[petsc-dev] DMCreateComposition crash in tests

Fri Mar 30 21:35:11 CDT 2012

Maybe that arch didn't get rebuilt?  The HG time stamp in your stack trace
says 'March 23'.
Hong alerted me to this bug today and the fix is here:
http://petsc.cs.iit.edu/petsc/petsc-dev/rev/de0779566bd9

Dmitry.
On Fri, Mar 30, 2012 at 9:27 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>  I will try again. But I just pulled before the test. Will see.
>
>   Barry
>
> On Mar 30, 2012, at 9:21 PM, Dmitry Karpeev wrote:
>
> > Barry,
> > This looks like petsc-dev from about a week ago -- I fixed this bug
> today.
> > It runs on my laptop right now.
> >
> > Dmitry.
> >
> > On Fri, Mar 30, 2012 at 9:00 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> > > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> > > [0]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> > > [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSCERROR: or try
> http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
> corruption errors
> > > [0]PETSC ERROR: likely location of problem given in stack below
> > > [0]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------
> > > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> > > [0]PETSC ERROR:       INSTEAD the line number of the start of the
> function
> > > [0]PETSC ERROR:       is given.
> > > [0]PETSC ERROR: [0] DMCreateDecomposition line 854
> /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c
> > > [0]PETSC ERROR: [0] PCSetUp_ASM line 161
> /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c
> > > [0]PETSC ERROR: [0] PCSetUp line 810
> /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c
> > > [0]PETSC ERROR: [0] KSPSetUp line 182
> /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c
> > > [0]PETSC ERROR: [0] KSPSolve line 339
> /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c
> > > [0]PETSC ERROR: [0] SNES_KSPSolve line 4169
> /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c
> > > [0]PETSC ERROR: [0] SNESSolve_LS line 143
> /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c
> > > [0]PETSC ERROR: [0] SNESSolve line 3345
> /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c
> > > [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> > > [0]PETSC ERROR: Signal received!
> > > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [0]PETSC ERROR: Petsc Development HG revision:
> ebfd90d136e614e3f7e877dc536ab77f25382894  HG Date: Fri Mar 23 21:43:17 2012
> -0500
> > > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > > [0]PETSC ERROR: See docs/index.html for manual pages.
> > > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [0]PETSC ERROR: ./ex50 on a arch-gnu named
> barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012
> > > [0]PETSC ERROR: Libraries linked from
> /Users/barrysmith/Src/petsc-dev/arch-gnu/lib
> > > [0]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012
> > > [0]PETSC ERROR: Configure options --download-blacs --download-fftw
> --download-hypre --download-metis --download-mpich --download-mumps
> --download-parmetis --download-ptscotch --download-scalapack
> --download-superlu --download-superlu_dist --download-yaml
> --with-shared-libraries PETSC_ARCH=arch-gnu
> > > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> > > [cli_0]: aborting job:
> > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> > > [1]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> > > [1]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> > > [1]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSCERROR: or try
> http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
> corruption errors
> > > [1]PETSC ERROR: likely location of problem given in stack below
> > > [1]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------
> > > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> > > [1]PETSC ERROR:       INSTEAD the line number of the start of the
> function
> > > [1]PETSC ERROR:       is given.
> > > [1]PETSC ERROR: [1] DMCreateDecomposition line 854
> /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c
> > > [1]PETSC ERROR: [1] PCSetUp_ASM line 161
> /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c
> > > [1]PETSC ERROR: [1] PCSetUp line 810
> /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c
> > > [1]PETSC ERROR: [1] KSPSetUp line 182
> /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c
> > > [1]PETSC ERROR: [1] KSPSolve line 339
> /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c
> > > [1]PETSC ERROR: [1] SNES_KSPSolve line 4169
> /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c
> > > [1]PETSC ERROR: [1] SNESSolve_LS line 143
> /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c
> > > [1]PETSC ERROR: [1] SNESSolve line 3345
> /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c
> > > [1]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> > > [1]PETSC ERROR: Signal received!
> > > [1]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [1]PETSC ERROR: Petsc Development HG revision:
> ebfd90d136e614e3f7e877dc536ab77f25382894  HG Date: Fri Mar 23 21:43:17 2012
> -0500
> > > [1]PETSC ERROR: See docs/changes/index.html for recent updates.
> > > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > > [1]PETSC ERROR: See docs/index.html for manual pages.
