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NASA NTRS1994

High performance computing applications in neurobiological research

The human nervous system is a massively parallel processor of information. The vast numbers of neurons, synapses and circuits is daunting to those seeking to understand the neural basis of consciousness and intellect. Pervading obstacles are lack of knowledge of the detailed, three-dimensional (3-D) organization of even a simple neural system and the paucity of large scale, biologically relevant computer simulations. We use high performance graphics workstations and supercomputers to study the 3-D organization of gravity sensors as a prototype architecture foreshadowing more complex systems. Scaled-down simulations run on a Silicon Graphics workstation and scale-up, three-dimensional versions run on the Cray Y-MP and CM5 supercomputers.

Ross, Muriel D.↗
NASA NTRS1995

CFD Research, Parallel Computation and Aerodynamic Optimization

During the last five years, CFD has matured substantially. Pure CFD research remains to be done, but much of the focus has shifted to integration of CFD into the design process. The work under these cooperative agreements reflects this trend. The recent work, and work which is planned, is designed to enhance the competitiveness of the US aerospace industry. CFD and optimization approaches are being developed and tested, so that the industry can better choose which methods to adopt in their design processes. The range of computer architectures has been dramatically broadened, as the assumption that only huge vector supercomputers could be useful has faded. Today, researchers and industry can trade off time, cost, and availability, choosing vector supercomputers, scalable parallel architectures, networked workstations, or heterogenous combinations of these to complete required computations efficiently.

Ryan, James S.↗
NASA NTRS1996

Towards the Interoperability of Web, Database, and Mass Storage Technologies for Petabyte Archives

At the San Diego Supercomputer Center, a massive data analysis system (MDAS) is being developed to support data-intensive applications that manipulate terabyte sized data sets. The objective is to support scientific application access to data whether it is located at a Web site, stored as an object in a database, and/or storage in an archival storage system. We are developing a suite of demonstration programs which illustrate how Web, database (DBMS), and archival storage (mass storage) technologies can be integrated. An application presentation interface is being designed that integrates data access to all of these sources. We have developed a data movement interface between the Illustra object-relational database and the NSL UniTree archival storage system running in a production mode at the San Diego Supercomputer Center. With this interface, an Illustra client can transparently access data on UniTree under the control of the Illustr DBMS server. The current implementation is based on the creation of a new DBMS storage manager class, and a set of library functions that allow the manipulation and migration of data stored as Illustra 'large objects'. We have extended this interface to allow a Web client application to control data movement between its local disk, the Web server, the DBMS Illustra server, and the UniTree mass storage environment. This paper describes some of the current approaches successfully integrating these technologies. This framework is measured against a representative sample of environmental data extracted from the San Diego Ba Environmental Data Repository. Practical lessons are drawn and critical research areas are highlighted.

Moore, Reagan↗
NASA NTRS1998

The Tera Multithreaded Architecture and Unstructured Meshes

The Tera Multithreaded Architecture (MTA) is a new parallel supercomputer currently being installed at San Diego Supercomputing Center (SDSC). This machine has an architecture quite different from contemporary parallel machines. The computational processor is a custom design and the machine uses hardware to support very fine grained multithreading. The main memory is shared, hardware randomized and flat. These features make the machine highly suited to the execution of unstructured mesh problems, which are difficult to parallelize on other architectures. We report the results of a study carried out during July-August 1998 to evaluate the execution of EUL3D, a code that solves the Euler equations on an unstructured mesh, on the 2 processor Tera MTA at SDSC. Our investigation shows that parallelization of an unstructured code is extremely easy on the Tera. We were able to get an existing parallel code (designed for a shared memory machine), running on the Tera by changing only the compiler directives. Furthermore, a serial version of this code was compiled to run in parallel on the Tera by judicious use of directives to invoke the "full/empty" tag bits of the machine to obtain synchronization. This version achieves 212 and 406 Mflop/s on one and two processors respectively, and requires no attention to partitioning or placement of data issues that would be of paramount importance in other parallel architectures.

