{"id":916,"date":"2020-11-09T10:58:31","date_gmt":"2020-11-09T09:58:31","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=916"},"modified":"2022-04-06T14:48:39","modified_gmt":"2022-04-06T12:48:39","slug":"trainings-2019-admin-hpc-module-1-sge-installation","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-admin-hpc-module-1\/trainings-2019-admin-hpc-module-1-sge-installation\/","title":{"rendered":"Trainings 2019 &#8211; Admin HPC &#8211; module 1 &#8211; sge installation"},"content":{"rendered":"<h2>SGE installation<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">Installation of Sun Grid Engine<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Related-course materials<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-admin-hpc-module-1\/\">HPC Administration Module1<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Authors<\/td>\n<td style=\"text-align: left;\">Ndomassi TANDO (ndomassi.tando@ird.fr)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Creation Date<\/td>\n<td style=\"text-align: left;\">23\/09\/2019<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">23\/09\/2019<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<h3>Summary<\/h3>\n<p><!-- TOC depthFrom:2 depthTo:2 withLinks:1 updateOnSave:1 orderedList:0 --><\/p>\n<ul>\n<li><a href=\"#part-1\">Definition<\/a><\/li>\n<li><a href=\"#part-2\">Prerequisites<\/a><\/li>\n<li><a href=\"#part-3\">SGE installation<\/a><\/li>\n<li><a href=\"#part-4\">Master Server installation<\/a><\/li>\n<li><a href=\"#part-5\">Nodes installation<\/a><\/li>\n<li><a href=\"#links\">Links<\/a><\/li>\n<li><a href=\"#license\">License<\/a><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"part-1\"><\/a><\/p>\n<h2>Definition<\/h2>\n<p>SGE (SUN Grid Engine) is a linux job scheduler able to handle from 2 to thousands of servers at the same time.<\/p>\n<p>One master server use the resources (CPU or RAM)of  one or several nodes to perform analyses. <\/p>\n<p>\u25cf An opensource tool<\/p>\n<p>\u25cf 3 main functions :<\/p>\n<ul>\n<li>\n<p>Allocates ressources (CPU,RAM) to users to allow them to<br \/>\nlaunch their analyses<\/p>\n<\/li>\n<li>\n<p>Provides a frame to launch,execute et monitore the jobs on the<br \/>\nwhole allocated nodes<\/p>\n<\/li>\n<li>\n<p>Deals with jobs in queue wait<\/p>\n<\/li>\n<\/ul>\n<p>RPMS :  <a href=\"https:\/\/copr.fedorainfracloud.org\/coprs\/loveshack\/SGE\/\">https:\/\/copr.fedorainfracloud.org\/coprs\/loveshack\/SGE\/<\/a><\/p>\n<p>SOURCE :    <a href=\"https:\/\/arc.liv.ac.uk\/downloads\/SGE\/releases\/\">https:\/\/arc.liv.ac.uk\/downloads\/SGE\/releases\/<\/a><\/p>\n<hr \/>\n<p><a name=\"part-2\"><\/a><\/p>\n<h2>Prerequisites:<\/h2>\n<p>you have to choose a nfs parttion shared between your master and your node.<\/p>\n<pre><code>$yum -y install epel-release\n$ yum -y install jemalloc-devel openssl-devel ncurses-devel pam-devel libXmu-devel hwloc-devel hwloc hwloc-libs java-devel javacc ant-junit libdb-devel motif-devel csh ksh xterm db4-utils perl-XML-Simple perl-Env xorg-x11-fonts- ISO8859-1-100dpi xorg-x11-fonts-ISO8859-1-75dpi\n$ yum install \u2013y gcc\n$ groupadd -g 490 sgeadmin\n$ useradd -u 495 -g 490 -r -m  -d \/home\/sgeadmin -s \/bin\/bash sgeadmin<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-3\"><\/a><\/p>\n<h2>SGE installation:<\/h2>\n<pre><code> $ wget https:\/\/arc.liv.ac.uk\/downloads\/SGE\/releases\/8.1.9\/sge-8.1.9.tar.gz\n $ cd sge-8.1.9\/source\/\n $ sh scripts\/bootstrap.sh &amp;&amp; .\/aimk &amp;&amp; .\/aimk \u2013man\n $ export SGE_ROOT=&lt;NFS_SHARE_DIR&gt; &amp;&amp; mkdir \u2013p $SGE_ROOT\n $ echo Y | .\/scripts\/distinst -local -allall -libs \u2013noexit\n $ chown -R sgeadmin.sgeadmin $SGE_ROOT<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-4\"><\/a><\/p>\n<h2>Master server installation:<\/h2>\n<p>On the master server type:<\/p>\n<pre><code>$ yum -y install nfs-utils\n$ cd $SGE_ROOT\n$ .