{"id":632,"date":"2016-05-31T14:19:33","date_gmt":"2016-05-31T12:19:33","guid":{"rendered":"http:\/\/vm-bioinfo-wp.toulouse.inra.fr\/?page_id=632"},"modified":"2020-07-29T10:42:51","modified_gmt":"2020-07-29T08:42:51","slug":"job_submission_faq","status":"publish","type":"page","link":"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/faq\/job_submission_faq\/","title":{"rendered":"Job submission"},"content":{"rendered":"<h6>SLURM Cluster<\/h6>\n<p>&nbsp;<\/p>\n\t\t\t\t\t\t<style>\r\n\t\t\t\t\t#wpsm_accordion_2591 .wpsm_panel-heading{\r\npadding:0px !important;\r\n}\r\n#wpsm_accordion_2591 .wpsm_panel-title {\r\nmargin:0px !important; \r\ntext-transform:none !important;\r\nline-height: 1 !important;\r\n}\r\n#wpsm_accordion_2591 .wpsm_panel-title a{\r\ntext-decoration:none;\r\ncolor:#000000 !important;\r\nfont-size:14px !important;\r\ndisplay:block;\r\npadding:0px;\r\nfont-family: Sans !important;\r\npadding-top: 10px;\r\npadding-bottom: 10px;\r\nborder-bottom:1px solid  #ddd !important;\r\n\r\n}\r\n#wpsm_accordion_2591 .wpsm_panel-title a:hover,#wpsm_accordion_2591 .wpsm_panel-title a:visited, #wpsm_accordion_2591 .wpsm_panel-title a:focus {\r\n\tcolor:#000000 !important;\r\n}\r\n#wpsm_accordion_2591 .acc-a{\r\n\tcolor: #000000 !important;\r\n\tbackground-color:#ffffff !important;\r\n\tborder-color: #ddd;\r\n}\r\n#wpsm_accordion_2591 .wpsm_panel-default > .wpsm_panel-heading{\r\n\tcolor: #000000 !important;\r\n\tbackground-color: #ffffff !important;\r\n\tborder-color: #ffffff !important;\r\n\tborder-top-left-radius: 0px;\r\n\tborder-top-right-radius: 0px;\r\n}\r\n#wpsm_accordion_2591 .wpsm_panel-default {\r\n\t\r\n\tborder:1px solid transparent !important;\r\n\r\n\t}\r\n#wpsm_accordion_2591 {\r\n\tmargin-bottom: 20px;\r\n\toverflow: hidden;\r\n\tfloat: left;\r\n\twidth: 100%;\r\n\tdisplay: block;\r\n}\r\n#wpsm_accordion_2591 .ac_title_class{\r\n\tdisplay: inline-block;\r\n    padding-top: 5px;\r\n    padding-bottom: 5px;\r\n    padding-left: 13px;\r\n    padding-right: 10px;\r\n    border: 0px solid #ddd;\r\n\tfont-size:14px !important;\r\nfont-family: Sans !important;\r\n\t\r\n\r\n}\r\n#wpsm_accordion_2591  .wpsm_panel {\r\n\toverflow:hidden;\r\n\t-webkit-box-shadow: 0 0px 0px rgba(0, 0, 0, .05);\r\n\tbox-shadow: 0 0px 0px rgba(0, 0, 0, .05);\r\n\t\r\n\t\tborder-radius: 4px;\r\n\t}\r\n#wpsm_accordion_2591  .wpsm_panel + .wpsm_panel {\r\n\t\tmargin-top: 5px;\r\n\t}\r\n#wpsm_accordion_2591  .wpsm_panel-body{\r\nbackground-color:#ffffff !important;\r\ncolor:#000000 !important;\r\nborder-top-color: #ffffff !important;\r\nfont-size:12px !important;\r\nfont-family: Sans !important;\r\noverflow: hidden;\r\n\r\nborder: 0px solid #ddd !important;\r\n\r\nborder-top:0px !important;\r\npadding-left: 60px;\r\n}\r\n\r\n#wpsm_accordion_2591 .ac_open_cl_icon{\r\n\tbackground-color:#ffffff;\r\n\tcolor: #ba195c;\r\n\t\r\n     padding-top: 5px; \r\n     padding-bottom: 5px; \r\n\t margin-left:10px;\r\n    line-height: 1.0;\r\n    font-size:14px !important;\r\ntext-align: center !important;\r\n     width: 32px !important;\r\n    display: inline-block;\r\n\t\r\n\t\r\n}\r\n#wpsm_accordion_2591 .ac_open_cl_number{\r\n width: 25px !important;\r\n    display: inline-block;\r\n\t margin-left:10px;\r\n\t text-align: center !important;\r\n\t font-size:14px !important;\r\n\r\n}\r\n\r\n\t\t\t\r\n\t\t\t\t\r\n.entry h4 span {\r\n\r\ncolor: #ba195c;\r\n\r\n}\t\t\t\t\t\r\n\t\t\t<\/style>\r\n\t\t\t<div class=\"wpsm_panel-group\" id=\"wpsm_accordion_2591\" >\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse1\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tTraining slides\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse1\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>Waiting for training\u00a0slides, please use these documents\u00a0 :<\/p>\r\n<ul>\r\n\t<li><a href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/wp-content\/uploads\/Bull_slurm_for_users.pdf\">Slurm_for_users<\/a><\/li>\r\n\t<li><a