AMBER Archive (2008)

Subject: Re: AMBER: sander.MPI / parallel

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Mon Jun 16 2008 - 12:56:57 CDT

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
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>> The AMBER Mail Reflector
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>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
>>
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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  

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