{"id":3812,"date":"2022-03-09T09:22:07","date_gmt":"2022-03-09T08:22:07","guid":{"rendered":"https:\/\/bioinfo.ird.fr\/?page_id=3812"},"modified":"2025-10-01T08:59:49","modified_gmt":"2025-10-01T06:59:49","slug":"tutorials-how-to-reserve-cluster-resources","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-how-to-reserve-cluster-resources\/","title":{"rendered":"Tutorials &#8211; How to reserve cluster resources?"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"3812\" class=\"elementor elementor-3812\">\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-25c1e48c elementor-section-boxed elementor-section-height-default elementor-section-height-default exad-glass-effect-no exad-sticky-section-no\" data-id=\"25c1e48c\" 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-2cfdeb76 exad-glass-effect-no exad-sticky-section-no\" data-id=\"2cfdeb76\" 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-8f42de2 exad-sticky-section-no exad-glass-effect-no elementor-widget elementor-widget-text-editor\" data-id=\"8f42de2\" 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>How to reserve cluster resources<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">How to reserve cluster resources<\/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:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/howtos-for-hpc-cluster-itrop\/\">Howtos cluster i-Trop <\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Authors<\/td>\n<td style=\"text-align: left;\">Julie Orjuela (julie.orjuela_AT_irf.fr), Christine Tranchant (christine.tranchant_AT_ird.fr)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Creation Date<\/td>\n<td style=\"text-align: left;\">10\/02\/2022<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">07\/03\/2025<\/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<p><a href=\"#how\">How to resource cluster resources ?<\/a><\/p>\n<ul>\n<li><a href=\"#who\">1. Who is working on the cluster ? <\/a><\/li>\n<li><a href=\"#partition\">2. How to choose a  adapted  partition for my data analysis ?<\/a><\/li>\n<li><a href=\"#node\">3. Which node to use for resources reservation ?<\/a><\/li>\n<li><a href=\"#scratch\">4. How to check \/scratch space ? <\/a><\/li>\n<li><a href=\"#summary\">5. Ressources summary <\/a><\/li>\n<p><a href=\"#license\">License<\/a>\n<\/p>\n<\/ul>\n<hr>\n<p><a><\/a><\/p>\n<h2>How to reserve cluster resources ?<\/h2>\n<p>If you start a new analysis, you wonder what partition, nodes and resources ( number of cpu and RAM memory) you need . <\/p>\n<p>In this tutorial, you can find a survival to know how to reserve cluster resources.<\/p>\n<p><a href=\"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/how_to_reserve_cluster_resources\/?preview=true#summary\">SUPER SUMMARY TABLE !! <\/a><\/p>\n<p><a><\/a><\/p>\n<h3>1. Who is working on the cluster ?<\/h3>\n<p>First, check who is working on the cluster to have an overview of load cluster.<\/p>\n<p>Using <code>squeue<\/code>  command,  you can observe jobs, users, partitions, state of every jobs and which nodes have been allocated to which jobs.  <\/p>\n<p>It can give you an idea of what nodes can  be used or not.<\/p>\n<pre><code>orjuela@master0 ~]$ squeue\n            JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)\n            983603    normal    beast   orjuela  R    5:23:05      1 node20\n            983602    normal    beast   orjuela  R    5:23:11      1 node20\n            983605    normal    beast   orjuela  R    5:16:24      1 node20\n            983604    normal    beast   orjuela  R    5:16:32      1 node20\n            983607    normal    beast   orjuela  R    5:09:15      1 node20\n            983606    normal    beast   orjuela  R    5:09:21      1 node20\n            983596    normal FlyeRave   tando  R    5:57:46      1 node20\n            983594    normal Unicycl_   tando  R    5:11:57      