href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/wp-content\/uploads\/Seminar_cluster_SLURM_15_03_18.pdf\">Genologin\/Slurm cluster presentation (15\/03\/2018)<\/a><\/li>\r\n<\/ul>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse2\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tWhich scheduler is used ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse2\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\tSLURM workload Manager :\r\n<a href=\"https:\/\/slurm.schedmd.com\">https:\/\/slurm.schedmd.com<\/a>\r\n\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse3\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tWhich commands can I use to submit my job ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse3\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p><strong><u>BATCH<\/u><\/strong><\/p>\r\n<p><strong>sbatch<\/strong>: submit a batch job to slurm (default workq partition).<br \/>\r\n<strong>sarray<\/strong>: submit a batch job-array to slurm.<\/p>\r\n<p><strong><u>INTERACTIVE<\/u><\/strong><\/p>\r\n<p><strong>srun --pty bash <\/strong>: submit an interactive session with a compute node (default workq partition).<\/p>\r\n<p><strong><u>INTERACTIVE with X11 forwarding<\/u><\/strong><\/p>\r\n<p>For the first time, create your public key as below (onto genologin server)<\/p>\r\n<p><code>$ ssh-keygen (and \"Enter\" for all question)<\/code><\/p>\r\n<p><code>$cat .ssh\/id_rsa.pub >> .ssh\/authorized_keys<\/code><\/p>\r\n<p><strong>srun --x11 --pty bash <\/strong>: submit an interactive session with X11 forwarding (default workq partition).<\/p>\r\n<p><strong><u>INTERACTIVE with graphical mode<\/u><\/strong><\/p>\r\n<p><strong>runVisuSession.sh<\/strong>: submit a TurboVNC \/ VirtualGL session with the graphical node (interq partition). Just for graphics jobs.<\/p>\r\n<p><strong><u>INTERACTIVE inside a batch job<\/u><\/strong><\/p>\r\n<p><strong>srun --pty --jobid jobid bash<\/strong>: convenient to follow a batch job (connection on the node where the batch is running<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse4\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tBasic parameters for srun command\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse4\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p><code>srun<\/code> <br \/>\r\n <code>-J <em>job name<\/em><\/code><em> \u00a0<\/em>-> for change the jobname<br \/>\r\n <code>-p <em>partition<\/em><\/code>\u00a0 -> which partition(~ queue) to use<br \/>\r\n <code>--time=<\/code><em><code>HH:MM:SS<\/code> -> <\/em>max time of the job<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse5\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tIO Redirection\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse5\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p><code>-o (--output) = output_filename<\/code> : to specify the stdout redirection. If -e (--error) is not specified both stdout ans stderr will be directed to the file name specified.<br \/>\r\n <code>-e (--error) = error_filename<\/code> : if specified, stderr will be redirected to different location as stdout<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse6\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tDefault job resources\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse6\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\tWithout any parameter, on any partition, each job is limited to <strong>1 cpu, 2G ram<\/strong> (cpus-per-task=1, mem=2G)\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse7\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow can I submit a simple job on the cluster ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse7\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>1 - First <strong>write a script<\/strong> (ex: myscript.sh) with the command line as following:<br \/>\r\n <br \/>\r\n <code>\r\n#!