A Hybrid Decomposition Parallel Implementation of the Car-Parrinello Method

We have developed a flexible hybrid decomposition parallel implementation of the first-principles molecular dynamics algorithm of Car and Parrinello. The code allows the problem to be decomposed either spatially, over the electronic orbitals, or any combination of the two. Performance statistics for 32, 64, 128 and 512 Si atom runs on the Touchstone Delta and Intel Paragon parallel supercomputers and comparison with the performance of an optimized code running the smaller systems on the Cray Y-MP and C90 are presented.Comment: Accepted by Computer Physics Communications, latex, 34 pages without figures, 15 figures available in PostScript form via WWW at http://www-theory.chem.washington.edu/~wiggs/hyb_figures.htm

High-performance computing for vision

Vision is a challenging application for high-performance computing (HPC). Many vision tasks have stringent latency and throughput requirements. Further, the vision process has a heterogeneous computational profile. Low-level vision consists of structured computations, with regular data dependencies. The subsequent, higher level operations consist of symbolic computations with irregular data dependencies. Over the years, many approaches to high-speed vision have been pursued. VLSI hardware solutions such as ASIC's and digital signal processors (DSP's) have provided good processing speeds on structured low-level vision tasks. Special purpose systems for vision have also been designed. Currently, there is growing interest in using general purpose parallel systems for vision problems. These systems offer advantages of higher performance, sofavare programmability, generality, and architectural flexibility over the earlier approaches. The choice of low-cost commercial-off-theshelf (COTS) components as building blocks for these systems leads to easy upgradability and increased system life. The main focus of the paper is on effectively using the COTSbased general purpose parallel computing platforms to realize high-speed implementations of vision tasks. Due to the successful use of the COTS-based systems in a variety of high performance applications, it is attractive to consider their use for vision applications as well. However, the irregular data dependencies in vision tasks lead to large communication overheads in the HPC systems. At the University of Southern California, our research efforts have been directed toward designing scalable parallel algorithms for vision tasks on the HPC systems. In our approach, we use the message passing programming model to develop portable code. Our algorithms are specified using C and MPI. In this paper, we summarize our efforts, and illustrate our approach using several example vision tasks. To facilitate the analysis and development of scalable algorithms, a realistic computational model of the parallel system must be used. Several such models have been proposed in the literature. We use the General-purpose Distributed Memory (GDM) model which is a simple but realistic model of state-of-theart parallel machines. Using the GDM model, generic algorithmic techniques such as data remapping, overlapping of communication with computation, message packing, asynchronous execution, and communication scheduling are developed. Using these techniques, we have developed scalable algorithms for many vision tasks. For instance, a scalable algorithm for linear approximation has been developed using the asynchronous execution technique. Using this algorithm, linear feature extraction can be performed in 0.065 s on a 64 node SP-2 for a 512 × 512 image. A serial implementation takes 3.45 s for the same task. Similarly, the communication scheduling and decomposition techniques lead to a scalable algorithm for the line grouping task. We believe that such an algorithmic approach can result in the development of scalable and portable solutions for vision tasks. © 1996 IEEE Publisher Item Identifier S 0018-9219(96)04992-4.published_or_final_versio

Performance of a finite volume CEM code on multicomputers

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/77161/1/AIAA-1994-236-711.pd

Contention-Free Complete Exchange Algorithms on Clusters

To construct a large commodity clustec a hierarchical network is generally adopted for connecting the host muchines, where a Gigabit backbone switch connects a few commodity switches with uplinks to achieve scaled bisectional bandwidth. This type of interconnection usually results in link contention and has congestion developed at the uplink ports. Moreover, the non-detenninistic delays on scheduling communication events in clusters accelerate the building up of congestion amongst these uplink ports, which lead to severe packets drop and hinder the overall performance. In this paper, we focus on the practical design of high-speed complete exchange algorithm on a commodity cluster interconnected by a hierarchical Ethemet-based network. By exploiting some architectural characteristics of the interconnection in optimizing the performunce of a complete exchange algorithm, we introduce a congestion control mechanism - global windowing that monitors and regulates the trafic load, together with a permutation scheme - reorder scheme that effectively alleviates the congestion problem. We evaluate our algorithm and compare its performance with other algorithms in a PC cluster connected by various types of switches, including Gigabit Ethernet, input-buffered and shared-memory Fast Ethernet switches.published_or_final_versio