1 node13\n         982965_71    normal range_r0     comte  R      13:36      1 node18\n         982965_70    normal range_r0     comte  R   15:01:36      1 node18\n         982965_69    normal range_r0     comte  R 1-04:32:15      1 node18\n         982965_68    normal range_r0     comte  R 1-07:58:54      1 node19\n         982965_67    normal range_r0     comte  R 1-13:14:58      1 node19\n         982965_66    normal range_r0     comte  R 1-22:58:13      1 node19<\/code><\/pre>\n<p><code>squeue<\/code> command has a lot of options, use <code>-u <\/code>  option to check  allocated resources to a user, in this case \u00ab\u00a0totoro\u00a0\u00bb, is waiting for resources but some jobs are running into node 18 and 19.<\/p>\n<pre><code>         JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)\n    982965_[74-89]    normal range_r0     totoro PD       0:00      1 (AssocGrpCpuLimit)\n         982965_73    normal range_r0     totoro  R    1:28:27      1 node19\n         982965_72    normal range_r0     totoro  R    3:31:51      1 node18\n         982965_71    normal range_r0     totoro  R    5:59:55      1 node18\n         982965_70    normal range_r0     totoro  R   20:47:55      1 node18\n         982965_69    normal range_r0     totoro  R 1-10:18:34      1 node18\n         982965_68    normal range_r0     totoro  R 1-13:45:13      1 node19<\/code><\/pre>\n<p><a><\/a><\/p>\n<h3>2. How to choose a adapted  partition for my data analysis ?<\/h3>\n<p>Depending on the type of jobs (analysis), you can choose between different partitions.<br>The partitions are waiting lists, each with specific priorities and constraints such as the size, the time limit of a job or  the users authorized to use it, etc.<\/p>\n<p>In this table, we list differents partitions availables on our cluster and some details about RAM and CPU number.<\/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<\/th>\n<th style=\"text-align: left;\">Number of Cores<\/th>\n<th style=\"text-align: left;\">Ram on nodes<\/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 (higher priority,interactive jobs)<\/td>\n<td style=\"text-align: left;\">13-16, 18,27<br><\/td>\n<td style=\"text-align: left;\">12 to 24 cores<\/td>\n<td style=\"text-align: left;\">48 to 144GB<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">normal<\/td>\n<td style=\"text-align: left;\">job of maximum 14 days<\/td>\n<td style=\"text-align: left;\">0,1,3,4,5,7,9, 13, 17, 20-24,27,30<\/td>\n<td style=\"text-align: left;\">12 to 48 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;\">14 days< long jobs< 45 days<\/td>\n<td style=\"text-align: left;\">8, 10, 12<\/td>\n<td style=\"text-align: left;\">12 to 24 cores<\/td>\n<td style=\"text-align: left;\">48 to 64GB<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">highmem<\/td>\n<td style=\"text-align: left;\">jobs with more memory needs<\/td>\n<td style=\"text-align: left;\">28,29<br><\/td>\n<td style=\"text-align: left;\">\u00a0112 cores<\/td>\n<td style=\"text-align: left;\">512GB<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">supermem<\/td>\n<td style=\"text-align: left;\">jobs with much more memory needs<\/td>\n<td style=\"text-align: left;\">node25<\/td>\n<td style=\"text-align: left;\">40 cores<\/td>\n<td style=\"text-align: left;\">1 TB<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">gpu<\/td>\n<td style=\"text-align: left;\">Need of 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>Jobs are prioritized and processed using the resources (CPU and RAM) of the nodes that make up these partitions.<\/p>\n<ul>\n<li>\n<p>By default, the chosen partition is the <em>normal<\/em> partition. On this partition, job are killed after 14 days !!<\/p>\n<\/li>\n<li>\n<p>If you need to test a command line or a script, use  the <em>short<\/em> partition.