Evaluation of six sugar kelp crosses selected for high yield at three Northeastern US farms
Not Available
Gonzalez, Sara T.↗
Engineering topics
Bailey, David
Publications and source records attributed to Bailey, David.
An Assessment of Southern Ocean Water Masses and Sea Ice During 1988-2007 in a Suite of Interannual CORE-II Simulations
We characterise the representation of the Southern Ocean water mass structure and sea ice within a suite of 15 global ocean-ice models run with the Coordinated Ocean-ice Reference Experiment Phase II (CORE-II) protocol. The main focus is the representation of the present (1988-2007) mode and intermediate waters, thus framing an analysis of winter and summer mixed layer depths; temperature, salinity, and potential vorticity structure; and temporal variability of sea ice distributions. We also consider the interannual variability over the same 20 year period. Comparisons are made between models as well as to observation-based analyses where available. The CORE-II models exhibit several biases relative to Southern Ocean observations, including an underestimation of the model mean mixed layer depths of mode and intermediate water masses in March (associated with greater ocean surface heat gain), and an overestimation in September (associated with greater high latitude ocean heat loss and a more northward winter sea-ice extent). In addition, the models have cold and fresh/warm and salty water column biases centred near 50 deg S. Over the 1988-2007 period, the CORE-II models consistently simulate spatially variable trends in sea-ice concentration, surface freshwater fluxes, mixed layer depths, and 200-700 m ocean heat content. In particular, sea-ice coverage around most of the Antarctic continental shelf is reduced, leading to a cooling and freshening of the near surface waters. The shoaling of the mixed layer is associated with increased surface buoyancy gain, except in the Pacific where sea ice is also influential. The models are in disagreement, despite the common CORE-II atmospheric state, in their spatial pattern of the 20-year trends in the mixed layer depth and sea-ice.
Sea ice↗
NASA Applications of Molecular Nanotechnology
Laboratories throughout the world are rapidly gaining atomically precise control over matter. As this control extends to an ever wider variety of materials, processes and devices, opportunities for applications relevant to NASA's missions will be created. This document surveys a number of future molecular nanotechnology capabilities of aerospace interest. Computer applications, launch vehicle improvements, and active materials appear to be of particular interest. We also list a number of applications for each of NASA's enterprises. If advanced molecular nanotechnology can be developed, almost all of NASA's endeavors will be radically improved. In particular, a sufficiently advanced molecular nanotechnology can arguably bring large scale space colonization within our grasp.
Globus, Al↗
Parallel Load Balancing for Adaptive Unstructured Meshes
Mesh adaption is a powerful tool for efficient unstructured-grid computations but causes load imbalance among processors on a parallel machine. We describe a novel method to dynamically balance the processor workloads with a global view. Mesh question, repartitioning, processor assignment, and remapping are critical components of the framework that must be accomplished rapidly and efficiently so as not to cause a significant overhead to the numerical simulation. A data redistribution model will also be presented that predicts the remapping cost. This model is required to determine whether the gain from a balanced workload distribution offsets the cost of data movement. Results presented will demonstrate that this is an effective dynamic load balancing strategy which remains viable on a large number of processors.
Biswas, Rupak↗
Trace-Driven Debugging of Message Passing Programs
In this paper we report on features added to a parallel debugger to simplify the debugging of parallel message passing programs. These features include replay, setting consistent breakpoints based on interprocess event causality, a parallel undo operation, and communication supervision. These features all use trace information collected during the execution of the program being debugged. We used a number of different instrumentation techniques to collect traces. We also implemented trace displays using two different trace visualization systems. The implementation was tested on an SGI Power Challenge cluster and a network of SGI workstations.
Frumkin, Michael↗
Challenges of Future High-End Computing
The next major milestone in high performance computing is a sustained rate of one Pflop/s (also written one petaflops, or 10(circumflex)15 floating-point operations per second). In addition to prodigiously high computational performance, such systems must of necessity feature very large main memories, as well as comparably high I/O bandwidth and huge mass storage facilities. The current consensus of scientists who have studied these issues is that "affordable" petaflops systems may be feasible by the year 2010, assuming that certain key technologies continue to progress at current rates. One important question is whether applications can be structured to perform efficiently on such systems, which are expected to incorporate many thousands of processors and deeply hierarchical memory systems. To answer these questions, advanced performance modeling techniques, including simulation of future architectures and applications, may be required. It may also be necessary to formulate "latency tolerant algorithms" and other completely new algorithmic approaches for certain applications. This talk will give an overview of these challenges.
