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NASA NTRS1994

Applications Performance Under MPL and MPI on NAS IBM SP2

On July 5, 1994, an IBM Scalable POWER parallel System (IBM SP2) with 64 nodes, was installed at the Numerical Aerodynamic Simulation (NAS) Facility Each node of NAS IBM SP2 is a "wide node" consisting of a RISC 6000/590 workstation module with a clock of 66.5 MHz which can perform four floating point operations per clock with a peak performance of 266 Mflop/s. By the end of 1994, 64 nodes of IBM SP2 will be upgraded to 160 nodes with a peak performance of 42.5 Gflop/s. An overview of the IBM SP2 hardware is presented. The basic understanding of architectural details of RS 6000/590 will help application scientists the porting, optimizing, and tuning of codes from other machines such as the CRAY C90 and the Paragon to the NAS SP2. Optimization techniques such as quad-word loading, effective utilization of two floating point units, and data cache optimization of RS 6000/590 is illustrated, with examples giving performance gains at each optimization step. The conversion of codes using Intel's message passing library NX to codes using native Message Passing Library (MPL) and the Message Passing Interface (NMI) library available on the IBM SP2 is illustrated. In particular, we will present the performance of Fast Fourier Transform (FFT) kernel from NAS Parallel Benchmarks (NPB) under MPL and MPI. We have also optimized some of Fortran BLAS 2 and BLAS 3 routines, e.g., the optimized Fortran DAXPY runs at 175 Mflop/s and optimized Fortran DGEMM runs at 230 Mflop/s per node. The performance of the NPB (Class B) on the IBM SP2 is compared with the CRAY C90, Intel Paragon, TMC CM-5E, and the CRAY T3D.

Saini, Subhash↗

NASA NTRS1994

Long Term Dynamic Stream Nitrate and Phosphate Changes Following Watershed Wildfires

During and following the 1988 Yellowstone National Park wildfires, airborne remotely sensed data were collected in order to characterize various vegetative components, fire front movements and bum intensities. ER-2 derived Thematic Mapper Simulator (TMS) data were used in conjunction with water sampling and chemistry analysis to determine fire intensities in various watersheds and aquatic system condition changes. The airborne Daedalus multispectral TMS data allowed the characterization of various bum intensities in watersheds. Stream sampling was then conducted in those various burned watersheds to determine nitrate and phosphate concentration changes. Six stream watersheds were monitored for five years (1989-1993) during non-snow periods (May/June through September): Cache Creek (intensely burned), Blacktail Deer Creek (intensely burned), Snake River (moderately burned), Lamar River (mixed burning), Soda Butte Creek (lightly burned), and Amphitheatre Creek (unburned). One litre samples were collected from those streams with ISCO water samplers every 12 hours. The samples were removed every 14 days .(28 Samples), and water chemistry analysis was performed. Chemistry analysis indicated that nitrate and phosphate concentrations were elevated in moderately burned watersheds and significantly elevated in severely burned watersheds. The results during the five year study indicate that bum intensities regulate stream water nitrate and phosphate concentrations, and that remotely sensed data can be used effectively to predict watershed chemical changes which will affect aquatic conditions.

Ambrosia, Vincent G.↗

NASA NTRS1994

Automated Instrumentation, Monitoring and Visualization of PVM Programs Using AIMS

