[gmx-users] Re: Segmentation fault, mdrun_mpi
blind.watchmaker at yahoo.com
Mon Oct 8 10:39:25 CEST 2012
Justin Lemkul wrote
> My first guess would be a buggy MPI implementation. I can't comment on
> specs, but usually the random failures seen in mdrun_mpi are a result of
> generic MPI failure. What MPI are you using?
I am using the OpenMPI package, version 1.4.3. It's one of three MPI
implementations which are included in the standard repositories of Ubuntu
Linux 11.10. I can also obtain MPICH2 and gromacs-mpich without jumping
through too many hoops. It looks like LAM is also available. However, if
GROMACS needs a special package to interface with LAM, it's not in the
Alternately, I could drop using the external MPI for now and just use the
new multi-threaded GROMACS defaults. I was trying to prepare for longer
runs on a cluster, however. If those runs are going to crash, I had better
know about it now.
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