[gmx-users] with mdrun-4.0.2 and mpi output is multiplicated

Berk Hess 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
> Hi,
> 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??
> cheers
> Michael
> ps: I DID make sure that no old output files are lying around
> in the directory where i start the run.
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