AMBER Archive (2008)

Subject: Re: AMBER: sander.MPI / parallel

From: David LeBard (david.lebard_at_asu.edu)
Date: Mon Jun 16 2008 - 13:07:21 CDT

Hi Arturas,

Have you tried to explicitly tell mpirun how many processors to use like
this?

mpirun -np $N $AMBERHOME/exe/sander.MPI ...

Just a thought,

David

On Mon, Jun 16, 2008 at 10:56 AM, Arturas Ziemys <arturas.ziemys_at_uth.tmc.edu>
wrote:

>
> Here is my PBS file:
> **************************************************************
> #! /bin/sh
> #PBS -N P_min_prl5
> #PBS -l cput=20:00:01
> #PBS -l walltime=22:00:00
> #PBS -l nodes=3:ppn=2
> #PBS -j oe
> #PBS -V
>
> echo
> echo -------------
> echo PBS_NODEFILE:
> cat $PBS_NODEFILE
> echo -------------
> echo
>
> N=`wc -l < $PBS_NODEFILE`
> echo this job has allocated $N nodes
>
> cd /home/aziemys/Works/Pep/AMBER/P/min
>
>
> #mpirun -np 6 $AMBERHOME/exe/sander.MPI -O -i min.in -o P_min_prl5.out -c
> BRCT.inpcrd -p BRCT.prmtop -r BRST_min_prl5.rst
>
> mpirun $AMBERHOME/exe/sander.MPI -O -i min.in -o P_min_prl5.out -c
> BRCT.inpcrd -p BRCT.prmtop -r BRST_min_prl5.rst
>
> **************************************************************
>
>
> Carlos Simmerling wrote:
>
>> can you show us your qsub script? what flags are you giving
>> to mpirun?
>>
>> On Mon, Jun 16, 2008 at 1:00 PM, Arturas Ziemys
>> <arturas.ziemys_at_uth.tmc.edu> wrote:
>>
>>
>>> Please, help me to setup AMBER 9 parallel (AMBER and openMPI compiled
>>> with
>>> g95,gcc4.3.x,redhat,xeon cpu). AMBER parallel test runs fine. Also, I run
>>> AMBER job fine from a command prompt. But if I submit job with 'qsub',
>>> AMBER
>>> runs just with a single CPU using sandes.MPI. What is wrong ?
>>>
>>> Arturas
>>>
>>> --
>>>
>>> Arturas Ziemys, PhD
>>> School of Health Information Sciences
>>> University of Texas Health Science Center at Houston
>>> 7000 Fannin, Suit 880
>>> Houston, TX 77030
>>> Phone: (713) 500-3975
>>> Fax: (713) 500-3929
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber_at_scripps.edu
>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>> to majordomo_at_scripps.edu
>>>
>>>
>>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
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>>
>>
>
>
> --
>
> Arturas Ziemys, PhD
> School of Health Information Sciences
> University of Texas Health Science Center at Houston
> 7000 Fannin, Suit 880
> Houston, TX 77030
> Phone: (713) 500-3975
> Fax: (713) 500-3929
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>

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