[GE users] how to define the nodes?

Ryoji Takahashi ryoji at cct.lsu.edu
Wed Jan 23 02:34:48 GMT 2008


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Reuti wrote:
> Hi,
>
> Am 22.01.2008 um 21:18 schrieb Ryoji Takahashi:
>
>> sorry, coming back to the same question.
>> So, for 8 processes per nodes, what should i do?
>> Can user specify in batch script?
>> #$ -pe mpich 2-8
>> (i know this is not right.)
>>
>> or root has to configure
>> this allocation_rule 8 ?  instead $round_robin?
>
> you could also use $pe_slots (see: man sge_pe). This will force to 
> allocate all 8 slots on one and the same machine. If you want to run 
> jobs with 8-16-24-32... slots, you will indeed need allocation_rule 8 
> to get the least amount of different nodes. $fill_up might also suits 
> your needs.
>
i am using first time, so , i am probably asking stupid question ...
this can be done by normal users?

in batch script, how i can specify exactly?
thanks,

>> how I can really do??
>>
>>
>> when i did by
>>
>> $ cat run.nim
>> #! /bin/sh
>> #$ -S /bin/sh
>> #$ -V
>> #$ -N dpb2005_s05_pr1
>> #$ -cwd
>> #$ -o /home/takahary/nimrod/rundir/dpb2005_s05_pr1/batch.out
>> #$ -e /home/takahary/nimrod/rundir/dpb2005_s05_pr1/batch.err
>> #$ -M ryoji-takahashi at utulsa.edu
>> #$ -m e
>> #$ -l h_cpu=48:00:00
>> ##$ -l h_vmem=2000M
>> #$ -pe mpich 2-8
>>
>> echo Running on host `hostname`
>> echo Time is `date`
>> echo Directory is `pwd`
>> set orig_dir=`pwd`
>> echo This job runs on the following processors:
>> cat $TMPDIR/machines
>> echo This job has allocated $NSLOTS processors
>>
>> mpirun  -hostfile  $TMPDIR/machines -np $NSLOTS 
>> /home/takahary/nimroot/nimrod-3.2.4/nimrod/nimrod
>>
>>
>> i see it only pick up 8 nodes?
>
> If always 8 are free, they will be taken. From the qsub man page:
>
> The range specification is processed as follows: The largest number of 
> queues requested  is
>               checked first. If enough queues meeting the specified 
> attribute list are available, all are allocated. If not, the
>               next smaller number of queues is checked, and so forth
>
> -- Reuti
>
>
>>>
>>> In SGE the allocation of number of slots per node is in the PE 
>>> definition. So maybe you need two PEs:
>>>
>>> - one with "allocation_rule 1"
>>>
>>> - one with "allocation_rule 2"
>>>
>>> if youn want to have one or two processes per node for this job. 
>>> Otherwise you can use $round_robin if you don't care.
>>>
>>> -- Reuti
>>
>>
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>
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