Bailey, David↗
Algebraic Nonoverlapping Domain Decomposition Methods for Stabilized FEM and FV Discretizations
We consider preconditioning methods for convection dominated fluid flow problems based on a nonoverlapping Schur complement domain decomposition procedure for arbitrary triangulated domains. The triangulation is first partitioned into a number of subdomains and interfaces which induce a natural 2 x 2 partitioning of the p.d.e. discretization matrix. We view the Schur complement induced by this partitioning as an algebraically derived coarse space approximation. This avoids the known difficulties associated with the direct formation of an effective coarse discretization for advection dominated equations. By considering various approximations of the block factorization of the 2 x 2 system, we have developed a family of robust preconditioning techniques. A computer code based on these ideas has been developed and tested on the IBM SP2 using MPI message passing protocol. A number of 2-D CFD calculations will be presented for both scalar advection-diffusion equations and the Euler equations discretized using stabilized finite element and finite volume methods. These results show very good scalability of the preconditioner for various discretizations as the number of processors is increased while the number of degrees of freedom per processor is fixed.
Barth, Timothy J.↗
Automated Generation of Message-Passing Programs: An Evaluation of CAPTools using NAS Benchmarks
Scientists at NASA Ames Research Center have been developing computational aeroscience applications on highly parallel architectures over the past ten years. During the same time period, a steady transition of hardware and system software also occurred, forcing us to expand great efforts into migrating and receding our applications. As applications and machine architectures continue to become increasingly complex, the cost and time required for this process will become prohibitive. Various attempts to exploit software tools to assist and automate the parallelization process have not produced favorable results. In this paper, we evaluate an interactive parallelization tool, CAPTools, for parallelizing serial versions of the NAB Parallel Benchmarks. Finally, we compare the performance of the resulting CAPTools generated code to the hand-coded benchmarks on the Origin 2000 and IBM SP2. Based on these results, a discussion on the feasibility of automated parallelization of aerospace applications is presented along with suggestions for future work.
Hribar, Michelle R.↗
NAS Parallel Benchmark Results 11-96
The NAS Parallel Benchmarks have been developed at NASA Ames Research Center to study the performance of parallel supercomputers. The eight benchmark problems are specified in a "pencil and paper" fashion. In other words, the complete details of the problem to be solved are given in a technical document, and except for a few restrictions, benchmarkers are free to select the language constructs and implementation techniques best suited for a particular system. These results represent the best results that have been reported to us by the vendors for the specific 3 systems listed. In this report, we present new NPB (Version 1.0) performance results for the following systems: DEC Alpha Server 8400 5/440, Fujitsu VPP Series (VX, VPP300, and VPP700), HP/Convex Exemplar SPP2000, IBM RS/6000 SP P2SC node (120 MHz), NEC SX-4/32, SGI/CRAY T3E, SGI Origin200, and SGI Origin2000. We also report High Performance Fortran (HPF) based NPB results for IBM SP2 Wide Nodes, HP/Convex Exemplar SPP2000, and SGI/CRAY T3D. These results have been submitted by Applied Parallel Research (APR) and Portland Group Inc. (PGI). We also present sustained performance per dollar for Class B LU, SP and BT benchmarks.
Bailey, David H.↗
The Automated Instrumentation and Monitoring System (AIMS): Design and Architecture
Whether a researcher is designing the 'next parallel programming paradigm', another 'scalable multiprocessor' or investigating resource allocation algorithms for multiprocessors, a facility that enables parallel program execution to be captured and displayed is invaluable. Careful analysis of such information can help computer and software architects to capture, and therefore, exploit behavioral variations among/within various parallel programs to take advantage of specific hardware characteristics. A software tool-set that facilitates performance evaluation of parallel applications on multiprocessors has been put together at NASA Ames Research Center under the sponsorship of NASA's High Performance Computing and Communications Program over the past five years. The Automated Instrumentation and Monitoring Systematic has three major software components: a source code instrumentor which automatically inserts active event recorders into program source code before compilation; a run-time performance monitoring library which collects performance data; and a visualization tool-set which reconstructs program execution based on the data collected. Besides being used as a prototype for developing new techniques for instrumenting, monitoring and presenting parallel program execution, AIMS is also being incorporated into the run-time environments of various hardware testbeds to evaluate their impact on user productivity. Currently, the execution of FORTRAN and C programs on the Intel Paragon and PALM workstations can be automatically instrumented and monitored. Performance data thus collected can be displayed graphically on various workstations. The process of performance tuning with AIMS will be illustrated using various NAB Parallel Benchmarks. This report includes a description of the internal architecture of AIMS and a listing of the source code.
