[petsc-users] signal received error; MatNullSpaceTest; Stokes flow solver with pc fieldsplit and schur complement
Matthew Knepley
knepley at gmail.com
Thu Oct 17 07:46:42 CDT 2013
On Thu, Oct 17, 2013 at 7:43 AM, Bishesh Khanal <bisheshkh at gmail.com> wrote:
>
>
>
> On Thu, Oct 17, 2013 at 1:07 PM, Matthew Knepley <knepley at gmail.com>wrote:
>
>> On Thu, Oct 17, 2013 at 3:42 AM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>>
>>>
>>>
>>>
>>> On Wed, Oct 16, 2013 at 8:04 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>>>
>>>> On Wed, 16 Oct 2013, Matthew Knepley wrote:
>>>>
>>>> > You can also try running under MPICH, which can be valgrind clean.
>>>>
>>>> Actually --download-mpich would configure/install mpich with
>>>> appropriate flags to be valgrind clean.
>>>>
>>>
>>> In my laptop (but not in the cluster, please look at the second part of
>>> this reply below for the cluster case) that's how I configured petsc and
>>> ran it under mpich. The following errors (which I do not understand what
>>> they mean) was reported by valgrind when using the mpich of the petsc in my
>>> laptop: Here is the command I used and the error:
>>>
>>
>> This is harmless, and as you can see it comes from gfortran
>> initialization.
>>
>>
>>> (Note: petsc is an alias in my .bashrc: alias
>>> petsc='/home/bkhanal/Documents/softwares/petsc-3.4.3/bin/petscmpiexec'
>>>
>>> petsc -n 2 valgrind src/AdLemMain -pc_type fieldsplit
>>> -pc_fieldsplit_type schur -pc_fieldsplit_dm_splits 0
>>> -pc_fieldsplit_0_fields 0,1,2 -pc_fieldsplit_1_fields 3
>>> -fieldsplit_0_pc_type hypre -fieldsplit_0_ksp_converged_reason
>>> -ksp_converged_reason
>>> ==3106== Memcheck, a memory error detector
>>> ==3106== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
>>> ==3106== Using Valgrind-3.6.1 and LibVEX; rerun with -h for copyright
>>> info
>>> ==3107== Memcheck, a memory error detector
>>> ==3107== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
>>> ==3107== Using Valgrind-3.6.1 and LibVEX; rerun with -h for copyright
>>> info
>>> ==3107== Command: src/AdLemMain -pc_type fieldsplit -pc_fieldsplit_type
>>> schur -pc_fieldsplit_dm_splits 0 -pc_fieldsplit_0_fields 0,1,2
>>> -pc_fieldsplit_1_fields 3 -fieldsplit_0_pc_type hypre
>>> -fieldsplit_0_ksp_converged_reason -ksp_converged_reason
>>> ==3107==
>>> ==3106== Command: src/AdLemMain -pc_type fieldsplit -pc_fieldsplit_type
>>> schur -pc_fieldsplit_dm_splits 0 -pc_fieldsplit_0_fields 0,1,2
>>> -pc_fieldsplit_1_fields 3 -fieldsplit_0_pc_type hypre
>>> -fieldsplit_0_ksp_converged_reason -ksp_converged_reason
>>> ==3106==
>>> ==3107== Conditional jump or move depends on uninitialised value(s)
>>> ==3107== at 0x32EEED9BCE: ??? (in /usr/lib64/libgfortran.so.3.0.0)
>>> ==3107== by 0x32EEED9155: ??? (in /usr/lib64/libgfortran.so.3.0.0)
>>> ==3107== by 0x32EEE185D7: ??? (in /usr/lib64/libgfortran.so.3.0.0)
>>> ==3107== by 0x32ECC0F195: call_init.part.0 (in /lib64/ld-2.14.90.so)
>>> ==3107== by 0x32ECC0F272: _dl_init (in /lib64/ld-2.14.90.so)
>>> ==3107== by 0x32ECC01719: ??? (in /lib64/ld-2.14.90.so)
>>> ==3107== by 0xE: ???
>>> ==3107== by 0x7FF0003EE: ???
>>> ==3107== by 0x7FF0003FC: ???
>>> ==3107== by 0x7FF000405: ???
>>> ==3107== by 0x7FF000410: ???
>>> ==3107== by 0x7FF000424: ???
>>> ==3107==
>>> ==3107== Conditional jump or move depends on uninitialised value(s)
>>> ==3107== at 0x32EEED9BD9: ??? (in /usr/lib64/libgfortran.so.3.0.0)
>>> ==3107== by 0x32EEED9155: ??? (in /usr/lib64/libgfortran.so.3.0.0)
>>> ==3107== by 0x32EEE185D7: ??? (in /usr/lib64/libgfortran.so.3.0.0)
>>> ==3107== by 0x32ECC0F195: call_init.part.0 (in /lib64/ld-2.14.90.so)
>>> ==3107== by 0x32ECC0F272: _dl_init (in /lib64/ld-2.14.90.so)
>>> ==3107== by 0x32ECC01719: ??? (in /lib64/ld-2.14.90.so)
>>> ==3107== by 0xE: ???
>>> ==3107== by 0x7FF0003EE: ???
>>> ==3107== by 0x7FF0003FC: ???
>>> ==3107== by 0x7FF000405: ???
>>> ==3107== by 0x7FF000410: ???
>>> ==3107== by 0x7FF000424: ???
