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en:documentation:tools:sge [2018/09/04 11:55] – [Comment choisir les files d'attente, de test ou de productions, adaptées ?] cpetiten:documentation:tools:sge [2020/08/25 15:58] – modification externe 127.0.0.1
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 ====== GridEngine ====== ====== GridEngine ======
  
-<WRAP center round todo 60%> 
-Under contruction... 
-</WRAP> 
  
 The job scheduler (or batch-queuing system) used in PSMN cluster is SGE,-previously Sun Grid Engine and now Son of Grid Engine-; it manages the execution of non-interactive jobs. The job scheduler (or batch-queuing system) used in PSMN cluster is SGE,-previously Sun Grid Engine and now Son of Grid Engine-; it manages the execution of non-interactive jobs.
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 ===== GridEngine : Submitting jobs ===== ===== GridEngine : Submitting jobs =====
  
-The normal way to submit jobs to the cluster is using the ''qsub'' command. For example: +<code> 
- +qsub programme <input >output
-<code bash> +
-qsub myscript.sh+
 </code> </code>
  
-The many options to the ''qsub'' command are described in the manpage, ''man qsub''.  
- 
-For example a more complex submission: 
 <code bash> <code bash>
-qsub -V -m b -m e -e /path/to/workdir/ -o /path/to/workdir/ -q $QUEUE script+qsub -V -e /path/to/workdir/ -o /path/to/workdir/ -q $QUEUE script
  
 -V : export environment variables -V : export environment variables
--m b : mail @begin 
--m e : mail @end 
 -e : where to put error files -e : where to put error files
 -o : where to put output files -o : where to put output files
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 </code> </code>
  
-** Nevertheless, it is easier to directly submit to GridEngine a script containing the desired options**. You can follow the documentation on [[documentation:tutorials:submit|how to submit a job (full documentation)]]. Moreover take a look at [[documentation:clusters:batch&#les_files_d_attente|the list of available queues for submission]].+**It is simpler to submit a script to GridEngine, which will contain more options**.  
 + 
 +<note important>Some options don't work directly in CLI, you have to use a script (example: send mails beginning and end).</note> 
 + 
 +Voir [[documentation:tutorials:submit:accueil|complete documentation to submit a job]], as well as [[documentation:clusters:batch&#les_files_d_attente|the queue list]].
  
 ==== How to choose the adapted queues for my needs? ==== ==== How to choose the adapted queues for my needs? ====
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   * if the main criterion is the large number of resources (//eg// a job with a lot of cores, a job with a lot of RAM,etc), then you have to move towards the queues that have a large number of resources (at least the resources requested by the job), even if waiting time in the queue is greater.   * if the main criterion is the large number of resources (//eg// a job with a lot of cores, a job with a lot of RAM,etc), then you have to move towards the queues that have a large number of resources (at least the resources requested by the job), even if waiting time in the queue is greater.
  
-Obviously, the above command (''qstat -g c'') and [[documentation:clusters:batch&#les_files_d_attente the list of queues]] should guide your choice.+Obviously, the above command (''qstat -g c'') and [[documentation:clusters:batch&#les_files_d_attente|the list of queues]] should guide your choice.
  
-And, of course, when tuning ypur code, you have to choose a test queue that is closest to the intended "production" queue (//i.e.// same type of compute nodes). //Eg// ''r815lin128ib'' was chosen for the production queue, you thus have to run your tests on''r815_ib_test''.+And, of course, when tuning ypur code, you have to choose a test queue that is closest to the intended "production" queue (//i.e.// same type of compute nodes). //Eg// ''r815lin128ib'' was chosen for the production queue, you thus have to run your tests on ''r815_ib_test''.
 ===== GridEngine : other useful commands ===== ===== GridEngine : other useful commands =====
  
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 <code>qstat -g c </code> <code>qstat -g c </code>
 +
 +  * display nodes status in a given queue: 
 +
 +<code>qstat -q <queue_name> -f </code>
  
     * display the running jobs of all users:      * display the running jobs of all users: 
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