We present views and analysis of the execution of several PVM codes for Computational Fluid Dynamics on a network of Sparcstations, including (a) NAS Parallel benchmarks CG and MG (White, Alund and Sunderam 1993); (b) a multi-partitioning algorithm for NAS Parallel Benchmark SP (Wijngaart 1993); and (c) an overset grid flowsolver (Smith 1993). These views and analysis were obtained using our Automated Instrumentation and Monitoring System (AIMS) version 3.0, a toolkit for debugging the performance of PVM programs. We will describe the architecture, operation and application of AIMS. The AIMS toolkit contains (a) Xinstrument, which can automatically instrument various computational and communication constructs in message-passing parallel programs; (b) Monitor, a library of run-time trace-collection routines; (c) VK (Visual Kernel), an execution-animation tool with source-code clickback; and (d) Tally, a tool for statistical analysis of execution profiles. Currently, Xinstrument can handle C and Fortran77 programs using PVM 3.2.x; Monitor has been implemented and tested on Sun 4 systems running SunOS 4.1.2; and VK uses X11R5 and Motif 1.2. Data and views obtained using AIMS clearly illustrate several characteristic features of executing parallel programs on networked workstations: (a) the impact of long message latencies; (b) the impact of multiprogramming overheads and associated load imbalance; (c) cache and virtual-memory effects; and (4significant skews between workstation clocks. Interestingly, AIMS can compensate for constant skew (zero drift) by calibrating the skew between a parent and its spawned children. In addition, AIMS' skew-compensation algorithm can adjust timestamps in a way that eliminates physically impossible communications (e.g., messages going backwards in time). Our current efforts are directed toward creating new views to explain the observed performance of PVM programs. Some of the features planned for the near future include: (a) ConfigView, showing the physical topology of the virtual machine, inferred using specially formatted IP (Internet Protocol) packets; and (b) LoadView, synchronous animation of PVM-program execution and resource-utilization patterns.

Mehra, Pankaj↗

NASA NTRS1994

Automated Instrumentation, Monitoring and Visualization of PVM Programs Using AIMS

We present views and analysis of the execution of several PVM (Parallel Virtual Machine) codes for Computational Fluid Dynamics on a networks of Sparcstations, including: (1) NAS Parallel Benchmarks CG and MG; (2) a multi-partitioning algorithm for NAS Parallel Benchmark SP; and (3) an overset grid flowsolver. These views and analysis were obtained using our Automated Instrumentation and Monitoring System (AIMS) version 3.0, a toolkit for debugging the performance of PVM programs. We will describe the architecture, operation and application of AIMS. The AIMS toolkit contains: (1) Xinstrument, which can automatically instrument various computational and communication constructs in message-passing parallel programs; (2) Monitor, a library of runtime trace-collection routines; (3) VK (Visual Kernel), an execution-animation tool with source-code clickback; and (4) Tally, a tool for statistical analysis of execution profiles. Currently, Xinstrument can handle C and Fortran 77 programs using PVM 3.2.x; Monitor has been implemented and tested on Sun 4 systems running SunOS 4.1.2; and VK uses XIIR5 and Motif 1.2. Data and views obtained using AIMS clearly illustrate several characteristic features of executing parallel programs on networked workstations: (1) the impact of long message latencies; (2) the impact of multiprogramming overheads and associated load imbalance; (3) cache and virtual-memory effects; and (4) significant skews between workstation clocks. Interestingly, AIMS can compensate for constant skew (zero drift) by calibrating the skew between a parent and its spawned children. In addition, AIMS' skew-compensation algorithm can adjust timestamps in a way that eliminates physically impossible communications (e.g., messages going backwards in time). Our current efforts are directed toward creating new views to explain the observed performance of PVM programs. Some of the features planned for the near future include: (1) ConfigView, showing the physical topology of the virtual machine, inferred using specially formatted IP (Internet Protocol) packets: and (2) LoadView, synchronous animation of PVM-program execution and resource-utilization patterns.

Mehra, Pankaj↗

NASA NTRS1996

RANS-MP: A Portable Parallel Navier-Stokes Solver

RANS-MP, a new implementation of a single-grid Navier-Stokes solver using the diagonalized Beam-Warming approximate-factorization scheme, is presented. This first release of the completely rewritten solver employs the following optimizations: (1) Bi-directional multi-partition method for the ADI solver part; this improves granularity and load balance; (2) Improved cache usage through elimination of non-unit-stride array access (possible in part due to multi-partitioning); (3) Preprocessing of communicating boundary conditions to streamline logic during time stepping; (4) Truly parallel, high-performance I/O using the newly-developed MPI-IO library; (5) Elimination of large amounts of redundant operations through efficient use of workspace. Results of some realistic wing computations on the IBM SP2 computer will be presented. We will demonstrate that excellent absolute performance and scalability are obtained with RANS-MP, even for relatively small grid sizes. Besides high performance, an outstanding feature of RANS-MP is its true portability, due to the use of the portable message passing and I/O libraries MPI and MPI-IO.