>>> ==3107==
>>> dmda of size: (8,8,8)
>>>
>>> using schur complement
>>>
>>> using user defined split
>>> Linear solve converged due to CONVERGED_ATOL iterations 0
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 3
>>> Linear solve converged due to CONVERGED_RTOL iterations 1
>>> ==3106==
>>> ==3106== HEAP SUMMARY:
>>> ==3106== in use at exit: 187,709 bytes in 1,864 blocks
>>> ==3106== total heap usage: 112,891 allocs, 111,027 frees, 19,838,487
>>> bytes allocated
>>> ==3106==
>>> ==3107==
>>> ==3107== HEAP SUMMARY:
>>> ==3107== in use at exit: 212,357 bytes in 1,870 blocks
>>> ==3107== total heap usage: 112,701 allocs, 110,831 frees, 19,698,341
>>> bytes allocated
>>> ==3107==
>>> ==3106== LEAK SUMMARY:
>>> ==3106== definitely lost: 0 bytes in 0 blocks
>>> ==3106== indirectly lost: 0 bytes in 0 blocks
>>> ==3106== possibly lost: 0 bytes in 0 blocks
>>> ==3106== still reachable: 187,709 bytes in 1,864 blocks
>>> ==3106== suppressed: 0 bytes in 0 blocks
>>> ==3106== Rerun with --leak-check=full to see details of leaked memory
>>> ==3106==
>>> ==3106== For counts of detected and suppressed errors, rerun with: -v
>>> ==3106== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 2 from 2)
>>> ==3107== LEAK SUMMARY:
>>> ==3107== definitely lost: 0 bytes in 0 blocks
>>> ==3107== indirectly lost: 0 bytes in 0 blocks
>>> ==3107== possibly lost: 0 bytes in 0 blocks
>>> ==3107== still reachable: 212,357 bytes in 1,870 blocks
>>> ==3107== suppressed: 0 bytes in 0 blocks
>>> ==3107== Rerun with --leak-check=full to see details of leaked memory
>>> ==3107==
>>> ==3107== For counts of detected and suppressed errors, rerun with: -v
>>> ==3107== Use --track-origins=yes to see where uninitialised values come
>>> from
>>> ==3107== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 2 from 2)
>>>
>>> In the above example, the solver iterates and gives results.
>>>
>>> Now the case in cluster: I had to configure petsc with the option:
>>> --with-mpi-dir=/opt/openmpi-gcc/current/ , that's how the cluster
>>> administrators asked me to install to get petsc running in many nodes of
>>> the clusters. I had tried on my own to configure with --download-mpich in
>>> the cluster too, but could not succeed with some errors. If you really
>>> think the errors could be from this configuration, I would retry to install
>>> with the petscmpich; please let me know.
>>> And the valgrind errors for the case where program terminates without
>>> completing normally (big sized domain), it has following errors just before
>>> abrupt termination:
>>>
>>> ... lots of other errors and then warnings such as:
>>>
>>
>> This appears to be a bug in OpenMPI, which would not be all that
>> surprising. First, you can try running
>> in the debugger and extracting a stack trace from the SEGV.
>>
>
> Just to make sure that I understood what you said before I talk with the
> cluster administrators:
> The program crashes only for a bigger domain size. Even in the cluster, it
> does not crash for the domain size up to a certain size. So I need to run
> in the debugger for the case when it crashes to get the stack trace from
> the SEGV, right ? I do not know how to attach a debugger when submitting a
> job to the cluster if that is possible at all! Or are you asking me to run
> the program in the debugger in my laptop for the biggest size ? (I have not
> tried running the code for the biggest size in my laptop fearing it might
> take forever)
>
There is no use being afraid. Run it both places. Ask the admins how to map
your display for the cluster and use -start_in_debugger.
Matt
> Then you could
>>
>> 1) Get the admin to install MPICH
>>
>> 2) Try running a PETSc example on the cluster
>>
>
>> 3) Try running on another machine
>>
>> Matt
>>
>>
>>> ==55437== Warning: set address range perms: large range [0xc4369040,
>>> 0xd6abb670) (defined)
>>> ==55438== Warning: set address range perms: large range [0xc4369040,
>>> 0xd6a6cd00) (defined)
>>> ==37183== Warning: set address range perms: large range [0xc4369040,
>>> 0xd69f57d8) (defined)
>>> ==37182== Warning: set address range perms: large range [0xc4369040,
>>> 0xd6a474f0) (defined)
>>> mpiexec: killing job...
>>>
>>>
>>> In between there are several errors such as:
>>> ==59334== Use of uninitialised value of size 8
>>> ==59334== at 0xD5B3704: mca_pml_ob1_send_request_put
>>> (pml_ob1_sendreq.c:1217)
>>> ==59334== by 0xE1EF01A: btl_openib_handle_incoming
>>> (btl_openib_component.c:3092)
>>> ==59334== by 0xE1F03E9: btl_openib_component_progress
>>> (btl_openib_component.c:3634)
>>> ==59334== by 0x81CF16A: opal_progress (opal_progress.c:207)
>>> ==59334== by 0x81153AC: ompi_request_default_wait_all (condition.h:92)
>>> ==59334== by 0xF4C25DD: ompi_coll_tuned_sendrecv_actual
>>> (coll_tuned_util.c:54)
>>> ==59334== by 0xF4C91FD:
>>> ompi_coll_tuned_allgatherv_intra_neighborexchange (coll_tuned_util.h:57)
>>> ==59334== by 0x8121783: PMPI_Allgatherv (pallgatherv.c:139)
>>> ==59334== by 0x5156D19: ISAllGather (iscoloring.c:502)
>>> ==59334== by 0x57A6B78: MatGetSubMatrix_MPIAIJ (mpiaij.c:3607)
>>> ==59334== by 0x532DB36: MatGetSubMatrix (matrix.c:7297)
>>> ==59334== by 0x5B97725: PCSetUp_FieldSplit(_p_PC*) (fieldsplit.c:524)
>>>
>>>
>>>
>>>
>>>
>>>
>>>>
>>>> Satish
>>>>
>>>
>>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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