[gmx-users] parallel run problem

[Ramachandra Rao Gullapalli]

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

# 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






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