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File-access characteristics of parallel scientific workloads

Phenomenal improvements in the computational performance of multiprocessors have not been matched by comparable gains in I/O system performance. This imbalance has resulted in I/O becoming a significant bottleneck for many scientific applications. One key to overcoming this bottleneck is improving the performance of parallel file systems. The design of a high-performance parallel file system requires a comprehensive understanding of the expected workload. Unfortunately, until recently, no general workload studies of parallel file systems have been conducted. The goal of the CHARISMA project was to remedy this problem by characterizing the behavior of several production workloads, on different machines, at the level of individual reads and writes. The first set of results from the CHARISMA project describe the workloads observed on an Intel iPSC/860 and a Thinking Machines CM-5. This paper is intended to compare and contrast these two workloads for an understanding of their essential similarities and differences, isolating common trends and platform-dependent variances. Using this comparison, we are able to gain more insight into the general principles that should guide parallel file-system design.

Nieuwejaar, Nils↗

Combining high performance simulation, data acquisition, and graphics display computers

Issues involved in the continuing development of an advanced simulation complex are discussed. This approach provides the capability to perform the majority of tests on advanced systems, non-destructively. The controlled test environments can be replicated to examine the response of the systems under test to alternative treatments of the system control design, or test the function and qualification of specific hardware. Field tests verify that the elements simulated in the laboratories are sufficient. The digital computer is hosted by a Digital Equipment Corp. MicroVAX computer with an Aptec Computer Systems Model 24 I/O computer performing the communication function. An Applied Dynamics International AD100 performs the high speed simulation computing and an Evans and Sutherland PS350 performs on-line graphics display. A Scientific Computer Systems SCS40 acts as a high performance FORTRAN program processor to support the complex, by generating numerous large files from programs coded in FORTRAN that are required for the real time processing. Four programming languages are involved in the process, FORTRAN, ADSIM, ADRIO, and STAPLE. FORTRAN is employed on the MicroVAX host to initialize and terminate the simulation runs on the system. The generation of the data files on the SCS40 also is performed with FORTRAN programs. ADSIM and ADIRO are used to program the processing elements of the AD100 and its IOCP processor. STAPLE is used to program the Aptec DIP and DIA processors.

Hickman, Robert J.↗

MODIS Technical Report Series. Volume 4: MODIS data access user's guide: Scan cube format

The software described in this document provides I/O functions to be used with Moderate Resolution Spectroradiometer (MODIS) level 1 and 2 data, and could be easily extended to other data sources. This data is in a scan cube data format: a 3-dimensional ragged array containing multiple bands which have resolutions ranging from 250 to 1000 meters. The complexity of the data structure is handled internally by the library. The I/O calls allow the user to access any pixel in any band through 'C' structure syntax. The high MODIS data volume (approaching half a terabyte per day) has been a driving factor in the library design. To avoid recopying data for user access, all I/O is performed through dynamic 'C' pointer manipulation. This manual contains background material on MODIS, several coding examples of library usage, in-depth discussions of each function, reference 'man' type pages, and several appendices with details of the included files used to customize a user's data product for use with the library.

Kalb, Virginia L.↗

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Kikuchi, Hideaki↗

Electrical Performance of a High Temperature 32-I/O HTCC Alumina Package

A high temperature co-fired ceramic (HTCC) alumina material was previously electrically tested at temperatures up to 550 C, and demonstrated improved dielectric performance at high temperatures compared with the 96% alumina substrate that we used before, suggesting its potential use for high temperature packaging applications. This paper introduces a prototype 32-I/O (input/output) HTCC alumina package with platinum conductor for 500 C low-power silicon carbide (SiC) integrated circuits. The design and electrical performance of this package including parasitic capacitance and parallel conductance of neighboring I/Os from 100 Hz to 1 MHz in a temperature range from room temperature to 550 C are discussed in detail. The parasitic capacitance and parallel conductance of this package in the entire frequency and temperature ranges measured does not exceed 1.5 pF and 0.05 microsiemens, respectively. SiC integrated circuits using this package and compatible printed circuit board have been successfully tested at 500 C for over 3736 hours continuously, and at 700 C for over 140 hours. Some test examples of SiC integrated circuits with this packaging system are presented. This package is the key to prolonged T greater than or equal to 500 C operational testing of the new generation of SiC high temperature integrated circuits and other devices currently under development at NASA Glenn Research Center.

