[gmx-users] Problems with simulation on multi-nodes cluster

James Starlight jmsstarlight at gmail.com
Thu Mar 15 08:04:49 CET 2012

Dear Gromacs Users!

I have some problems with running my simulation on multi-modes station wich
use open_MPI

I've launch my jobs by means of that script. The below example of running
work on 1 node ( 12 cpu).

#PBS -N gromacs
#PBS -l nodes=1:red:ppn=12
#PBS -o gromacs.out
#PBS -e gromacs.err

cd /globaltmp/xz/job_name
grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o job.tpr
mpiexec -np 12 mdrun_mpi_d.openmpi -v -deffnm job

All nodes of my cluster consist of 12 CPU. When I'm using just 1 node on
that cluster I have no problems with running of my jobs but when I try to
use more than one nodes I've obtain error ( the example is attached in the
gromacs.err file as well as mmd.mdp of that system). Another outcome of
such multi-node simulation is that my job has been started but no
calculation were done ( the name_of_my_job.log file was empty and no update
of .trr file was seen ). Commonly this error occurs when I uses many nodes
(8-10) Finally sometimes I've obtain some errors with the PME order ( this
time I've used 3 nodes). The exactly error differs when I varry the number
of nodes.

Could you tell me whats wrong could be with my cluster?

Thanks for help

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