<\/p>\n<\/li>\n<li>\n<p>The <em>highmem<\/em> partition should only be used for jobs requiring at least 35-40GB of memory.<\/p>\n<\/li>\n<li>\n<p>The <em>supermem<\/em> partition has to be used for large assemblies and jobs requiring more than 100GB of memory.<\/p>\n<\/li>\n<li>\n<p>The <em>gpu<\/em> partition is used for nanopore basecalling, polishing\/correction and for machine learning algorithms.<\/p>\n<\/li>\n<\/ul>\n<p>The partition can be chosen following this scheme. But in a general way, check cpu number and memory needed by the tool you want to use.<\/p>\n<p>Time estimation can be tricky, we recommended to seek for advice from the bioinformaticians in your UMR (error\/experience balance !).<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2025\/03\/choix_partitions-1.png\" width=\"60%\"><\/p>\n<p>In below table, we put in some examples, with usecases to help you in the choice of partitions.<\/p>\n<table>\n<thead>\n<tr>\n<th>Rules<\/th>\n<th>Partition<\/th>\n<th>Some tools<\/th>\n<th>Comments<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td>basecalling\/demultiplexing\/correction<\/td>\n<td>gpu<\/td>\n<td>medaka\/guppy\/machine learning tools<\/td>\n<td>request for access to the necessary partition<\/td>\n<\/tr>\n<tr>\n<td>assemblies >100G RAM<\/td>\n<td>supermem<\/td>\n<td>miniasm\/flye\/raven\/smartdenovo<\/td>\n<td>genome target > 400 Mb (riz genome assembly does not consume 100GB)<\/td>\n<\/tr>\n<tr>\n<td>genomicsbd (gatk) > 100G RAM<\/td>\n<td>supermem<\/td>\n<td>GATK genomicsDB<\/td>\n<td>genome target > 400 Mb (>10 samples)<\/td>\n<\/tr>\n<tr>\n<td>assemblies => 35G et < 100G RAM<\/td>\n<td>highmem<\/td>\n<td>miniasm\/flye\/raven\/smartdenovo<\/td>\n<td>100 Mb > genome target > 400 Mb<\/td>\n<\/tr>\n<tr>\n<td>population genomics<\/td>\n<td>long<\/td>\n<td><br><\/td>\n<td><br><\/td>\n<\/tr>\n<tr>\n<td>simulations<\/td>\n<td>long<\/td>\n<td><br><\/td>\n<td><br><\/td>\n<\/tr>\n<tr>\n<td>metagenomics<\/td>\n<td>normal<\/td>\n<td>quiime2\/frogs<\/td>\n<td><br><\/td>\n<\/tr>\n<tr>\n<td>mapping<\/td>\n<td>normal<\/td>\n<td>bwa\/minimap2\/hisat2<\/td>\n<td>need a lot of cores but not a lot of RAM. It is necessary to reserve the number of cores that the tool will use.<\/td>\n<\/tr>\n<tr>\n<td>genotyping<\/td>\n<td>normal<\/td>\n<td>GATK haplotypecaller\/samtools mpileup\/bcftools<\/td>\n<td>need a lot of cores but not a lot of RAM. It is necessary to reserve the number of cores that the tool will use.<\/td>\n<\/tr>\n<tr>\n<td>statistics<\/td>\n<td>normal<\/td>\n<td>R<\/td>\n<td><br><\/td>\n<\/tr>\n<tr>\n<td>scripts debugging and test<\/td>\n<td>short<\/td>\n<td>bash\/python\/R<\/td>\n<td><br><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>In any case, to use a determinate partition, use the <code>-p<\/code> option (or <code>--partition<\/code> parameter) with the <code>srun<\/code> or <code>sbatch<\/code> command line, in which <em>partition<\/em>  can be normal, long, supermem, highmem, highmemplus, or gpu.<\/p>\n<pre><code>sbatch -p partition\nsrun -p partition<\/code><\/pre>\n<p><a><\/a><\/p>\n<h3>3.  Which node to use for resources reservation  ?<\/h3>\n<p>Once you have decided what partition to use, check nodes! .<\/p>\n<p>So, you  now need to know if people is working in the nodes of this partition.<\/p>\n<p>Several options are possible for you.<\/p>\n<p>We suggest to use <code>squeue<\/code> to check allocated resources in this particular node. For example in node8.<\/p>\n<pre><code>[orjuela@master0 ~]$ squeue | grep 'node18' -\n         982965_72    normal range_r0     elie  R    4:19:51      1 node18\n         982965_71    normal range_r0     elie  R    6:47:55      1 node18\n         982965_70    normal range_r0     elie  R   21:35:55      1 node18\n         982965_69    normal range_r0     elie  R 1-11:06:34      1 node18\n         982965_65    normal range_r0     elie  R 2-08:11:31      1 node18\n         982965_60    normal range_r0     elie  R 2-19:40:38      1 node18\n         982965_57    normal range_r0     elie  R 3-17:21:45      1 node18<\/code><\/pre>\n<p><code>squeue<\/code> command with more options can help you to ckeck cpu and mem allocated by user in the chosen node  . <\/p>\n<p>In this example, 4 threads per job has been reserved but RAM memory was not specified.