Bokhari, Shahid H.↗
NASA NTRS1998

COOP 3D ARPA Experiment 109 National Center for Atmospheric Research

Coupled atmospheric and hydrodynamic forecast models were executed on the supercomputing resources of the National Center for Atmospheric Research (NCAR) in Boulder, Colorado and the Ohio Supercomputing Center (OSC)in Columbus, Ohio. respectively. The interoperation of the forecast models on these geographically diverse, high performance Cray platforms required the transfer of large three dimensional data sets at very high information rates. High capacity, terrestrial fiber optic transmission system technologies were integrated with those of an experimental high speed communications satellite in Geosynchronous Earth Orbit (GEO) to test the integration of the two systems. Operation over a spacecraft in GEO orbit required modification of the standard configuration of legacy data communications protocols to facilitate their ability to perform efficiently in the changing environment characteristic of a hybrid network. The success of this performance tuning enabled the use of such an architecture to facilitate high data rate, fiber optic quality data communications between high performance systems not accessible to standard terrestrial fiber transmission systems. Thus obviating the performance degradation often found in contemporary earth/satellite hybrids.

Source record↗
NASA NTRS1999

MOD Tool (Microwave Optics Design Tool)

The Jet Propulsion Laboratory (JPL) is currently designing and building a number of instruments that operate in the microwave and millimeter-wave bands. These include MIRO (Microwave Instrument for the Rosetta Orbiter), MLS (Microwave Limb Sounder), and IMAS (Integrated Multispectral Atmospheric Sounder). These instruments must be designed and built to meet key design criteria (e.g., beamwidth, gain, pointing) obtained from the scientific goals for the instrument. These criteria are frequently functions of the operating environment (both thermal and mechanical). To design and build instruments which meet these criteria, it is essential to be able to model the instrument in its environments. Currently, a number of modeling tools exist. Commonly used tools at JPL include: FEMAP (meshing), NASTRAN (structural modeling), TRASYS and SINDA (thermal modeling), MACOS/IMOS (optical modeling), and POPO (physical optics modeling). Each of these tools is used by an analyst, who models the instrument in one discipline. The analyst then provides the results of this modeling to another analyst, who continues the overall modeling in another discipline. There is a large reengineering task in place at JPL to automate and speed-up the structural and thermal modeling disciplines, which does not include MOD Tool. The focus of MOD Tool (and of this paper) is in the fields unique to microwave and millimeter-wave instrument design. These include initial design and analysis of the instrument without thermal or structural loads, the automation of the transfer of this design to a high-end CAD tool, and the analysis of the structurally deformed instrument (due to structural and/or thermal loads). MOD Tool is a distributed tool, with a database of design information residing on a server, physical optics analysis being performed on a variety of supercomputer platforms, and a graphical user interface (GUI) residing on the user's desktop computer. The MOD Tool client is being developed using Tcl/Tk, which allows the user to work on a choice of platforms (PC, Mac, or Unix) after downloading the Tcl/Tk binary, which is readily available on the web. The MOD Tool server is written using Expect, and it resides on a Sun workstation. Client/server communications are performed over a socket, where upon a connection from a client to the server, the server spawns a child which is be dedicated to communicating with that client. The server communicates with other machines, such as supercomputers using Expect with the username and password being provided by the user on the client.

Katz, Daniel S.↗
NASA NTRS1999

An Integrated Architecture for Onboard Spacecraft

As increasingly complex scientific and environmental observation spacecraft are deployed, the burden on the downlink assets, and ground-based systems complexity and cost is becoming a major problem. Already, the limitations of communications bandwidth and processing throughput limit the science data gathering, both in volume and in rate. This poses a dilemma to the scientist experimenter forcing choices between data collection and bandwidth/processing/archiving. Advances in ground based processing and space-to-Earth links have fallen behind the requirements for observation data, at increasing rates, over the last few decades. As NASA achieves its 40th anniversary, the ability to observe and capture phenomena of theoretical and practical interest to life on Earth far outstrips the ability to transfer, process, or store these data. NASA recognizes the need to invest on technological advancements that will enable both the space and ground systems to address the limitations. Spacecraft onboard computing power is a clear one. The capability of creating data products onboard the spacecraft adds a new level of flexibility to address the more demanding observation needs. Current spacecraft computing power is limited and incapable of addressing the needs of the new generation of observation satellites because extensive onboard data processing is required. Traditional spacecraft architectures only collect, package, and transmit to Earth the data acquired by multiple instruments. Conversely, the experience on developing ground data systems shows the need for high performance computing systems to process and create information from the instrumentation data. The expectation is that supercomputing technology is required to enable spacecraft to create information onboard. Moving supercomputing capability onboard spacecraft requires an approach that considers an integrated data architecture. Otherwise, it may simply convert a compute-bound problem into a communications bound problem, as has been shown numerous times in the context of massively parallel architectures. What is left to determine are the technologies that will enable spacecraft high performance computing.

