On 15/03/2012 6:04 PM, James Starlight wrote:
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).
#!/bin/sh
#PBS -N gromacs
#PBS -l nodes=1:red:ppn=12
#PBS -V
#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?
The error message is quite explicit and is clearly nothing to do with
GROMACS. Your invocation of mpiexec is malformed. You need to consult
your local documentation.
Mark
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