[gmx-users] GPU running problem with GMX-4.6 beta2

[Albert]

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