{"id":913,"date":"2020-11-09T10:54:56","date_gmt":"2020-11-09T09:54:56","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=913"},"modified":"2022-04-06T14:48:39","modified_gmt":"2022-04-06T12:48:39","slug":"trainings-2019-admin-hpc-module-1-module-env-en","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-module-env-en\/","title":{"rendered":"Trainings 2019 &#8211; Admin HPC &#8211; module 1 &#8211; module env &#8211; EN"},"content":{"rendered":"<h2>Module Environment installation<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">Installation of Module Environment<\/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;\">20\/09\/2019<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">20\/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\">Installation<\/a><\/li>\n<li><a href=\"#part-3\">Configuration<\/a><\/li>\n<li><a href=\"#part-4\">Create a personal modulefile repository<\/a><\/li>\n<li><a href=\"#part-5\">Create a module file<\/a><\/li>\n<li><a href=\"#part-6\">Module commands<\/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>URL: <a href=\"https:\/\/github.com\/cea-hpc\/modules\">https:\/\/github.com\/cea-hpc\/modules<\/a><\/p>\n<p>Environment Modules: provides dynamic modification of a user's environment <a href=\"http:\/\/modules.sourceforge.net\/\">http:\/\/modules.sourceforge.net\/<\/a><\/p>\n<p>It allows the user to switch between several version of a program<\/p>\n<hr \/>\n<p><a name=\"part-2\"><\/a><\/p>\n<h2>Installation:<\/h2>\n<pre><code>$ yum install tcl tcl-devel -y\n$ wget https:\/\/github.com\/cea-hpc\/modules\/releases\/download\/v4.2.1\/modules-4.2.1.tar.gz\n$ tar xvfz module-4.2.1.tar.gz\n$ cd module-4.2.1\n$ .\/configure --prefix=\/usr\/local\/modules-4.2.1\n$ make\n$ make install<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-3\"><\/a><\/p>\n<h2>Configuration:<\/h2>\n<h3>Activate the Modules at  shell startup:<\/h3>\n<p>Enable Modules initialization at shell startup. An easy way to get module function defined and its associated configuration setup<br \/>\nat shell startup is to make the initialization scripts part of the system-wide environment setup in <code>\/etc\/profile.d<\/code>. To do so, make a<br \/>\nlink in this directory to the profile scripts that can be found in your Modules installation init directory:<\/p>\n<pre><code>$ ln -s \/usr\/local\/modules-4.2.1\/init\/profile.sh \/etc\/profile.d\/modules.sh\n$ ln -s \/usr\/local\/modules-4.2.1\/init\/profile.csh \/etc\/profile.d\/modules.csh<\/code><\/pre>\n<h3>Define module path to enable by default:<\/h3>\n<p>Edit <code>\/usr\/local\/modules-4.2.1\/modulerc<\/code> configuration file.<\/p>\n<p>Add there all the modulefile    directories you want to activate by default at Modules initialization time.<\/p>\n<p>Add one line mentioning each modulefile directory prefixed by the <code>module use<\/code> command:<\/p>\n<pre><code>$ module use \/usr\/local\/modules-4.2.1\/modulefiles\n$ module use \/path\/to\/other\/modulefiles<\/code><\/pre>\n<h3>Define the modulefiles to load by default<\/h3>\n<p>Edit <code>\/usr\/local\/modules-4.2.1\/modulerc<\/code> configuration file.<\/p>\n<p>Add one line mentioning each modulefile to load prefixed by the <code>module load<\/code> command:<\/p>\n<pre><code>$ module load foo\n$ module load bar<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-4\"><\/a><\/p>\n<h2>Define a personal module file repository:<\/h2>\n<p>Each user can create his personal module file repository<\/p>\n<h3>create  your  own repository<\/h3>\n<pre><code>mkdir \/home\/path_to_my_modulefiles<\/code><\/pre>\n<h3>Add the repository in your shell:<\/h3>\n<p>In your <code>\/home\/user\/.bashrc<\/code>, add the following line:<\/p>\n<pre><code>module use \u2013append \/home\/path_to_my_modulefiles<\/code><\/pre>\n<h3>Define the module to  launch at shell startup:<\/h3>\n<p>In your <code>\/home\/user\/.bash_profile<\/code>, add the following line:<\/p>\n<pre><code>module load program<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-5\"><\/a><\/p>\n<h2>Create a modulefile:<\/h2>\n<p>We are going to split the modulefiles in two categories:<\/p>\n<p>system: corresponding to the system programs<\/p>\n<p>bioinfo: corresponding to the bioinformatics programs<\/p>\n<pre><code>$ mkdir \/usr\/local\/modules-4.2.1\/modulefiles\/system\n$ mkdir \/usr\/local\/modules-4.2.1\/modulefiles\/bioinfo<\/code><\/pre>\n<p>For  each program you  will have to create a directory with the name of the program and a modulefile with the version number.