{"id":2955,"date":"2021-03-06T00:01:31","date_gmt":"2021-03-05T23:01:31","guid":{"rendered":"https:\/\/bioinfo.ird.fr\/?page_id=2955"},"modified":"2026-03-13T12:20:27","modified_gmt":"2026-03-13T11:20:27","slug":"tutorials-howtos-i-trop-cluster","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/","title":{"rendered":"Tutorials &#8211; HowTos i-Trop cluster"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"2955\" class=\"elementor elementor-2955\">\n\t\t\t\t\t\t<div class=\"elementor-inner\">\n\t\t\t\t<div class=\"elementor-section-wrap\">\n\t\t\t\t\t\t\t\t\t<section class=\"has_eae_slider elementor-section elementor-top-section elementor-element elementor-element-44bf0fa3 elementor-section-boxed elementor-section-height-default elementor-section-height-default exad-glass-effect-no exad-sticky-section-no\" data-id=\"44bf0fa3\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t\t\t<div class=\"elementor-row\">\n\t\t\t\t\t<div class=\"has_eae_slider elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-38f45cc9 exad-glass-effect-no exad-sticky-section-no\" data-id=\"38f45cc9\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-column-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t<div class=\"elementor-widget-wrap\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-5ec12d9c exad-sticky-section-no exad-glass-effect-no elementor-widget elementor-widget-text-editor\" data-id=\"5ec12d9c\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-text-editor elementor-clearfix\">\n\t\t\t\t<h2>Howtos cluster i-Trop<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">HowTos for i-Trop Cluster<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Author<\/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;\">08\/11\/19<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\"> Modification date<\/td>\n<td style=\"text-align: left;\">13\/03\/2026<\/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=\"#preambule\">Preambule: Architecture of the Itrop Cluster and Softwares to install before connecting to the cluster  <\/a><\/li>\n<li><a href=\"#howto-12\">How to: Add ssh keys to connect to the cluster<\/a><\/li>\n<li><a href=\"#howto-1\">How to:Transfer files with filezilla <code>sftp<\/code> on the i-Trop cluster<\/a><\/li>\n<li><a href=\"#howto-2\">How to: Connect to the i-Trop cluster via <code>ssh<\/code><\/a><\/li>\n<li><a href=\"#howto-3\">How to: Reserve one or several cores of a node <\/a><\/li>\n<li><a href=\"#howto-4\">How to: Transfer my data from the san server to the node <\/a><\/li>\n<li><a href=\"#howto-5\">How to: Use the Module Environment <\/a><\/li>\n<li><a href=\"#howto-6\">How to: Launch a job with Slurm  <\/a><\/li>\n<li><a href=\"#howto-7\">How to: Choose a particular partition <\/a><\/li>\n<li><a href=\"#howto-9\">How to: See or delete your data on the \/scratch partition of the nodes<\/a><\/li>\n<li><a href=\"#howto-10\">How to: Use a singularity container <\/a><\/li>\n<li><a href=\"#howto-11\">How to: Cite the Itrop platform in your publications<\/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><\/a><\/p>\n<h3>Preambule<\/h3>\n<h5>Architecture of the i-Trop cluster :<\/h5>\n<p>The i-Trop computing cluster is made up of a set of computing servers accessible via a front-end machine. Connections to these compute servers are made via this master machine, which ensures the distribution of the different analyses between the machines available at any given moment. <\/p>\n<p>The computing cluster is composed of :<\/p>\n<ul>\n<li>1 master machine<\/li>\n<li>1 san bay for temporary storage of project data up to 800TB <\/li>\n<li>32 CPU computing nodes with a total capacity of 1404 cores and 8392GB of RAM and a GPU server with 8 RTX 2080 graphics cards..<\/li>\n<\/ul>\n<p>Here is the architecture:<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2023\/09\/schema_cluster_110923-1024x871.png\" alt=\"\"><\/p>\n<h5>Connecting to a server in ssh from a Windows machine<\/h5>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">System<\/th>\n<th style=\"text-align: left;\">Softwares<\/th>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">url<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\"><img decoding=\"async\" width=\"20%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/tpLinux\/osWin.png\"><\/td>\n<td style=\"text-align: left;\">mobaXterm<\/td>\n<td style=\"text-align: left;\">an advanced terminal for Windows with an X11 server and an SSH client<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/mobaxterm.mobatek.net\/\">Download<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\"><img decoding=\"async\" width=\"20%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/tpLinux\/osWin.png\"><\/td>\n<td style=\"text-align: left;\">putty<\/td>\n<td style=\"text-align: left;\">Putty allows to connect to a Linux server from a Windows machine .