[gmx-users] segmentation fault - extending trajectory uwing gmx4.0.4 on 16 processors with PME

Ángel Piñeiro angel.pineiro at usc.es
Fri May 15 10:26:49 CEST 2009

Dear all,
I have some membrane protein systems running in our cluster using
gmx4.0.4. The minimizations finish with reasonable potential energy
values (of the order of 10^-5 with maximum forces of the order of
10^-3). Then I am trying to run several 1-ns-long equilibration MD
trajectories with progressive relaxation of the protein positional
restraints decreasing the force constant from 1000 kJ/mol/nm^2 to 0, all
using PME on 16 processors. The PME load is about 25% in all cases. Some
systems run with no problem but others abort with final lines in the
mdrun.log file like these:
MPI Application rank 4 killed before MPI_Finalize() with signal 11
MPI Application rank 15 killed before MPI_Finalize() with signal 11

It is worth to mention that some of the simulations that present this
segmentation fault are just extensions of trajectories that finished
successfully, with the only change of reducing the force constant in 200
KJ/mol/nm^2, for example from 800 to 600 or from 1000 to 800. Other
simulations present this problem just during the first equilibration
step with a force constant of 1000.

IMPORTANT: A copy of the same topol.tpr files run on my local computer
(on one processor) with no problem, so I do believe that it is not a
problem of the initial configuration.

Anyone knows the source of this problem?

Thanks a lot for any help...


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