[gmx-developers] When will 4.6 kernels be back?

Christoph Junghans junghans at votca.org
Mon Nov 19 18:29:59 CET 2012 

2012/11/19 ms <devicerandom at gmail.com>:
>
> 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).
Can you post this error on the votca mailing list, it fits better there.
If it is actually a gromacs problem, we can open a bug on Redmine.

Christoph
>
> 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
> --
> 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

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