\/install_qmaster<\/code><\/pre>\n<p>You will be asked to mention:<\/p>\n<ul>\n<li>\n<p>The Grid Engine administrator name<\/p>\n<\/li>\n<li>\n<p>The value of $SGE_ROOT<\/p>\n<\/li>\n<li>\n<p>The number of the TCP port ( 6444 by default)<\/p>\n<\/li>\n<li>\n<p>The Grid Engine service Name<\/p>\n<\/li>\n<li>\n<p>The number of the TCP port for sge_execd (6445 by default)<\/p>\n<\/li>\n<li>\n<p>The Grid Engine cell name (leave default)<\/p>\n<\/li>\n<li>\n<p>The spool directory path<\/p>\n<\/li>\n<li>\n<p>The spooling method<\/p>\n<\/li>\n<li>\n<p>group ID range for Grid Engine<\/p>\n<\/li>\n<li>\n<p>Accept the installation of booting scripts<\/p>\n<\/li>\n<li>\n<p>Do not install shadow server<\/p>\n<\/li>\n<li>\n<p>The list of administration and submit hosts : put your master server in both<\/p>\n<\/li>\n<\/ul>\n<p>To finish the installation, launch the following commands:<\/p>\n<pre><code>$  cp $SGE_ROOT\/default\/common\/settings.sh \/etc\/profile.d\/SGE.sh\n$ cp $SGE_ROOT\/default\/common\/settings.csh \/etc\/profile.d\/SGE.csh<\/code><\/pre>\n<p>If you have serveral nodes: allow the nfs export of the SGE PATH to the other nodes of the cluster:<\/p>\n<p>In <code>\/etc\/exports<\/code> add:<\/p>\n<pre><code>$ \/usr\/local\/sge  IP_range_nodes\/24(rw,no_root_squash)<\/code><\/pre>\n<p>Start and enable the nfs service:<\/p>\n<pre><code>$ systemctl start rpcbind nfs-server\n$ systemctl enable rpcbind nfs-server<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-5\"><\/a><\/p>\n<h2>Nodes installation:<\/h2>\n<p>if you have several nodes, make sure they appear in the <code>\/etc\/hosts<\/code> file<\/p>\n<p>Mount the SGE_ROOT path on the node:<\/p>\n<pre><code> $ yum -y install nfs-utils\n $ systemctl start rpcbind\n $ systemctl enable rpcbind\n $ mount \u2013t nfs &lt;master&gt;:\/usr\/local\/sge \/usr\/local\/sge\n $ systemctl start rpcbind nfs-server\n $ systemctl enable rpcbind nfs-server<\/code><\/pre>\n<p>Launch the installation of the node:<\/p>\n<pre><code> $ export SGE_ROOT=\/usr\/local\/sge\n $ export SGE_CELL=default\n $ cd $SGE_ROOT\n $ .\/install_execd <\/code><\/pre>\n<p>After answering all the questions:<\/p>\n<pre><code>$ cp $SGE_ROOT\/default\/common\/settings.sh \/etc\/profile.d\/SGE.sh\n$ cp $SGE_ROOT\/default\/common\/settings.csh \/etc\/profile.d\/SGE.csh<\/code><\/pre>\n<hr \/>\n<h3>Links<\/h3>\n<p><a name=\"links\"><\/a><\/p>\n<ul>\n<li>Related courses : [HPC Trainings]((<a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-hpc\/\">https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-hpc\/<\/a>)<\/li>\n<\/ul>\n<hr \/>\n<h3>License<\/h3>\n<p><a name=\"license\"><\/a><\/p>\n<div>\nThe resource material is licensed under the Creative Commons Attribution 4.0 International License (<a href=\"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/\">here<\/a>).<br \/>\n<center><img decoding=\"async\" width=\"25%\" class=\"img-responsive\" src=\"http:\/\/creativecommons.org.nz\/wp-content\/uploads\/2012\/05\/by-nc-sa1.png\"\/><br \/>\n<\/center>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>SGE installation Description Installation of Sun Grid Engine Related-course materials HPC Administration Module1 Authors Ndomassi TANDO (ndomassi.tando@ird.fr) Creation Date 23\/09\/2019&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-admin-hpc-module-1\/trainings-2019-admin-hpc-module-1-sge-installation\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":893,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-916","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Trainings 2019 - Admin HPC - module 1 - sge installation - itrop<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-admin-hpc-module-1\/trainings-2019-admin-hpc-module-1-sge-installation\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Trainings 2019 - Admin HPC - module 1 - sge installation - itrop\" \/>\n<meta property=\"og:description\" content=\"SGE installation Description Installation of Sun Grid Engine Related-course materials HPC Administration Module1 Authors Ndomassi TANDO (ndomassi.tando@ird.fr) Creation Date 23\/09\/2019&hellip; 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