[GE users] how to define the nodes?

Reuti reuti at staff.uni-marburg.de
Wed Jan 23 14:09:48 GMT 2008


Hi,

Am 23.01.2008 um 03:34 schrieb Ryoji Takahashi:

> 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?

no. The SGE admin has to set up different PEs for the same nodes, if  
you want to use different slot->hosts allocations from job to job.

> in batch script, how i can specify exactly?

You will need to specify one of the different PEs in your job script,  
which could use names like:

-pe mpich_smp 4
-pe mpich_8 16
-pe mpich 8

(with the default mpich using $round_robin) and so on.

-- Reuti


> 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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