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
--
========================================
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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