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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 15 08:25:15 CET 2012

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.


> 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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