<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/www.chiark.greenend.org.uk\/~sgtatham\/putty\/latest.html\">T\u00e9l\u00e9charger<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h5>Transfer files from your computer to Linux servers with SFTP<\/h5>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Systems<\/th>\n<th style=\"text-align: left;\">Softwares<\/th>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">url<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\"><img decoding=\"async\" width=\"10%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/tpLinux\/osApple.png\"> <img decoding=\"async\" width=\"10%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/tpLinux\/osLinux.png\"> <img decoding=\"async\" width=\"10%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/tpLinux\/osWin.png\"><\/td>\n<td style=\"text-align: left;\"><img decoding=\"async\" width=\"20%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/tpLinux\/filezilla.png\"> filezilla<\/td>\n<td style=\"text-align: left;\">FTP and SFTP client<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/filezilla-project.org\/\">Download<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h5>View and edit files locally or on a remote server<\/h5>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Type<\/th>\n<th style=\"text-align: left;\" softwares<=\"\" th=\"\">\n<\/th>\n<th style=\"text-align: left;\">url<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Distant, console mode<\/td>\n<td style=\"text-align: left;\">nano<\/td>\n<td style=\"text-align: left;\"><a href=\"http:\/\/www.howtogeek.com\/howto\/42980\/\">Tutorial<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Distant, console mode<\/td>\n<td style=\"text-align: left;\">vi<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/www.washington.edu\/computing\/unix\/vi.html\">Tutorial<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Distant, graphic mode<\/td>\n<td style=\"text-align: left;\">komodo edit<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/www.activestate.com\/komodo-ide\/downloads\/edit\">T\u00e9l\u00e9charger<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Linux &#038; windows \u00e9diteur<\/td>\n<td style=\"text-align: left;\">Notepad++<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/notepad-plus-plus.org\/download\/v7.5.5.html\">T\u00e9l\u00e9charger<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr>\n<p><a><\/a><\/p>\n<h3>How to : Add ssh keys to connect to the cluster <\/h3>\n<p><a><\/a><\/p>\n<h3><span style=\"color: var( --e-global-color-text ); font-family: var( --e-global-typography-text-font-family ), Sans-serif; font-weight: var( --e-global-typography-text-font-weight ); font-size: 16px;\">Follow the instructions here:\u00a0<\/span><a href=\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-add-ssh-keys\/\" target=\"_blank\" style=\"font-family: var( --e-global-typography-text-font-family ), Sans-serif; font-weight: var( --e-global-typography-text-font-weight ); font-size: 16px;\">https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-add-ssh-keys\/<\/a><br><\/h3>\n<div><br><\/div>\n<h3>How to : Transfer files with filezilla <code>sftp<\/code><\/h3>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p><code>\n<h5>Open FileZilla and save the i-Trop cluster into the site manager<\/h5>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2023\/09\/filezilla1-1024x431.png\" alt=\"\" width=\"1024\" height=\"431\"><\/p>\n<p>In the FileZilla menu, go to  <em>File > Site Manager<\/em>. Then go through these 5 steps:<\/p>\n<ol>\n<li>Click on\u00a0<em>New Site<\/em>.<\/li>\n<li>Add an explicit name.<\/li>\n<li>\n<p>Choose host bioinfo-san.ird.fr<\/p>\n<\/li>\n<\/ol>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2023\/09\/partition_san.png\" alt=\"\" width=\"605\" height=\"710\"><\/p>\n<ol start=\"4\">\n<li>Put the Logon Type to \"key File\" and choose the id_rsa.ppk key retreived before<\/li>\n<li>Choose port 22 and press the \"Connect\" button.<\/li>\n<\/ol>\n<h5>Transferring files<\/h5>\n<p><img decoding=\"async\" width=\"100%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/tpLinux\/tp-filezilla2.png\"><\/p>\n<ol>\n<li>From your computer to the cluster : click and drag an text file item from the left local column to the right remote column<\/li>\n<li>From the cluster to your computer: click and drag an text file item from he right remote column to the left local column<\/li>\n<\/ol>\n<hr>\n<p><a><\/a><\/p>\n<h3>How to : How to: Connect to the i-Trop cluster via <code>ssh<\/code><\/h3>\n<h4><span style=\"font-size: 1.1rem; letter-spacing: 0.0625rem;\">From a windows computer :<\/span><br><\/h4>\n<p>with mobaXterm:<\/p>\n<ol>\n<li>Click the session button and choose SSH.