Justin Lemkul wrote > Random segmentation faults are really hard to debug. Can you resume the > run > using a checkpoint file? That would suggest maybe an MPI problem or > something > else external to Gromacs. Without a reproducible system and a debugging > backtrace, it's going to be hard to figure out where the problem is coming > from.
Thanks for that tip, Justin. I tried to resume one run which failed at 1.06 million cycles, and it WORKED. It proceeded all the way to the 2.50 million cycles that I designated. I now have two separate .trr files, but I suppose they can be merged. I don't know whether my crashes are random yet. I will try re-running that simulation again from time zero, to see whether it segfaults at the same place. If it doesn't, then I have a problem which may have nothing to do with GROMACS. I looked in on memory usage several times while mdrun_mpi was executing. Over all, about 3 GB of my computer's 8 GB of RAM were in use. As I expected, GROMACS used very little of this. The mpirun process used a constant 708K. I had five mdrun_mpi processes, all of which used slightly more RAM as they worked, but I didn't notice anything which suggested a gross memory leak. The process which used the most RAM was using 14.4 MB right after it started, rose to 15.9 MB within the first ten minutes or so, and reached 16.0 MB after four hours. The process which used the least RAM started at 10.6 MB and finished at 10.8 MB. All together, GROMACS was using about 64 MB. I have a well-cooled CPU, core temperatures are under 50 degrees when the system is running under full load. My system doesn't lock up or crash on me. I think that my hardware is good. -- View this message in context: http://gromacs.5086.n6.nabble.com/Segmentation-fault-mdrun-mpi-tp5001601p5001760.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
