{"id":4532,"date":"2025-03-07T18:28:20","date_gmt":"2025-03-07T17:28:20","guid":{"rendered":"https:\/\/bioinfo.ird.fr\/?page_id=4532"},"modified":"2025-10-01T09:30:47","modified_gmt":"2025-10-01T07:30:47","slug":"how-to-utiliser-le-scratch-mutualise","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/how-to-utiliser-le-scratch-mutualise\/","title":{"rendered":"How to utiliser le scratch mutualise: scratch-ib"},"content":{"rendered":"

How to - Utiliser le scratch mutualis\u00e9 \/scratch-ib<\/h2>\n\n\n\n\n\n\n\n
Description<\/th>\nUtiliser \/scratch-ib<\/th>\n<\/tr>\n<\/thead>\n
Auteur<\/td>\nndomassi TANDO (ndomassi.tando@ird.fr)<\/td>\n<\/tr>\n
Creation Date<\/td>\n21\/01\/2025<\/td>\n<\/tr>\n
Date de modification<\/td>\n01\/10\/2025<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Role de la partition \/scratch-ib<\/h3>\n

La partition \/scratch-ib est une partition scratch mutualis\u00e9e h\u00e9berg\u00e9e sur bioinfo-san.ird.fr destin\u00e9e \u00e0 accueillir des donn\u00e9es \u00e0 analyser de mani\u00e8re temporarire<\/p>\n

Elle est partag\u00e9e entre tous les noeuds de calcul ayant la feature infiniband (acc\u00e8s \u00e0 un r\u00e9seau haut-d\u00e9bit)<\/p>\n

Les utilisateurs peuvent positionner leur donn\u00e9es directement dans \/scratch-ib sur bioinfo-san.ird.fr puis utiliser un ou plusieurs noeuds de calcul ayant la feature infiniband. pour les traiter directement dans \/scratch-ib <\/p>\n

Les calculs peuvent \u00eatre lanc\u00e9s en parall\u00e8le sur plusieurs noeuds \u00e0 la fois sur les m\u00eames donn\u00e9es. <\/p>\n

Caract\u00e9ristiques de la partition \/scratch-ib<\/h3>\n

- La partition \/scratch-ib est accessible depuis internet sur le serveur bioinfo-san.ird.fr<\/p>\n

\n - Elle a une taille de 128To\n <\/p>\n

- Les donn\u00e9es de cette partition ne sont accessibles que pour les noeuds avec la feature infiniband. <\/p>\n

Utiliser la partition \/scratch-ib<\/h3>\n

\"\"<\/p>\n

1) Placer vos donn\u00e9es dans \/scratch-ib en vous connectant sur bioinfo-san.ird.fr<\/h4>\n

Voir le processus de transfert ici: https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/howtos-for-hpc-cluster-itrop\/#howto-1<\/a><\/p>\n

