{"id":953,"date":"2020-11-09T15:06:28","date_gmt":"2020-11-09T14:06:28","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=953"},"modified":"2022-04-06T14:48:55","modified_gmt":"2022-04-06T12:48:55","slug":"trainings-2019-admin-hpc-module-2-slurm-usage","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-admin-hpc-module-2\/trainings-2019-admin-hpc-module-2-slurm-usage\/","title":{"rendered":"Trainings 2019 &#8211; Admin HPC &#8211; module 2 &#8211; slurm usage"},"content":{"rendered":"<h2>Utilisation de Slurm<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th>Savoir utiliser Slurm<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Cours li\u00e9<\/td>\n<td><a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-admin-hpc-module-2\/\">HPC Administration Module2<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Auteur<\/td>\n<td>Ndomassi TANDO (ndomassi.tando@ird.fr)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Date de cr\u00e9ation<\/td>\n<td>27\/09\/2019<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Date de modification<\/td>\n<td>27\/09\/2019<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<h3>Summary<\/h3>\n<p><!-- TOC depthFrom:2 depthTo:2 withLinks:1 updateOnSave:1 orderedList:0 --><\/p>\n<ul>\n<li><a href=\"#part-1\">Objectif<\/a><\/li>\n<li><a href=\"#part-2\">Lancer des jobs sous Slurm<\/a><\/li>\n<li><a href=\"#part-3\">Superviser des ressources sous Slurm<\/a><\/li>\n<li><a href=\"#part-3\">Commandes d'administration sous Slurm<\/a><\/li>\n<li><a href=\"#links\">Links<\/a><\/li>\n<li><a href=\"#license\">License<\/a><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"part-1\"><\/a><\/p>\n<h2>Objectif<\/h2>\n<p>Pouvoir lancer des jobs de diff\u00e9rents types sous Slurm.<\/p>\n<p>Monitorer les ressources sous Slurm<\/p>\n<hr \/>\n<p><a name=\"part-2\"><\/a><\/p>\n<h2>Lancer des jobs sous Slurm:<\/h2>\n<h3>Lancer des commandes depuis la machine ma\u00eetre s'ex\u00e9cutant les ressources de calcul<\/h3>\n<p>La commande suivante alloue des ressources de calcul (noeuds, cpus, m\u00e9moire) et lance la commande imm\u00e9diatement sur chaque ressource allou\u00e9e<\/p>\n<pre><code>$ srun + commande<\/code><\/pre>\n<p>Exemple:<\/p>\n<pre><code>$ srun hostname<\/code><\/pre>\n<p>Permet d'obtenir le nom de la ressource de calcul utilis\u00e9<\/p>\n<h3>R\u00e9server des ressources de calcul pour lancer des commandes avec Slurm<\/h3>\n<p>On utilise la commande:<\/p>\n<pre><code>$ salloc<\/code><\/pre>\n<p>Cette commande permet de r\u00e9server une ou pusieurs ressources de calcul tout en continuant \u00e0 travailler sur la machine ma\u00eetre.<\/p>\n<p>Les commandes \u00e0 lancer sur le ressources de calcul peuvent \u00eatre lanc\u00e9es plus tard avec la commande <code>srun + arguments<\/code>.<\/p>\n<p>Il est important quand on utilise cette commande pr\u00e9ciser un temps de r\u00e9servation avec l'option --time <\/p>\n<p>Exemple: On r\u00e9serve 2 noeuds de calcul( options -N) \u00e0 la fois pour 5 minutes et on lance plus tard la commande hostname sur ces 2 noeuds avec srun<\/p>\n<pre><code>$ salloc --time=05:00 -N 2\n$ srun hostname<\/code><\/pre>\n<p>Nous obtiendrons une r\u00e9ponse du type:<\/p>\n<pre><code>$[tando@master0 ~]$ srun hostname\nnode21.alineos.net\nnode14.alineos.net<\/code><\/pre>\n<h3>Lancer des commandes apr\u00e8s connexion \u00e0 un noeud de mani\u00e8re