<\/p>\n<pre><code>[orjuela@master0 ~]$ squeue -O jobID,name:40,partition,nodelist,NumCPUs,MinMemory,state,timeused  | grep 'node18' -\n983654              range_r0                                normal              node18              4                   0                   RUNNING             4:23:09             \n983634              range_r0                                normal              node18              4                   0                   RUNNING             6:51:13             \n983587              range_r0                                normal              node18              4                   0                   RUNNING             21:39:13            \n983538              range_r0                                normal              node18              4                   0<\/code><\/pre>\n<p>You can also go inside node and use the <code>htop<\/code> command  to visualize the memory consumed by a process.<\/p>\n<pre><code>ssh node18\nhtop<\/code><\/pre>\n<p><a><\/a><\/p>\n<h3>4. How to check \/scratch space ?<\/h3>\n<p>If you have decided to work in a specific node, you also have  to check \/scratch space. <\/p>\n<p>To check  occupancy percent of \/scratch temporal repertory in each node, use the <code>df -h <\/code> command line.<\/p>\n<p>In the node8 for example the <code>\/scratch<\/code> is ocupated to 1% from 13To.<\/p>\n<pre><code>Sys. de fichiers   Taille Utilis\u00e9 Dispo Uti% Mont\u00e9 sur\n\/dev\/sda2             29G    8,8G   19G  33% \/\ndevtmpfs              24G       0   24G   0% \/dev\ntmpfs                 24G       0   24G   0% \/dev\/shm\ntmpfs                 24G     57M   24G   1% \/run\ntmpfs                 24G       0   24G   0% \/sys\/fs\/cgroup\n\/dev\/sdb1             13T    734M   12T   1% \/scratch\n\/dev\/sda1            477M    145M  308M  32% \/boot\n\/dev\/sda5            257G     78M  244G   1% \/tmp\nnas3:\/data3           66T     61T  4,9T  93% \/data3\nnas2:\/data            44T     41T  3,3T  93% \/data\nnas:\/home            5,9T    5,4T  546G  91% \/home\nnas:\/teams           5,0T    3,2T  1,9T  63% \/teams\nmaster0:\/usr\/local   2,5T    1,7T  824G  68% \/usr\/local\nmaster0:\/opt          50G     21G   30G  42% \/opt\ntmpfs                4,8G       0  4,8G   0% \/run\/user\/0\nnas:\/data2            28T     25T  3,1T  89% \/data2\ntmpfs                4,8G       0  4,8G   0% \/run\/user\/35449<\/code><\/pre>\n<p><em>NOTE<\/em> :  In some nodes, check <code>\/tmp<\/code> line percentage instead of <code>\/scratch<\/code>.<\/p>\n<p><a><\/a><\/p>\n<h3>5. Resources summary<\/h3>\n<p>You can find here a summary of   nodes resources. You can find the node composition of each partition, the number of CPU  available and the total RAM memory total of the node and its memory\/cpu.<\/p>\n<p><code>srun<\/code> or <code>sbatch<\/code> arguments can be set easily with the <code>--mem<\/code> to reserve the total memory for a job.<\/p>\n<p>For the <code>--mem-per-cpu<\/code> argument, you need to know how many Gb\/cpu to use. <\/p>\n<p>With this table, you know it all now !!<\/p>\n<p><strong>NOTE<\/strong>: New nodes specifications (in blue) can be found at the end of this table !! Check it out !<\/p>\n<p><b>NEW AND IMPORTANT<\/b> : Now you can use some nodes with infiniband to acelerate data transfert between san and nodes but also between nodes directly !