Random segfault for MPI based REMD at startup

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Apr 02 2014 - 00:34:20 CDT



for those of you that suffer from random segfaults during startup of MPI
based replica exchange md with NAMD 2.10, you might want to replace the 1st
line of "replica.namd" :






after 5000 replicaBarrier


The segfaults seem to come due asynchronous startups of MPI processes, so
that 1st replicas "replicaBarrier" will send into the nowhere of cyberspace,
cause not all replica processes are already there, and that of course comes
with a segmentation violation. If you still observe the error, but less
frequent, increase the waiting time for "after" as it depends on your
cluster environment.


Good luck


Norman Geist



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