[gmx-users] parallel run problem

[David]

On Tue, 2005-04-05 at 15:05 -0400, Ramachandra Rao Gullapalli wrote:
> Hi all,
> Im just getting into Md simulations and as a part of the learning process, i
> tried to run the tutorial ribonuclease protein in parallel on our cluster.
> 
> I received the following error message when i tried to run in parallel
> 
> Back Off! I just backed up md.log to ./#md.log.2#
> Sorry couldn't backup md.log to ./#md.log.2#
> Fatal error: File topol.tpr not found
> Fatal error: File topol.tpr not found
> Fatal error: File topol.tpr not found
> Fatal error: File topol.tpr not found
> /var/spool/pbs/mom_priv/jobs/566534.lion.SC: full.tpr: command not found
> 
> My PBS script which i prepared to run this thing is as follows
> 
> #PBS -l nodes=2:myrinet:ppn=2
> #PBS -l walltime=2:00:00
> #PBS -j oe
> #PBS -q lionxm-mcd18
> 
> # change the current working directory to the directory where
> # the executable file 'foo' can be found
> cd /home6/rrg142/gromacs/testfiles/speptide300

try replacing the above with
cd $PBS_O_WORKDIR

> 
> # run the executable file 'foo' using the qmpirun script
> /usr/global/bin/mmpirun  /usr/global/gromacs/i686-pc-linux-gnu/bin/mdrun -s
> full.tpr -o full.trr -c after_md.gro -v -g after_md.log
> 
> I have the file "full.tpr" in my current working directory.
> Also is it necessary to specify the number of nodes in the mdrun command? For
> the current file, i specified grompp with 2 nodes.
> 
> Thanks a lot for your help.
> Sincerely
> Regards
> Rama
> 
> 
> 
> 
> 
> 
> The important thing is not to stop questioning. Curiosity has its own reason for existing...
> -Einstein 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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