2012/11/24 ms <[email protected]>: > Hi, > > I am trying to run the VOTCA spce/tf tutorial (v.1.2.3) using a 4.6 revision > of gromacs I've been advised (because it still has fast kernels and AdResS > support). Unfortunately mdrun segfaults. Any hint on how to troubleshoot > this is appreciated :) > > gromacs has been compiled following the following steps: > ---- > git clone git://git.gromacs.org/gromacs.git > > cd gromacs > > git checkout --track -b release-4-6 origin/release-4-6 > > git checkout 5ba7125c5972f2aafde2310eaa4a345cbac55da5^ > > mkdir build-single-5ba7 > > mkdir exec-single-5ba7 > > cd build-single-5ba7/ > > CC=mpicc CXX=mpiCC cmake ../ -DGMX_MPI=ON -DGMX_DEFAULT_SUFFIX=OFF > -DGMX_BINARY_SUFFIX="_git4.6" -DGMX_LIBS_SUFFIX="_git4.6" -DGMX_GPU=OFF > -DCMAKE_INSTALL_PREFIX=../exec-single-5ba7/ > > make -j 8 > > make install > ---- > Segfault log below: > > > Reading file topol.tpr, VERSION 4.6-dev-20120605-c7a8265 (single precision) > [francy:17387] *** Process received signal *** > [francy:17387] Signal: Segmentation fault (11) > [francy:17387] Signal code: Address not mapped (1) > [francy:17387] Failing at address: (nil) > [francy:17390] *** Process received signal *** > [francy:17392] *** Process received signal *** > [francy:17392] Signal: Segmentation fault (11) > [francy:17392] Signal code: Address not mapped (1) > [francy:17392] Failing at address: (nil) > [francy:17386] *** Process received signal *** > [francy:17386] Signal: Segmentation fault (11) > [francy:17386] Signal code: Address not mapped (1) > [francy:17386] Failing at address: (nil) > [francy:17388] *** Process received signal *** > [francy:17388] Signal: Segmentation fault (11) > [francy:17388] Signal code: Address not mapped (1) > [francy:17388] Failing at address: (nil) > [francy:17391] *** Process received signal *** > [francy:17391] Signal: Segmentation fault (11) > [francy:17391] Signal code: Address not mapped (1) > [francy:17391] Failing at address: (nil) > [francy:17390] Signal: Segmentation fault (11) > [francy:17390] Signal code: Address not mapped (1) > [francy:17390] Failing at address: (nil) > [francy:17392] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f95a82f8cb0] > [francy:17387] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7faf1e2fbcb0] > [francy:17387] [ 1] /usr/lib/libmpi.so.0(ompi_dpm_base_mark_dyncomm+0x34) > [0x7faf1e78c724] > [francy:17387] [ 2] /usr/lib/libmpi.so.0(ompi_comm_set+0x165) > [0x7faf1e736fd5] > [francy:17387] [ 3] /usr/lib/libmpi.so.0(+0x2113f) [0x7faf1e73813f] > [francy:17387] [ 4] /usr/lib/libmpi.so.0(MPI_Comm_create+0xae) > [0x7faf1e7650be] > [francy:17387] [ 5] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(+0x108aee) > [0x7faf1f10aaee] > [francy:17387] [ 6] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(setup_dd_grid+0x7ae) > [0x7faf1f12a79e] > [francy:17387] [ 7] mdrun_git4.6(mdrunner+0xe5b) [0x4103cb] > [francy:17387] [ 8] mdrun_git4.6(main+0x160b) [0x407d3b] > [francy:17387] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7faf1df5076d] > [francy:17387] [10] mdrun_git4.6() [0x408079] > [francy:17387] *** End of error message *** > [francy:17391] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f2d49e30cb0] > [francy:17391] [ 