Hi Albert, Thanks for the testing.
Last questions. - What version are you using? Is it beta2 release or latest git? if it's the former, getting the latest git might help if... - (do) you happen to be using GMX_GPU_ACCELERATION=None (you shouldn't!)? A bug triggered only with this setting has been fixed recently. If the above doesn't help, please file a bug report and attach a tpr so we can reproduce. Cheers, -- Szilárd On Mon, Dec 17, 2012 at 6:21 PM, Albert <mailmd2...@gmail.com> wrote: > On 12/17/2012 06:08 PM, Szilárd Páll wrote: > >> Hi, >> >> How about GPU emulation or CPU-only runs? Also, please try setting the >> number of therads to 1 (-ntomp 1). >> >> >> -- >> Szilárd >> >> > hello: > > I am running in GPU emulation mode with the GMX_EMULATE_GPU=1 env. var > set (and to match closer the GPU setup with -ntomp 12), it failed with log: > > Back Off! I just backed up step33b.pdb to ./#step33b.pdb.2# > > Back Off! I just backed up step33c.pdb to ./#step33c.pdb.2# > > Wrote pdb files with previous and current coordinates > [CUDANodeA:20753] *** Process received signal *** > [CUDANodeA:20753] Signal: Segmentation fault (11) > [CUDANodeA:20753] Signal code: Address not mapped (1) > [CUDANodeA:20753] Failing at address: 0x106ae6a00 > > [1] Segmentation fault mdrun_mpi -v -s nvt.tpr -c nvt.gro -g > nvt.log -x nvt.xtc -ntomp 12 > > > > > I also tried , number of therads to 1 (-ntomp 1), it failed with following > messages: > > > Back Off! I just backed up step33c.pdb to ./#step33c.pdb.1# > > Wrote pdb files with previous and current coordinates > [CUDANodeA:20740] *** Process received signal *** > [CUDANodeA:20740] Signal: Segmentation fault (11) > [CUDANodeA:20740] Signal code: Address not mapped (1) > [CUDANodeA:20740] Failing at address: 0x1f74a96ec > [CUDANodeA:20740] [ 0] /lib64/libpthread.so.0(+**0xf2d0) [0x2b351d3022d0] > [CUDANodeA:20740] [ 1] /opt/gromacs-4.6/lib/libmd_**mpi.so.6(+0x11020f) > [0x2b351a99c20f] > [CUDANodeA:20740] [ 2] /opt/gromacs-4.6/lib/libmd_**mpi.so.6(+0x111c94) > [0x2b351a99dc94] > [CUDANodeA:20740] [ 3] > /opt/gromacs-4.6/lib/libmd_**mpi.so.6(gmx_pme_do+0x1d2e) > [0x2b351a9a1bae] > [CUDANodeA:20740] [ 4] /opt/gromacs-4.6/lib/libmd_** > mpi.so.6(do_force_lowlevel+**0x1eef) [0x2b351a97262f] > [CUDANodeA:20740] [ 5] /opt/gromacs-4.6/lib/libmd_** > mpi.so.6(do_force_cutsVERLET+**0x1756) [0x2b351aa04736] > [CUDANodeA:20740] [ 6] /opt/gromacs-4.6/lib/libmd_**mpi.so.6(do_force+0x3bf) > [0x2b351aa0a0df] > [CUDANodeA:20740] [ 7] mdrun_mpi(do_md+0x8133) [0x4334c3] > [CUDANodeA:20740] [ 8] mdrun_mpi(mdrunner+0x19e9) [0x411639] > [CUDANodeA:20740] [ 9] mdrun_mpi(main+0x17db) [0x4373db] > [CUDANodeA:20740] [10] /lib64/libc.so.6(__libc_start_**main+0xfd) > [0x2b351d52ebfd] > [CUDANodeA:20740] [11] mdrun_mpi() [0x407f09] > [CUDANodeA:20740] *** End of error message *** > > [1] Segmentation fault mdrun_mpi -v -s nvt.tpr -c nvt.gro -g > nvt.log -x nvt.xtc -ntomp 1 > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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