<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 TRANSITIONAL//EN">
<HTML>
<HEAD>
<META http-equiv="Content-Type" content="text/html; CHARSET=UTF-8">
<META name="GENERATOR" content="GtkHTML/3.16.1">
</HEAD>
<BODY>
What i was trying to do is to run a parallel simulation. I have successfully compiled mdrun with mpi support. <BR>
<BR>
This is my grompp command<BR>
<BR>
grompp -f md.mdp -c rec_pr.gro -p rec.top -o rec.tpr -np 12<BR>
<BR>
And this is the script I sent to the cluster:<BR>
<BR>
#!/bin/bash<BR>
<BR>
cd /home/yunierkis/MD<BR>
export LAMRSH="ssh -x"<BR>
lamboot -v .nodes<BR>
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 &<BR>
<BR>
<BR>
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.<BR>
It sounds very strange for me and I can't find an explanation.<BR>
<BR>
Yunierkis<BR>
<BR>
<BR>
On Tue, 2008-01-15 at 11:54 +1100, Mark Abraham wrote:
<BLOCKQUOTE>
<PRE>
<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">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">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">Mark</FONT>
<FONT color="#000000">_______________________________________________</FONT>
<FONT color="#000000">gmx-users mailing list <A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></FONT>
<FONT color="#000000"><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></FONT>
<FONT color="#000000">Please search the archive at <A href="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!</FONT>
<FONT color="#000000">Please don't post (un)subscribe requests to the list. Use the </FONT>
<FONT color="#000000">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</FONT>
<FONT color="#000000">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></FONT>q
</PRE>
</BLOCKQUOTE>
<HR>Servicio de Correos del Grupo de Redes. UCLV <BR>-Universidad 2008 del 11 al 15 de febrero del 2008.<BR>Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu<BR>- II Taller internacional -Virtualización en la Educación Superior-, del 11 al 15 de febrero de 2008 <BR>Palacio de Convenciones. La Habana, Cuba. http://virtual-es.uclv.edu.cu<HR>
</BODY>
</HTML>