Figueiredo, Marco A.↗
NASA NTRS1999

Research on Spectroscopy, Opacity, and Atmospheres

A web site has been set up to make the calculations accessible; (i.e., cfakus.harvard.edu) This data can also be accessed by FTP. It has all of the atomic and diatomic molecular data, tables of distribution function opacities, grids of model atmospheres, colors, fluxes, etc, programs that are ready for distribution, and most of recent papers developed during this grant. Atlases and computed spectra will be added as they are completed. New atomic and molecular calculations will be added as they are completed. The atomic programs that had been running on a Cray at the San Diego Supercomputer Center can now run on the Vaxes and Alpha. The work started with Ni and Co because there were new laboratory analyses that included isotopic and hyperfine splitting. Those calculations are described in the appended abstract for the 6th Atomic Spectroscopy and oscillator Strengths meeting in Victoria last summer. A surprising finding is that quadrupole transitions have been grossly in error because mixing with higher levels has not been included. All levels up through n=9 for Fe I and II, the spectra for which the most information is available, are now included. After Fe I and Fe II, all other spectra are "easy". ATLAS12, the opacity sampling program for computing models with arbitrary abundances, has been put on the web server. A new distribution function opacity program for workstations that replaces the one used on the Cray at the San Diego Supercomputer Center has been written. Each set of abundances would take 100 Cray hours costing $100,000.

Kurucz, Robert L.↗
NASA NTRS1998

The SGI/Cray T3E: Experiences and Insights

The NASA Goddard Space Flight Center is home to the fifth most powerful supercomputer in the world, a 1024 processor SGI/Cray T3E-600. The original 512 processor system was placed at Goddard in March, 1997 as part of a cooperative agreement between the High Performance Computing and Communications Program's Earth and Space Sciences Project (ESS) and SGI/Cray Research. The goal of this system is to facilitate achievement of the Project milestones of 10, 50 and 100 GFLOPS sustained performance on selected Earth and space science application codes. The additional 512 processors were purchased in March, 1998 by the NASA Earth Science Enterprise for the NASA Seasonal to Interannual Prediction Project (NSIPP). These two "halves" still operate as a single system, and must satisfy the unique requirements of both aforementioned groups, as well as guest researchers from the Earth, space, microgravity, manned space flight and aeronautics communities. Few large scalable parallel systems are configured for capability computing, so models are hard to find. This unique environment has created a challenging system administration task, and has yielded some insights into the supercomputing needs of the various NASA Enterprises, as well as insights into the strengths and weaknesses of the T3E architecture and software. The T3E is a distributed memory system in which the processing elements (PE's) are connected by a low latency, high bandwidth bidirectional 3-D torus. Due to the focus on high speed communication between PE's, the T3E requires PE's to be allocated contiguously per job. Further, jobs will only execute on the user specified number of PE's and PE timesharing is possible but impractical. With a highly varied job mix in both size and runtime of jobs, the resulting scenario is PE fragmentation and an inability to achieve near 100% utilization. SGI/Cray has provided several scheduling and configuration tools to minimize the impact of fragmentation. These tools include PScheD (the political scheduler), GRM (the global resource manager) and NQE (the Network Queuing Environment). Features and impact of these tools will be discussed, as will resulting performance and utilization data. As a distributed memory system, the T3E is designed to be programmed through explicit message passing. Consequently, certain assumptions related to code design are made by the operating system (UNICOS/mk) and its scheduling tools. With the exception of HPF, which does run on the T3E, however poorly, alternative programming styles have the potential to impact the T3E in unexpected and undesirable ways. Several examples will be presented (preceeded with the disclaimer, "Don't try this at home! Violators will be prosecuted!")

