Design and evaluation of a high performance file system for message passing parallel computers

2002 ◽  
Author(s):  
U. Nagaraj ◽  
U.S. Shukla ◽  
A. Paulraj
Keyword(s):  
Message Passing ◽  
High Performance ◽  
File System ◽  
Parallel Computers

High-Performance Implementation

1995 ◽  
Author(s):  
E. A. Ashcroft ◽  
A. A. Faustini ◽  
R. Jaggannathan ◽  
W. W. Wadge
Keyword(s):  
Message Passing ◽  
High Performance ◽  
Interconnection Network ◽  
Matrix Multiplication ◽  
Parallel Computers ◽  
Parallel Applications ◽  
Low Level ◽  
Two Factors ◽  
Hybrid Language ◽  
Memory Architectures

In Chapter 1, we saw how Lucid could be used to express solutions to standard problems such as sorting and matrix multiplication. One of the unique characteristics of Lucid is not only that it can be used as a programming language but it can also be used as a “composition” language. That is, instead of using Lucid to specify computations, it can be used to express how computation components (expressed in some other language) can be “glued” together to form a coherent application. By doing so, the resulting application can enjoy some of the practical benefits attributable to Lucid such as high performance through exploitation of implicit parallelism and robustness through software fault tolerance. In this chapter, we discuss one such use of Lucid—as part of a hybrid language to construct parallel applications to be executed on conventional parallel computers. A conventional parallel computer either consists of a number of processors each with local memory interconnected by a network (as in distributed memory architectures) or a number of processors that share memory possibly using an interconnection network (as in shared memory architectures). The past decade has seen the advent of conventional parallel computers starting with the Denelcor HEP evolving to the CM-2 and Intel Hypercube and further evolving to the CM-5, Intel Paragon, Cray T3D, and IBM SP-2. Even networks of workstations (or workstation clusters) are seen as low-cost (“poor man’s”) parallel computers. Programming of conventional parallel computers has proven to be far more challenging than had been expected. Part of the reason is the continued use of low-level, explicitly parallel programming models such as PVM [42], Linda [10]. Two factors have fueled the continuing use of such languages despite their limited success. 1. The need to reuse existing sequential code because the cost of rewriting legacy applications from scratch is considered prohibitive both in economic and technical terms. 2. The need to run on conventional parallel computers that view a “parallel program” at a low level—as consisting of sequential processes that frequently synchronize and communicate with each other using some form of message passing.

scholarly journals A Universal, Dynamically Adaptable and Programmable Network Router for Parallel Computers

VLSI Design ◽  
2001 ◽  
Vol 12 (1) ◽  
pp. 25-52 ◽  
Author(s):  
Taras I. Golota ◽  
Sotirios G. Ziavras
Keyword(s):  
Message Passing ◽  
High Performance ◽  
Interconnection Network ◽  
Vlsi Design ◽  
Parallel Computers ◽  
System Level ◽  
Current Configuration ◽  
Data Channel ◽  
Vhdl Code ◽  
Or Applications

Existing message-passing parallel computers employ routers designed for a specific interconnection network and deal with fixed data channel width. There are disadvantages to this approach, because the system design and development times are significant and these routers do not permit run time network reconfiguration. Changes in the topology of the network may be required for better performance or faulttolerance. In this paper, we introduce a class of high-performance universal (statically and dynamically adaptable) programmable routers (UPRs) for message-passing parallel computers. The universality of these routers is based on their capability to adapt at run and/or static times according to the characteristics of the systems and/or applications. More specifically, the number of bidirectional data channels, the channel size and the I/O port mappings (for the implementation of a particular topology) can change dynamically and statically. Our research focuses on system-level specification issues of the UPRs, their VLSI design and their simulation to estimate their performance. Our simulation of data transfers via UPR routers employs VHDL code in the Mentor Graphics environment. The results show that the performance of the routers depends mostly on their current configuration. Details of the simulation and synthesis are presented.