Yan, Jerry C.↗
NAS Parallel Benchmark. Results 11-96: Performance Comparison of HPF and MPI Based NAS Parallel Benchmarks
High Performance Fortran (HPF), the high-level language for parallel Fortran programming, is based on Fortran 90. HALF was defined by an informal standards committee known as the High Performance Fortran Forum (HPFF) in 1993, and modeled on TMC's CM Fortran language. Several HPF features have since been incorporated into the draft ANSI/ISO Fortran 95, the next formal revision of the Fortran standard. HPF allows users to write a single parallel program that can execute on a serial machine, a shared-memory parallel machine, or a distributed-memory parallel machine. HPF eliminates the complex, error-prone task of explicitly specifying how, where, and when to pass messages between processors on distributed-memory machines, or when to synchronize processors on shared-memory machines. HPF is designed in a way that allows the programmer to code an application at a high level, and then selectively optimize portions of the code by dropping into message-passing or calling tuned library routines as 'extrinsics'. Compilers supporting High Performance Fortran features first appeared in late 1994 and early 1995 from Applied Parallel Research (APR) Digital Equipment Corporation, and The Portland Group (PGI). IBM introduced an HPF compiler for the IBM RS/6000 SP/2 in April of 1996. Over the past two years, these implementations have shown steady improvement in terms of both features and performance. The performance of various hardware/ programming model (HPF and MPI (message passing interface)) combinations will be compared, based on latest NAS (NASA Advanced Supercomputing) Parallel Benchmark (NPB) results, thus providing a cross-machine and cross-model comparison. Specifically, HPF based NPB results will be compared with MPI based NPB results to provide perspective on performance currently obtainable using HPF versus MPI or versus hand-tuned implementations such as those supplied by the hardware vendors. In addition we would also present NPB (Version 1.0) performance results for the following systems: DEC Alpha Server 8400 5/440, Fujitsu VPP Series (VX, VPP300, and VPP700), HP/Convex Exemplar SPP2000, IBM RS/6000 SP P2SC node (120 MHz) NEC SX-4/32, SGI/CRAY T3E, SGI Origin2000.
Saini, Subash↗
By Hand or Not By-Hand: A Case Study of Alternative Approaches to Parallelize CFD Applications
While parallel processing promises to speed up applications by several orders of magnitude, the performance achieved still depends upon several factors, including the multiprocessor architecture, system software, data distribution and alignment, as well as the methods used for partitioning the application and mapping its components onto the architecture. The existence of the Gorden Bell Prize given out at Supercomputing every year suggests that while good performance can be attained for real applications on general purpose multiprocessors, the large investment in man-power and time still has to be repeated for each application-machine combination. As applications and machine architectures become more complex, the cost and time-delays for obtaining performance by hand will become prohibitive. Computer users today can turn to three possible avenues for help: parallel libraries, parallel languages and compilers, interactive parallelization tools. The success of these methodologies, in turn, depends on proper application of data dependency analysis, program structure recognition and transformation, performance prediction as well as exploitation of user supplied knowledge. NASA has been developing multidisciplinary applications on highly parallel architectures under the High Performance Computing and Communications Program. Over the past six years, the transition of underlying hardware and system software have forced the scientists to spend a large effort to migrate and recede their applications. Various attempts to exploit software tools to automate the parallelization process have not produced favorable results. In this paper, we report our most recent experience with CAPTOOL, a package developed at Greenwich University. We have chosen CAPTOOL for three reasons: 1. CAPTOOL accepts a FORTRAN 77 program as input. This suggests its potential applicability to a large collection of legacy codes currently in use. 2. CAPTOOL employs domain decomposition to obtain parallelism. Although the fact that not all kinds of parallelism are handled may seem unappealing, many NASA applications in computational aerosciences as well as earth and space sciences are amenable to domain decomposition. 3. CAPTOOL generates code for a large variety of environments employed across NASA centers: MPI/PVM on network of workstations to the IBS/SP2 and CRAY/T3D.
Yan, Jerry C.↗
The First Three Years of the Parallel Tools Consortium -- A Review
The Parallel Tools Consortium (or PTOOLS) was established in late 1993 in response to concerns that effective parallel tool development requires more input from the user community. The group consists of real users and real developers who actually talk to each other and who are completing the development of 100% user-specified tools. We have found that developers -- some from academia, others from the major HPC vendors (H-P/Convex, IBM, Intel, Meiko, SGI/Cray Research, etc.) and the government -- are very open to end-users' needs and opinions. The main activities of PTOOLS include the PTOOLS Annual Meeting and various sponsored projects.
