[gmx-users] gromacs on glacier.westgrid.ca

[Justin A. Lemkul]

Payman Pirzadeh wrote:
> 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.

"Whatever was produced" does not inspire confidence.  You're sure that 
--enable-mpi was used during configuration, right?

> 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).

There has to be something different about this one.  If everything worked, we 
wouldn't be having this conversation :)

> 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`"
> 
> 

Based on the error messages, it appears that mpirun is interpreting everything 
you have specified as a command line argument (the call to mdrun_d, -deffnm, 
npttest).  We have the same version of mpirun on our cluster, and -path does not 
appear to be a valid argument.  Perhaps try something like:

MDRUN="/global/home/prizadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest"

${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE ${MDRUN}

-Justin

> 
> 
> 
> Payman
> 
> 
> 
> 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at 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-bounces at gromacs.org [mailto:gmx-users-bounces at 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 <ppirzade at 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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> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================