[gmx-users] RHEL OS, g_mdrun

[Justin A. Lemkul]

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
> 
> #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.
> 

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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