[gmx-developers] When will 4.6 kernels be back?
ms
devicerandom at gmail.com
Mon Nov 19 11:14:25 CET 2012
Ok, thanks for helping me again with my subpar git-fu (I use it for
internal version control but I rarely have to deal with branches/coming
back to previous revisions) - it's at least the second time you rescue
me from my git clumsiness, apparently :)
It seems the previous problems are solved, but now mdrun segfaults. I am
trying to run the VOTCA spce/tf tutorial (v.1.2.3).
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)
####################################################################################################
#
#
# 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
> 2012/11/18 ms <devicerandom at gmail.com>:
>> On 14/11/12 19:44, Christoph Junghans wrote:
>>>
>>> 2012/11/14 ms <devicerandom at gmail.com>:
>>>>
>>>> On 13/11/12 19:26, Christoph Junghans wrote:
>>>>
>>>>>> ERROR 1 [file grompp.mdp]:
>>>>>> AdResS is currently disabled
>>>>>
>>>>>
>>>>> Sorry, I think, there was a misunderstanding.
>>>>> 5ba7125c5972f2aafde2310eaa4a345cbac55da5^ is the last revision, which
>>>>> has AdResS and SSE kernels.
>>>>> We are working on re-enabling AdResS, but it will take a while.
>>>>>
>>>>
>>>> Awww. Ok, sorry. Now, what I would need (I am just teaching myself
>>>> adress...) is the last revision of gmx which was both adress-enabled and
>>>> with fast kernels.
>>>
>>> 5ba7125c5972f2aafde2310eaa4a345cbac55da5 is the revision, where Erik
>>> removed the assembly kernels, hence
>>> 5ba7125c5972f2aafde2310eaa4a345cbac55da5^ (mind the ^) is the one
>>> which still has them.
>>> Does that work for you?
>>
>>
>> Thanks for pointing at the missed ^, but still the result is the same:
>> adress is disabled.
>>
>> ---
>>
>> ERROR 1 [file grompp.mdp]:
>> AdResS is currently disabled
> Something must have went wrong:
> $git blame ./src/kernel/readir.c | grep "AdResS is currently"
> f40969c2 (Erik Lindahl 2012-10-28 14:45:52 -0400 1153)
> warning_error(wi,"AdResS is currently disabled\n");
> This from a much later commit.
>
>> ---
>>
>> Steps as before except for the git reset:
>>
>> ---
>>
>> git clone git://git.gromacs.org/gromacs.git
>>
>> cd gromacs
>>
>> git checkout --track -b release-4-6 origin/release-4-6
>>
>> git reset --soft 5ba7125c5972f2aafde2310eaa4a345cbac55da5^
> why git reset?
> $ git checkout 5ba7125c5972f2aafde2310eaa4a345cbac55da5^
> should do it. And check again with "git status" that you don't have
> any unwanted modification in the workdir.
>
> Christoph
>>
>>
>> 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
>>
>> ---
>>
>> thanks and sorry!
>> M.
>>
>>
>>>
>>>>
>>>> Any chance of remembering what it was? :)
>>>>
>>>> thanks!
>>>>
>>>> M.
>>>>
>>>>>>
>>>>>> does it mean AdResS is disabled in that revision or did I forget some
>>>>>> compilation flag?
>>>>>>
>>>>>> thanks!
>>>>>> M.
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Massimo Sandal, Ph.D.
>>>>>> http://devicerandom.org
>>>>>> --
>>>>>> gmx-developers mailing list
>>>>>> gmx-developers at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface
>>>>>> or send it to gmx-developers-request at gromacs.org.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Christoph Junghans
>>>>> Web: http://www.compphys.de
>>>>>
>>>>
>>>>
>>>> --
>>>> Massimo Sandal, Ph.D.
>>>> http://devicerandom.org
>>>> --
>>>> gmx-developers mailing list
>>>> gmx-developers at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface
>>>> or send it to gmx-developers-request at gromacs.org.
>>>
>>>
>>>
>>>
>>> --
>>> Christoph Junghans
>>> Web: http://www.compphys.de
>>>
>>
>>
>> --
>> Massimo Sandal, Ph.D.
>> http://devicerandom.org
>> --
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-developers-request at gromacs.org.
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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