\n<ul>\n<li>In the remote host box, type: bioinfo-master1.ird.fr<\/li>\n<li>Check the  specify username  box and enter your login<\/li>\n<\/ul>\n<\/li>\n<li>Choose Advanced SSH settings<\/li>\n<li>Tick the \u00ab Use private key \u00bb box and provides your id_rsa.ppk from your ssh-login.zip then press OKs<\/li>\n<\/ol>\n<h4>From a MAC or Linux:<\/h4>\n<p>Open terminal application  and type the following command:<\/p>\n<p><code>ssh login@bioinfo-master1.ird.fr<\/code><\/p>\n<p>with login: your cluster account<\/p>\n<p><br><\/p>\n<hr>\n<p><a><\/a><\/p>\n<h3>How to : Reserve one or several cores of a node<\/h3>\n<p>Cluster uses Slurm (<a href=\"https:\/\/slurm.schedmd.com\/documentation.html\">https:\/\/slurm.schedmd.com\/documentation.html<\/a>) to deal with users analyses<\/p>\n<p>It monitors available resources (CPU et RAM ) and allocate them to the users for job launching<\/p>\n<p> When you are connected on bioinfo-master1.ird.fr, you have the possibily to reserve one or serveral cores among them of the 28 nodes available<\/p>\n<h4>Reserving one core<\/h4>\n<p>Type the following command:<\/p>\n<p><code>srun -p short --pty bash -i<\/code><\/p>\n<p>You will be randomly connected to one of the nodes of the short partition  with one core reserved. <\/p>\n<h4>Reserving several cores at the same time <\/h4>\n<p>Typ\u00ea the following command:<\/p>\n<p><code>srun -p short -c X --pty bash -i<\/code><\/p>\n<p>With X the number of cores between 2 and 12.<\/p>\n<p>You will be randomly connected to one of the nodes of the short partition  with X reserved cores<\/p>\n<h4>Reserving one core of a specific node:<\/h4>\n<p> type the following command<\/p>\n<p><code>srun -p short  --nodelist=nodeX --pty bash -i<\/code><\/p>\n<p>With nodeX belonging to the short partition<\/p>\n<h4>Reserving one or several cores of a\u00a0 node using\u00a0 --constraint option:<\/h4>\n<p>Features\/Constraints allow users to make very specific requests to the scheduler. On our cluster, with have different features depending on what you need.<\/p>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Features<\/th>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">Nodes<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">512<\/td>\n<td style=\"text-align: left;\"> allows to select 512 GB RAM memory nodes in highmem partition<\/td>\n<td style=\"text-align: left;\">node5, node28,node29,node30<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">avx<\/td>\n<td style=\"text-align: left;\">allows to select nodes with avx processors <\/td>\n<td style=\"text-align: left;\">node0, node1, node4, node5, node7, node17, node18, node20, node21, node22, node23, node24, node25, node26, node27, node28, node29, node31<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">BEAST<\/td>\n<td style=\"text-align: left;\">allows to select  nodes to use BEAST with beagle<\/td>\n<td style=\"text-align: left;\">node4, node7, node28, node29, node30<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">dell<\/td>\n<td style=\"text-align: left;\">allows to select dell nodes<\/td>\n<td style=\"text-align: left;\">node28,node29,node30<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">geforce<\/td>\n<td style=\"text-align: left;\">allows to choose gpu nodes with geforce graphical card<\/td>\n<td style=\"text-align: left;\">node26<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">infiniband<\/td>\n<td style=\"text-align: left;\">allows to select infiniband nodes to speed up your data transfer<\/td>\n<td style=\"text-align: left;\">node0, node1, node4, node5, node7, node8, node11, node17, node20, node21, node22, node24, node25, node26, node27<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">rtx2080<\/td>\n<td style=\"text-align: left;\">allows to select nodes with rtx2080 gpu cards<\/td>\n<td style=\"text-align: left;\">node26<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">xeon<\/td>\n<td style=\"text-align: left;\">allows to select nodes with intel xeon processors<\/td>\n<td style=\"text-align: left;\">node0, node1, node5,node8, node10, node11, node12, node13, node14, node15, node16, node17, node18, node20, node21, node22, node23, node24, node25, node27  <\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">xeon-gold <\/td>\n<td style=\"text-align: left;\">allows to select nodes with intel xeon-gold processors<\/td>\n<td style=\"text-align: left;\">node4, node7, node26, node28, node29, node30, node31  <\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>To use one o several features, you have to use the <code> --constraint<\/code> option<\/p>\n<p>For example, to choose a node with avx processors , you will type:<\/p>\n<p><code>srun constraint=avx --pty bash -i<\/code><\/p>\n<p>For example, to choose a node with infiniband and 512 GB of ram on highmem partition, you will type:<\/p>\n<p><code>srun -p highmem --constraint=512,infiniband --pty bash -i<\/code><\/p>\n<p><br><\/p>\n<hr>\n<p><a><\/a><\/p>\n<h3>How to : Transfer my data from the san bay to nodes<\/h3>\n<p> On the cluster, every node has its own local partition called \/scratch. <\/p>\n<p><strong>\/scratch is used to receive data to  analyse, perform analyses on them and produces data results temporarly.