Hi Justin,
Following is the script I use. But remember several points:
1. I compiled the gmx with double precision and did not rename the code to
mpi. I kept whatever was produced with _d suffix.
2. I use the same script for other codes and they work (I am using other MD
code for special purposes and a QM code as well).
3. This script follows the guidelines of glacier as well. It is available
online at http://www.westgrid.ca/support/quickstart/glacier
#!/bin/bash
#PBS -S /bin/bash
# Torque script for running an MPI program pn on glacier
# 2005-05-26 DSP
# This presumes code compiled with the Intel compiler.
# For example:
# /global/software/mpich-1.2.5.2/ssh/bin/mpif90 pn.f -o pn
#PBS -N sixsite-test
#PBS -l walltime=240:00:00
#PBS -l nodes=2:ppn=2
#PBS -l qos=parallel
MPIRUN="/global/software/mpich-1.2.5.2/ssh/bin/mpirun"
cd $PBS_O_WORKDIR
echo "Current working directory is `pwd`"
echo "Node file: $PBS_NODEFILE :"
echo "---------------------"
cat $PBS_NODEFILE
echo "---------------------"
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo "Running on $NUM_PROCS processors."
echo "Starting run at: `date`"
${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest
echo "Job finished at: `date`"
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: May 19, 2009 12:36 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] gromacs on glacier.westgrid.ca
Dear Tsjerk,
Thanks for your e-mail. The message that cluster sends is:
"Running on 4 processors.
Starting run at: Sat May 16 17:13:28 PDT 2009
Warning: Command line arguments for program should be given
after the program name. Assuming that
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming that -s is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name. Assuming that npttest is a
command line argument for the program.
Missing: program name
Program -path either does not exist, is not
executable, or is an erroneous argument to mpirun.
Job finished at: Sat May 16 17:13:28 PDT 2009"
The message that GROMACS has in log file is:
"Program mdrun, VERSION 3.3.1
Source code file: gmxfio.c, line: 706
Can not open file:
topol.tpr"
This is while I have the topology file in the same folder.
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Tsjerk Wassenaar
Sent: May 19, 2009 12:25 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca
Hi Payman,
That is probably not the only grid facility on which Gromacs may be
run and it would be helpful if you could give specifications of it
(WMS software e.g.), which could give you more response. Also, it
would be helpful if you'd be able to give more information regarding
the output. Then you'd also have to ask the question whether your
problem is grid related or gromacs related. In the former case you'd
better consult support from the facility you're trying to use.
Cheers,
Tsjerk
On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh <ppirz...@ucalgary.ca>
wrote:
> Hi All,
>
> Is there anyone who is running gromacs on glacier.westgrid.ca machine? If
> yes, I will be appreciated if he/she can tell me how to run gmx on this
> facility. I either get error messages which says either the executable or
> the topology file can not be found.
>
> Regards,
>
>
>
> Payman
>
>
>
>
>
> _______________________________________________
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>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
_______________________________________________
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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