[gmx-users] mpich job hangs on exit
David van der Spoel
spoel at xray.bmc.uu.se
Wed Aug 4 12:44:26 CEST 2004
On Wed, 4 Aug 2004, Anton Feenstra wrote:
>David van der Spoel wrote:
>> Maybe time to make a short test problem...
>> It could also be due to a combination of MPI and queueing system, but if
>> you can reproduce it in a ten step simulation you can try running with
>OK, did that. I now have a 40k atom system (protein + water) that runs for
>10 steps on 8 CPU's and than hangs during exit, as I described previously.
>Turning on -debug eliminates the problem. What is the next step?
See where it hangs in the mdrunXX.log files.
The question is whether the nodes ever reach the mpi_finalize call, or
whether they are killed by the queue system.
Maybe you have to put in extra debug statements.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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