dielectric performance↗

File-System Workload on a Scientific Multiprocessor

Many scientific applications have intense computational and I/O requirements. Although multiprocessors have permitted astounding increases in computational performance, the formidable I/O needs of these applications cannot be met by current multiprocessors a their I/O subsystems. To prevent I/O subsystems from forever bottlenecking multiprocessors and limiting the range of feasible applications, new I/O subsystems must be designed. The successful design of computer systems (both hardware and software) depends on a thorough understanding of their intended use. A system designer optimizes the policies and mechanisms for the cases expected to most common in the user's workload. In the case of multiprocessor file systems, however, designers have been forced to build file systems based only on speculation about how they would be used, extrapolating from file-system characterizations of general-purpose workloads on uniprocessor and distributed systems or scientific workloads on vector supercomputers (see sidebar on related work). To help these system designers, in June 1993 we began the Charisma Project, so named because the project sought to characterize 1/0 in scientific multiprocessor applications from a variety of production parallel computing platforms and sites. The Charisma project is unique in recording individual read and write requests-in live, multiprogramming, parallel workloads (rather than from selected or nonparallel applications). In this article, we present the first results from the project: a characterization of the file-system workload an iPSC/860 multiprocessor running production, parallel scientific applications at NASA's Ames Research Center.

Kotz, David↗

Diskless supercomputers: Scalable, reliable I/O for the Tera-Op technology base

Computing is seeing an unprecedented improvement in performance; over the last five years there has been an order-of-magnitude improvement in the speeds of workstation CPU's. At least another order of magnitude seems likely in the next five years, to machines with 500 MIPS or more. The goal of the ARPA Teraop program is to realize even larger, more powerful machines, executing as many as a trillion operations per second. Unfortunately, we have seen no comparable breakthroughs in I/O performance; the speeds of I/O devices and the hardware and software architectures for managing them have not changed substantially in many years. We have completed a program of research to demonstrate hardware and software I/O architectures capable of supporting the kinds of internetworked 'visualization' workstations and supercomputers that will appear in the mid 1990s. The project had three overall goals: high performance, high reliability, and scalable, multipurpose system.

Katz, Randy H.↗

The FTIO Benchmark

We introduce a new benchmark for measuring the performance of parallel input/ouput. This benchmark has flexible initialization. size. and scaling properties that allows it to satisfy seven criteria for practical parallel I/O benchmarks. We obtained performance results while running on the a SGI Origin2OOO computer with various numbers of processors: with 4 processors. the performance was 68.9 Mflop/s with 0.52 of the time spent on I/O, with 8 processors the performance was 139.3 Mflop/s with 0.50 of the time spent on I/O, with 16 processors the performance was 173.6 Mflop/s with 0.43 of the time spent on I/O. and with 32 processors the performance was 259.1 Mflop/s with 0.47 of the time spent on I/O.

Fagerstrom, Frederick C.↗

A case for Redundant Arrays of Inexpensive Disks (RAID)

Increasing performance of CPUs and memories will be squandered if not matched by a similar performance increase in I/O. While the capacity of Single Large Expensive Disks (SLED) has grown rapidly, the performance improvement of SLED has been modest. Redundant Arrays of Inexpensive Disks (RAID), based on the magnetic disk technology developed for personal computers, offers an attractive alternative to SLED, promising improvements of an order of magnitude in performance, reliability, power consumption, and scalability. This paper introduces five levels of RAIDs, giving their relative cost/performance, and compares RAID to an IBM 3380 and a Fujitsu Super Eagle.