\/bin\/bash<br \/>\r\n#SBATCH -J test<br \/>\r\n#SBATCH -o output.out<br \/>\r\n#SBATCH -e error.out<br \/>\r\n#SBATCH -t 01:00:00<br \/>\r\n#SBATCH --mem=8G<br \/>\r\n#SBATCH --mail-type=BEGIN,END,FAIL<\/code> (the email address is automatically LDAP account's one)<code><br \/>\r\n#Purge any previous modules<br \/>\r\nmodule purge<br \/>\r\n<br \/>\r\n#Load the application<br \/>\r\nmodule load bioinfo\/ncbi-blast-2.2.29+<br \/>\r\n<br \/>\r\n# My command lines I want to run on the cluster<br \/>\r\nblastall ...<\/code><\/p>\r\n<p>2 - To submit the job, use the<strong> sbatch<\/strong> command line as following:<br \/>\r\n <br \/>\r\n <code>sbatch myscript.sh<\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse8\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow to book more memory than default (2G) ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse8\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>To change memory reservation, <strong>add this option<\/strong> to the submission command (sbatch, srun, sarray):<\/p>\r\n<p><code>--mem=XG<\/code> (default value is 2G)<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse9\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow can I book more than 1 cpu ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse9\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>With default parameters, each job is limited to 1 cpu.<br \/>\r\n To book more, use the following options:<\/p>\r\n<p># Book n cpus on the <strong>same node<\/strong> (up to 64)<br \/>\r\n <code>-c ncpus (--cpus-per-task=ncpus)<\/code><\/p>\r\n<p># Book n cpus on <strong>any nodes<\/strong> in case of MPI jobs<br \/>\r\n <code>-N nnodes (--nodes=nnodes)<\/code><\/p>\r\n <code>-n ntasks (--ntasks=ntasks)<\/code><\/p>\r\n <code>--ntasks_per_node<\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse10\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tWhich are the available queues\/partitions ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse10\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>Each job is submitted to a specific partition (the default one is the workq).<br \/>\r\nEach partition has a different priority considering the maximum time of execution allowed.<\/p>\r\n<p>The partition is configurable with -p option.<\/p>\r\n<p>\n<table id=\"tablepress-7\" class=\"tablepress tablepress-id-7\">\n<thead>\n<tr class=\"row-1 odd\">\n\t<th class=\"column-1\">Queue<\/th><th class=\"column-2\">Access<\/th><th class=\"column-3\">Priority<\/th><th class=\"column-4\">Max time<\/th><th class=\"column-5\">Max slots<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr class=\"row-2 even\">\n\t<td class=\"column-1\">workq<\/td><td class=\"column-2\">everyone<\/td><td class=\"column-3\">100<\/td><td class=\"column-4\">4 days (96h)<\/td><td class=\"column-5\">3072<\/td>\n<\/tr>\n<tr class=\"row-3 odd\">\n\t<td class=\"column-1\">unlimitq<\/td><td class=\"column-2\">everyone<\/td><td class=\"column-3\">1<\/td><td class=\"column-4\">180 days<\/td><td class=\"column-5\">500<\/td>\n<\/tr>\n<tr class=\"row-4 even\">\n\t<td class=\"column-1\">interq (runVisuSession.sh)<\/td><td class=\"column-2\"><a href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/ask-for\/resources-request\/\">on demand<\/a><\/td><td class=\"column-3\"><\/td><td class=\"column-4\">2 days (48h)<\/td><td class=\"column-5\">32<\/td>\n<\/tr>\n<tr class=\"row-5 odd\">\n\t<td class=\"column-1\">smpq<\/td><td class=\"column-2\"><a href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/ask-for\/resources-request\/\">on demand<\/a><\/td><td class=\"column-3\"><\/td><td class=\"column-4\">180 days<\/td><td class=\"column-5\">96<\/td>\n<\/tr>\n<tr class=\"row-6 even\">\n\t<td class=\"column-1\">wflowq<\/td><td class=\"column-2\">specific software<\/td><td class=\"column-3\"><\/td><td class=\"column-4\">180 days<\/td><td class=\"column-5\">3072<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-7 from cache --><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse11\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tSubmit an array of jobs ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse11\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>To submit an array of jobs, use <strong>sarray<\/strong> command (same sbatch options):<\/p>\r\n<p>1. create a file with one command per line (prefix by module load if needed)<\/p>\r\n<p>eg : file star_cmd.txt contains:<\/p>\r\n<p style=\"font-size: 10px;\">module load bioinfo\/STAR-2.6.0c; STAR -genomeDir referenceModel --readFilesIn ech1.R1.fastq ech1.R2.fastq ...