\u00a0 \u00a0 Don&rsquo;t forget to use rsync with infiniband such as `rsync node0-ib:\/scratch\/user\/data.txt node1-ib:\/scratch\/user\/` &#8230; More details on\u00a0 <a target=\"_blank\" data-stringify-link=\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/\" data-sk=\"tooltip_parent\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/\" rel=\"noopener noreferrer\" style=\"box-sizing: inherit; color: rgba(var(--sk_highlight, 18, 100, 163), 1); text-decoration: none; font-family: Slack-Lato, Slack-Fractions, appleLogo, sans-serif; font-size: 15px; font-style: normal; font-variant-ligatures: common-ligatures; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; white-space: normal; background-color: rgb(248, 248, 248);\">https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-howtos-i-trop-cluster\/<\/a> <\/p>\n<table>\n<thead>\n<tr>\n<th>NODELIST<\/th>\n<th>PARTITION<\/th>\n<th>CPUS<\/th>\n<th>TOTAL MEMORY (Gb)<\/th>\n<th>RAM PER CPU (Gb)<\/th>\n<th>SCRATCH (To)<\/th>\n<th>INFINIBAND<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td>node0<\/td>\n<td>normal*<\/td>\n<td>24<\/td>\n<td>144<\/td>\n<td>6<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node1<\/td>\n<td>normal*<\/td>\n<td>24<\/td>\n<td>144<\/td>\n<td>6<\/td>\n<td>1.8<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node2<\/td>\n<td>supermem<\/td>\n<td>256<\/td>\n<td>2063<\/td>\n<td>7<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node3<\/td>\n<td>normal*<\/td>\n<td>64<\/td>\n<td>144<\/td>\n<td>2.25<\/td>\n<td>13<\/td>\n<td><br><\/td>\n<\/tr>\n<tr>\n<td>node4<\/td>\n<td>normal*<\/td>\n<td>72<\/td>\n<td>257<\/td>\n<td>4<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node5<\/td>\n<td>normal*<\/td>\n<td>88<\/td>\n<td>515<\/td>\n<td>6<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node7<\/td>\n<td>normal*<\/td>\n<td>48<\/td>\n<td>385<\/td>\n<td>8<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node8<\/td>\n<td>long<\/td>\n<td>12<\/td>\n<td>48<\/td>\n<td>4<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node9<\/td>\n<td>normal*<\/td>\n<td>64<\/td>\n<td>144<\/td>\n<td>2.25<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node10<\/td>\n<td>long<\/td>\n<td>12<\/td>\n<td>48<\/td>\n<td>4<\/td>\n<td>2.7<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node11<\/td>\n<td>runner<\/td>\n<td>12<\/td>\n<td>48<\/td>\n<td>4<\/td>\n<td>2.7<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node12<\/td>\n<td>long<\/td>\n<td>12<\/td>\n<td>64<\/td>\n<td>5<\/td>\n<td>13<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node13<\/td>\n<td>short,normal*<\/td>\n<td>12<\/td>\n<td>64<\/td>\n<td>5<\/td>\n<td>13<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node14<\/td>\n<td>short<\/td>\n<td>12<\/td>\n<td>64<\/td>\n<td>5<\/td>\n<td>13<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node15<\/td>\n<td>short<\/td>\n<td>12<\/td>\n<td>64<\/td>\n<td>5<\/td>\n<td>2.5<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node16<\/td>\n<td>short<\/td>\n<td>12<\/td>\n<td>64<\/td>\n<td>5<\/td>\n<td>13<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node17<\/td>\n<td>normal*<\/td>\n<td>48<\/td>\n<td>144<\/td>\n<td>3<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node18<\/td>\n<td>short<\/td>\n<td>12<\/td>\n<td>64<\/td>\n<td>5<\/td>\n<td>2.5<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node20<\/td>\n<td>normal*<\/td>\n<td>20<\/td>\n<td>64<\/td>\n<td>3<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node21<\/td>\n<td>normal*<\/td>\n<td>24<\/td>\n<td>144<\/td>\n<td>6<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node22<\/td>\n<td>normal*<\/td>\n<td>20<\/td>\n<td>64<\/td>\n<td>3<\/td>\n<td>13<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node23<\/td>\n<td>normal*<\/td>\n<td>20<\/td>\n<td>64<\/td>\n<td>3<\/td>\n<td>13<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node24<\/td>\n<td>normal*<\/td>\n<td>20<\/td>\n<td>64<\/td>\n<td>3<\/td>\n<td>2.5<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node25<\