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.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.scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo.scripps.edu
>>
>>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
>
--
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.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Wed Jun 18 2008 - 06:07:32 PDT
