I decided to recompile mdrun with mpi support again and restart the simulation again. I also checked for lam running on the nodes and it was still running nevertheless I tried to halt lam. Now everything seems to be running ok.
On Tue, 2008-01-15 at 12:24 -0500, [EMAIL PROTECTED] wrote: > > 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 > > > > _______________________________________________ > 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.php __________________________________________________________________ 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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