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 #cat $PBS_NODEFILE NP=`wc -l < $PBS_NODEFILE` cd $PBS_O_WORKDIR #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. Thanks Ram -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
