On 15/03/2012 6:13 PM, Peter C. Lai wrote:
Try separating your grompp run from your mpirun:
You should not really be having the scheduler execute the grompp. Run
your grompp step to generate a .tpr either on the head node or on your local
machine (then copy it over to the cluster).
Good advice.
(The -p that the scheduler is complaining about only appears in the grompp
step, so don't have the scheduler run it).
grompp is running successfully, as you can see from the output
I think "mpiexec -np 12" is being interpreted as "mpiexec -n 12 -p", and
the process of separating the grompp stage from the mdrun stage would
help make that clear - read documentation first, however.
Mark
On 2012-03-15 10:04:49AM +0300, 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?
Thanks for help
James
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