Multi-level Parallelization of Genotype Imputation on Supercomputers

2020 ◽  
Vol 15 ◽  
Author(s):  
Weiwen Zhang ◽  
Long Wang ◽  
Theint Theint Aye ◽  
Juniarto Samsudin ◽  
Yongqing Zhu
Keyword(s):  
Association Study ◽  
Message Passing ◽  
High Performance ◽  
Message Passing Interface ◽  
Genome Wide Association Study ◽  
Job Scheduling ◽  
Genotype Imputation ◽  
Job Level ◽  
Multi Level ◽  
High Performance Requirement

Background: Genotype imputation as a service is developed to enable researchers to estimate genotypes on haplotyped data without performing whole genome sequencing. However, genotype imputation is computation intensive and thus it remains a challenge to satisfy the high performance requirement of genome wide association study (GWAS). Objective: In this paper, we propose a high performance computing solution for genotype imputation on supercomputers to enhance its execution performance. Method: We design and implement a multi-level parallelization that includes job level, process level and thread level parallelization, enabled by job scheduling management, message passing interface (MPI) and OpenMP, respectively. It involves job distribution, chunk partition and execution, parallelized iteration for imputation and data concatenation. Due to the design of multi-level parallelization, we can exploit the multi-machine/multi-core architecture to improve the performance of genotype imputation. Results: Experiment results show that our proposed method can outperform the Hadoop-based implementation of genotype imputation. Moreover, we conduct the experiments on supercomputers to evaluate the performance of the proposed method. The evaluation shows that it can significantly shorten the execution time, thus improving the performance for genotype imputation. Conclusion: The proposed multi-level parallelization, when deployed as an imputation as a service, will facilitate bioinformatics researchers in Singapore to conduct genotype imputation and enhance the association study.

Microstructures in Elastic Media

1994 ◽  
Author(s):  
Nhan Phan-Thien ◽  
Sangtae Kim
Keyword(s):  
Computational Methods ◽  
High Performance ◽  
Chemical Engineering ◽  
Elliptic Partial Differential Equations ◽  
Parallel Computers ◽  
Computational Algorithms ◽  
Applied Physics ◽  
Advanced Students ◽  
Particulate Solids ◽  
Modeling Software

This monograph describes various methods for solving deformation problems of particulate solids, taking the reader from analytical to computational methods. The book is the first to present the topic of linear elasticity in mathematical terms that will be familiar to anyone with a grounding in fluid mechanics. It incorporates the latest advances in computational algorithms for elliptic partial differential equations, and provides the groundwork for simulations on high performance parallel computers. Numerous exercises complement the theoretical discussions, and a related set of self-documented programs is available to readers with Internet access. The work will be of interest to advanced students and practicing researchers in mechanical engineering, chemical engineering, applied physics, computational methods, and developers of numerical modeling software.

A high-performance, portable implementation of the MPI message passing interface standard

1996 ◽  
Vol 22 (6) ◽  
pp. 789-828 ◽  
Author(s):  
William Gropp ◽  
Ewing Lusk ◽  
Nathan Doss ◽  
Anthony Skjellum
Keyword(s):  
Message Passing ◽  
High Performance ◽  
Message Passing Interface

Based on Numerical Simulation of High-Performance Parallel Machine Muffler Experimental Calibration

2013 ◽  
Vol 718-720 ◽  
pp. 1645-1650
Author(s):  
Gen Yin Cheng ◽  
Sheng Chen Yu ◽  
Zhi Yong Wei ◽  
Shao Jie Chen ◽  
You Cheng
Keyword(s):  
Numerical Simulation ◽  
Finite Element ◽  
Boundary Element ◽  
Message Passing ◽  
High Performance ◽  
Message Passing Interface ◽  
Parallel Machine ◽  
Simulation Software ◽  
Experimental Calibration ◽  
The Cost

Commonly used commercial simulation software SYSNOISE and ANSYS is run on a single machine (can not directly run on parallel machine) when use the finite element and boundary element to simulate muffler effect, and it will take more than ten days, sometimes even twenty days to work out an exact solution as the large amount of numerical simulation. Use a high performance parallel machine which was built by 32 commercial computers and transform the finite element and boundary element simulation software into a program that can running under the MPI (message passing interface) parallel environment in order to reduce the cost of numerical simulation. The relevant data worked out from the simulation experiment demonstrate that the result effect of the numerical simulation is well. And the computing speed of the high performance parallel machine is 25 ~ 30 times a microcomputer.

