[GE users] how to define the nodes?

Reuti reuti at staff.uni-marburg.de
Tue Jan 22 23:06:25 GMT 2008


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.

> 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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