Hi everyone, I had some time on the weekend to try to troubleshoot this. Updating the BIOS and trying different compilers didn’t help, but updating the kernel to 4.11.12 has made for a much more stable system. I ran a 1 ns five times and it only crashed once.
Regards, Steffen > On Aug 8, 2017, at 6:03 PM, Steffen Graether <graet...@uoguelph.ca> wrote: > > Hi, > > I am trying to run a protein/water simulation using a new computer (Ryzen > 1700X, Nvidia GTX 1070 running Ubuntu 17.04). I compiled GROMACS 2016.3 with > gcc-5 (CUDA 8.0 complained that it only supports up to version 5) and > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON, otherwise defaults were > used. The build passed all make check tests. > > During the production mdrun, I would get core dumps almost all of the time > (mostly segmentation faults, sometimes illegal instructions, once it actually > completed the 1 ps run). I also tried different water (TIP4P2005 and SPCE), > but no change. I haven’t tried a different forcefield yet (just Amber > ff03WS), but feel like that isn’t the problem. > > Suggestions I found online seem to be mostly about not having compiled gmx on > the current machine, which I had done. I also tried recompiling with SSE4.1, > but still got a core dump. Interestingly restricting the program to the > number of physical cores (-nt 8) lets the run complete more often (3/4 > attempts), but still crash. > > I would be appreciative of any suggestions people may have for compiling a > more stable executable. > > Thanks, > Steffen -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
