On 10/8/12 4:39 AM, Ladasky wrote:
Justin Lemkul wrote
My first guess would be a buggy MPI implementation. I can't comment on
hardware
specs, but usually the random failures seen in mdrun_mpi are a result of
some
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
repositories.
This all seems reasonable. I asked about the MPI implementation because people
have previously reported that using LAM (which is really outdated) causes random
seg faults and errors. I would not necessarily implicate OpenMPI, as I use it
routinely. I never use repositories (I always compile from source) as I have
gotten buggy packages in the past, but I don't know if that's relevant here or
not. I'm not trying to implicate the package maintainer in any way, just noting
that long ago (5-6 years) the Gromacs package had some issues.
-Justin
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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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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