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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 15 08:09:17 CET 2012

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.


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