[gmx-users] RHEL OS, g_mdrun

ram bio rmbio861 at gmail.com
Wed May 18 22:24:15 CEST 2011

Dear Justin,

Thanks for the suggestion.
Do we need to install FFTW libraries also while installing gromacs as
I think FFT pack got installed as default when the gromacs is
installed by the system admin using yum i.e. yum install gromacs.

yum install gromacs_openmpi /
yum install gromacs_mpich2,

because when i asked my system administrator he mentioned that he
installed mpich2 version of gromacs, but when i tried to locate
g_mdrun_mpich2, i could not find it in the path, instead i found
g_mdrun_openmpi and so i tried to run the job with g_mdrun_openmpi,
but could not run the job.

So it is difficult now to figure out why I could not use
g_mdrun_openmpi, even though the file exists in the


On Wed, May 18, 2011 at 3:00 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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