[petsc-users] signal received error; MatNullSpaceTest; Stokes flow solver with pc fieldsplit and schur complement

Matthew Knepley knepley at gmail.com
Thu Oct 17 06:07:39 CDT 2013 

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. 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
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