VanderWijngaart, Rob F.↗

NASA NTRS2001

A Parallel Cartesian Approach for External Aerodynamics of Vehicles with Complex Geometry

This workshop paper presents the current status in the development of a new approach for the solution of the Euler equations on Cartesian meshes with embedded boundaries in three dimensions on distributed and shared memory architectures. The approach uses adaptively refined Cartesian hexahedra to fill the computational domain. Where these cells intersect the geometry, they are cut by the boundary into arbitrarily shaped polyhedra which receive special treatment by the solver. The presentation documents a newly developed multilevel upwind solver based on a flexible domain-decomposition strategy. One novel aspect of the work is its use of space-filling curves (SFC) for memory efficient on-the-fly parallelization, dynamic re-partitioning and automatic coarse mesh generation. Within each subdomain the approach employs a variety reordering techniques so that relevant data are on the same page in memory permitting high-performance on cache-based processors. Details of the on-the-fly SFC based partitioning are presented as are construction rules for the automatic coarse mesh generation. After describing the approach, the paper uses model problems and 3- D configurations to both verify and validate the solver. The model problems demonstrate that second-order accuracy is maintained despite the presence of the irregular cut-cells in the mesh. In addition, it examines both parallel efficiency and convergence behavior. These investigations demonstrate a parallel speed-up in excess of 28 on 32 processors of an SGI Origin 2000 system and confirm that mesh partitioning has no effect on convergence behavior.

Aftosmis, M. J.↗

NASA NTRS1997

NAS Applications and Advanced Algorithms

This paper examines the applications most commonly run on the supercomputers at the Numerical Aerospace Simulation (NAS) facility. It analyzes the extent to which such applications are fundamentally oriented to vector computers, and whether or not they can be efficiently implemented on hierarchical memory machines, such as systems with cache memories and highly parallel, distributed memory systems.

Bailey, David H.↗

NASA NTRS1997

NAS Applications and Advanced Architectures

Bailey, David H.↗

NASA NTRS1998

Achieving High Performance on the i860 Microprocessor

The i860 is a high performance microprocessor used in the Intel Touchstone project. This paper proposes a paradigm for programming the i860 that is modelled on the vector instructions of the Cray computers. Fortran callable assembler subroutines were written that mimic the concurrent vector instructions of the Cray. Cache takes the place of vector registers. Using this paradigm we have achieved twice the performance of compiled code on a traditional solve.

Lee, King↗

NASA NTRS1997

Communication Improvement for the LU NAS Parallel Benchmark: A Model for Efficient Parallel Relaxation Schemes

The first release of the MPI version of the LU NAS Parallel Benchmark (NPB2.0) performed poorly compared to its companion NPB2.0 codes. The later LU release (NPB2.1 & 2.2) runs up to two and a half times faster, thanks to a revised point access scheme and related communications scheme. The new scheme sends substantially fewer messages. is cache "friendly", and has a better load balance. We detail the, observations and modifications that resulted in this efficiency improvement, and show that the poor behavior of the original code resulted from deriving a message passing scheme from an algorithm originally devised for a vector architecture.