scholarly journals A lightweight approach to performance portability with targetDP

2016 ◽  
Vol 32 (2) ◽  
pp. 288-301
Author(s):  
Alan Gray ◽  
Kevin Stratford
Keyword(s):  
Particle Physics ◽  
Message Passing ◽  
Graphics Processing Units ◽  
High Performance ◽  
Large Scale ◽  
Message Passing Interface ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Performance Portability ◽  
Graphics Processing

Leading high performance computing systems achieve their status through use of highly parallel devices such as NVIDIA graphics processing units or Intel Xeon Phi many-core CPUs. The concept of performance portability across such architectures, as well as traditional CPUs, is vital for the application programmer. In this paper we describe targetDP, a lightweight abstraction layer which allows grid-based applications to target data parallel hardware in a platform agnostic manner. We demonstrate the effectiveness of our pragmatic approach by presenting performance results for a complex fluid application (with which the model was co-designed), plus separate lattice quantum chromodynamics particle physics code. For each application, a single source code base is seen to achieve portable performance, as assessed within the context of the Roofline model. TargetDP can be combined with Message Passing Interface (MPI) to allow use on systems containing multiple nodes: we demonstrate this through provision of scaling results on traditional and graphics processing unit-accelerated large scale supercomputers.

Message-Passing-Interface MPI Parallelization of Iteratively Coupled Fluid Flow and Geomechanics Codes for the Simulation of System Behavior in Hydrate-Bearing Geologic Media

2021 ◽  
Author(s):  
Jiecheng Zhang ◽  
George Moridis ◽  
Thomas Blasingame
Keyword(s):  
Message Passing ◽  
High Performance ◽  
Message Passing Interface ◽  
Gas Production ◽  
Parallel Performance ◽  
Group 3 ◽  
Linux Cluster ◽  
Group 2 ◽  
3D Problem ◽  
Group 1

Abstract The Reservoir GeoMechanics Simulator (RGMS), a geomechanics simulator based on the finite element method and parallelized using the Message Passing Interface (MPI), is developed in this work to model the stresses and deformations in subsurface systems. RGMS can be used stand-alone, or coupled with flow and transport models. pT+H V1.5, a parallel MPI-based version of the serial T+H V1.5 code that describes mass and heat flow in hydrate-bearing porous media, is also developed. Using the fixed-stress split iterative scheme, RGMS is coupled with the pT+H V1.5 to investigate the geomechanical responses associated with gas production from hydrate accumulations. The code development and testing process involve evaluation of the parallelization and of the coupling method, as well as verification and validation of the results. The parallel performance of the codes is tested on the Ada Linux cluster of the Texas A&M High Performance Research Computing using up to 512 processors, and on a Mac Pro computer with 12 processors. The investigated problems are: Group 1: Geomechanical problems solved by RGMS in 2D Cartesian and cylindrical domains and a 3D problem, involving 4x106 and 3.375 x106 elements, respectively; Group 2: Realistic problems of gas production from hydrates using pT+H V1.5 in 2D and 3D systems with 2.45x105 and 3.6 x106 elements, respectively; Group 3: The 3D problem in Group 2 solved with the coupled RGMS-pT+H V1.5 simulator, fully accounting for geomechanics. Two domain partitioning options are investigated on the Ada Linux cluster and the Mac Pro, and the code parallel performance is monitored. On the Ada Linux cluster using 512 processors, the simulation speedups (a) of RGMS are 218.89, 188.13, and 284.70 in the Group 1 problems, (b) of pT+H V1.5 are 174.25 and 341.67 in the Group 2 cases, and (c) of the coupled simulators is 331.80 in Group 3. The results produced in this work show the necessity of using full geomechanics simulators in marine hydrate-related studies because of the associated pronounced geomechanical effects on production and displacements and (b) the effectiveness of the parallel simulators developed in this study, which can be the only realistic option in these complex simulations of large multi-dimensional domains.

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