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Sun HPC Software, Linux Edition 2.0.1, Deployment and User Guide

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Sun HPC Software, Linux Edition 2.0.1, Deployment and User Guide Gree SunTM HPC Software, Linux Edition 2.0.1 Deployment and User Guide Sun Microsystems, Inc. www.sun.com Part No. 821-0375-10 July 2009 Copyright © 2009 Sun Microsystems, Inc., 4150 Network Circle, Santa Clara, California 95054, U.S.A. All rights reserved. U.S. Government Rights - Commercial software. Government users are subject to the Sun Microsystems, Inc. standard license agreement and applicable provisions of the FAR and its supplements. This distribution may include materials developed by third parties. Sun, Sun Microsystems, the Sun logo, and Lustre are trademarks or registered trademarks of Sun Microsystems, Inc. in the U.S. and other countries. Products covered by and information contained in this service manual are controlled by U.S. Export Control laws and may be subject to the export or import laws in other countries. Nuclear, missile, chemical biological weapons or nuclear maritime end uses or end users, whether direct or indirect, are strictly prohibited. Export or reexport to countries subject to U.S. embargo or to entities identified on U.S. export exclusion lists, including, but not limited to, the denied persons and specially designated nationals lists is strictly prohibited. DOCUMENTATION IS PROVIDED "AS IS" AND ALL EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS AND WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT, ARE DISCLAIMED, EXCEPT TO THE EXTENT THAT SUCH DISCLAIMERS ARE HELD TO BE LEGALLY INVALID. This product includes source code for the Berkeley Database, a product of Sleepycat Software, Inc. Your development of software that uses the Berkeley Database application programming interfaces is subject to additional licensing conditions and restrictions imposed by Sleepycat Software Inc. Sun Microsystems, Inc iii Table of Contents 1. Introduction ............................................................................1 What is the Sun HPC Software, Linux Edition ...............................................1 Who should use this document ..................................................................1 What are the system requirements ............................................................1 How is this document organized ................................................................2 Where can I find additional information .....................................................2 2. Overview and Preparation .........................................................3 Installation Overview................................................................................3 Planning and Preparation .........................................................................4 Installation considerations.....................................................................................4 Preparing to install the software............................................................................4 Obtaining the software..........................................................................................4 3. Installing the Software and Provisioning the Cluster ....................6 Step A. Install the Sun HPC Software on the Head Node................................7 Overview..............................................................................................................7 Method 1: Install the Sun HPC Software from an ISO image......................................7 Method 2. Use Kickstart to install RHEL and the Sun HPC Software..........................12 Step B. Prepare the Head Node to Provision the Cluster..............................14 Overview............................................................................................................14 Preparing a head node running RHEL 5.3 ..............................................................17 Preparing a head node running SLES 10 SP2..........................................................21 Step C. Prepare to Provision the Client Nodes.............................................23 Overview............................................................................................................23 Introduction to the Sun HPC Software Management Database and Tools.................23 Preparing to provision the Client nodes.................................................................26 Step D. Provision the Client Nodes............................................................33 Configuring a Serial Console (Optional)......................................................35 Configuring the Lustre File System (Optional).............................................35 4. Managing the HPC Cluster .......................................................36 Setting Up SSH Keys................................................................................36 Creating SSH keys ...............................................................................................36 Generating SSH keys for hosts defined in a Genders configuration file.....................37 Configuring the PowerMan Power Management Tool.................................39 Configuring the ConMan Console Management Tool...................................41 Setting Up and Using pdsh.......................................................................43 iv Sun Microsystems, Inc. Setting up Cfengine to Manage Configuration Files on Clients......................44 Setting up Cfengine on a head node......................................................................45 Adding Cfengine configuration files.......................................................................45 Customizing the Cfengine configuration................................................................46 Using the Cobbler Provisioning Tool..........................................................48 Adding a node.....................................................................................................48 Deleting a node...................................................................................................49 Changing options in a Cobbler profile....................................................................49 Starting OpenSM.....................................................................................51 5. Monitoring the HPC Cluster .....................................................52 Using ConMan to Capture and View Console Logs.......................................52 Using Ganglia to Monitor the Cluster.........................................................52 Setting up and starting Ganglia............................................................................53 Customizing the Ganglia configuration..................................................................54 Using Nagios to Monitor the Cluster..........................................................56 Nagios on a SunHPC system.................................................................................56 Customizing Nagios.............................................................................................57 6. Parallel Computing .................................................................61 Using the Sun HPC ClusterTools................................................................61 Features of the Sun HPC ClusterTools MPI module.................................................61 Checking to see if MPI has been installed correctly.................................................62 Setting up user accounts .....................................................................................62 Using mpirun .....................................................................................................63 A basic MPI example ...........................................................................................64 Using the ClusterTools libraries with gcc and makefile...........................................68 Using the ClusterTools libraries with mpicc and makefile........................................68 Running an MPI application.................................................................................69 Using the Sun Studio/PGI/Intel/Pathscale Compilers..................................70 Installing additional MPI distributions..................................................................70 Using MVAPICH2.................................................................................................73 Building an MPI application.................................................................................74 Running an MPI application.................................................................................74 Running an Intel MPI Benchmark..........................................................................75 Using Modules to Handle Additional MPI Distributions................................77 7. Managing Compute Resources .................................................79 Sun Grid Engine ......................................................................................79 Overview of Sun Grid Engine ................................................................................79 Preparing a Sun Grid Engine installation................................................................80 Sun Microsystems, Inc v Install Sun Grid Engine on a shared file system......................................................81 Installing Sun Grid Engine on non-shared file systems............................................83 Configuring and testing the installed Sun Grid Engine instance...............................85 SLURM...................................................................................................86
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