1] /usr/lib/libmpi.so.0(ompi_dpm_base_mark_dyncomm+0x34) > [0x7f2d4a2c1724] > [francy:17391] [ 2] /usr/lib/libmpi.so.0(ompi_comm_set+0x165) > [0x7f2d4a26bfd5] > [francy:17391] [ 3] /usr/lib/libmpi.so.0(+0x2113f) [0x7f2d4a26d13f] > [francy:17391] [ 4] /usr/lib/libmpi.so.0(MPI_Comm_create+0xae) > [0x7f2d4a29a0be] > [francy:17391] [ 5] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(+0x108aee) > [0x7f2d4ac3faee] > [francy:17391] [ 6] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(setup_dd_grid+0x7ae) > [0x7f2d4ac5f79e] > [francy:17391] [ 7] mdrun_git4.6(mdrunner+0xe5b) [0x4103cb] > [francy:17391] [ 8] mdrun_git4.6(main+0x160b) [0x407d3b] > > [francy:17387] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7faf1df5076d] > [francy:17387] [10] mdrun_git4.6() [0x408079] > [francy:17387] *** End of error message *** > [francy:17391] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f2d49e30cb0] > [francy:17391] [ 1] /usr/lib/libmpi.so.0(ompi_dpm_base_mark_dyncomm+0x34) > [0x7f2d4a2c1724] > [francy:17391] [ 2] /usr/lib/libmpi.so.0(ompi_comm_set+0x165) > [0x7f2d4a26bfd5] > [francy:17391] [ 3] /usr/lib/libmpi.so.0(+0x2113f) [0x7f2d4a26d13f] > [francy:17391] [ 4] /usr/lib/libmpi.so.0(MPI_Comm_create+0xae) > [0x7f2d4a29a0be] > [francy:17391] [ 5] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(+0x108aee) > [0x7f2d4ac3faee] > [francy:17391] [ 6] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(setup_dd_grid+0x7ae) > [0x7f2d4ac5f79e] > [francy:17391] [ 7] mdrun_git4.6(mdrunner+0xe5b) [0x4103cb] > [francy:17391] [ 8] mdrun_git4.6(main+0x160b) [0x407d3b] > [francy:17391] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f2d49a8576d] > [francy:17391] [10] mdrun_git4.6() [0x408079] > [francy:17391] *** End of error message *** > [francy:17386] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7fe55580dcb0] > [francy:17386] [ 1] /usr/lib/libmpi.so.0(ompi_dpm_base_mark_dyncomm+0x34) > [0x7fe555c9e724] > [francy:17386] [ 2] /usr/lib/libmpi.so.0(ompi_comm_set+0x165) > [0x7fe555c48fd5] > [francy:17386] [ 3] /usr/lib/libmpi.so.0(+0x2113f) [0x7fe555c4a13f] > [francy:17386] [ 4] /usr/lib/libmpi.so.0(MPI_Comm_create+0xae) > [0x7fe555c770be] > [francy:17386] [ 5] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(+0x108aee) > [0x7fe55661caee] > [francy:17386] [ 6] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(setup_dd_grid+0x7ae) > [0x7fe55663c79e] > [francy:17386] [ 7] mdrun_git4.6(mdrunner+0xe5b) [0x4103cb] > [francy:17386] [ 8] mdrun_git4.6(main+0x160b) [0x407d3b] > [francy:17386] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7fe55546276d] > [francy:17386] [10] mdrun_git4.6() [0x408079] > [francy:17386] *** End of error message *** > [francy:17388] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f404dddecb0] > [francy:17388] [ 1] /usr/lib/libmpi.so.0(ompi_dpm_base_mark_dyncomm+0x34) > [0x7f404e26f724] > [francy:17388] [ 2] /usr/lib/libmpi.so.0(ompi_comm_set+0x165) > [0x7f404e219fd5] > [francy:17388] [ 3] /usr/lib/libmpi.so.0(+0x2113f) [0x7f404e21b13f] > [francy:17388] [ 4] /usr/lib/libmpi.so.0(MPI_Comm_create+0xae) > [0x7f404e2480be] > [francy:17388] [ 5] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(+0x108aee) > [0x7f404ebedaee] > [francy:17388] [ 6] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(setup_dd_grid+0x7ae) > [0x7f404ec0d79e] > [francy:17388] [ 