Yan, Jerry C.↗
Methodologies and Tools for Tuning Parallel Programs: 80% Art, 20% Science, and 10% Luck
The need for computing power has forced a migration from serial computation on a single processor to parallel processing on multiprocessors. However, without effective means to monitor (and analyze) program execution, tuning the performance of parallel programs becomes exponentially difficult as program complexity and machine size increase. In the past few years, the ubiquitous introduction of performance tuning tools from various supercomputer vendors (Intel's ParAide, TMC's PRISM, CRI's Apprentice, and Convex's CXtrace) seems to indicate the maturity of performance instrumentation/monitor/tuning technologies and vendors'/customers' recognition of their importance. However, a few important questions remain: What kind of performance bottlenecks can these tools detect (or correct)? How time consuming is the performance tuning process? What are some important technical issues that remain to be tackled in this area? This workshop reviews the fundamental concepts involved in analyzing and improving the performance of parallel and heterogeneous message-passing programs. Several alternative strategies will be contrasted, and for each we will describe how currently available tuning tools (e.g. AIMS, ParAide, PRISM, Apprentice, CXtrace, ATExpert, Pablo, IPS-2) can be used to facilitate the process. We will characterize the effectiveness of the tools and methodologies based on actual user experiences at NASA Ames Research Center. Finally, we will discuss their limitations and outline recent approaches taken by vendors and the research community to address them.
Yan, Jerry C.↗
Computational Nanotechnology at NASA Ames Research Center, 1996
Some forms of nanotechnology appear to have enormous potential to improve aerospace and computer systems; computational nanotechnology, the design and simulation of programmable molecular machines, is crucial to progress. NASA Ames Research Center has begun a computational nanotechnology program including in-house work, external research grants, and grants of supercomputer time. Four goals have been established: (1) Simulate a hypothetical programmable molecular machine replicating itself and building other products. (2) Develop molecular manufacturing CAD (computer aided design) software and use it to design molecular manufacturing systems and products of aerospace interest, including computer components. (3) Characterize nanotechnologically accessible materials of aerospace interest. Such materials may have excellent strength and thermal properties. (4) Collaborate with experimentalists. Current in-house activities include: (1) Development of NanoDesign, software to design and simulate a nanotechnology based on functionalized fullerenes. Early work focuses on gears. (2) A design for high density atomically precise memory. (3) Design of nanotechnology systems based on biology. (4) Characterization of diamonoid mechanosynthetic pathways. (5) Studies of the laplacian of the electronic charge density to understand molecular structure and reactivity. (6) Studies of entropic effects during self-assembly. Characterization of properties of matter for clusters up to sizes exhibiting bulk properties. In addition, the NAS (NASA Advanced Supercomputing) supercomputer division sponsored a workshop on computational molecular nanotechnology on March 4-5, 1996 held at NASA Ames Research Center. Finally, collaborations with Bill Goddard at CalTech, Ralph Merkle at Xerox Parc, Don Brenner at NCSU (North Carolina State University), Tom McKendree at Hughes, and Todd Wipke at UCSC are underway.
Globus, Al↗
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.↗
Constructing Space-Time Views from Fixed Size Statistical Data: Getting the Best of Both Worlds
Many performance monitoring tools are currently available to the super-computing community. The performance data gathered and analyzed by these tools fall under two categories: statistics and event traces. Statistical data is much more compact but lacks the probative power event traces offer. Event traces, on the other hand, can easily fill up the entire file system during execution such that the instrumented execution may have to be terminated half way through. In this paper, we propose an innovative methodology for performance data gathering and representation that offers a middle ground. The user can trade-off tracing overhead, trace data size vs. data quality incrementally. In other words, the user will be able to limit the amount of trace collected and, at the same time, carry out some of the analysis event traces offer using spacetime views for the entire execution. Two basic ideas are employed: the use of averages to replace recording data for each instance and "formulae" to represent sequences associated with communication and control flow. With the help of a few simple examples, we illustrate the use of these techniques in performance tuning and compare the quality of the traces we collected vs. event traces. We found that the trace files thus obtained are, in deed, small, bounded and predictable before program execution and that the quality of the space time views generated from these statistical data are excellent. Furthermore, experimental results showed that the formulae proposed were able to capture 100% of all the sequences associated with 11 of the 15 applications tested. The performance of the formulae can be incrementally improved by allocating more memory at run-time to learn longer sequences.
Schmidt, Melisa↗
The NAS parallel benchmarks
A new set of benchmarks was developed for the performance evaluation of highly parallel supercomputers. These benchmarks consist of a set of kernels, the 'Parallel Kernels,' and a simulated application benchmark. Together they mimic the computation and data movement characteristics of large scale computational fluid dynamics (CFD) applications. The principal distinguishing feature of these benchmarks is their 'pencil and paper' specification - all details of these benchmarks are specified only algorithmically. In this way many of the difficulties associated with conventional benchmarking approaches on highly parallel systems are avoided.
Bailey, David↗