interactive:<\/h3>\n<p>Pour se connecter de mani\u00e8re int\u00e9ractive  pendant un temps X \u00e0 un noeud, on utilise la commande:<\/p>\n<pre><code>$ srun --time=X:00 --pty bash -i<\/code><\/pre>\n<p>Une fois connect\u00e9 sur le noeud, on peut lancer les commandes d\u00e9sir\u00e9es sans le pr\u00e9fixe <code>srun<\/code>qui s'ex\u00e9cuteront sur le noeud<\/p>\n<h3>Les principales options disponibles pour lancer une analyse sous Slurm:<\/h3>\n<p>Toutes les commandes <code>salloc<\/code>, <code>srun<\/code> et <code>sbatch<\/code> peuvent \u00eatre utilis\u00e9es avec les options suivantes:<\/p>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">actions<\/th>\n<th style=\"text-align: left;\">Option<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Pr\u00e9ciser une partition<\/td>\n<td style=\"text-align: left;\">-p [queue]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Nombre de noeuds \u00e0 utiliser<\/td>\n<td style=\"text-align: left;\">-N [min[-max]]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Nombre de cpus \u00e0 utiliser<\/td>\n<td style=\"text-align: left;\">-n [count]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">limite de temps<\/td>\n<td style=\"text-align: left;\">-t [min] ou -t [days-hh:mm:ss]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">pr\u00e9ciser un fichier de sortie<\/td>\n<td style=\"text-align: left;\">-o [file_name]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">pr\u00e9ciser un fichier d'erreur<\/td>\n<td style=\"text-align: left;\">-e [file_name]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Combiner les fichiers STDOUT et STDERR files<\/td>\n<td style=\"text-align: left;\">utiliser -o sans -e<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Copier l'environnement<\/td>\n<td style=\"text-align: left;\">--export=[ALL , NONE , variables]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Type de notifications \u00e0 envoyer<\/td>\n<td style=\"text-align: left;\">--mail-type=[events]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Envoi d'un email<\/td>\n<td style=\"text-align: left;\">--mail-user=[address]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Nom du job<\/td>\n<td style=\"text-align: left;\">--job-name=[name]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Relancer un job si probl\u00e8me<\/td>\n<td style=\"text-align: left;\">--requeue<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Preciser le r\u00e9pertoire de travail<\/td>\n<td style=\"text-align: left;\">--workdir=[dir_name]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Taille de la m\u00e9moire \u00e0 r\u00e9server<\/td>\n<td style=\"text-align: left;\">--mem=[mem][M,G,T] ou-mem-per-cpu=[mem][M,G,T]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Pr\u00e9ciser un account<\/td>\n<td style=\"text-align: left;\">--account=[account]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Nombre de t\u00e2ches par noeud<\/td>\n<td style=\"text-align: left;\">--tasks-per-node=[count]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Nombre de cpus par t\u00e2che<\/td>\n<td style=\"text-align: left;\">--cpus-per-task=[count]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">D\u00e9pendance \u00e0 un autre noeud<\/td>\n<td style=\"text-align: left;\">--depend=[state:job_id]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Choisir des h\u00f4tes de pr\u00e9f\u00e9rence<\/td>\n<td