Yarrow, Maurice↗

NASA NTRS2002

Effects of Ordering Strategies and Programming Paradigms on Sparse Matrix Computations

The Conjugate Gradient (CG) algorithm is perhaps the best-known iterative technique to solve sparse linear systems that are symmetric and positive definite. For systems that are ill-conditioned, it is often necessary to use a preconditioning technique. In this paper, we investigate the effects of various ordering and partitioning strategies on the performance of parallel CG and ILU(O) preconditioned CG (PCG) using different programming paradigms and architectures. Results show that for this class of applications: ordering significantly improves overall performance on both distributed and distributed shared-memory systems, that cache reuse may be more important than reducing communication, that it is possible to achieve message-passing performance using shared-memory constructs through careful data ordering and distribution, and that a hybrid MPI+OpenMP paradigm increases programming complexity with little performance gains. A implementation of CG on the Cray MTA does not require special ordering or partitioning to obtain high efficiency and scalability, giving it a distinct advantage for adaptive applications; however, it shows limited scalability for PCG due to a lack of thread level parallelism.

Oliker, Leonid↗

NASA NTRS2002

VEXT: A Virtual Observatory Exploration Toolkit

This final report consists of two main parts. The first is taken from a paper by the PiCA (Pittsburgh Computational Astrostatistics) Group which describes our ongoing work in fast computation of n-point correlation functions. We present here a new algorithm for the fast computation of N-point correlation functions in large astronomical data sets. The algorithm is based on kd-trees which are decorated with cached sufficient statistics thus allowing for orders of magnitude speed-ups over the naive non-tree-based implementation of correlation functions. We further discuss the use of controlled approximations within the computation which allows for further acceleration. In summary, our algorithm now makes it possible to compute exact, all-pairs, measurements of the two, three and four-point correlation functions for cosmological data sets like the Sloan Digital Sky Survey and the next generation of Cosmic Microwave Background experiments. The second part summarizes the progress made by the PiCA Group in this area through the AISR grant.

Schneider, Jeff↗

NASA NTRS2002

The Efficiency and the Scalability of an Explicit Operator on an IBM POWER4 System

We present an evaluation of the efficiency and the scalability of an explicit CFD operator on an IBM POWER4 system. The POWER4 architecture exhibits a common trend in HPC architectures: boosting CPU processing power by increasing the number of functional units, while hiding the latency of memory access by increasing the depth of the memory hierarchy. The overall machine performance depends on the ability of the caches-buses-fabric-memory to feed the functional units with the data to be processed. In this study we evaluate the efficiency and scalability of one explicit CFD operator on an IBM POWER4. This operator performs computations at the points of a Cartesian grid and involves a few dozen floating point numbers and on the order of 100 floating point operations per grid point. The computations in all grid points are independent. Specifically, we estimate the efficiency of the RHS operator (SP of NPB) on a single processor as the observed/peak performance ratio. Then we estimate the scalability of the operator on a single chip (2 CPUs), a single MCM (8 CPUs), 16 CPUs, and the whole machine (32 CPUs). Then we perform the same measurements for a chache-optimized version of the RHS operator. For our measurements we use the HPM (Hardware Performance Monitor) counters available on the POWER4. These counters allow us to analyze the obtained performance results.

Frumkin, Michael↗

NASA NTRS2002

The Computing and Data Grid Approach: Infrastructure for Distributed Science Applications

With the advent of Grids - infrastructure for using and managing widely distributed computing and data resources in the science environment - there is now an opportunity to provide a standard, large-scale, computing, data, instrument, and collaboration environment for science that spans many different projects and provides the required infrastructure and services in a relatively uniform and supportable way. Grid technology has evolved over the past several years to provide the services and infrastructure needed for building 'virtual' systems and organizations. We argue that Grid technology provides an excellent basis for the creation of the integrated environments that can combine the resources needed to support the large- scale science projects located at multiple laboratories and universities. We present some science case studies that indicate that a paradigm shift in the process of science will come about as a result of Grids providing transparent and secure access to advanced and integrated information and technologies infrastructure: powerful computing systems, large-scale data archives, scientific instruments, and collaboration tools. These changes will be in the form of services that can be integrated with the user's work environment, and that enable uniform and highly capable access to these computers, data, and instruments, regardless of the location or exact nature of these resources. These services will integrate transient-use resources like computing systems, scientific instruments, and data caches (e.g., as they are needed to perform a simulation or analyze data from a single experiment); persistent-use resources. such as databases, data catalogues, and archives, and; collaborators, whose involvement will continue for the lifetime of a project or longer. While we largely address large-scale science in this paper, Grids, particularly when combined with Web Services, will address a broad spectrum of science scenarios. both large and small scale.

