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. 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. -- View this message in context: http://gromacs.5086.n6.nabble.com/Segmentation-fault-mdrun-mpi-tp5001601p5001776.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