Patterson, David A.↗

An open, parallel I/O computer as the platform for high-performance, high-capacity mass storage systems

APTEC Computer Systems is a Portland, Oregon based manufacturer of I/O computers. APTEC's work in the context of high density storage media is on programs requiring real-time data capture with low latency processing and storage requirements. An example of APTEC's work in this area is the Loral/Space Telescope-Data Archival and Distribution System. This is an existing Loral AeroSys designed system, which utilizes an APTEC I/O computer. The key attributes of a system architecture that is suitable for this environment are as follows: (1) data acquisition alternatives; (2) a wide range of supported mass storage devices; (3) data processing options; (4) data availability through standard network connections; and (5) an overall system architecture (hardware and software designed for high bandwidth and low latency). APTEC's approach is outlined in this document.

Abineri, Adrian↗

A 500 megabyte/second disk array

Applications at the Army High Performance Computing Research Center's (AHPCRC) Graphic and Visualization Laboratory (GVL) at the University of Minnesota require a tremendous amount of I/O bandwidth and this appetite for data is growing. Silicon Graphics workstations are used to perform the post-processing, visualization, and animation of multi-terabyte size datasets produced by scientific simulations performed of AHPCRC supercomputers. The M.A.X. (Maximum Achievable Xfer) was designed to find the maximum achievable I/O performance of the Silicon Graphics CHALLENGE/Onyx-class machines that run these applications. Running a fully configured Onyx machine with 12-150MHz R4400 processors, 512MB of 8-way interleaved memory, 31 fast/wide SCSI-2 channel each with a Ciprico disk array controller we were able to achieve a maximum sustained transfer rate of 509.8 megabytes per second. However, after analyzing the results it became clear that the true maximum transfer rate is somewhat beyond this figure and we will need to do further testing with more disk array controllers in order to find the true maximum.

Ruwart, Thomas M.↗

Exploring the use of I/O nodes for computation in a MIMD multiprocessor

As parallel systems move into the production scientific-computing world, the emphasis will be on cost-effective solutions that provide high throughput for a mix of applications. Cost effective solutions demand that a system make effective use of all of its resources. Many MIMD multiprocessors today, however, distinguish between 'compute' and 'I/O' nodes, the latter having attached disks and being dedicated to running the file-system server. This static division of responsibilities simplifies system management but does not necessarily lead to the best performance in workloads that need a different balance of computation and I/O. Of course, computational processes sharing a node with a file-system service may receive less CPU time, network bandwidth, and memory bandwidth than they would on a computation-only node. In this paper we begin to examine this issue experimentally. We found that high performance I/O does not necessarily require substantial CPU time, leaving plenty of time for application computation. There were some complex file-system requests, however, which left little CPU time available to the application. (The impact on network and memory bandwidth still needs to be determined.) For applications (or users) that cannot tolerate an occasional interruption, we recommend that they continue to use only compute nodes. For tolerant applications needing more cycles than those provided by the compute nodes, we recommend that they take full advantage of both compute and I/O nodes for computation, and that operating systems should make this possible.

Kotz, David↗

I/O Parallelization for the Goddard Earth Observing System Data Assimilation System (GEOS DAS)

