[votca] gromacs parallel run

[Sikandar Mashayak]

hi

I was running the spce ibm tutorial script and observed that gromacs simulations are done in serial, considering number of iterations (gromacs CG simulations) it may require to converge, I would like to run gromacs in parallel.

So I am wondering , is it possible to run gromacs in parallel? If yes, how can it be achieved?

thanks
sikandar

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[Christoph Junghans]

> So I am wondering , is it possible to run gromacs in parallel? If yes, how
> can it be achieved?

First you will need a parallel(mpi) version of gromacs, that means
configure with "--enable-mpi" option.
Second you will have to add a mpi block to <cg>. <inverse> section in
your settings xml file.
<cg>
....
....
<inverse>
....
.....
<mpi>
<tasks>8</tasks>
<cmd>/opt/lam/bin/mpirun -np 8</cmd>
</mpi>
</inverse>
</cg>

Also see: http://groups.google.com/group/votca/browse_thread/thread/b6ec755d531042cb?hl=en

Third do NOT execute cg_inverse using mpirun, this is handled
internally. Gromacs will be called with the command given in
<cg>.<inverse>.<mpi>.<cmd> and multi_g_rdf will be used instead of
g_rdf.

Cheers,

Christoph

[Sikandar Mashayak]

well I have modified settings.xml file as suggested. I submit the job on the server (managed as OpenPBS), by the command qsub bat.sh (attched below).
But I get the error saying

Missing: program name
Program mdrun either does not exist, is not
executable, or is an erroneous argument to mpirun.
run_or_exit: '/opt/mpich-mx-gcc-32/bin/mpirun -np 8 mdrun -s topol.tpr ' failed

though mdrun is in my path.

-------------------
bat.sh
--------------------
# supported.  Request nodes only as above.
##PBS -l ncpus=16
#
#
# Option: -l walltime, request this amount of wall
# clock time for your job.  Format is hh:mm:ss
# The default is 1 hour, the limit is 3 days.
# The following requests 5 hours.
#PBS -l walltime=01:10:00
#
#
# Option: -j oe, combines stdout and stderr into a
# single file.
#PBS -j oe
#
# Option: -o, specifies the name of the output file
# which will be found in ${PBS_O_WORKDIR} after your
# job completes.
#PBS -o spce_ibm.out
#
# Option: -N, names the job
#PBS -N spce_ibm
#
# Change directories to the directory where the qsub
# command was issued.
#cd ${PBS_O_WORKDIR}
#
# Copy in a fresh version of the hello++. 
cd $HOME/VOTCA/tutorials/spce/ibm
rjq -mpirun run.sh


thanks
sikandar

[Christoph Junghans]

2010/4/27 Sikandar Mashayak <symas...@gmail.com>:

> well I have modified settings.xml file as suggested. I submit the job on the
> server (managed as OpenPBS), by the command qsub bat.sh (attched below).
> But I get the error saying
>
> Missing: program name
> Program mdrun either does not exist, is not
> executable, or is an erroneous argument to mpirun.
> run_or_exit: '/opt/mpich-mx-gcc-32/bin/mpirun -np 8 mdrun -s topol.tpr '
> failed
>
> though mdrun is in my path.

PBS sometimes does not inherit the setting of an interactive shell, try to add
'source path/to/gromacs/bin/GMXRC.bash'
in your bat.sh somewhere before the call of run.sh.

Cheers,

Christoph