Dear All,
Thanks a lot. This really helped me understanding of the mpirun and parallelization, I can now better understand that qsub and mpirun have different roles. My experiments are working now. I really appreciate all of you for your cooperation and continuous support.
Regards
Imtiaz
On 30 Jan 2010, at 20:10, Mengjuei Hsieh wrote:
> Hi,
> I belive that you need to use 'mpirun C' before the actual executable.
>
> So it should become:
> /opt/lam/7.1.3/bin/mpirun C /opt/amber10/bin/sander.MPI -O -i heat.in -o heat.out -p SAMP.prmtop -c min.rst -r heat.rst -x heat.mdcrd -ref min.rst
>
> Of course if your lammpi is not compiled with tm modual, you need to specify -np 16 instead of 'C'....
>
> Best,
> --mj
>
> On Jan 30, 2010, at 7:20, MUHAMMAD IMTIA SHAFIQ <imtiazshafiq.gmail.com> wrote:
>> Dear All,
>> I am submitting my sander.MPI job with qsub using the following script
>> #!/bin/sh
>> #$ -S /bin/bash
>> # This is file Run__amber
>> #PBS -l nodes=4:ppn=4
>> #PBS -V
>> #PBS -N Imtiaz
>> #PBS -l walltime=03:59:00
>> cd $PBS_O_WORKDIR
>>
>> echo "simulation started at" `date`
>>
>> /opt/lam/7.1.3/bin/lamboot
>>
>> /opt/amber10/bin/sander.MPI -O -i heat.in -o heat.out -p SAMP.prmtop -c min.rst -r heat.rst -x heat.mdcrd -ref min.rst
>>
>> echo "simulation end at" `date`
>>
>>
>> When I submit the job with qsub I get a job ID and showq indicate that job is running on 16 processors and 4 nodes.
>>
>> 414013 mis9 Running 16 03:55:33 Sat Jan 30 00:58:54
>> 1 Active Job 16 of 36 Processors Active (44.44%)
>> 4 of 9 Nodes Active (44.44%)
>>
>> When I noticed the this job is taking very long time then an average estimate I used ssh to each note and run top command. I found sander.MPI is running only on one node.
>>
>> What could be the potential reasons that despite job is submitted to 4 nodes and showq also show that it is running on four nodes but in reality it is taking unnecessarily very long time and top command on each individual nodes shows that sander.MPI is actually running only on one node ? Do I need to change or submit some environmental variables in the job submission script
>>
>> Waiting for some suggestion in this regards.
>>
>> Imtiaz
>
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Received on Sat Jan 30 2010 - 15:30:02 PST