<br \/>\r\nmodule load bioinfo\/STAR-2.6.0c; STAR -genomeDir referenceModel --readFilesIn ech2.R1.fastq ech2.R2.fastq ...<br \/>\r\nmodule load bioinfo\/STAR-2.6.0c; STAR -genomeDir referenceModel --readFilesIn ech3.R1.fastq ech3.R2.fastq ...<\/p>\r\n<p>2. launch sarray with sbatch option<\/p>\r\n<p><code>sarray -J jobName -o %j.out -e %j.err -t 01:00:00 --mem=8G --mail-type=BEGIN,END,FAIL star_cmd.txt<\/code><\/p>\r\n<p>For more information about how to create the command file go to <a href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/faq\/bioinfo_tips_faq\/\">FAQ Bioinfo tips<\/a> (\"How to generate an sarray command file with ....\")<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse12\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tWhat is my CPU time quota ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse12\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>To know your quota, use the command: <br \/>\r\n <br \/>\r\n<code>squota_cpu<\/code><\/p>\r\n<p><strong>Academic account quota<\/strong>: 100 000 h\/per calendar year<br \/>\r\n Beyond these 100,000 hours, you will need to submit a science project (by the <a href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/ask-for\/resources-request\/\">resources request form<\/a>) to estimate the real needs of the bioinformatics environment.<\/p>\r\n<p>According to results from this evaluation, but also their geographical and institutional origin, users can then either continue their treatments or be invited to contribute financially to infrastructure, or be redirected to regional or national m\u00e9socentres calculation.<\/p>\r\n<p><strong>Non-academic account quota<\/strong>: \u00a0500 h\/per calendar year for testing the infrastructure.<br \/>\r\n Overtime calculation will be charged (price on request).<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse13\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow can I know my quota usage on \/work directory ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse13\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>Use the following command line (on genologin server):<\/p>\r\n<p><code>mmlsquota -u <em>username <\/em>--block-size G<em><\/em><\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse14\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow can I submit a MPI job ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse14\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p> Example of a full bash script :<br \/>\r\n<code>#!\/bin\/bash<br \/>\r\n#SBATCH -J mpi_job<br \/>\r\n#SBATCH --nodes=2<br \/>\r\n#SBATCH --tasks-per-node=6<br \/>\r\n#SBATCH --time=00:10:00<br \/>\r\ncd $SLURM_SUBMIT_DIR<br \/>\r\nmodule purge<br \/>\r\nmodule load compiler\/intel-2018.0.128 mpi\/openmpi-1.8.8-intel2018.0.128<br \/>\r\nmpirun -n $SLURM_NTASKS --map-by ppr:$SLURM_NTASKS_PER_NODE:node .\/hello_world<\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse15\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow can I monitor a running job ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse15\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>To do so, you can use the <strong>squeue<\/strong> command, following are some usefull options:<\/p>\r\n<p><code>squeue -u <em>username<\/em><\/code> : list only the specified user's jobs.<br \/>\r\n <code>squeue -j <em>job_id<\/em><\/code> : provide several informations on the specified job.<\/p>\r\n<p>(see <code>squeue --help<\/code> or <code>man squeue<\/code> for more options)<\/p>\r\n<p>For more detail:<\/p>\r\n<p><code>scontrol show job\u00a0<em>job_id<\/em><\/code><\/p>\r\n<p>You can also have access to a graphical user interface which provides the same informations.