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

Michael Brunsteiner mbx0009 at yahoo.com
Thu Dec 11 10:32:14 CET 2008


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.


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