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Intel® Cluster Toolkit 2.0 Tutorial (Revision 20051122)

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Intel® Cluster Toolkit 2.0 Tutorial (Revision 20051122) Intel® Cluster Toolkit 2.0 Tutorial (Revision 20051122) Table of Contents 1. Disclaimer and Legal Information ........................................................................................... 2 2. Introduction ............................................................................................................................. 3 3. Synopsis of New Features...................................................................................................... 4 4. Acronyms and Definitions ....................................................................................................... 6 5. Conventions ............................................................................................................................ 7 6. Intel Software Downloads and Installation for the Intel® Cluster Toolkit................................ 8 6.1 Installation of Intel® Cluster Toolkit on 32 Bit and 64 Bit Nodes which Share a Common /opt Directory ............................................................................................................................. 13 7. The Parallel Install Capability for the Intel® Cluster Toolkit Installer.................................... 14 8. The Software Architecture of the Intel® Cluster Toolkit........................................................ 15 9. Getting Started with Intel® MPI Library ................................................................................ 17 9.1 Launching MPD Daemons ........................................................................................... 18 9.1.1 How to Set Up MPD Daemons............................................................................ 19 9.2 The mpdboot Command .............................................................................................. 20 9.3 Compiling and Linking with Intel® MPI Library ............................................................ 20 9.4 Selecting a Network Fabric or Device.......................................................................... 20 9.5 Running an MPI Program Using Intel® MPI Library .................................................... 21 9.6 Experimenting with Intel® MPI Library......................................................................... 21 9.7 Controlling MPI Process Placement............................................................................. 22 10. Interoperability of Intel® MPI Library with the Intel® Trace Collector and Intel® Trace Analyzer......................................................................................................................................... 24 10.1 Compiling MPI Programs in Conjunction with the Intel® Trace Collector Header Files 26 10.2 Linking MPI Programs with the Intel® Trace Collector Libraries ................................. 27 10.2.1 Simplifying the Compile and Link Command between Intel® MPI Library and the Intel® Trace Collector ........................................................................................................... 46 10.2.2 Internal Intel® MPI Library State Tracing with Intel® Trace Collector................. 47 10.2.3 How to Get Additional Help Regarding the Intel® Trace Collector ..................... 51 10.3 Experimenting with the MPI Examples in the Directory ${VT_ROOT}/examples ........ 51 10.4 Experimenting with Intel® Trace Analyzer Examples in the Directory <directory-path- to-ITA>/examples ...................................................................................................................... 57 10.4.1 How to Get Additional Help Regarding the Intel® Trace Analyzer...................... 59 10.5 Experimenting with Intel® Trace Analyzer and Collector in a Fail-Safe Mode ............ 59 11. Getting Started in Using the Intel® Cluster Math Kernel Library (Intel® Cluster MKL) ........ 61 11.1 Gathering Instrumentation Data and Analyzing the ScaLAPACK Examples with the Intel® Trace Collector and Intel® Trace Analyzer..................................................................... 65 11.2 Experimenting with the Cluster DFT Software ............................................................. 69 12. Experimenting with the Intel® MPI Benchmarks .................................................................. 73 13. Hardware and Recommendations for Installation ................................................................ 86 14. System Administrator Checklist ............................................................................................ 86 15. User Checklist ...................................................................................................................... 