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

Thu Oct 17 03:42:33 CDT 2013

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:
(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:

==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
>
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