<\/strong><br><strong>Data on \/scratch is hosted for  30 days max  expect for the nodes from the long partition until 45 day<\/strong><br><strong>It is mandatory to transfer its data to the \/scratch of the reserved node before launching its analyses.<\/strong> <\/p>\n<p>The \/scratch volumes range from 1TB to 14TB depending on the chosen node.<\/p>\n<p>When the analyses are finished, consider recovering your data.<\/p>\n<h4> scp command:<\/h4>\n<p>To transfer data between 2 remote servers, we use the command scp<\/p>\n<p><code>scp -r source destination<\/code><\/p>\n<p>There are 2 possible syntaxes:<\/p>\n<h5>Retrieve data from the san:<\/h5>\n<p><code>scp -r san:path_to_files\/file local_destination<\/code><\/p>\n<h5>Transfer data to the san:<\/h5>\n<p><code>scp -r \/local_path_to_files\/file san:remote_destination<\/code><\/p>\n<h4>Description of the partitions:<\/h4>\n<h5> User data<\/h5>\n<p> Each user has a 100GB personal volume to host data.  <\/p>\n<p> This personal folders are hosted into the <b>\/users<\/b> partition of the bioinfo-san.ird.fr<\/p>\n<p> For example for user test is personal folder will be \/users\/test<\/p>\n<p><strong>Be careful<\/strong>:On bioinfo-master1.ird.fr and the nodes, the \/users and the \/home partitions contain the same data . <b>This is not the case for bioinfo-san.ird.fr : \/home is different from \/users<\/b><\/p>\n<h5> Projects partitions <\/h5>\n<ul>\n<li>\/projects\/medium: hosts small or temporary  projects up to 1000 GB<\/li>\n<li>\/projects\/large: hosts normal projects from 1 to 4,9TB<\/li>\n<li>\/projects\/xl: hosts big projects from 5 to 9,9TB<\/li>\n<\/ul>\n<h5> share partitions <\/h5>\n<p> the \/share partition is used to hosts data such as banks or  to make available temporary data<\/p>\n<p><br><\/p>\n<h4>Use the infiniband nodes to transfer:<\/h4>\n<div><br><\/div>\n<div>\n<div>\n<div>The infiniband network (192.168.4.0)\u00a0 allows users to have access to an high speed network to transfer their data from the san to the nodes or between infiniband nodes.<\/div>\n<div><br><\/div>\n<div>Only certain nodes are equiped with infiniband for now :\u00a0 node0, node1, node4, node5, node7, node8, node9, node11, node17, node20, node21, node22, node23, node24, node25, node26, node27<\/div>\n<p><\/p>\n<div>To use the infiniband network,  we have to add the \"-ib\" siffix to the alias of the machine, for example san will become san-ib, node0 will become node0-ib etc...<\/div>\n<\/div>\n<div><br><\/div>\n<div><br><\/div>\n<div>Use the options\u00a0 \u00a0 -p partition ( with partition being the node partition) --constraint=infiniband to reserve one or several cores on a infiniband node:<\/div>\n<div><br><\/div>\n<div>For example, we want to reserve an infiniband node on highmem partition in a interactive mode, type the following command:<\/div>\n<div><br><\/div>\n<div><br><\/div>\n<div><span style=\"font-size: 12.25px;\">srun -p highmem --constraint=infiniband --pty bash -i<\/span><\/div>\n<\/div>\n<p>you now have access to the infiniband network, to use it just change the alias san to san-ib to  do your transfers <\/p>\n<p>There are 2 possible syntaxes:<\/p>\n<h5>Retrieve data from the san:<\/h5>\n<p><code>scp -r san-ib:path_to_files\/file local_destination<\/code><\/p>\n<h5>Transfer data to the san:<\/h5>\n<p><code>scp -r \/local_path_to_files\/file san-ib:remote_destination<\/code><\/p>\n<div><span style=\"font-size: 12.25px;\"><br><\/span><\/div>\n<div><span style=\"font-size: 12.25px;\"><br><\/span><\/div>\n<div><span style=\"font-size: 12.25px;\">\u00a0<\/span><\/div>\n<div><br><\/div>\n<div><br><\/div>\n<div><br><\/div>\n<div><br><\/div>\n<div>\u00a0\u00a0<\/div>\n<div><br><\/div>\n<div><br><\/div>\n<div><br><\/div>\n<hr>\n<p><a><\/a><\/p>\n<a name=\"howto-5\"><\/a>\n<h3>How to : Use module Environnement<\/h3>\n<p>Module Environment allows you to dynamically change your environment variable(PATH, LD_LIBRARY_PATH) and then choose your version software.