[gmx-users] about parallel run
Yunierkis Perez Castillo
yunierkis at uclv.edu.cu
Tue Jan 15 18:08:37 CET 2008
What i was trying to do is to run a parallel simulation. I have
successfully compiled mdrun with mpi support.
This is my grompp command
grompp -f md.mdp -c rec_pr.gro -p rec.top -o rec.tpr -np 12
And this is the script I sent to the cluster:
export LAMRSH="ssh -x"
lamboot -v .nodes
nohup mpirun -np 12 mdrun_mpi -s rec_md.tpr -o rec_md.trr -c rec_md.gro
-e rec.edr -g rec_md.log -nice 0 -np 12 &
I have deleted all #md.trr.*# files and the simulation is still running
on all the 6 nodes and no new #md.trr.*# file have been created.
It sounds very strange for me and I can't find an explanation.
On Tue, 2008-01-15 at 11:54 +1100, Mark Abraham wrote:
> Yunierkis Perez Castillo wrote:
> > Hi all, I'm new to gromacs. I have setup a protein MD simulation in a
> > cluster, I'm using 6 computers with 2 CPUs each one.
> > After gromacs begun running I had 12 trajectory files in the folder the
> > output is written:
> > md.trr
> > #md.trr.1#
> > #md.trr.2#
> > ................
> > #md.trr.11#
> > It seems like the trajectory is replicated by each CPU the simulation is
> > running on.
> > All files has the same size, and grows simultaneously as the simulation
> > advances.
> > Is that a normal thing??
> > Can I delete the #* files??
> I infer from your results that you've run 12 single-processor
> simulations from the same working directory. GROMACS makes backups of
> files when you direct it to write to an existing file, and these are
> numbered as #filename.index#. Your 12 simulations are all there, but you
> can't assume that those files with number 5 are all from the same
> simulation, because of the possibility of filesystem asynchronicities in
> creating the files.
> If you're trying to run 12 single-processor simulations in the same
> working directory, then you need to rethink your strategy. If you're
> trying to do something else, then you also need to rethink :-)
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