[gmx-users] RHEL OS, g_mdrun

Justin A. Lemkul jalemkul at vt.edu
Wed May 18 22:00:35 CEST 2011

ram bio wrote:
> 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.

MPI and threading are mutually exclusive; you can't launch a multi-thread 
process (mdrun -nt) via mpirun.  The mdrun executable must be MPI-enabled to run 
on this system.  Perhaps the pre-compiled binary is not, in which case you 
should install from source with --enable-mpi and --disable-threads.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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