Escali 4.4 manual Chapter, Scali MPI Connect product context

Page 17

Chapter 1

Introduction

 

 

 

 

This manual describes Scali MPI Connect (SMC) in detail. SMC is sold as a separate stand-alone product, with an SMC distribution, and integrated with Scali Manage in the SSP distribution. Some integration issues and features of the MPI are also discussed in the Scali Manage Users Guide, the user's manual for Scali Manage.

This manual is written for users who have a basic programming knowledge of C or Fortran, as well as an understanding of MPI.

1.1 Scali MPI Connect product context

Figure 1-1:A cluster system

Figure 1-1:shows a simplified view of the underlying architecture of clusters using Scali MPI

Connect: A number of compute nodes are connected together in a Ethernet network through which a front-end interfaces the cluster with the corporate network. A high performance interconnect can be attached to service communication requirements of key applications. The front-end imports services like file systems from the corporate network to allow users to run applications and access their data.

Scali MPI Connect implements the MPI standard for a number of popular high performance interconnects, like Gigiabit Ethenet, Infiniband, Myrinet and SCI.

While the high performance interconnect is optional, the networking infrastructure is mandatory. Without it the nodes in the cluster will have no way of sharing resources. TCP/IP functionality implemented by the Ethernet network enables the front-end to issue commands to the nodes, provide them with data and application images, and collect results from the processing the nodes perform.

The Scali Software Platform provides the necessary software components to combine a number of commodity computers running Linux into a single computer entity, henceforth called a cluster.

Scali is targeting its software at users involved in High Performance Computing, also known as supercomputing, which typically includes CPU-intensive parallel applications. Scali aims to produce software tools which assist its users in maximizing the power and ease of use of the computing hardware purchased.

Scali MPI Connect Release 4.4 Users Guide

5

Image 17
Contents Scali MPI ConnectTM Users Guide Copyright 1999-2005 Scali AS. All rights reserved AcknowledgementScali Bronze Software Certificate Grant of License MaintenanceII Software License Terms Commencement License Manager SupportSub-license and distribution Export RequirementsLICENSEE’s Obligations SCALI’s ObligationsTransfer Title to Intellectual Property RightsCompliance with Licenses Warranty of Title and Substantial PerformanceScali MPI Connect Release 4.4 Users Guide Vii Limitation on Remedies and LiabilitiesMiscellaneous Proprietary InformationGoverning Law Scali MPI Connect Release 4.4 Users Guide Table of contents Profiling with Scali MPI Connect Appendix a Example MPI code Scali MPI Connect Release 4.4 Users Guide Scali MPI Connect product context ChapterProblem reports Scali mailing lists SMC FAQ SMC release documentsSupport Platforms supportedAcronyms and abbreviations How to read this guideLicensing FeedbackNIC GUI style font Terms and conventionsTypographic conventions Typographic conventions Scali MPI Connect components Description of Scali MPI ConnectSMC network devices Network devices Direct Access Transport DATShared Memory Device Ethernet Devices3.2 DET Using detctlUsing detstat Infiniband Myrinet4.1 GM 5.1 IBChannel buffer Communication protocols on DAT-devices6 SCI Transporter protocol Inlining protocolEagerbuffering protocol Zerocopy protocol MPI-2 FeaturesSupport for other interconnects Scali MPI Connect Release 4.4 Users Guide MPI-2 Features Compiling and linking Setting up a Scali MPI Connect environmentScali MPI Connect environment variables RunningLinker flags Compiler supportNaming conventions Running Scali MPI Connect programsIdentity of parallel processes Mpimon monitor programBasic usage Standard input Controlling options to mpimonStandard output Program specNetwork options How to provide options to mpimonMpirun usage Mpirun wrapper scriptSuspending and resuming jobs Running with tcp error detection TfdrRunning with dynamic interconnect failover capabilities Part partDebugging with a sequential debugger Debugging and profilingBuilt-in-tools for debugging Using built-in segment protect violation handlerAssistance for external profiling Debugging with Etnus TotalviewChannelinlinethreshold size to set threshold for inlining Controlling communication resourcesCommunication resources on DAT-devices Using MPIBsend Using MPIIsend, MPIIrecvGood programming practice with SMC Matching MPIRecv with MPIProbeUser interface errors and warnings Error and warning messagesFatal errors Unsafe MPI programsMpimon options Postfix Giving numeric values to mpimonPrefix Scali MPI Connect Release 4.4 Users Guide Example Profiling with Scali MPI ConnectTracing Using Scali MPI Connect built-in trace+relSecs S eTime where AbsRank MPIcallcommNamerankcall-dependant-parameters whereExample FeaturesTiming Using Scali MPI Connect built-in timingMPIcallDcallsDtimeDfreq TcallsTtimeTfreq Commrank recv from fromworldFromcommonFields Using the scanalyzeCommrank send to toworldTocommonFields where Count!avrLen!zroLen!inline!eager!transporter! whereFor timing This produces the following report Using SMCs built-in CPU-usage functionalityScali MPI Connect Release 4.4 Users Guide Automatic buffer management Tuning communication resourcesBenchmarking How to optimize MPI performanceCaching the application program on the nodes First iteration is very slowMemory consumption increase after warm-up Collective operationsFinding the best algorithm Image contrast enhancement Appendix aPrograms in the ScaMPItst package Scali MPI Connect Release 4.4 Users Guide Original File formatAppendix B When things do not work troubleshootingWhy does not my program start to run? General problems Why can I not start mpid?Why does my program terminate abnormally? Appendix C Per node installation of Scali MPI ConnectInstall Scali MPI Connect for Direct Ethernet Install Scali MPI Connect for TCP/IPInstall Scali MPI Connect for Myrinet ExampleInstall Scali MPI Connect for SCI Install Scali MPI Connect for InfinibandInstall and configure SCI management software License optionsScali kernel drivers Uninstalling SMCTroubleshooting Network providers Troubleshooting the GM provider Troubleshooting 3rdparty DAT providersScali MPI Connect Release 4.4 Users Guide Grouping Appendix D Bracket expansion and groupingBracket expansion Scali MPI Connect Release 4.4 Users Guide Related documentation Appendix EScali MPI Connect Release 4.4 Users Guide List of figures Scali MPI Connect Release 4.4 Users Guide Transporter protocol IndexSSP