Bernard, Lisa Hamet↗
NASA NTRS1999

Research on Spectroscopy, Opacity, and Atmospheres

To make my calculations more readily accessible I have set up a web site cfaku5.harvard.edu that can also be accessed by FTP. it has 5 9GB disks that hold all of my atomic and diatomic molecular data, my tables of distribution function opacities, my grids of model atmospheres, colors, fluxes, etc, my program that are ready for distribution, most of my recent papers. Atlases and computed spectra will be added as they are completed. New atomic and molecular calculations will be added as they are completed. I got my atomic programs that had been running on a Cray at the San Diego Supercomputer Center to run on my Vaxes and Alpha. I started with Ni and Co because there were new laboratory analyses that included isotopic and hyperfine splitting. Those calculations are described in the appended abstract for the 6th Atomic Spectroscopy and oscillator Strengths meeting in Victoria last summer. A surprising finding is that quadrupole transitions have been grossly in error because mixing with higher levels has not been included. I now have enough memory in my Alpha to treat 3000 x 3000 matrices. I now include all levels up through n=9 for Fe I and 11, the spectra for which the most information is available. I am finishing those calculations right now. After Fe I and Fe 11, all other spectra are "easy", and I will be in mass production. ATL;LS12, my opacity sampling program for computing models with arbitrary abundances, has been put on the web server. I wrote a new distribution function opacity program for workstations that replaces the one I used on the Cray at the San Diego Supercomputer Center. Each set of abundances would take 100 Cray hours costing $100,000. 1 ran 25 cases. Each of my opacity CDs contains three abundances. I have a new program -iinning on the Alpha that takes about a week. I am going to have to get a faster processor or I will have to dedicate a whole workstation just to opacities.

Kurucz, Robert L.↗
NASA NTRS2000

Computing Needs for Astrobiology: Models of Planetary Formation

Theories of planet formation indicate that a diverse range of physical and chemical processes determine the characteristics of a planetary system. Extensive numerical modeling is required to understand how planetary systems form, and to make quantitative assessments of the factors which determine the masses, spacings and volatile compound inventories of planets and small bodies within a planetary system. Fluid flow problems associated with the formation and evolution of protoplanetary disks include specific local calculations to provide physical insight, which are best performed on workstations, and large multifaceted simulations which require supercomputers with large memories. Formation and early growth of planetesimals display a similar range of computational requirements. Modeling the late stages of planetary accumulation is very CPU intensive, as it requires following a simple system of approx. hundreds of bodies for millions of dynamical (orbital) times. These varied computational needs could be met in the most cost-effective manner by a diverse set of computers, including workstations for individual PI's and dedicated time on various types of supercomputers which are specialized for differing tasks.

Lissauer, Jack J.↗
NASA NTRS2000

An Advanced User Interface Approach for Complex Parameter Study Process Specification in the Information Power Grid

The creation of parameter study suites has recently become a more challenging problem as the parameter studies have now become multi-tiered and the computational environment has become a supercomputer grid. The parameter spaces are vast, the individual problem sizes are getting larger, and researchers are now seeking to combine several successive stages of parameterization and computation. Simultaneously, grid-based computing offers great resource opportunity but at the expense of great difficulty of use. We present an approach to this problem which stresses intuitive visual design tools for parameter study creation and complex process specification, and also offers programming-free access to grid-based supercomputer resources and process automation.

Yarrow, Maurice↗
NASA NTRS1994

High Performance Computing at NASA

The speaker will give an overview of high performance computing in the U.S. in general and within NASA in particular, including a description of the recently signed NASA-IBM cooperative agreement. The latest performance figures of various parallel systems on the NAS Parallel Benchmarks will be presented. The speaker was one of the authors of the NAS (National Aerospace Standards) Parallel Benchmarks, which are now widely cited in the industry as a measure of sustained performance on realistic high-end scientific applications. It will be shown that significant progress has been made by the highly parallel supercomputer industry during the past year or so, with several new systems, based on high-performance RISC processors, that now deliver superior performance per dollar compared to conventional supercomputers. Various pitfalls in reporting performance will be discussed. The speaker will then conclude by assessing the general state of the high performance computing field.

