AMBER Archive (2008)

Subject: Re: AMBER: sander.MPI / parallel

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jun 16 2008 - 13:28:04 CDT

the uncommented one doesn't specify -np or -mfile.
I use something like this:

set sanderexe="/mnt/raidb/programs/amber9.ifort9/exe/sander.MPI"
set sander = "mpirun -machinefile $PBS_NODEFILE -np `wc -l <
$PBS_NODEFILE` $sanderexe"

check also the test cases, did they work in parallel?
read the scripts for those.

On Mon, Jun 16, 2008 at 1:56 PM, 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
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>>>
>>>
>>
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>>
>
>
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