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| en:documentation:tools:sge [2018/09/04 11:37] – [Jobs qui ont des problèmes :] cpetit | en:documentation:tools:sge [2023/12/12 12:55] (Version actuelle) – supprimée ltaulell | ||
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| - | ====== GridEngine ====== | ||
| - | |||
| - | <WRAP center round todo 60%> | ||
| - | Under contruction... | ||
| - | </ | ||
| - | |||
| - | The job scheduler (or batch-queuing system) used in PSMN cluster is SGE, | ||
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| - | ● __Infrastructure__: | ||
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| - | * the **compilation servers** are described [[documentation: | ||
| - | * the **cluster hardware configuration** is described [[documentation: | ||
| - | * the **queues for job submission** are described [[documentation: | ||
| - | {{ : | ||
| - | ==== Optimum use of resources ==== | ||
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| - | To make the best use of resources, it is important to fill up the servers. For this, they are two strategies: | ||
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| - | * fill in "at best" (a best effort strategy), | ||
| - | * fill in with multiple of n cores (where n is the number of physical cores per server). | ||
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| - | Filling at best quickly leads to a fragmentation between the servers, of parallel applications via mpi. | ||
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| - | Filling at best is therefore only implemented on a few queues for parallel applications. On other queues, the fill in with the multiple of n cores of an entire server is used. | ||
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| - | ==== Priorities ==== | ||
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| - | Job priority is: | ||
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| - | * inversely proportional to the calculation time already consumed, | ||
| - | * proportional to waiting time and number of hearts requested. | ||
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| - | This is to distribute the available resources more equitably. | ||
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| - | ===== GridEngine : Submitting jobs ===== | ||
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| - | The normal way to submit jobs to the cluster is using the '' | ||
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| - | <code bash> | ||
| - | qsub myscript.sh | ||
| - | </ | ||
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| - | The many options to the '' | ||
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| - | For example a more complex submission: | ||
| - | <code bash> | ||
| - | qsub -V -m b -m e -e / | ||
| - | |||
| - | -V : export environment variables | ||
| - | -m b : mail @begin | ||
| - | -m e : mail @end | ||
| - | -e : where to put error files | ||
| - | -o : where to put output files | ||
| - | -q : queue (file d' | ||
| - | </ | ||
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| - | ** Nevertheless, | ||
| - | |||
| - | ==== Comment choisir les files d' | ||
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| - | De par les achats successifs de nœuds de calcul avec des architectures de génération différente, | ||
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| - | Concrètement le choix de la file d' | ||
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| - | * si le critère principal est la rapidité de l' | ||
| - | * si le critère principal est le grand nombre de ressources (p.ex. un job avec beaucoup de cœurs, un job avec beaucoup de mémoire RAM), alors il faut plutôt s' | ||
| - | |||
| - | Évidemment, | ||
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| - | Et bien sur, pour la mise au point du code, il faut choisir une file d' | ||
| - | ===== GridEngine : Les autres commandes utiles ===== | ||
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| - | ==== Checking job status ==== | ||
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| - | * display job status of a specific user: | ||
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| - | < | ||
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| - | * display queues status (and list of queues): | ||
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| - | < | ||
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| - | * display the running jobs of all users: | ||
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| - | < | ||
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| - | * display the pending jobs of all users: | ||
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| - | < | ||
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| - | * display the status of a job in progress: | ||
| - | |||
| - | < | ||
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| - | * display the status of a job in progress with more details (longer): | ||
| - | |||
| - | < | ||
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| - | * display the status of a job in progress with even more details (even longer): | ||
| - | |||
| - | < | ||
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| - | * display information on a job afetr its completion (long): | ||
| - | |||
| - | < | ||
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| - | * delete a job: | ||
| - | |||
| - | < | ||
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| - | * delete a job (force deletion) : | ||
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| - | < | ||
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| - | ==== Accounting ==== | ||
| - | |||
| - | <note important> | ||
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| - | * Détails des jobs sur les 30 derniers jours : | ||
| - | |||
| - | < | ||
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| - | * Consommation d' | ||
| - | |||
| - | < | ||
| - | |||
| - | ou | ||
| - | |||
| - | < | ||
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| - | * Consommation d' | ||
| - | |||
| - | < | ||
| - | |||
| - | ==== Troubleshootings: | ||
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| - | Run the command: | ||
| - | < | ||
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| - | on the output, look at the last two columns: | ||
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| - | * **aoACD** : Number of cores that are at least in one of the following states: | ||
| - | * **a** Load threshold alarm | ||
| - | * **o** Orphaned | ||
| - | * **A**** Suspend threshold alarm | ||
| - | * **C Suspended by calendar | ||
| - | * **D** Disabled by calendar | ||
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| - | * **cdsuE** : Number of cores that are at least in one of the following states: | ||
| - | * **c** Configuration ambiguous | ||
| - | * **d** Disabled | ||
| - | * **s** Suspended | ||
| - | * **u** Unknown | ||
| - | * **E** Error | ||
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| - | ==== Possible job status: ==== | ||
| - | |||
| - | * **d**(eletion), | ||
| - | * **E**(rror), | ||
| - | * **h**(old), | ||
| - | * **r**(unning), | ||
| - | * **R**(estarted), | ||
| - | * **s**(uspended), | ||
| - | * **S**(uspended), | ||
| - | * **t**(ransfering), | ||
| - | * **T**(hreshold), | ||
| - | * **w**(aiting). | ||
| - | |||
| - | ===== GridEngine : Variables d' | ||
| - | |||
| - | <note important>''# | ||
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| - | * SGE_O_WORKDIR : répertoire d'où à été soumis le job, utilisable dans les scripts | ||
| - | * NSLOTS : nombre de coeurs demandé | ||
| - | * JOB_ID : ID du job (unique) assigné par GridEngine | ||
| - | * JOB_NAME : nom du job (-N) | ||
| - | * PE_HOSTFILE : fichier de hosts | ||
| - | |||
| - | |||
| - | ===== Références : ===== | ||
| - | |||
| - | * http:// | ||
| - | * http:// | ||
| - | * http:// | ||
| - | * http:// | ||
| - | * https:// | ||
| - | * https:// | ||
| - | * https:// | ||
| - | * https:// | ||
| - | * http:// | ||
| - | * http:// | ||
| - | * https:// | ||
| - | * http:// | ||