Bailey, David H.↗
NASA NTRS1994

New Computer Simulations of Macular Neural Functioning

We use high performance graphics workstations and supercomputers to study the functional significance of the three-dimensional (3-D) organization of gravity sensors. These sensors have a prototypic architecture foreshadowing more complex systems. Scaled-down simulations run on a Silicon Graphics workstation and scaled-up, 3-D versions run on a Cray Y-MP supercomputer. A semi-automated method of reconstruction of neural tissue from serial sections studied in a transmission electron microscope has been developed to eliminate tedious conventional photography. The reconstructions use a mesh as a step in generating a neural surface for visualization. Two meshes are required to model calyx surfaces. The meshes are connected and the resulting prisms represent the cytoplasm and the bounding membranes. A finite volume analysis method is employed to simulate voltage changes along the calyx in response to synapse activation on the calyx or on calyceal processes. The finite volume method insures that charge is conserved at the calyx-process junction. These and other models indicate that efferent processes act as voltage followers, and that the morphology of some afferent processes affects their functioning. In a final application, morphological information is symbolically represented in three dimensions in a computer. The possible functioning of the connectivities is tested using mathematical interpretations of physiological parameters taken from the literature. Symbolic, 3-D simulations are in progress to probe the functional significance of the connectivities. This research is expected to advance computer-based studies of macular functioning and of synaptic plasticity.

Ross, Muriel D.↗
NASA NTRS1995

RISC Processors and High Performance Computing

In this tutorial, we will discuss top five current RISC microprocessors: The IBM Power2, which is used in the IBM RS6000/590 workstation and in the IBM SP2 parallel supercomputer, the DEC Alpha, which is in the DEC Alpha workstation and in the Cray T3D; the MIPS R8000, which is used in the SGI Power Challenge; the HP PA-RISC 7100, which is used in the HP 700 series workstations and in the Convex Exemplar; and the Cray proprietary processor, which is used in the new Cray J916. The architecture of these microprocessors will first be presented. The effective performance of these processors will then be compared, both by citing standard benchmarks and also in the context of implementing a real applications. In the process, different programming models such as data parallel (CM Fortran and HPF) and message passing (PVM and MPI) will be introduced and compared. The latest NAS Parallel Benchmark (NPB) absolute performance and performance per dollar figures will be presented. The next generation of the NP13 will also be described. The tutorial will conclude with a discussion of general trends in the field of high performance computing, including likely future developments in hardware and software technology, and the relative roles of vector supercomputers tightly coupled parallel computers, and clusters of workstations. This tutorial will provide a unique cross-machine comparison not available elsewhere.

