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

Peter C. Lai pcl at uab.edu
Thu Mar 15 08:13:15 CET 2012

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).

(The -p that the scheduler is complaining about only appears in the grompp
step, so don't have the scheduler run it).

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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Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
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