AMBER Archive (2008)

Subject: Re: AMBER: sander.MPI / parallel

From: David LeBard (david.lebard_at_asu.edu)
Date: Mon Jun 16 2008 - 13:08:20 CDT

Sorry, I see you commented this out. Please forget my last email.

On Mon, Jun 16, 2008 at 11:07 AM, David LeBard <david.lebard_at_asu.edu> wrote:

> 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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