Saini, Subhash↗
NASA NTRS1995

The NAS Computational Aerosciences Archive

In order to further the state-of-the-art in computational aerosciences (CAS) technology, researchers must be able to gather and understand existing work in the field. One aspect of this information gathering is studying published work available in scientific journals and conference proceedings. However, current scientific publications are very limited in the type and amount of information that they can disseminate. Information is typically restricted to text, a few images, and a bibliography list. Additional information that might be useful to the researcher, such as additional visual results, referenced papers, and datasets, are not available. New forms of electronic publication, such as the World Wide Web (WWW), limit publication size only by available disk space and data transmission bandwidth, both of which are improving rapidly. The Numerical Aerodynamic Simulation (NAS) Systems Division at NASA Ames Research Center is in the process of creating an archive of CAS information on the WWW. This archive will be based on the large amount of information produced by researchers associated with the NAS facility. The archive will contain technical summaries and reports of research performed on NAS supercomputers, visual results (images, animations, visualization system scripts), datasets, and any other supporting meta-information. This information will be available via the WWW through the NAS homepage, located at http://www.nas.nasa.gov/, fully indexed for searching. The main components of the archive are technical summaries and reports, visual results, and datasets. Technical summaries are gathered every year by researchers who have been allotted resources on NAS supercomputers. These summaries, together with supporting visual results and references, are browsable by interested researchers. Referenced papers made available by researchers can be accessed through hypertext links. Technical reports are in-depth accounts of tools and applications research projects performed by NAS staff members and collaborators. Visual results, which may be available in the form of images, animations, and/or visualization scripts, are generated by researchers with respect to a certain research project, depicting dataset features that were determined important by the investigating researcher. For example, script files for visualization systems (e.g. FAST, PLOT3D, AVS) are provided to create visualizations on the user's local workstation to elucidate the key points of the numerical study. Users can then interact with the data starting where the investigator left off. Datasets are intended to give researchers an opportunity to understand previous work, 'mine' solutions for new information (for example, have you ever read a paper thinking "I wonder what the helicity density looks like?"), compare new techniques with older results, collaborate with remote colleagues, and perform validation. Supporting meta-information associated with the research projects is also important to provide additional context for research projects. This may include information such as the software used in the simulation (e.g. grid generators, flow solvers, visualization). In addition to serving the CAS research community, the information archive will also be helpful to students, visualization system developers and researchers, and management. Students (of any age) can use the data to study fluid dynamics, compare results from different flow solvers, learn about meshing techniques, etc., leading to better informed individuals. For these users it is particularly important that visualization be integrated into dataset archives. Visualization researchers can use dataset archives to test algorithms and techniques, leading to better visualization systems, Management can use the data to figure what is really going on behind the viewgraphs. All users will benefit from fast, easy, and convenient access to CFD datasets. The CAS information archive hopes to serve as a useful resource to those interested in computational sciences. At present, only information that may be distributed internationally is made available via the archive. Studies are underway to determine security requirements and solutions to make additional information available. By providing access to the archive via the WWW, the process of information gathering can be more productive and fruitful due to ease of access and ability to manage many different types of information. As the archive grows, additional resources from outside NAS will be added, providing a dynamic source of research results.

Miceli, Kristina D.↗
NASA NTRS1995

Monitoring Object Library Usage and Changes

The NASA Ames Numerical Aerodynamic Simulation program Aeronautics Consolidated Supercomputing Facility (NAS/ACSF) supercomputing center services over 1600 users, and has numerous analysts with root access. Several tools have been developed to monitor object library usage and changes. Some of the tools do "noninvasive" monitoring and other tools implement run-time logging even for object-only libraries. The run-time logging identifies who, when, and what is being used. The benefits are that real usage can be measured, unused libraries can be discontinued, training and optimization efforts can be focused at those numerical methods that are actually used. An overview of the tools will be given and the results will be discussed.

Owen, R. K.↗
NASA NTRS1996

The " Swarm of Ants vs. Herd of Elephants" Debated Revisited: Performance Measurements of PVM-Overflow Across a Wide Spectrum of Architectures

The Gorden Bell Prizes given out at Supercomputing every year includes at least two catergories: performance (highest GFLOP count) and price-performance (GFLOP/million $$) for real applications. In the past five years, the winners of the price-performance categories all came from networks of work-stations. This reflects three important facts: 1. supercomputers are still too expensive for the masses; 2. achieving high performance for real applications takes real work; and, most importantly; 3. it is possible to obtain acceptable performance for certain real applications on network of work stations. With the continued advance of network technology as well as increased performance of "desktop" workstation, the "Swarm of Ants vs. Herd of Elephants" debate, which began with vector multiprocessors (VPPs) against SIMD type multiprocessors (e.g. CM2), is now recast as VPPs against Symetric Multiprocessors (SMPs, e.g. SGI PowerChallenge). This paper reports on performance studies we performed solving a large scale (2-million grid pt.s) CFD problem involving a Boeing 747 based on a parallel version of OVERFLOW that utilizes message passing on PVM. A performance monitoring tool developed under NASA HPCC, called AIMS, was used to instrument and analyze the the performance data thus obtained. We plan to compare its performance data obtained across a wide spectrum of architectures including: the Cray C90, IBM/SP2, SGI/Power Challenge Cluster, to a group of workstations connected over a simple network. The metrics of comparison includes speed-up, price-performance, throughput, and turn-around time. We also plan to present a plan of attack for various issues that will make the execution of Grand Challenge Applications across the Global Information Infrastructure a reality.

Yan, Jerry C.↗