[gmx-users] with mdrun-4.0.2 and mpi output is multiplicated
gmx3 at hotmail.com
Thu Dec 11 10:49:21 CET 2008
Your results indicate that you are running two independent mdrun processes simultaneously.
Did you configure gromacs with --enable-mpi?
> Date: Thu, 11 Dec 2008 01:32:14 -0800
> From: mbx0009 at yahoo.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] with mdrun-4.0.2 and mpi output is multiplicated
> when i start a job with gmx version 4.0.2 as in:
> mpirun -np 2 --hostfile my-hostfile mdrun_d -s topol.tpr -np 2 >& err &
> then mdrun writes a traj.trr, traj.xtc and ener.edr output files, but does so twice
> so that one ends up being renamed to #ener.edr.1# etc...
> it seems as if each processor tried to write its own output file.
> (with -np 4 four files are written)
> My OS/hardware are Linux 2.6.9, 32-bit, on a rocks cluster of dual
> procesor/dual core PCs. I use double precision gmx. What i describe
> above happens if i run 2 or 4 jobs on the same machine, I didn't test
> what happens if I use more than one node.
> I assume this is harmless and the content of the two output files should
> be identical, is that correct??
> ps: I DID make sure that no old output files are lying around
> in the directory where i start the run.
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users