<br \/>\r\n This interface is accessible with the <strong>sview<\/strong> command.<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse16\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow to use srun to check running jobs?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse16\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>The srun command can be used to check in on a running job in the cluster.<\/p>\r\n<p><code>srun --pty --jobid= bash<\/code> : starts a shell, where you can run any command, on the first allocated node in a specific job.<\/p>\r\n<p>To check processor and memory usage quickly, you can run top directly:<\/p>\r\n<p><code>srun --pty --jobid= top -u login<\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse17\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow can I retrieve informations on a finished job ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse17\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>To do so, use the <strong>sacct<\/strong> command line as following:<br \/>\r\n <br \/>\r\n <code>sacct -j <em>job_id<\/em><\/code><\/p>\r\n<p>(see <code>sacct --help<\/code> or <code>man sacct<\/code> for more options)<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse18\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow can I kill my job ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse18\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>To do so, you can use the<strong> scancel<\/strong> command, following are some usefull options:<\/p>\r\n<p># Kill the specified job<br \/>\r\n <code>scancel <em>job_id<\/em><\/code><\/p>\r\n<p><br \/>\r\n # Kill all job launched by the specified user<br \/>\r\n <code>scancel -u <em>username<\/em><\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse19\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow to specify a processor architecture ?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse19\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>Add the following flag to address the ivy or broadwell processor architecture : <\/p>\r\n<p>-C,<br\/> --constraint=ivy <br\/>(old compute nodes 001 to 068)<\/p>\r\n<p>-C, <br\/>--constraint=broadwell <br\/>(new computes nodes 101 to 148)<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse20\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow to use visualization node?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse20\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p><strong>Prerequisites<\/strong><\/p>\r\n<p>-> Request access to the visualization node <a href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/ask-for\/resources-request\/\">here<\/a>.<br \/>\r\n-> The turboVnc software must be installed on your workstation. <span lang=\"en\" tabindex=\"0\">You do not need the entire package, only the client part (vncviewer).<\/span> You can download it <a href=\"https:\/\/sourceforge.net\/projects\/turbovnc\/files\/\" target=\"_blank\" rel=\"noopener\">here<\/a>.<\/p>\r\n<p><strong>How to connect?<\/strong><\/p>\r\n<p>Connect on <span lang=\"en\" tabindex=\"0\">front-end server<\/span>:<\/p>\r\n<p><code>ssh <em>username<\/em>@genologin.toulouse.inra.fr<\/code><\/p>\r\n<p>Then, on <span lang=\"en\" tabindex=\"0\">front-end server<\/span>:<\/p>\r\n<p><code>$ runVisuSession.sh<\/code><\/p>\r\n<p><code>Desktop 'TurboVNC' started on display genoview:1<\/code><\/p>\r\n<p><code>Starting applications specified in \/tools\/bin\/node\/xstartup.mate<\/code><br \/>\r\n<code>Log file is \/home\/\/.vnc\/genoview:1.log<\/code><\/p>\r\n<p><code><\/code><code>=================================================================<\/code><br \/>\r\n<code>+ VNC Session name: TurboVNC<\/code><br \/>\r\n<code>+ Your TurboVNC session is available on genoview.toulouse.inra.fr <\/code><br \/>\r\n<code>+<\/code><br \/>\r\n<code>+ CAUTION: If you close this interactive SLURM job,<\/code><br \/>\r\n<code>+ your VNC session will be destroyed !