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I decided to recompile mdrun with mpi support again and restart the simulation again.<BR>
I also checked for lam running on the nodes and it was still running nevertheless I tried to halt lam.<BR>
Now everything seems to be running ok.<BR>
<BR>
<BR>
<BR>
On Tue, 2008-01-15 at 12:24 -0500, chris.neale@utoronto.ca wrote:
<BLOCKQUOTE>
<PRE>
<FONT color="#000000">> What i was trying to do is to run a parallel simulation. I have</FONT>
<FONT color="#000000">> successfully compiled mdrun with mpi support.</FONT>
<FONT color="#000000">></FONT>
<FONT color="#000000">> This is my grompp command</FONT>
<FONT color="#000000">></FONT>
<FONT color="#000000">> grompp -f md.mdp -c rec_pr.gro -p rec.top -o rec.tpr -np 12</FONT>
<FONT color="#000000">></FONT>
<FONT color="#000000">> And this is the script I sent to the cluster:</FONT>
<FONT color="#000000">></FONT>
<FONT color="#000000">> #!/bin/bash</FONT>
<FONT color="#000000">></FONT>
<FONT color="#000000">> cd /home/yunierkis/MD</FONT>
<FONT color="#000000">> export LAMRSH="ssh -x"</FONT>
<FONT color="#000000">> lamboot -v .nodes</FONT>
<FONT color="#000000">> nohup mpirun -np 12 mdrun_mpi -s rec_md.tpr -o rec_md.trr -c rec_md.gro</FONT>
<FONT color="#000000">> -e rec.edr -g rec_md.log -nice 0 -np 12 &</FONT>
<FONT color="#000000">></FONT>
<FONT color="#000000">Are you sure that you are running Lam correctly on your machine?</FONT>
<FONT color="#000000">I would personally run it like this:</FONT>
<FONT color="#000000">/tools/lam/lam-7.1.2/bin/mpirun C mdrun_mpi -np 12 -deffnm rec_md</FONT>
<FONT color="#000000">></FONT>
<FONT color="#000000">> I have deleted all #md.trr.*# files and the simulation is still running</FONT>
<FONT color="#000000">> on all the 6 nodes and no new #md.trr.*# file have been created.</FONT>
<FONT color="#000000">> It sounds very strange for me and I can't find an explanation.</FONT>
<FONT color="#000000">Did you have other #files# ? e.g. the .edr or .log ?</FONT>
<FONT color="#000000">Do you lamhalt properly after previous attempts?</FONT>
<FONT color="#000000">></FONT>
<FONT color="#000000">> Yunierkis</FONT>
<FONT color="#000000">></FONT>
<FONT color="#000000">></FONT>
<FONT color="#000000">> On Tue, 2008-01-15 at 11:54 +1100, Mark Abraham wrote:</FONT>
<FONT color="#000000">></FONT>
<FONT color="#000000">>> Yunierkis Perez Castillo wrote:</FONT>
<FONT color="#000000">>> > Hi all, I'm new to gromacs. I have setup a protein MD simulation in a</FONT>
<FONT color="#000000">>> > cluster, I'm using 6 computers with 2 CPUs each one.</FONT>
<FONT color="#000000">>> > After gromacs begun running I had 12 trajectory files in the folder the</FONT>
<FONT color="#000000">>> > output is written:</FONT>
<FONT color="#000000">>> ></FONT>
<FONT color="#000000">>> > md.trr</FONT>
<FONT color="#000000">>> > #md.trr.1#</FONT>
<FONT color="#000000">>> > #md.trr.2#</FONT>
<FONT color="#000000">>> > ................</FONT>
<FONT color="#000000">>> > #md.trr.11#</FONT>
<FONT color="#000000">>> ></FONT>
<FONT color="#000000">>> > It seems like the trajectory is replicated by each CPU the simulation is</FONT>
<FONT color="#000000">>> > running on.</FONT>
<FONT color="#000000">>> > All files has the same size, and grows simultaneously as the simulation</FONT>
<FONT color="#000000">>> > advances.</FONT>
<FONT color="#000000">>> > Is that a normal thing??</FONT>
<FONT color="#000000">>> > Can I delete the #* files??</FONT>
<FONT color="#000000">>></FONT>
<FONT color="#000000">>> I infer from your results that you've run 12 single-processor</FONT>
<FONT color="#000000">>> simulations from the same working directory. GROMACS makes backups of</FONT>
<FONT color="#000000">>> files when you direct it to write to an existing file, and these are</FONT>
<FONT color="#000000">>> numbered as #filename.index#. Your 12 simulations are all there, but you</FONT>
<FONT color="#000000">>> can't assume that those files with number 5 are all from the same</FONT>
<FONT color="#000000">>> simulation, because of the possibility of filesystem asynchronicities in</FONT>
<FONT color="#000000">>> creating the files.</FONT>
<FONT color="#000000">>></FONT>
<FONT color="#000000">>> If you're trying to run 12 single-processor simulations in the same</FONT>
<FONT color="#000000">>> working directory, then you need to rethink your strategy. If you're</FONT>
<FONT color="#000000">>> trying to do something else, then you also need to rethink :-)</FONT>
<FONT color="#000000">>></FONT>
<FONT color="#000000">>> Mark</FONT>
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</PRE>
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