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 & 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. 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 > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.phpq __________________________________________________________________ Servicio de Correos del Grupo de Redes. UCLV - Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu - II Taller internacional -Virtualizaci�n en la Educaci�n Superior-, del 11 al 15 de febrero de 2008 Palacio de Convenciones. La Habana, Cuba. http://virtual-es.uclv.edu.cu
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