Dear all, I am trying to install GROMACS on the server with CUDA and MPI support. I figured it out with CUDA (tried it in the MPI-less version). The problem was with the memory that 'gmx mdrun' uses out of GPUs - 'nvidia-msi' showed that only ~350 MB (of ~16000MB) has been used by 'mdrun' from 2 accelerators, which is... low result I guess?
Nevertheless, I tried to install GROMACS with MPI support now, mayve this will improve the final result. As a result - many tests during 'make check' procedure failed and after installation when I try 'gmx_mpi mdrun -h' it shows options for the command, but with such message in the end: simulacrum-PowerEdge-R740:03726] *** Process received signal *** [simulacrum-PowerEdge-R740:03726] Signal: Segmentation fault (11) [simulacrum-PowerEdge-R740:03726] Signal code: Address not mapped (1) [simulacrum-PowerEdge-R740:03726] Failing at address: 0x99 [simulacrum-PowerEdge-R740:03726] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7f9a33b44890] [simulacrum-PowerEdge-R740:03726] [ 1] /usr/lib/x86_64-linux-gnu/libopen-pal.so.20(opal_hwloc_base_free_topology+0x76)[0x7f9a33279ca6] [simulacrum-PowerEdge-R740:03726] [ 2] /usr/lib/x86_64-linux-gnu/libopen-pal.so.20(+0x6f830)[0x7f9a33276830] [simulacrum-PowerEdge-R740:03726] [ 3] /usr/lib/x86_64-linux-gnu/libopen-pal.so.20(mca_base_framework_close+0x71)[0x7f9a332551c1] [simulacrum-PowerEdge-R740:03726] [ 4] /usr/lib/x86_64-linux-gnu/libopen-pal.so.20(opal_finalize+0x95)[0x7f9a3322e365] [simulacrum-PowerEdge-R740:03726] [ 5] /usr/lib/x86_64-linux-gnu/libmpi.so.20(ompi_mpi_finalize+0x69d)[0x7f9a3496638d] [simulacrum-PowerEdge-R740:03726] [ 6] gmx_mpi(+0x93de6)[0x562531385de6] [simulacrum-PowerEdge-R740:03726] [ 7] gmx_mpi(+0x8be33)[0x56253137de33] [simulacrum-PowerEdge-R740:03726] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f9a33762b97] [simulacrum-PowerEdge-R740:03726] [ 9] gmx_mpi(+0x8f88a)[0x56253138188a] [simulacrum-PowerEdge-R740:03726] *** End of error message *** Segmentation fault (core dumped) How can I solve this issue? I'm not very expirienced user, that's why I'm writing here. Hope for the solution soon. -- With best wishes, Dudarie Dmytro -- 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 [email protected].
