[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:


cd /home/yunierkis/MD
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 :-)
> Mark
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