[gmx-users] parallel run stops writing in output files

elena.mol at mail.com elena.mol at mail.com
Fri Nov 6 17:06:59 CET 2009


Dear gmx users

i'm trying to run gromacs
4.0.5 (mdrun with replica exchange) in parallel on a cluster, with the command:

mpirun -np n  mdrun_mpi -multi m 
(.........other mdrun options....)

(where n is the number of
“processes” and m the n. of replicas)

and after some time it
stops writing in the output files, .log, .edr, .xtc...., although
from “top” it seems it's still running. It stops writing
“simultaneously” (after the same n. of steps) in  all these
files, I checked it by plotting energies etc from .edr, and rmsd from

I have done many tests
changing the number of processes, their distribution among nodes, the
nst.... options (how frequently to write in output files, in order to check if
the problem was due to file size..), but it always shows the same
kind of behaviour. 

The number of steps
performed before stopping is not constant, but it corresponds to a cpu
time of some minutes, while the same calculations run on a single
processor work fine (for much longer times).

Does anyone have ideas on
how to solve this problem? ...which input parameters to change...?

Many thanks in advance

Elena Molteni 

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