[gmx-users] RHEL OS, g_mdrun

ram bio rmbio861 at gmail.com
Wed May 18 21:54:59 CEST 2011

Dear Gromacs Users,

I am trying to run a gromacs mdrun  job (pbs script) on the cluster
(RHEL operating system) using the recently installed gromacs version
4.5.3, but  i think i could not run it paralleled on the nodes, as it
is taking a long time to finish the job.

The information regarding the  installed gromacs on the server is as follows:

Scheduler: Moab/Torque
Mpi Version: Mpich2
OS: RHEL 5.5
Compiler: gcc  version 4.4 enterprise linux 5
FFT – FFT Pack

I am running a batch job using the script as under:

#PBS -S /bin/bash
#PBS -N aarontest
#PBS -o aaronout.txt
#PBS -j oe
#PBS -l nodes=2:ppn=4
#PBS -l walltime=336:00:00

NP=`wc -l < $PBS_NODEFILE`
#export MPI_GROUP_MAX=128

/usr/local/bin/mpirun -np 8 /usr/bin/g_mdrun -nt 8 -deffnm testnpt3ns
-v dlb yes -rdd 1.2

Please let me know your suggestions for correcting the error.


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