<br>The nomenclature use for modules is package_name\/package_version<br>Softwares are divided in 2 environnements:<\/p>\n<ul>\n<li>bioinfo-itrop: Load the list of the bioinformatics software installed by i-Trop<\/li>\n<li>bioinfo-shared: Load the list of the\u00a0 bioinformatics\u00a0 softwares provided by the IFB Core cluster<\/li>\n<\/ul>\n<h4 style=\"margin-top: 0px;\">Choose the environment to work on<\/h4><div><span style=\"font-size: 12.25px;\">\u00a0 module load bioinfo-itrop\u00a0 \u00a0or module load bioinfo-shared<\/span><\/div><div><br><\/div>\n\nYou can work with only one environment loaded : bioinfo-itrop or bioinfo-shared, if you want to use  softwares from the other make sure  to unload the loaded environment first with:\n\n<p>\n<code>module unload bioinfo-itrop or module unload bioinfo-shared<\/code><\/p> <h4>Displaying the available software<\/h4>\n<p><code>module avail<\/code><\/p>\n<h4>Displaying the description of a sotfware<\/h4>\n<p><code>module whatis module_name\/version<\/code><\/p>\n<p><br>with module_name: the name of themodule.<\/p>\n<p>For example :  samtools version 1.7:<\/p>\n<p><code>module whatis samtools\/1.7<\/code><\/p>\n<h4>load a software:<\/h4>\n<p><code>module load module_name\/version<\/code><\/p>\n<p><br>with module_name: module name.<\/p>\n<p>For example :  samtools version 1.7:<\/p>\n<p><code>module load samtools\/1.7<\/code><\/p>\n<h4>unload a software<\/h4>\n<p><code>module unload module_name\/version<\/code><\/p>\n<p><br>with module_name: module name.<\/p>\n<p>For example :  samtools version 1.7:<\/p>\n<p><code>module unload samtools\/1.7<\/code><\/p>\n<h4>Displaying the loaded modules<\/h4>\n<p><code>module list<\/code><\/p>\n<h4>Unloading all the modules<\/h4>\n<p><code>module purge<\/code><\/p>\n<hr>\n<p><a><\/a><\/p>\n<h3>How to : Launch a job with Slurm<\/h3>\n<p> Cluster uses  <a href=\"https:\/\/slurm.schedmd.com\/documentation.html\">Slurm<\/a> to manage and prioritize users jobs .<\/p>\n<p>It checks the ressources availables (CPU and RAM ) and allocate them to the users to perform their analyses.<\/p>\n<p>Connected to bioinfo-master1.ird.fr, we can launch a command with <code>srun<\/code> or a script with<code>sbatch<\/code>. <\/p>\n<h4>Use srun with a command:<\/h4>\n<p>If you simply want to launch a command that will be executed on a node:.<\/p>\n<pre><code>        $ srun + command<\/code><\/pre>\n<p>Example:<\/p>\n<pre><code>        $ srun hostname<\/code><\/pre>\n<p>will launch the command hostname on the node choose by Slurm..<\/p>\n<h4>Use sbatch to launch a script:<\/h4>\n<p>Lthe batch mode allows to launch a analysis in several setps defined in a script.<\/p>\n<p>Slurm allows to use several scripts languages<br> such as  bash, perl or python.<\/p>\n<p>Slurm allocates the desired resources and launches the analyses in background. <\/p>\n<p>To be interpreted by Slurm, a script must contain a header with the Slurm  options beginning by the keyword <code>#BATCH<\/code>.<\/p>\n<p>Slurm example script:<\/p>\n<pre><code>#!\/bin\/bash\n## Define the job name\n#SBATCH --job-name=test\n## Define the output file\n#SBATCH --output=res.txt\n## Define the number of tasks\n#SBATCH --ntasks=1\n## Define the execution limit\n#SBATCH --time=10:00\n## Define 100Mb of memory per cpu\n#SBATCH --mem-per-cpu=100\nsleep 180 #lance une pause de 180s<\/code><\/pre>\n<p> to launch a analysis via a script:<\/p>\n<pre><code>$ sbatch script.sh<\/code><\/pre>\n<p>With<code>script.sh<\/code> the script to use<\/p>\n<p>More Slurm options here: <a href=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/cluster-itrop\/Slurm\/#\">Slurm options<\/a><\/p>\n<h4>Example of script :<\/h4>\n<p><a href=\"https:\/\/itrop.ird.fr\/cluster\/template_abyss_script.sh\">template for a abyss script<\/a> <\/p>\n<hr>\n<p><a><\/a><\/p>\n<h3>How to:  Choose a particular partition<\/h3>\n<p>Depending on the type of jobs (analyses) you want to run, you can choose between different partitions.<\/p>\n<p>Partitions are analysis queues with specific priorities and constraints such as the size or time limit of a job, the users authorized to use it, etc...<\/p>\n<p>Jobs are prioritized and processed using the resources (CPU and RAM) of the nodes making up these partitions.   <\/p>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">partition<\/th>\n<th style=\"text-align: left;\">role<\/th>\n<th style=\"text-align: left;\">nodes list<\/th>\n<th style=\"text-align: left;\">Number of cores<\/th>\n<th style=\"text-align: left;\">Ram<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">short<\/td>\n<td style=\"text-align: left;\">short jobs < 1 day (high priority,interactive jobs)<\/td>\n<td style=\"text-align: left;\">node13,node14,node15,node16,node18,node27<\/td>\n<td style=\"text-align: left;\">12 to 24 cores<\/td>\n<td style=\"text-align: left;\">48 to 144 Gb<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">normal<\/td>\n<td style=\"text-align: left;\">jobs < 7 days<\/td>\n<td style=\"text-align: left;\">node0,node1,node3,node4,node5,node7, node9,node13,node17,node20,node21,node22,node23,node24, node27,node30<\/td>\n<td style=\"text-align: left;\">20 to 112 cores<\/td>\n<td style=\"text-align: left;\">64 to 512Gb<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">long<\/td>\n<td style=\"text-align: left;\"><7 dayss< long jobs< 45 days<\/td>\n<td style=\"text-align: left;\">node8,node10,node12<\/td>\n<td style=\"text-align: left;\">12 to 24 cores<\/td>\n<td style=\"text-align: left;\">48 to 64 Gb<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">highmem<\/td>\n<td style=\"text-align: left;\">jobs with memory needs<\/td>\n<td style=\"text-align: left;\">node25,node28,node29<\/td>\n<td style=\"text-align: left;\">40 to 112 cores<\/td>\n<td style=\"text-align: left;\">512Gb to 1 Tb<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">global<\/td>\n<td style=\"text-align: left;\">partition for the GLOBAL project<\/td>\n<td style=\"text-align: left;\">node31<\/td>\n<td style=\"text-align: left;\">112 cores<\/td>\n<td style=\"text-align: left;\">512 Gb<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">supermem<\/td>\n<td style=\"text-align: left;\">jobs with important memory needs<\/td>\n<td style=\"text-align: left;\">node2<\/td>\n<td style=\"text-align: left;\">256 coeurs<\/td>\n<td style=\"text-align: left;\">2 Tb<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">gpu<\/td>\n<td style=\"text-align: left;\">analyses on GPU cores<\/td>\n<td style=\"text-align: left;\">node26<\/td>\n<td style=\"text-align: left;\">24 cpus and 8 GPUS cores<\/td>\n<td style=\"text-align: left;\">192 Gb<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>The access to the gpu partition is restricted . A request can be made here: : <a href=\"https:\/\/itrop-glpi.ird.fr\/plugins\/formcreator\/front\/formdisplay.php?id=15\">request access to gpu<\/a><\/p>\n<p>The partition can be chosen following this scheme:<\/p>\n<p><img decoding=\"async\" width=\"100%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/partition_choice.png\"><\/p>\n<p>By default, the chosen partition is the normal partition.<\/p>\n<p>Warning, highmem and highmemplus should only be used for jobs requiring at least 35-40GB of memory..<\/p>\n<p>The supermem partition should be used for large assemblies and jobs requiring more than 100GB of memory.  <\/p>\n<p> You can use the <code>htop<\/code> on a node to visualize the memory consumed by a process.<\/p>\n<p>To choose a partition, use the -p option.<\/p>\n<p><code>sbatch -p partition<\/code><br><code>srun -p partition<\/code><\/p>\n<p>With <code>partition<\/code> the chosen partition.<\/p>\n<hr>\n<p><a><\/a><\/p>\n<h3>How to :  View and delete your data contained in the \/scratch partition of the nodes<\/h3>\n<p>the 2 scripts are located here<code>\/opt\/scripts\/scratch-scripts\/<\/code><\/p>\n<p>To see your data contained in the \/scratch of the nodes:<\/p>\n<pre><code><code>sh \/opt\/scripts\/scratch-scripts\/scratch_use.sh<\/code>\n<\/code><\/pre>\n<p> and follow the instructions<\/p>\n<p>To delete your data contained in the \/scratch partition of the nodes: launch the following command:<\/p>\n<pre><code><code>sh \/opt\/scripts\/scratch-scripts\/clean_scratch.sh<\/code><\/code><\/pre>\n<p><code><code><br><\/code><\/code><\/p>\n<p><code><code><\/code><br>and follow the instructions<\/code><\/p>\n<hr>\n<p><a><\/a><\/p>\n<h3>How to : Use a singularity container<\/h3>\n<p><psingularity enables=\"\" users=\"\" to=\"\" have=\"\" full=\"\" control=\"\" of=\"\" their=\"\" environment.=\"\" singularity=\"\" containers=\"\" can=\"\" be=\"\" used=\"\" package=\"\" entire=\"\" scientific=\"\" workflows,=\"\" software=\"\" and=\"\" libraries,=\"\" even=\"\" data.=\"\" this=\"\" means=\"\" that=\"\" you=\"\" don\u2019t=\"\" ask=\"\" your=\"\" cluster=\"\" admin=\"\" install=\"\" anything=\"\" for=\"\" -=\"\" put=\"\" it=\"\" in=\"\" a=\"\" container=\"\" run.<=\"\" p=\"\">\n<\/psingularity><\/p>\n<p>Singularity is installed on the Itrop Cluster with several versions<\/p>\n<p>Containers are located in  <code>\/usr\/local\/bioinfo\/containers<\/code><\/p>\n<p>You first need to load the environment with the command:<\/p>\n<p><code>module load singularity<\/code> or <code>module load singularity\/version_wanted<\/code><\/p>\n<h5>Get help:<\/h5>\n<p>Use the command:<\/p>\n<p><code>singularity help \/usr\/local\/bioinfo\/containers\/singularity_version\/container.simg<\/code> <\/p>\n<p>with container.simg the container name .