2) Choisir un noeud infiniband<\/h4>\n

Seuls les noeuds dans la liste ci-dessous sont en infiniband:<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
node<\/th>\npartitions<\/th>\nCPU<\/th>\nRAM total (Gb)<\/th>\nRAM by CPU (Gb\/cpu)<\/th>\nscratch size (To)<\/th>\n<\/tr>\n<\/thead>\n
node0<\/td>\nnormal<\/td>\n24<\/td>\n144<\/td>\n6<\/td>\n13<\/td>\n<\/tr>\n
node1<\/td>\nnormal<\/td>\n24<\/td>\n144<\/td>\n6<\/td>\n2<\/td>\n<\/tr>\n
node2<\/td>\nsupermem<\/td>\n256<\/td>\n2063<\/td>\n7<\/td>\n13<\/td>\n<\/tr>\n
node4<\/td>\nnormal<\/td>\n72<\/td>\n257<\/td>\n4<\/td>\n13<\/td>\n<\/tr>\n
node5<\/td>\nnormal<\/td>\n88<\/td>\n516<\/td>\n6<\/td>\n13<\/td>\n<\/tr>\n
node7<\/td>\nnormal<\/td>\n24<\/td>\n145<\/td>\n6<\/td>\n3<\/td>\n<\/tr>\n
node8<\/td>\nlong<\/td>\n24<\/td>\n48<\/td>\n2<\/td>\n13<\/td>\n<\/tr>\n
node9<\/td>\nnormal<\/td>\n64<\/td>\n144<\/td>\n2<\/td>\n13<\/td>\n<\/tr>\n
node11<\/td>\nrunner<\/td>\n24<\/td>\n48<\/td>\n2<\/td>\n3<\/td>\n<\/tr>\n
node17<\/td>\nnormal<\/td>\n48<\/td>\n144<\/td>\n3<\/td>\n13<\/td>\n<\/tr>\n
node20<\/td>\nnormal<\/td>\n20<\/td>\n64<\/td>\n3<\/td>\n13<\/td>\n<\/tr>\n
node21<\/td>\nnormal<\/td>\n24<\/td>\n144<\/td>\n6<\/td>\n13<\/td>\n<\/tr>\n
node24<\/td>\nnormal<\/td>\n20<\/td>\n64<\/td>\n3<\/td>\n13<\/td>\n<\/tr>\n
node25<\/td>\nhighmem<\/td>\n40<\/td>\n1\u202f032<\/td>\n26<\/td>\n14<\/td>\n<\/tr>\n
node26<\/td>\ngpu<\/td>\n24<\/td>\n192<\/td>\n8<\/td>\n14<\/td>\n<\/tr>\n
node27<\/td>\nnormal<\/td>\n24<\/td>\n144<\/td>\n6<\/td>\n14<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Pour pouvoir choisir un noeud infiniband, il faut rajouter \u00e0 Slurm l'option<\/p>\n

--constraint=infiniband<\/code><\/p>\n

Par exemple, pour se connecter en mode int\u00e9ractif \u00e0 un noeud infiniband de la partition short on \u00e9crira:<\/p>\n

srun -p short --constraint=infiniband --pty bash -i<\/code><\/p>\n

Dans un script \u00e0 lancer avec sbatch, on rajoutera les options suivantes en d\u00e9but de script:<\/p>\n

#SBATCH -p short\n#SBATCH --constraint=infiniband<\/code><\/pre>\n
3) Lancer votre analyse directement  dans le r\u00e9pertoire \/scratch-ib<\/h4>\n
cd \/scratch-ib\n<\/code><\/pre>\n
Penser \u00e0 modifier  son script avec \/scratch-ib \u00e0 la place de \/scratch<\/strong><\/p>\n
Si les donn\u00e9es sont dans le r\u00e9pertoire \/projects, on va pouvoir int\u00e9grer le transfert dans le script  en rempla\u00e7ant san  par san-ib (comme infiniband)   et \/scratch par \/scratch-ib  <\/p>\n
scp -r san-ib:path_to_files\/file \/scratch-ib\/folder<\/code><\/p>\n
Plus d'informations sur l'utilisation de l'infiniband ici:<\/p>\n
Transfert en infiniband<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"
How to – Utiliser le scratch mutualis\u00e9 \/scratch-ib Description Utiliser \/scratch-ib Auteur ndomassi TANDO (ndomassi.tando@ird.fr) Creation Date 21\/01\/2025 Date de… 
 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-4532","page","type-page","status-publish","hentry"],"yoast_head":"\nHow to utiliser le scratch mutualise: scratch-ib - 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\/how-to-utiliser-le-scratch-mutualise\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"How to utiliser le scratch mutualise: scratch-ib - itrop\" \/>\n<meta property=\"og:description\" content=\"How to - Utiliser le scratch mutualis\u00e9 \/scratch-ib Description Utiliser \/scratch-ib Auteur ndomassi TANDO (ndomassi.tando@ird.fr) Creation Date 21\/01\/2025 Date de… Lire la suite\" \/>\n<meta property=\"og:url\" content=\"https:\/\/bioinfo.ird.fr\/index.php\/how-to-utiliser-le-scratch-mutualise\/\" \/>\n<meta property=\"og:site_name\" content=\"itrop\" \/>\n<meta property=\"article:modified_time\" content=\"2025-10-01T07:30:47+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/bioinfo.ird.fr\/wp-content\/uploads\/2025\/03\/scratch-ib.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=\"2 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\/how-to-utiliser-le-scratch-mutualise\/\",\"url\":\"https:\/\/bioinfo.ird.fr\/index.php\/how-to-utiliser-le-scratch-mutualise\/\",\"name\":\"How to utiliser le scratch mutualise: scratch-ib - 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