/td>\n<td>highmem<\/td>\n<td>40<\/td>\n<td>1030<\/td>\n<td>26<\/td>\n<td>2.5<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node26<\/td>\n<td>gpu<\/td>\n<td>24<\/td>\n<td>192<\/td>\n<td>8<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node27<\/td>\n<td>short<\/td>\n<td>24<\/td>\n<td>144<\/td>\n<td>6<\/td>\n<td>13<\/td>\n<td>X<\/td>\n<\/tr>\n<tr>\n<td>node28<\/td>\n<td>highmem<\/td>\n<td>112<\/td>\n<td>514<\/td>\n<td>5<\/td>\n<td>7<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node29<\/td>\n<td>highmem<\/td>\n<td>112<\/td>\n<td>514<\/td>\n<td>5<\/td>\n<td>7<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node30<\/td>\n<td>normal*<\/td>\n<td>112<\/td>\n<td>514<\/td>\n<td>5<\/td>\n<td>7<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td>node31<\/td>\n<td>global<\/td>\n<td>112<\/td>\n<td>514<\/td>\n<td>5<\/td>\n<td>7<\/td>\n<td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>All informations regarding a node can be also obtained with the <code>scontrol<\/code> or <code>sinfo -Nl<\/code> command line.<\/p>\n<p>with <code>scontrol<\/code> &#8230;<\/p>\n<pre><code>[orjuela@node18 ~]$ scontrol show nodes node18\nNodeName=node18 Arch=x86_64 CoresPerSocket=6 \n   CPUAlloc=12 CPUTot=12 CPULoad=12.01\n   AvailableFeatures=(null)\n   ActiveFeatures=(null)\n   Gres=(null)\n   NodeAddr=node18 NodeHostName=node18 \n   OS=Linux 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 01:06:37 UTC 2018 \n   RealMemory=64232 AllocMem=0 FreeMem=9361 Sockets=2 Boards=1\n   State=ALLOCATED ThreadsPerCore=1 TmpDisk=2700000 Weight=1 Owner=N\/A MCS_label=N\/A\n   Partitions=normal \n   BootTime=2021-03-17T16:07:03 SlurmdStartTime=2021-05-20T12:30:01\n   CfgTRES=cpu=12,mem=64232M,billing=12\n   AllocTRES=cpu=12\n   CapWatts=n\/a\n   CurrentWatts=0 AveWatts=0\n   ExtSensorsJoules=n\/s ExtSensorsWatts=0 ExtSensorsTemp=n\/s<\/code><\/pre>\n<p>or with <code>sinfo<\/code> &#8230;<\/p>\n<pre><code>[orjuela@node18 ~]$ sinfo -Nl\nThu Feb 10 23:40:09 2022\nNODELIST   NODES   PARTITION       STATE CPUS    S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON              \nnode0          1       short        idle   24   2:12:1 144786  1334989      1   (null) none                \nnode0          1     normal*        idle   24   2:12:1 144786  1334989      1   (null) none                \nnode1          1       short        idle   24   2:12:1 144786  1800000      1   (null) none                \nnode1          1     normal*        idle   24   2:12:1 144786  1800000      1   (null) none                \n...\nnode27         1     highmem        idle   24   2:12:1 144785  1321002      1   (null) none                \nnode28         1 highmemdell       mixed  112   2:28:2 514258  7626760      1   (null) none                \nnode29         1 highmemdell        idle  112   2:28:2 514247  7626760      1   (null) none                \nnode30         1 highmemdell        idle  112   2:28:2 514258  7626760      1   (null) none                \nnode31         1      global        idle  112   2:28:2 514258  7626760      1   (null) none <\/code><\/pre>\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>)\n<\/div>\n<p>no<\/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>How to reserve cluster resources Description How to reserve cluster resources Related-course materials Howtos cluster i-Trop Authors Julie Orjuela (julie.orjuela_AT_irf.fr),&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/en\/tutorials-how-to-reserve-cluster-resources\/\">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-3812","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 - How to reserve cluster resources? - 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-how-to-reserve-cluster-resources\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tutorials - How to reserve 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