style=\"text-align: left;\">--nodelist=[nodes] ET\/OU --exclude=[nodes]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Job arrays<\/td>\n<td style=\"text-align: left;\">--array=[array_spec]<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Heure de d\u00e9marrage<\/td>\n<td style=\"text-align: left;\">--begin=YYYY-MM-DD[THH:MM[:SS]]<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>Lancer des jobs via un script<\/h3>\n<p>Lancer est job est l'action de lancer une analyse dont le d\u00e9roulement est d\u00e9crite \u00e0 l'int\u00e9rieur d'un script.<\/p>\n<p>Slurm permet d'utiliser des scripts de type bash, perl ou python.<\/p>\n<p>Slurm alloue les ressources demand\u00e9es et lance les analyses sur celles-ci en arri\u00e8re plan.<\/p>\n<p>Un script cr\u00e9\u00e9 doit cependant contenir une ent\u00eate afin que celui-ci soit interpr\u00e9t\u00e9 par Slurm.<\/p>\n<p>Pour que chaque option du script soit interpr\u00e9t\u00e9 par Slurm, il faut les faire pr\u00e9c\u00e9der par le mot cl\u00e9 <code>#BATCH<\/code><\/p>\n<p>Exemple  de script slurm:<\/p>\n<pre><code>#!\/bin\/bash\n## On d\u00e9finit le nom du job\n#SBATCH --job-name=test\n## On d\u00e9finit le nom du fichier de sortie\n#SBATCH --output=res.txt\n## On d\u00e9finit le nombre de t\u00e2ches\n#SBATCH --ntasks=1\n## On d\u00e9finit le temps limit d&#039;\u00e9x\u00e9cution\n#SBATCH --time=10:00\n## On d\u00e9finit 100Mo de m\u00e9moire par cpu\n#SBATCH --mem-per-cpu=100\nsleep 00:03:00 #on lance un sleep de 3 minutes<\/code><\/pre>\n<p>Une analyse sera lanc\u00e9 gr\u00e2ce \u00e0 la commande:<\/p>\n<pre><code>$ sbatch script.sh<\/code><\/pre>\n<p>Avec <code>script.sh<\/code> le nom du script \u00e0 utiliser<\/p>\n<h3>Supprimer un job sous Slurm<\/h3>\n<pre><code>$ scancel &lt;job_id&gt;<\/code><\/pre>\n<p>Avec <code>&lt;job_id&gt;<\/code>: le num\u00e9ro du job  <\/p>\n<hr \/>\n<p><a name=\"part-3\"><\/a><\/p>\n<h2>Superviser des ressources sous Slurm:<\/h2>\n<h3>Avoir des informations sur les jobs :<\/h3>\n<p>On utilise la commande<\/p>\n<pre><code>$ squeue<\/code><\/pre>\n<p>Pour que les informations sur les jobs se rafraichissent toutes les 5 secondes<\/p>\n<pre><code>$ squeue -i 5<\/code><\/pre>\n<p>Pour avoir des infos sur un job en particulier<\/p>\n<pre><code>$ scontrol show job &lt;job_id&gt;<\/code><\/pre>\n<p>Avec <code>&lt;job_id&gt;<\/code>: le num\u00e9ro du job  <\/p>\n<p>Pour avoir des infos sur les jobs d'un utilisateur en particulier<\/p>\n<pre><code>$ squeue -u &lt;user&gt;<\/code><\/pre>\n<p>Avec <code>&lt;user&gt;<\/code>: le login de l'utilisateur<\/p>\n<p>Pour avoir des informations pr\u00e9cises sur tous les jobs:<\/p>\n<pre><code>$ sacct --format=JobID,elapsed,ncpus,ntasks,state,node<\/code><\/pre>\n<p>Pour avoir des informations sur les ressources utilis\u00e9es par un job termin\u00e9:<\/p>\n<pre><code>$ seff &lt;job_id&gt;<\/code><\/pre>\n<p>Avec <code>&lt;job_id&gt;<\/code>: le num\u00e9ro du job <\/p>\n<p>On peut \u00e9galement rajouter la commande suivante en fin de script pour obtenir des informations sur les informations utilis\u00e9es dans le fichier de sortie:<\/p>\n<pre><code>$ seff $SLURM_JOB_ID<\/code><\/pre>\n<h3>Avoir des infos sur les partitions (files d'attentes)<\/h3>\n<p>Taper la commande:<\/p>\n<pre><code>$ sinfo<\/code><\/pre>\n<p>Cette commande donne des informations sur les partitions et les noeuds qui leur sont rattach\u00e9s.