On 29/09/2011 12:44 PM, Tandia, Adama wrote:
Dear Co-users,
I have a systems made of simple molecules, KNO3 to say. A classical MD
runs to completion on a supercomputer when using 24 CPUs only and fails
after few hundreds of ps, not always at the same step, when I increase
the number of CPUs to 72, 84, 96 ...
"The error message is as follows: " 1 particles communicated to PME node
1 are more than 2/3 times the cut-off out of the domain decomposition
cell of their charge group in dimension x. This usually means that your
system is not well equilibrated."
A given simulation system and code cannot scale efficiently to an
arbitrary number of processors. GROMACS needs about 500-1000 atoms per
processor to get good value. Close to the lower limit, things become
increasingly likely to break. However, it is likely that your system is
not actually equilibrated.
I do know for facts that the system is very well equilibrated since the
system had previously been equilibrated with EM on another machine until
the energy does not change any more.
Successful EM does not imply equilibration, or nobody would ever worry
about equilibration once EM succeeded...
Mark
Is there any brilliant idea out there?
Thanks in advance for your help.
Regards,
Adama
__
Dr. Adama Tandia | Modeling& Simulation, Corning INC, Corning, NY 14831
USA | Tel: (+1) 607 248 1036
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