7] mdrun_git4.6(mdrunner+0xe5b) [0x4103cb] > [francy:17388] [ 8] mdrun_git4.6(main+0x160b) [0x407d3b] > [francy:17388] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f404da3376d] > [francy:17388] [10] mdrun_git4.6() [0x408079] > [francy:17388] *** End of error message *** > [francy:17392] [ 1] /usr/lib/libmpi.so.0(ompi_dpm_base_mark_dyncomm+0x34) > [0x7f95a8789724] > [francy:17392] [ 2] /usr/lib/libmpi.so.0(ompi_comm_set+0x165) > [0x7f95a8733fd5] > [francy:17392] [ 3] /usr/lib/libmpi.so.0(+0x2113f) [0x7f95a873513f] > [francy:17392] [ 4] /usr/lib/libmpi.so.0(MPI_Comm_create+0xae) > [0x7f95a87620be] > [francy:17392] [ 5] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(+0x108aee) > [0x7f95a9107aee] > [francy:17392] [ 6] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(setup_dd_grid+0x7ae) > [0x7f95a912779e] > [francy:17392] [ 7] mdrun_git4.6(mdrunner+0xe5b) [0x4103cb] > [francy:17392] [ 8] mdrun_git4.6(main+0x160b) [0x407d3b] > [francy:17392] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f95a7f4d76d] > [francy:17392] [10] mdrun_git4.6() [0x408079] > [francy:17392] *** End of error message *** > [francy:17390] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) > [0x7f98741a0cb0] > [francy:17390] [ 1] /usr/lib/libmpi.so.0(ompi_dpm_base_mark_dyncomm+0x34) > [0x7f9874631724] > [francy:17390] [ 2] /usr/lib/libmpi.so.0(ompi_comm_set+0x165) > [0x7f98745dbfd5] > [francy:17390] [ 3] /usr/lib/libmpi.so.0(+0x2113f) [0x7f98745dd13f] > [francy:17390] [ 4] /usr/lib/libmpi.so.0(MPI_Comm_create+0xae) > [0x7f987460a0be] > [francy:17390] [ 5] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(+0x108aee) > [0x7f9874fafaee] > [francy:17390] [ 6] > /home/massimo/gromacs/gromacs-4.6git/gromacs/exec-single-5ba7/lib/libmd_git4.6.so.6(setup_dd_grid+0x7ae) > [0x7f9874fcf79e] > [francy:17390] [ 7] mdrun_git4.6(mdrunner+0xe5b) [0x4103cb] > [francy:17390] [ 8] mdrun_git4.6(main+0x160b) [0x407d3b] > [francy:17390] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) > [0x7f9873df576d] > [francy:17390] [10] mdrun_git4.6() [0x408079] > [francy:17390] *** End of error message *** > Making 3D domain decomposition 2 x 2 x 2 > -------------------------------------------------------------------------- > mpirun noticed that process rank 3 with PID 17388 on node francy exited on > signal 11 (Segmentation fault). > -------------------------------------------------------------------------- > 4 total processes killed (some possibly by mpirun during cleanup) That is strange, isn't 2x2x2=8 ? Why 4 ? > #################################################################################################### > # # > # ERROR: # > # critical: 'mpirun -np 8 mdrun_git4.6 -s topol.tpr -c confout.gro -o > traj.trr -x traj.xtc' failed # > # # > #################################################################################################### > For details see /home/massimo/gromacs/cg-adress-tests/tf/inverse.log > die: (called from 17268) CSG_MASTER_PID is 16311
It is hard to derive what went wrong, but you could try: - run mdrun on 1 core only - run the same simulation with adress=no on 8 cores - export GMX_NB_GENERIC=1 Christoph > > > > -- > Massimo Sandal, Ph.D. > http://devicerandom.org > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