<\/p>\n<p>Pour des informations plus pr\u00e9cises:<\/p>\n<pre><code>$ scontrol show partitions<\/code><\/pre>\n<p>De mani\u00e8re g\u00e9n\u00e9rale <code>scontrol show<\/code> peut \u00eatre utiliser avec nodes, user, account etc...<\/p>\n<p>Connaitre la limite de temps par parttion:<\/p>\n<pre><code>$sinfo -o &quot;%10P %.11L %.11l&quot;<\/code><\/pre>\n<h3>Avoir des infos sur le noeuds de calcul<\/h3>\n<p>Taper le commande:<\/p>\n<pre><code>$ sinfo -N -l<\/code><\/pre>\n<p>Plusieurs \u00e9tats sont possibles:<\/p>\n<ul>\n<li>\n<p>alloc : le noeud est utilis\u00e9 enti\u00e8rement<\/p>\n<\/li>\n<li>\n<p>mix : le noeud est partiellement utilis\u00e9<\/p>\n<\/li>\n<li>\n<p>idle : Aucun job ne tourne sur le noeud<\/p>\n<\/li>\n<li>\n<p>drain :Le noeud est entrain de finir des jobs re\u00e7us mais n'en accepte pas de nouveaux ( quand le noeud va \u00eatre arr\u00eat\u00e9 pour maintenance).   <\/p>\n<\/li>\n<\/ul>\n<p>Pour obtenir des informations encore plus pr\u00e9cises:<\/p>\n<pre><code>$ scontrol show nodes<\/code><\/pre>\n<hr \/>\n<p><a name=\"part-4\"><\/a><\/p>\n<h2>Commandes d'administration sous Slurm:<\/h2>\n<p>La commande <code>sacctmgr<\/code>suivie d'options permet de modifier des valeurs sur diff\u00e9rents param\u00e8tre: account, user, ressources, nodes, partitions etc<\/p>\n<h3>Rajouter un utilisateur \u00e0 un account (group).<\/h3>\n<p>Sous Slurm faire appartenir un user \u00e0 un account permet de g\u00e9rer ses droits et ses privil\u00e8ges sous slurm.<\/p>\n<p>Par exemple si on veut que l'utilisateur dom appartienne au group bioinfo, on \u00e9crira:<\/p>\n<pre><code>$ sacctmgr create user dom account=bioinfo fairshare=1000<\/code><\/pre>\n<h3>Changer les limites de ressources pour un account<\/h3>\n<p>On utilisera la commande<\/p>\n<pre><code>$ sacctmgr modify + options<\/code><\/pre>\n<p>Par exemple pour imposer une limite \u00e0 100 cpus pour le compte bioinfo:<\/p>\n<pre><code>$ sacctmgr modify  account bioinfo set GrpTRES=cpu=100<\/code><\/pre>\n<p>Pour supprimer la limite du nombre de cpus pour le compte bioinfo:<\/p>\n<pre><code>$ sacctmgr modify  account bioinfo set GrpTRES=cpu=-1<\/code><\/pre>\n<hr \/>\n<h3>Links<\/h3>\n<p><a name=\"links\"><\/a><\/p>\n<ul>\n<li>Cours li\u00e9s : <a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-hpc\/\">HPC Trainings<\/a><\/li>\n<\/ul>\n<hr \/>\n<h3>License<\/h3>\n<p><a name=\"license\"><\/a><\/p>\n<div>\nThe resource material is licensed under the Creative Commons Attribution 4.0 International License (<a href=\"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/\">here<\/a>).<br \/>\n<center><img decoding=\"async\" width=\"25%\" class=\"img-responsive\" src=\"http:\/\/creativecommons.org.nz\/wp-content\/uploads\/2012\/05\/by-nc-sa1.png\"\/><br \/>\n<\/center>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Utilisation de Slurm Description Savoir utiliser Slurm Cours li\u00e9 HPC Administration Module2 Auteur Ndomassi TANDO (ndomassi.tando@ird.fr) Date de cr\u00e9ation 27\/09\/2019&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-admin-hpc-module-2\/trainings-2019-admin-hpc-module-2-slurm-usage\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":928,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-953","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This 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