<\/code><br \/>\r\n<code>+<\/code><br \/>\r\n<code>+ Please use your LDAP login and password to authenticate<\/code><br \/>\r\n<code>+<\/code><br \/>\r\n<code>+ Connection summary<\/code><br \/>\r\n<code>+ ------------------<\/code><br \/>\r\n<code>+ VNC_URL : genoview.toulouse.inra.fr:1<\/code><br \/>\r\n<code>+ HTTP_URL : http:\/\/genoview.toulouse.inra.fr:5801<\/code><br \/>\r\n<code>+ Authentication : LDAP<\/code><br \/>\r\n<code>=================================================================<\/code><\/p>\r\n<p><strong>Access the visualization node<\/strong><\/p>\r\n<p>\u00a0Then, you can acces to the visualization node using:<\/p>\r\n<p>- your web browser with the HTTP_URL: http:\/\/genoview.toulouse.inra.fr:5801<br \/>\r\n- a vnc client with VNC_URL : genoview.toulouse.inra.fr:1<\/p>\r\n<p>(on Windows, run vncviewer-java.bat)<\/p>\r\n<p><strong>Ask for more ressources (cpus, mem)<\/strong><\/p>\r\n<p>On <span lang=\"en\" tabindex=\"0\">front-end server<\/span>, replace the command \"runVisuSession.sh\" by the following command (example for cpus=4 and mem=16G):<\/p>\r\n<p><code>$ srun --partition=interq -c 4 --mem=16gb --job-name=TurboVNC \/tools\/bin\/node\/runVisuSession_node.sh 1024x768 mate<\/code><\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse21\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow to set my cpu and memory pre-allocation?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse21\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>On a test job in COMPLETED state, check the result of the seff command:<\/p>\r\n<p><code>seff <em>jobid<\/em><\/code><\/p>\r\n<p>and adjust time with -t , memory with --mem et cpu with --cpus-per-task options.<\/p>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"collapsed\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2591 \" href=\"#ac_2591_collapse22\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tHow can I get my jobs processed faster on the cluster?\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2591_collapse22\" class=\"wpsm_panel-collapse collapse_2591 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t<p>The smaller a job, the faster it is processed. Set your different pre-allocations (time, memory and cpu) as closely as possible to your needs.<\/p>\r\n<p>On a test job in COMPLETED state, check the result of the seff command:<\/p>\r\n<p><code>seff <em>jobid<\/em><\/code><\/p>\r\n<p>and adjust time with -t , memory with --mem et cpu with --cpus-per-task options.<\/p>\r\n<div id=\"s3gt_translate_tooltip_mini\" class=\"s3gt_translate_tooltip_mini_box\" style=\"background: initial !important; border: initial !important; border-radius: initial !important; border-spacing: initial !important; border-collapse: initial !important; direction: ltr !important; flex-direction: initial !important; font-weight: initial !important; height: initial !important; letter-spacing: initial !important; min-width: initial !important; max-width: initial !important; min-height: initial !important; max-height: initial !important; margin: auto !important; outline: initial !important; padding: initial !important; position: absolute; table-layout: initial !important; text-align: initial !important; text-shadow: initial !important; width: initial !important; word-break: initial !important; word-spacing: initial !important; overflow-wrap: initial !important; box-sizing: initial !important; display: initial !important; color: inherit !important; font-size: 13px !important; font-family: X-LocaleSpecific, sans-serif, Tahoma, Helvetica !important; line-height: 13px !important; vertical-align: top !important; white-space: inherit !important; left: 95px; top: 136px; opacity: 0.5;\">\r\n<div id=\"s3gt_translate_tooltip_mini_logo\" class=\"s3gt_translate_tooltip_mini\" title=\"Traduire le texte s\u00e9lectionn\u00e9\">\u00a0<\/div>\r\n<div id=\"s3gt_translate_tooltip_mini_sound\" class=\"s3gt_translate_tooltip_mini\" title=\"Lecture\">\u00a0<\/div>\r\n<div