<\/p>\n<h5>Shell connection to a container:<\/h5>\n<p><code>singularity shell \/usr\/local\/bioinfo\/containers\/singularity_version\/container.simg<\/code><\/p>\n<h5> Launch a container with only one application:<\/h5>\n<p><code>singularity run \/usr\/local\/bioinfo\/containers\/singularity_version\/container.simg + arguments<\/code><\/p>\n<h5>Launch a container with several applications:<\/h5>\n<p><code>singularity exec \/usr\/local\/bioinfo\/containers\/singularity_version\/container.simg + tools + arguments<\/code><\/p>\n<h5>Bind a host folder to a singularity container.<\/h5>\n<p>Use the option <code>--bind \/host_partition:\/container_partition<\/code><\/p>\n<p>Example:<\/p>\n<p><code>singularity exec --bind \/toto2:\/tmp \/usr\/local\/bioinfo\/containers\/singularity_version\/container.simg + tools + arguments<\/code><\/p>\n<p>The container will have access to  the file of the partition <code>\/toto2<\/code> of the host in its <code>\/tmp<\/code> partition<\/p>\n<p>By default, partitions \/home, \/opt,\/scratch, \/projects\/medium, projects\/large\/projects\/xl, \/users and \/share are already binded.  <\/p>\n<hr>\n<p><a><\/a><\/p>\n<h3>How to : Cite the Itrop platform in your publications<\/h3>\n<p>\nPlease just copy the following sentence:<\/p>\n<p><code>\u201cThe authors acknowledge the  ISO 9001 certified IRD i-Trop HPC (South Green Platform) at IRD montpellier for providing HPC resources that have contributed to the research results reported within this paper.<br>    URL: https:\/\/bioinfo.ird.fr\/- http:\/\/www.southgreen.fr<br>\u201d<\/code> <\/p>\n<hr>\n<h3>Links<\/h3>\n<p><a><\/a><\/p>\n<ul>\n<li>Related courses : <a href=\"https:\/\/southgreenplatform.github.io\/trainings\/linux\/\">Linux for Dummies<\/a><\/li>\n<li>Related courses : <a href=\"https:\/\/southgreenplatform.github.io\/trainings\/HPC\/\">HPC<\/a><\/li>\n<li>Tutorials : <a href=\"https:\/\/southgreenplatform.github.io\/trainings\/linux\/linuxTuto\/\">Linux Command-Line Cheat Sheet<\/a><\/li>\n<\/ul>\n<hr>\n<h3>License<\/h3>\n<p><a><\/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><center><img decoding=\"async\" width=\"25%\" src=\"http:\/\/creativecommons.org.nz\/wp-content\/uploads\/2012\/05\/by-nc-sa1.png\">i1148s<br><\/center>\n<\/div>\n<\/code><p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\n<p><code><\/code><\/p>\t\t\t\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Howtos cluster i-Trop Description HowTos for i-Trop Cluster Author Ndomassi TANDO (ndomassi.tando@ird.fr) Creation date 08\/11\/19 Modification date 13\/03\/2026 Summary Preambule:&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":5,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-2955","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>Tutorials - HowTos i-Trop cluster - 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\/en\/tutorials-howtos-i-trop-cluster\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tutorials - HowTos i-Trop cluster - itrop\" \/>\n<meta property=\"og:description\" content=\"Howtos cluster i-Trop Description HowTos for i-Trop Cluster Author Ndomassi TANDO (ndomassi.tando@ird.fr) Creation date 08\/11\/19 Modification date 13\/03\/2026 Summary Preambule:&hellip; Lire la suite\" \/>\n<meta property=\"og:url\" content=\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/\" \/>\n<meta property=\"og:site_name\" content=\"itrop\" \/>\n<meta property=\"article:modified_time\" content=\"2026-03-13T11:20:27+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2023\/09\/schema_cluster_110923-1024x871.png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@ItropBioinfo\" \/>\n<meta name=\"twitter:label1\" content=\"Dur\u00e9e de lecture estim\u00e9e\" \/>\n\t<meta name=\"twitter:data1\" content=\"15 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/\",\"url\":\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/\",\"name\":\"Tutorials - HowTos i-Trop cluster - itrop\",\"isPartOf\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2023\/09\/schema_cluster_110923-1024x871.png\",\"datePublished\":\"2021-03-05T23:01:31+00:00\",\"dateModified\":\"2026-03-13T11:20:27+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/#breadcrumb\"},\"inLanguage\":\"fr-FR\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"fr-FR\",\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/#primaryimage\",\"url\":\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2023\/09\/schema_cluster_110923.png\",\"contentUrl\":\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2023\/09\/schema_cluster_110923.png\",\"width\":1221,\"height\":1039},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Accueil\",\"item\":\"https:\/\/bioinfo.ird.fr\/index.php\/en\/front-page-2\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Tutorials &#8211; HowTos i-Trop cluster\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/bioinfo.ird.fr\/#website\",\"url\":\"https:\/\/bioinfo.ird.fr\/\",\"name\":\"itrop\",\"description\":\"\",\"publisher\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/bioinfo.ird.fr\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"fr-FR\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/bioinfo.ird.fr\/#organization\",\"name\":\"i-Trop\",\"url\":\"https:\/\/bioinfo.ird.fr\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"fr-FR\",\"@id\":\"https:\/\/bioinfo.ird.fr\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2021\/10\/i-tropTwt5.png\",\"contentUrl\":\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2021\/10\/i-tropTwt5.png\",\"width\":1356,\"height\":1356,\"caption\":\"i-Trop\"},\"image\":{\"@id\":\"https:\/\/bioinfo.ird.fr\/#\/schema\/logo\/image\/\"},\"sameAs\":[\"https:\/\/x.com\/ItropBioinfo\"]}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Tutorials - HowTos i-Trop cluster - itrop","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/","og_locale":"fr_FR","og_type":"article","og_title":"Tutorials - HowTos i-Trop cluster - itrop","og_description":"Howtos cluster i-Trop Description HowTos for i-Trop Cluster Author Ndomassi TANDO (ndomassi.tando@ird.fr) Creation date 08\/11\/19 Modification date 13\/03\/2026 Summary Preambule:&hellip; Lire la suite","og_url":"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/","og_site_name":"itrop","article_modified_time":"2026-03-13T11:20:27+00:00","og_image":[{"url":"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2023\/09\/schema_cluster_110923-1024x871.png","type":"","width":"","height":""}],"twitter_card":"summary_large_image","twitter_site":"@ItropBioinfo","twitter_misc":{"Dur\u00e9e de lecture estim\u00e9e":"15 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/","url":"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/","name":"Tutorials - HowTos i-Trop cluster - itrop","isPartOf":{"@id":"https:\/\/bioinfo.ird.fr\/#website"},"primaryImageOfPage":{"@id":"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/#primaryimage"},"image":{"@id":"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/#primaryimage"},"thumbnailUrl":"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2023\/09\/schema_cluster_110923-1024x871.png","datePublished":"2021-03-05T23:01:31+00:00","dateModified":"2026-03-13T11:20:27+00:00","breadcrumb":{"@id":"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/#breadcrumb"},"inLanguage":"fr-FR","potentialAction":[{"@type":"ReadAction","target":["https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/"]}]},{"@type":"ImageObject","inLanguage":"fr-FR","@id":"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/#primaryimage","url":"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2023\/09\/schema_cluster_110923.png","contentUrl":"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2023\/09\/schema_cluster_110923.png","width":1221,"height":1039},{"@type":"BreadcrumbList","@id":"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Accueil","item":"https:\/\/bioinfo.ird.fr\/index.php\/en\/front-page-2\/"},{"@type":"ListItem","position":2,"name":"Tutorials &#8211; HowTos i-Trop cluster"}]},{"@type":"WebSite","@id":"https:\/\/bioinfo.ird.fr\/#website","url":"https:\/\/bioinfo.ird.fr\/","name":"itrop","description":"","publisher":{"@id":"https:\/\/bioinfo.ird.fr\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/bioinfo.ird.fr\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"fr-FR"},{"@type":"Organization","@id":"https:\/\/bioinfo.ird.fr\/#organization","name":"i-Trop","url":"https:\/\/bioinfo.ird.fr\/","logo":{"@type":"ImageObject","inLanguage":"fr-FR","@id":"https:\/\/bioinfo.ird.fr\/#\/schema\/logo\/image\/","url":"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2021\/10\/i-tropTwt5.png","contentUrl":"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2021\/10\/i-tropTwt5.png","width":1356,"height":1356,"caption":"i-Trop"},"image":{"@id":"https:\/\/bioinfo.ird.fr\/#\/schema\/logo\/image\/"},"sameAs":["https:\/\/x.com\/ItropBioinfo"]}]}},"_links":{"self":[{"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/pages\/2955","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/comments?post=2955"}],"version-history":[{"count":276,"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/pages\/2955\/revisions"}],"predecessor-version":[{"id":4846,"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/pages\/2955\/revisions\/4846"}],"wp:attachment":[{"href":"https:\/\/bioinfo.ird.fr\/index.php\/wp-json\/wp\/v2\/media?parent=2955"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}