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Subject: Re: [OMPI users] restricting a job to a set of hosts
From: Reuti (reuti_at_[hidden])
Date: 2012-07-26 17:56:17


Am 26.07.2012 um 23:48 schrieb Reuti:

> Am 26.07.2012 um 23:33 schrieb Erik Nelson:
>
>> I have a purely parallel job that runs ~100 processes. Each process has ~identical
>> overhead so the speed of the program is dominated by the slowest processor.
>>
>> For this reason, I would like to restrict the job to a specific set of identical (fast)
>> processors on our cluster.
>>
>> I read the FAQ on -hosts and -hostfile, but it is still unclear to me what affect these
>> directives will have in a queuing environment.
>>
>> Currently, I submit the job using the "qsub" command in the "sge" environment as :
>>
>> qsub -pe mpich 101 jobfile.job
>>
>> where jobfile contains the command
>>
>> mpirun -np 101 -nolocal ./executable
>
> I would leave -nolocal out here.
>
> $ qsub -l "h=compute-5-[1-9]|compute-5-1[0-9]|compute-5-2[0-9]|compute-5-3[0-2]" -pe mpich 101 jobfile.job

Or shorter:

$ qsub -l "h=compute-5*&(*-[1-9]|*-[1-2][0-9]|*-3[0-2])" -pe mpich 101 jobfile.job

-- Reuti

> -- Reuti
>
>
>> I would like to restrict the job to nodes compute-5-1 to compute-5-32 on our machine,
>> each containing 8 cpu's (slots). How do I go about this?
>>
>> Thanks, Erik
>>
>> --
>> Erik Nelson
>>
>> Howard Hughes Medical Institute
>> 6001 Forest Park Blvd., Room ND10.124
>> Dallas, Texas 75235-9050
>>
>> p : 214 645 5981
>> f : 214 645 5948
>> _______________________________________________
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>
>
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