87 1 1. Disclaimer and Legal Information This installation and tutorial document, called Intel® Cluster Toolkit Tutorial, as well as the software described in it, is subject to change without notice and Intel Corporation assumes no responsibility or liability for any errors or inaccuracies that may appear in this document or any software that may be provided in association with this document. This document and the software described in it are furnished under license and may only be used or copied in accordance with the terms of the license. No license, express or implied, by estoppel or otherwise, to any intellectual property rights is granted by this document. The information in this document is provided in connection with Intel products and should not be construed as a commitment by Intel Corporation. EXCEPT AS PROVIDED IN INTEL'S TERMS AND CONDITIONS OF SALE FOR SUCH PRODUCTS, INTEL ASSUMES NO LIABILITY WHATSOEVER, AND INTEL DISCLAIMS ANY EXPRESS OR IMPLIED WARRANTY, RELATING TO SALE AND/OR USE OF INTEL PRODUCTS INCLUDING LIABILITY OR WARRANTIES RELATING TO FITNESS FOR A PARTICULAR PURPOSE, MERCHANTABILITY, OR INFRINGEMENT OF ANY PATENT, COPYRIGHT OR OTHER INTELLECTUAL PROPERTY RIGHT. Intel products are not intended for use in medical, life saving, life sustaining, critical control or safety systems, or in nuclear facility applications. Designers must not rely on the absence or characteristics of any features or instructions marked "reserved" or "undefined." Intel reserves these for future definition and shall have no responsibility whatsoever for conflicts or incompatibilities arising from future changes to them. The software described in this document may contain software defects which may cause the product to deviate from published specifications. Current characterized software defects are available on request. Intel, the Intel logo, Intel SpeedStep, Intel NetBurst, Intel NetStructure, MMX, i386, i486, Intel386, Intel486, Intel740, IntelDX2, IntelDX4, IntelSX2, Celeron, Intel Centrino, Intel Xeon, Intel XScale, Itanium, Pentium, Pentium II Xeon, Pentium III Xeon, Pentium M, and VTune are trademarks or registered trademarks of Intel Corporation or its subsidiaries in the United States and other countries. * Other names and brands may be claimed as the property of others. All trademarks and registered trademarks referenced in this Intel® Cluster Toolkit document are the property of their respective holders. Copyright © Intel Corporation 2004 – 2005. 2 2. Introduction At the time of this writing, the Intel® Cluster Toolkit 2.0 release consists of: 1. Intel® MPI Library 2.0 2. Intel® Cluster Math Kernel Library 8.0.1 (Intel® Cluster MKL 8.0.1), which includes ScaLAPACK and Cluster DFT (Discrete Fourier Transform) 3. Intel® Trace Analyzer1 and Collector2 4. Intel® MPI Benchmarks3 This Intel® Cluster Toolkit 2.0 Tutorial contains information for installing software packages to support homogeneous cluster computing for Intel® Pentium® 4, Intel® Xeon®, Intel® Itanium® 2, and Intel® EM64T-based processors running Red Hat Enterprise Linux* 3.0, Red Hat Enterprise Linux 4.0, SUSE Linux Enterprise Server* 9, SUSE Linux 9.0, or SUSE Linux 9.1. The tutorial was last checked and validated on November 22, 2005. The emphasis of this tutorial is on the interoperability of the software components listed above. The user of the Intel® Cluster Toolkit may need assistance from their system administrator in installing the associated software packages on their cluster system, if the installation directory requires system administrative write privileges (e.g. /opt/intel). This assumes that the user’s login account does not have administrative privileges. 1 Intel® Trace Analyzer was formerly known as Vampir. 2 Intel® Trace Collector was formerly known as Vampirtrace. 3 Intel® MPI Benchmarks was formerly known as the Pallas MPI Benchmarks (PMB). 3 3. Synopsis of New Features Intel® Cluster Toolkit 2.0 • There is additional operating system support • The Intel® Cluster Toolkit has an expect script called sshconnectivity.exp which the user may find useful in establishing secure shell connectivity on a cluster system. Please see chapter 6 titled “Intel Software Downloads and Installation for the Intel® Cluster Toolkit” Intel® Cluster MKL 8.0.1 • Cluster DFTs (Discrete Fourier Transforms) o There are examples of using the Cluster Fast Fourier Transform within the chapter on Intel® Cluster MKL • Iterative sparse solver • Increased sparse solver support o Sparse level 2 and 3 BLAS • Interval Arithmetic o Solvers for interval systems of linear equations o Interval matrix inversion o Functions for testing regularity/singularity of interval matrices • Vector Statistical Library additions o Convolution and correlation o New random number generators and service functions • FFTW (“Fastest Fourier Transform in the West”) interface to the MKL DFTs • Fortran 90/95 interfaces
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