ICASE

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in the areas of (1) applied and numerical mathematics, including numerical analysis and algorithm development; (2) theoretical and computational research in fluid mechanics in selected areas of interest, including acoustics and combustion; (3) experimental research in transition and turbulence and aerodynamics involving Langley facilities and scientists; and (4) computer science

Practical Prefetching Techniques for Multiprocessor File Systems

Improvements in the processing speed of multiprocessors are outpacing improvements in the speed of disk hardware. Parallel disk I/O subsystems have been proposed as one way to close the gap between processor and disk speeds. In a previous paper we showed that prefetching and caching have the potential to deliver the performance benefits of parallel file systems to parallel applications. In this paper we describe experiments with practical prefetching policies that base decisions only on on-line reference history, and that can be implemented efficiently. We also test the ability of these policies across a range of architectural parameters

High-Performance Parallel Analysis of Coupled Problems for Aircraft Propulsion

Applications are described of high-performance computing methods to the numerical simulation of complete jet engines. The methodology focuses on the partitioned analysis of the interaction of the gas flow with a flexible structure and with the fluid mesh motion driven by structural displacements. The latter is treated by a ALE technique that models the fluid mesh motion as that of a fictitious mechanical network laid along the edges of near-field elements. New partitioned analysis procedures to treat this coupled three-component problem were developed. These procedures involved delayed corrections and subcycling, and have been successfully tested on several massively parallel computers, including the iPSC-860, Paragon XP/S and the IBM SP2. The NASA-sponsored ENG10 program was used for the global steady state analysis of the whole engine. This program uses a regular FV-multiblock-grid discretization in conjunction with circumferential averaging to include effects of blade forces, loss, combustor heat addition, blockage, bleeds and convective mixing. A load-balancing preprocessor for parallel versions of ENG10 was developed as well as the capability for the first full 3D aeroelastic simulation of a multirow engine stage. This capability was tested on the IBM SP2 parallel supercomputer at NASA Ames

Practical Prefetching Techniques for Multiprocessor File Systems

Improvements in the processing speed of multiprocessors are outpacing improvements in the speed of disk hardware. Parallel disk I/O subsystems have been proposed as one way to close the gap between processor and disk speeds. In a previous paper we showed that prefetching and caching have the potential to deliver the performance benefits of parallel file systems to parallel applications. In this paper we describe experiments with practical prefetching policies that base decisions only on on-line reference history, and that can be implemented efficiently. We also test the ability of these policies across a range of architectural parameters

[Research activities in applied mathematics, fluid mechanics, and computer science]

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, fluid mechanics, and computer science during the period April 1, 1995 through September 30, 1995

High-Performance Parallel Analysis of Coupled Problems for Aircraft Propulsion

This research program dealt with the application of high-performance computing methods to the numerical simulation of complete jet engines. The program was initiated in January 1993 by applying two-dimensional parallel aeroelastic codes to the interior gas flow problem of a bypass jet engine. The fluid mesh generation, domain decomposition and solution capabilities were successfully tested. Attention was then focused on methodology for the partitioned analysis of the interaction of the gas flow with a flexible structure and with the fluid mesh motion driven by these structural displacements. The latter is treated by a ALE technique that models the fluid mesh motion as that of a fictitious mechanical network laid along the edges of near-field fluid elements. New partitioned analysis procedures to treat this coupled three-component problem were developed during 1994 and 1995. These procedures involved delayed corrections and subcycling, and have been successfully tested on several massively parallel computers, including the iPSC-860, Paragon XP/S and the IBM SP2. For the global steady-state axisymmetric analysis of a complete engine we have decided to use the NASA-sponsored ENG10 program, which uses a regular FV-multiblock-grid discretization in conjunction with circumferential averaging to include effects of blade forces, loss, combustor heat addition, blockage, bleeds and convective mixing. A load-balancing preprocessor tor parallel versions of ENG10 was developed. During 1995 and 1996 we developed the capability tor the first full 3D aeroelastic simulation of a multirow engine stage. This capability was tested on the IBM SP2 parallel supercomputer at NASA Ames. Benchmark results were presented at the 1196 Computational Aeroscience meeting