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

[Payman Pirzadeh]

Hi Nicolas,
Thanks for the tips!
Yes, that's what I thought yesterday. Main problem is I think there is an
older version of GROMACS installed on Glacier and if I do not source the
path, it will take the cluster one not mine. I passed that phase. Now I am
checking if I can run the job in parallel with no problems.
Are you in UofC?

Payman

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Nicolas Sapay
Sent: May 20, 2009 2:26 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca

Hello Payman,

Westgrid (and Glacier) has several pages of doc on its website about running
Gromacs and compiling softwares. I used to run (my own compilation of)
Gromacs on Glacier and never had any particular problem. 
You just have to make sure you compile it with the correct mpicc and fftw
libraries. You also have make sure that you source the appropriate path to
mdrun in your script and that your GMXLIB  path is correctly set.

Hope that helps,
Nicolas

Payman Pirzadeh a écrit :
> 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-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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