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:
#!/bin/bash
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 &
Are you sure that you are running Lam correctly on your machine?
I would personally run it like this:
/tools/lam/lam-7.1.2/bin/mpirun C mdrun_mpi -np 12 -deffnm rec_md
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.
Did you have other #files# ? e.g. the .edr or .log ?
Do you lamhalt properly after previous attempts?
Yunierkis
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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