id=\"s3gt_translate_tooltip_mini_copy\" class=\"s3gt_translate_tooltip_mini\" title=\"Copier le texte dans le presse-papiers\">\u00a0<\/div>\r\n<\/div>\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End -->\r\n\t\t\t\t\r\n\t\t\t\t\t\t<\/div>\r\n\t\t\t\t<script>\r\n\tjQuery(document).ready(function() {\r\n\t\t\r\n\t\t\tjQuery('.collapse_2591').on('shown.bs.collapse', function(){jQuery(this).parent().find(\".fa-plus\").removeClass(\"fa-minus\").addClass(\"fa-minus\"); jQuery(this).parent().find(\".wpsm_panel-heading\").addClass(\"acc-a\"); }).on('hidden.bs.collapse', function(){jQuery(this).parent().find(\".fa-minus\").removeClass(\"fa-minus\").addClass(\"fa-plus\"); jQuery(this).parent().find(\".wpsm_panel-heading\").removeClass(\"acc-a\");});\r\n\t\t\r\n\t\t});\r\n\t<\/script>\r\n\t\t\n&nbsp;<\/p>\n<h6>SGE to SLURM<\/h6>\n\t\t\t\t\t\t<style>\r\n\t\t\t\t\t#wpsm_accordion_2780 .wpsm_panel-heading{\r\npadding:0px !important;\r\n}\r\n#wpsm_accordion_2780 .wpsm_panel-title {\r\nmargin:0px !important; \r\ntext-transform:none !important;\r\nline-height: 1 !important;\r\n}\r\n#wpsm_accordion_2780 .wpsm_panel-title a{\r\ntext-decoration:none;\r\ncolor:#000000 !important;\r\nfont-size:14px !important;\r\ndisplay:block;\r\npadding:0px;\r\nfont-family: Sans !important;\r\npadding-top: 10px;\r\npadding-bottom: 10px;\r\nborder-bottom:1px solid  #ddd !important;\r\n\r\n}\r\n#wpsm_accordion_2780 .wpsm_panel-title a:hover,#wpsm_accordion_2780 .wpsm_panel-title a:visited, #wpsm_accordion_2780 .wpsm_panel-title a:focus {\r\n\tcolor:#000000 !important;\r\n}\r\n#wpsm_accordion_2780 .acc-a{\r\n\tcolor: #000000 !important;\r\n\tbackground-color:#ffffff !important;\r\n\tborder-color: #ddd;\r\n}\r\n#wpsm_accordion_2780 .wpsm_panel-default > .wpsm_panel-heading{\r\n\tcolor: #000000 !important;\r\n\tbackground-color: #ffffff !important;\r\n\tborder-color: #ffffff !important;\r\n\tborder-top-left-radius: 0px;\r\n\tborder-top-right-radius: 0px;\r\n}\r\n#wpsm_accordion_2780 .wpsm_panel-default {\r\n\t\r\n\tborder:1px solid transparent !important;\r\n\r\n\t}\r\n#wpsm_accordion_2780 {\r\n\tmargin-bottom: 20px;\r\n\toverflow: hidden;\r\n\tfloat: left;\r\n\twidth: 100%;\r\n\tdisplay: block;\r\n}\r\n#wpsm_accordion_2780 .ac_title_class{\r\n\tdisplay: inline-block;\r\n    padding-top: 5px;\r\n    padding-bottom: 5px;\r\n    padding-left: 13px;\r\n    padding-right: 10px;\r\n    border: 0px solid #ddd;\r\n\tfont-size:14px !important;\r\nfont-family: Sans !important;\r\n\t\r\n\r\n}\r\n#wpsm_accordion_2780  .wpsm_panel {\r\n\toverflow:hidden;\r\n\t-webkit-box-shadow: 0 0px 0px rgba(0, 0, 0, .05);\r\n\tbox-shadow: 0 0px 0px rgba(0, 0, 0, .05);\r\n\t\r\n\t\tborder-radius: 4px;\r\n\t}\r\n#wpsm_accordion_2780  .wpsm_panel + .wpsm_panel {\r\n\t\tmargin-top: 5px;\r\n\t}\r\n#wpsm_accordion_2780  .wpsm_panel-body{\r\nbackground-color:#ffffff !important;\r\ncolor:#000000 !important;\r\nborder-top-color: #ffffff !important;\r\nfont-size:12px !important;\r\nfont-family: Sans !important;\r\noverflow: hidden;\r\n\r\nborder: 0px solid #ddd !important;\r\n\r\nborder-top:0px !important;\r\npadding-left: 60px;\r\n}\r\n\r\n#wpsm_accordion_2780 .ac_open_cl_icon{\r\n\tbackground-color:#ffffff;\r\n\tcolor: #ba195c;\r\n\t\r\n     padding-top: 5px; \r\n     padding-bottom: 5px; \r\n\t margin-left:10px;\r\n    line-height: 1.0;\r\n    font-size:14px !important;\r\ntext-align: center !important;\r\n     width: 32px !important;\r\n    display: inline-block;\r\n\t\r\n\t\r\n}\r\n#wpsm_accordion_2780 .ac_open_cl_number{\r\n width: 25px !important;\r\n    display: inline-block;\r\n\t margin-left:10px;\r\n\t text-align: center !important;\r\n\t font-size:14px !important;\r\n\r\n}\r\n\r\n\t\t\t\r\n\t\t\t\t\r\n\t\t\t\t\t\r\n\t\t\t<\/style>\r\n\t\t\t<div class=\"wpsm_panel-group\" id=\"wpsm_accordion_2780\" >\r\n\t\t\t\t\r\n\t\t\t\t\t\t\r\n\t\t\t\t  <!