<\/p>\n<p>For example, the bioinformatics software ncbi-blast v 2.4.0+  will have the modulefile 2.4.0+ according to this path:<\/p>\n<pre><code>\/usr\/local\/modules-4.2.1\/modulefiles\/bioinfo\/ncbi-blast\/2.4.0+<\/code><\/pre>\n<h3>Module file template<\/h3>\n<p>Modulefiles are written in tcl language.<\/p>\n<p>Here is  a example for the program <code>program 1.0<\/code><\/p>\n<pre><code class=\"language-#%Module1.0#####################################################################\">       ##\n       ##\n\n       ## Define the  &quot;module help \u2026&quot; command below:\n       proc ModulesHelp { } {\n       global name version prefix man_path\n       puts stderr &quot;\\t[module-info name] - loads the compiler env variables&quot;\n       puts stderr &quot;\\tThe following env variables are set:&quot;\n       puts stderr &quot;\\t\\t\\$COMPILER, \\$COMPILER_VER, \\$CC, \\$FC&quot;\n       puts stderr &quot;\\tThe following env variables are modified:&quot;\n       puts stderr &quot;\\t\\t\\$PATH, \\$MANPATH, \\$LD_LIBRARY_PATH&quot;\n       }\n       ## Define the &quot;module whatis \u2026&quot; comman with the line below\n      module-whatis   &quot;loads the [module-info name] environment&quot;\n\n        ## if some modules interfers with this one you can use conflict\n       conflict bioinfo\/program\/2.0\n\n        ## Set the version nuber of your program\n         set     version      &quot;1.0&quot;\n\n        ## Set the install path of your program\n         set     topdir          \/usr\/local\/bioinfo\/program-1.0\n\n        ## Define the PATH and other variable\n        prepend-path   PATH             $topdir\/bin\n        prepend-path   LD_LIBRARY_PATH $topdir\/lib\n        setenv  CC     gcc    # setenv attributes only  one value  to the variable<\/code><\/pre>\n<h3>Example of modulefile:<\/h3>\n<pre><code class=\"language-#%Module1.0#####################################################################\">    ##\n    ## modules modulefile\n    ##\n    ## modulefiles\/modules.  Generated from modules.in by configure.\n    ##\n    proc ModulesHelp { } {\n    global version modroot\n\n    puts stderr &quot;blast\/2.4.0+ version 2.4.0 of blast&quot;\n     }\n\n     module-whatis   &quot;Loads version 2.4.0 of blast. BLAST finds regions of similarity between biological sequences&quot;\n     conflict bioinfo\/blast\/2.3.0+\n\n    # for Tcl script use only\n    set     version         2.4.0+\n    set     topdir          \/usr\/local\/ncbi-blast-2.4.0+\n\n    prepend-path    PATH            $topdir\/bin\n    prepend-path    MANPATH         $topdir\/man<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-6\"><\/a><\/p>\n<h2>Module commands:<\/h2>\n<p>See the available modules :<\/p>\n<pre><code>$ module avail<\/code><\/pre>\n<p>Obtain infos on a particular module:<\/p>\n<pre><code>$ module whatis + module name<\/code><\/pre>\n<p>Load a module :<\/p>\n<pre><code>$ module load + modulename<\/code><\/pre>\n<p>List the loaded module :<\/p>\n<pre><code>$ module list<\/code><\/pre>\n<p>Unload a module :<\/p>\n<pre><code>$ module unload + modulename<\/code><\/pre>\n<p>Unload all  modules :<\/p>\n<pre><code>$ module purge<\/code><\/pre>\n<hr \/>\n<h3>Links<\/h3>\n<p><a name=\"links\"><\/a><\/p>\n<ul>\n<li>Related courses : <a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-hpc\/\">HPC Trainings<\/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>Module Environment installation Description Installation of Module Environment Related-course materials HPC Administration Module1 Authors Ndomassi TANDO (ndomassi.tando@ird.fr) Creation Date 20\/09\/2019&hellip; 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