The National Aeronautics and Space Administration (NASA) Data Assimilation Office (DAO) at the Goddard Space Flight Center (GSFC) has developed the GEOS DAS, a data assimilation system that provides production support for NASA missions and will support NASA's Earth Observing System (EOS) in the coming years. The DAO's support of the EOS project along with the requirement of producing long-term reanalysis datasets with an unvarying system levy a large I/O burden on the future system. The DAO has been involved in prototyping parallel implementations of the GEOS DAS for a number of years and is now converting the production version from shared-memory parallelism to distributed-memory parallelism using the portable Message-Passing Interface (MPI). If the MPI-based GEOS DAS is to meet these production requirements, we must make I/O from the parallel system efficient. We have designed a scheme that allows efficient I/O processing while retaining portability, reducing the need for post-processing, and producing data formats that are required by our users, both internal and external. The first phase of the GEOS DAS Parallel I/O System (GPIOS) will expand upon the common method of gathering global data to a Single PE for output. Instead of using a PE also tasked with primary computation, a number of PEs will be dedicated to I/O and its related tasks. This allows the data transformations and formatting required prior to output to take place asynchronously with respect to the GEOS DAS assimilation cycle, improving performance and generating output data sets in a format convenient for our users. I/O PEs can be added as needed to handle larger data volumes or to meet user file specifications. We will show I/O performance results from a prototype MPI GCM integrated with GPIOS. Phase two of GPIOS development will examine ways of integrating new software technologies to further improve performance and build scalability into the system. The maturing of MPI-IO implementations and other supporting libraries such as parallel HDF should provide performance gains while retaining portability.

Lucchesi, R.↗

Characterizing parallel file-access patterns on a large-scale multiprocessor

Rapid increases in the computational speeds of multiprocessors have not been matched by corresponding performance enhancements in the I/O subsystem. To satisfy the large and growing I/O requirements of some parallel scientific applications, we need parallel file systems that can provide high-bandwidth and high-volume data transfer between the I/O subsystem and thousands of processors. Design of such high-performance parallel file systems depends on a thorough grasp of the expected workload. So far there have been no comprehensive usage studies of multiprocessor file systems. Our CHARISMA project intends to fill this void. The first results from our study involve an iPSC/860 at NASA Ames. This paper presents results from a different platform, the CM-5 at the National Center for Supercomputing Applications. The CHARISMA studies are unique because we collect information about every individual read and write request and about the entire mix of applications running on the machines. The results of our trace analysis lead to recommendations for parallel file system design. First the file system should support efficient concurrent access to many files, and I/O requests from many jobs under varying load conditions. Second, it must efficiently manage large files kept open for long periods. Third, it should expect to see small requests predominantly sequential access patterns, application-wide synchronous access, no concurrent file-sharing between jobs appreciable byte and block sharing between processes within jobs, and strong interprocess locality. Finally, the trace data suggest that node-level write caches and collective I/O request interfaces may be useful in certain environments.

Purakayastha, Apratim↗

System monitors discrete computer inputs

Computer system monitors inputs from checkout devices. The comparing, addressing, and controlling functions are performed in the I/O unit. This leaves the computer main frame free to handle memory, access priority, and interrupt instructions.

Burns, J. J.↗

The graphics and data acquisition software package

A software package was developed for use with micro and minicomputers, particularly the LSI-11/DPD-11 series. The package has a number of Fortran-callable subroutines which perform a variety of frequently needed tasks for biomedical applications. All routines are well documented, flexible, easy to use and modify, and require minimal programmer knowledge of peripheral hardware. The package is also economical of memory and CPU time. A single subroutine call can perform any one of the following functions: (1) plot an array of integer values from sampled A/D data, (2) plot an array of Y values versus an array of X values; (3) draw horizontal and/or vertical grid lines of selectable type; (4) annotate grid lines with user units; (5) get coordinates of user controlled crosshairs from the terminal for interactive graphics; (6) sample any analog channel with program selectable gain; (7) wait a specified time interval, and (8) perform random access I/O of one or more blocks of a sequential disk file. Several miscellaneous functions are also provided.

Crosier, W. G.↗

Universal computer control system (UCCS) for space telerobots

A universal computer control system (UCCS) is under development for all motor elements of a space telerobot. The basic hardware architecture and software design of UCCS are described, together with the rich motor sensing, control, and self-test capabilities of this all-computerized motor control system. UCCS is integrated into a multibus computer environment with direct interface to higher level control processors, uses pulsewidth multiplier power amplifiers, and one unit can control up to sixteen different motors simultaneously at a high I/O rate. UCCS performance capabilities are illustrated by a few data.

Bejczy, Antal K.↗