[gmx-users] help on mdrun

raghuvir at bcpindia.org raghuvir at bcpindia.org
Fri Jul 8 19:37:39 CEST 2011


 I have a problem related to submitting a mdrun job on cluster.  I tried 
 to ask help or gromacs and rocks users-group.

 My machine specs.
 Cluster of Intel Xeon processors:QC with Rocks Cluster.  8 processors 
 (16 threads)

 When I submit mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px 
 pullx-umbrella0.xvg on the localhost, the job takes note of 16 threads 
 and the job completes in a day.  But when I try submitting it to the 
 cluster using following qsub script the job takes ~16 days

 #$ -cwd
 #$ -S /bin/bash
 #$ -N umbrella0
 #$ -e umbrella0.errout
 #$ -o umbrella0.out
 #$ -pe mpi 16

 echo -n "Running on: "

 /opt/openmpi/bin/mpirun -np 16 -machinefile /home/raghuvir/machines 
 /share/apps/gromacs-4.5.3/bin/mdrunmpi -deffnm umbrella0 -pf 
 pullf-umbrella0.xvg -px pullx-umbrella0.xvg

 echo "Done."

 Please help me if possible

 Thanks N Regards


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