Johnston, William E.↗

NASA NTRS2003

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↗

NASA NTRS2003

Robotic Mars Sample Return: Risk Assessment and Analysis Report

A comparison of the risk associated with two alternative scenarios for a robotic Mars sample return mission was conducted. Two alternative mission scenarios were identified, the Jet Propulsion Lab (JPL) reference Mission and a mission proposed by Johnson Space Center (JSC). The JPL mission was characterized by two landers and an orbiter, and a Mars orbit rendezvous to retrieve the samples. The JSC mission (Direct/SEP) involves a solar electric propulsion (SEP) return to earth followed by a rendezvous with the space shuttle in earth orbit. A qualitative risk assessment to identify and characterize the risks, and a risk analysis to quantify the risks were conducted on these missions. Technical descriptions of the competing scenarios were developed in conjunction with NASA engineers and the sequence of events for each candidate mission was developed. Risk distributions associated with individual and combinations of events were consolidated using event tree analysis in conjunction with Monte Carlo techniques to develop probabilities of mission success for each of the various alternatives. The results were the probability of success of various end states for each candidate scenario. These end states ranged from complete success through various levels of partial success to complete failure. Overall probability of success for the Direct/SEP mission was determined to be 66% for the return of at least one sample and 58% for the JPL mission for the return of at least one sample cache. Values were also determined for intermediate events and end states as well as for the probability of violation of planetary protection. Overall mission planetary protection event probabilities of occurrence were determined to be 0.002% and 1.3% for the Direct/SEP and JPL Reference missions respectively.

Lalk, Thomas R.↗

NASA NTRS2003

Performance Analysis of a Hybrid Overset Multi-Block Application on Multiple Architectures

This paper presents a detailed performance analysis of a multi-block overset grid compu- tational fluid dynamics app!ication on multiple state-of-the-art computer architectures. The application is implemented using a hybrid MPI+OpenMP programming paradigm that exploits both coarse and fine-grain parallelism; the former via MPI message passing and the latter via OpenMP directives. The hybrid model also extends the applicability of multi-block programs to large clusters of SNIP nodes by overcoming the restriction that the number of processors be less than the number of grid blocks. A key kernel of the application, namely the LU-SGS linear solver, had to be modified to enhance the performance of the hybrid approach on the target machines. Investigations were conducted on cacheless Cray SX6 vector processors, cache-based IBM Power3 and Power4 architectures, and single system image SGI Origin3000 platforms. Overall results for complex vortex dynamics simulations demonstrate that the SX6 achieves the highest performance and outperforms the RISC-based architectures; however, the best scaling performance was achieved on the Power3.

Djomehri, M. Jahed↗

NASA NTRS1995

Performance Modeling of Network-Attached Storage Device Based Hierarchical Mass Storage Systems

Network attached storage devices improve I/O performance by separating control and data paths and eliminating host intervention during the data transfer phase. Devices are attached to both a high speed network for data transfer and to a slower network for control messages. Hierarchical mass storage systems use disks to cache the most recently used files and a combination of robotic and manually mounted tapes to store the bulk of the files in the file system. This paper shows how queuing network models can be used to assess the performance of hierarchical mass storage systems that use network attached storage devices as opposed to host attached storage devices. Simulation was used to validate the model. The analytic model presented here can be used, among other things, to evaluate the protocols involved in 1/0 over network attached devices.

Menasce, Daniel A.↗