symposium on Analytical Chemistry, Penn State University, June 18-21,1968. (3) Ziegler, E., Pittsburgh Conference on Analytical Chemistry and Applied Spectroscopy, March 1969. (4) Ziegler, E., Henneberg, D., and Schomburg, G., Pittsburgh Conference on Analytical Chemistry and Applied Spectroscopy, March 1970. (5) For a more general discussion : J. W. Frazer, Pittsburgh Conference on Analytical Chemistry and Applied Spectroscopy, March 1970.

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Mulheim Computer System for Analytical Instrumentation

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