-- Inner panel Start -->\r\n\t\t\t\t  <div class=\"wpsm_panel wpsm_panel-default\">\r\n\t\t\t\t\t<div class=\"wpsm_panel-heading\" role=\"tab\" >\r\n\t\t\t\t\t  <h4 class=\"wpsm_panel-title\">\r\n\t\t\t\t\t\t<a  class=\"\"  data-toggle=\"collapse\" data-parent=\"#wpsm_accordion_2780 \" href=\"#ac_2780_collapse1\"  >\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span  class=\"ac_open_cl_icon fa fa-plus\"><\/span>\r\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"ac_title_class\">\r\n\t\t\t\t\t\t\t\tUseful commands\t\t\t\t\t\t\t<\/span>\r\n\t\t\t\t\t\t<\/a>\r\n\t\t\t\t\t  <\/h4>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t\t<div id=\"ac_2780_collapse1\" class=\"wpsm_panel-collapse collapse_2780 collapse \"  >\r\n\t\t\t\t\t  <div class=\"wpsm_panel-body\">\r\n\t\t\t\t\t\t\n<table id=\"tablepress-13\" class=\"tablepress tablepress-id-13\">\n<thead>\n<tr class=\"row-1 odd\">\n\t<th class=\"column-1\">SGE<\/th><th class=\"column-2\">SLURM<\/th><th class=\"column-3\">Comments<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"row-hover\">\n<tr class=\"row-2 even\">\n\t<td class=\"column-1\">qsub script.sh<\/td><td class=\"column-2\">sbatch script.sh<\/td><td class=\"column-3\">sbatch is only for script<\/td>\n<\/tr>\n<tr class=\"row-3 odd\">\n\t<td class=\"column-1\">qsub -l mem=XG -l h_vmem=YG -b y <command><\/td><td class=\"column-2\">srun --mem=YG<\/td><td class=\"column-3\">No h_vmem parameters with Slurm. <\/td>\n<\/tr>\n<tr class=\"row-4 even\">\n\t<td class=\"column-1\">qsub -m bea<\/td><td class=\"column-2\">sbatch\/srun --mail-type=BEGIN,END,FAIL<\/td><td class=\"column-3\">Notify user by email when certain event types occur. <\/td>\n<\/tr>\n<tr class=\"row-5 odd\">\n\t<td class=\"column-1\">qsub -b y \"command\"<\/td><td class=\"column-2\">sbatch --wrap=\"command\"<\/td><td class=\"column-3\">submit command line<\/td>\n<\/tr>\n<tr class=\"row-6 even\">\n\t<td class=\"column-1\">qsub -sync  y \"command\"<\/td><td class=\"column-2\">srun \"command\"<\/td><td class=\"column-3\">submit a job in real time<\/td>\n<\/tr>\n<tr class=\"row-7 odd\">\n\t<td class=\"column-1\">qsub -pe parallel_smp 8<\/td><td class=\"column-2\">sbatch\/srun -c 8 (--cpus-per-task=8)<\/td><td class=\"column-3\">by default, job are on one node (-N=1 <--> --nodes=nnodes)<\/td>\n<\/tr>\n<tr class=\"row-8 even\">\n\t<td class=\"column-1\">qsub -pe parallel_fill n or<br \/>\nqsub -pe parallel_rr n<\/td><td class=\"column-2\">sbatch\/srun<br \/>\n<br \/>\n -N=nnodes (--nodes=nnodes)<br \/>\n<br \/>\n-n=ntasks (--ntasks=ntasks)<br \/>\n-c=ncpus (--cpus-per-task)ncpus<\/td><td class=\"column-3\">No parallel environnement with slurm<\/td>\n<\/tr>\n<tr class=\"row-9 odd\">\n\t<td class=\"column-1\">qstat -u login<\/td><td class=\"column-2\">squeue -u login<\/td><td class=\"column-3\">See all your submitted jobs<\/td>\n<\/tr>\n<tr class=\"row-10 even\">\n\t<td class=\"column-1\">qstat -j job_id<\/td><td class=\"column-2\">scontrol show job job_id<\/td><td class=\"column-3\">Running job details<\/td>\n<\/tr>\n<tr class=\"row-11 odd\">\n\t<td class=\"column-1\">qacct -j job_id<\/td><td class=\"column-2\">sacct --unit=G --format JobID,jobname,NTasks,nodelist,CPUTime,ReqMem,MaxVMSize,Elapsed -j job_id<\/td><td class=\"column-3\">Finished job  details. <\/td>\n<\/tr>\n<tr class=\"row-12 even\">\n\t<td class=\"column-1\">qquota_cpu login<\/td><td class=\"column-2\">squota_cpu<\/td><td class=\"column-3\">See your CPU time quota<\/td>\n<\/tr>\n<tr class=\"row-13 odd\">\n\t<td class=\"column-1\">qdel -j job_id<\/td><td class=\"column-2\">scancel job_id<\/td><td class=\"column-3\">Kill a job<\/td>\n<\/tr>\n<tr class=\"row-14 even\">\n\t<td class=\"column-1\">qrsh<\/td><td class=\"column-2\">srun --pty bash<\/td><td class=\"column-3\">Interactive job<\/td>\n<\/tr>\n<tr class=\"row-15 odd\">\n\t<td class=\"column-1\">qlogin<\/td><td class=\"column-2\">srun --x11 --pty bash<\/td><td class=\"column-3\">Interactive jgraphical ob with X11 forwarding<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-13 from cache -->\t\t\t\t\t  <\/div>\r\n\t\t\t\t\t<\/div>\r\n\t\t\t\t  <\/div>\r\n\t\t\t\t   <!-- Inner panel End 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