> > > [1]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [1]PETSC ERROR: ./ex50 on a arch-gnu named
> barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012
> > > [1]PETSC ERROR: Libraries linked from
> /Users/barrysmith/Src/petsc-dev/arch-gnu/lib
> > > [1]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012
> > > [1]PETSC ERROR: Configure options --download-blacs --download-fftw
> --download-hypre --download-metis --download-mpich --download-mumps
> --download-parmetis --download-ptscotch --download-scalapack
> --download-superlu --download-superlu_dist --download-yaml
> --with-shared-libraries PETSC_ARCH=arch-gnu
> > > [1]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [1]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
> > > [cli_1]: aborting job:
> > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
> > > [2]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> > > [2]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> > > [2]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[2]PETSCERROR: or try
> http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
> corruption errors
> > > [2]PETSC ERROR: likely location of problem given in stack below
> > > [2]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------
> > > [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> > > [2]PETSC ERROR:       INSTEAD the line number of the start of the
> function
> > > [2]PETSC ERROR:       is given.
> > > [2]PETSC ERROR: [2] DMCreateDecomposition line 854
> /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c
> > > [2]PETSC ERROR: [2] PCSetUp_ASM line 161
> /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c
> > > [2]PETSC ERROR: [2] PCSetUp line 810
> /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c
> > > [2]PETSC ERROR: [2] KSPSetUp line 182
> /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c
> > > [2]PETSC ERROR: [2] KSPSolve line 339
> /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c
> > > [2]PETSC ERROR: [2] SNES_KSPSolve line 4169
> /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c
> > > [2]PETSC ERROR: [2] SNESSolve_LS line 143
> /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c
> > > [2]PETSC ERROR: [2] SNESSolve line 3345
> /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c
> > > [2]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> > > [2]PETSC ERROR: Signal received!
> > > [2]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [2]PETSC ERROR: Petsc Development HG revision:
> ebfd90d136e614e3f7e877dc536ab77f25382894  HG Date: Fri Mar 23 21:43:17 2012
> -0500
> > > [2]PETSC ERROR: See docs/changes/index.html for recent updates.
> > > [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > > [2]PETSC ERROR: See docs/index.html for manual pages.
> > > [2]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [2]PETSC ERROR: ./ex50 on a arch-gnu named
> barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012
> > > [2]PETSC ERROR: Libraries linked from
> /Users/barrysmith/Src/petsc-dev/arch-gnu/lib
> > > [2]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012
> > > [2]PETSC ERROR: Configure options --download-blacs --download-fftw
> --download-hypre --download-metis --download-mpich --download-mumps
> --download-parmetis --download-ptscotch --download-scalapack
> --download-superlu --download-superlu_dist --download-yaml
> --with-shared-libraries PETSC_ARCH=arch-gnu
> > > [2]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [2]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2
> > > [cli_2]: aborting job:
> > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2
> > > [3]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> > > [3]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> > > [3]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[3]PETSCERROR: or try
> http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
> corruption errors
> > > [3]PETSC ERROR: likely location of problem given in stack below
> > > [3]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------
> > > [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> > > [3]PETSC ERROR:       INSTEAD the line number of the start of the
> function
> > > [3]PETSC ERROR:       is given.
> > > [3]PETSC ERROR: [3] DMCreateDecomposition line 854
> /Users/barrysmith/Src/petsc-dev/src/dm/interface/dm.c
> > > [3]PETSC ERROR: [3] PCSetUp_ASM line 161
> /Users/barrysmith/Src/petsc-dev/src/ksp/pc/impls/asm/asm.c
> > > [3]PETSC ERROR: [3] PCSetUp line 810
> /Users/barrysmith/Src/petsc-dev/src/ksp/pc/interface/precon.c
> > > [3]PETSC ERROR: [3] KSPSetUp line 182
> /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c
> > > [3]PETSC ERROR: [3] KSPSolve line 339
> /Users/barrysmith/Src/petsc-dev/src/ksp/ksp/interface/itfunc.c
> > > [3]PETSC ERROR: [3] SNES_KSPSolve line 4169
> /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c
> > > [3]PETSC ERROR: [3] SNESSolve_LS line 143
> /Users/barrysmith/Src/petsc-dev/src/snes/impls/ls/ls.c
> > > [3]PETSC ERROR: [3] SNESSolve line 3345
> /Users/barrysmith/Src/petsc-dev/src/snes/interface/snes.c
> > > [3]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> > > [3]PETSC ERROR: Signal received!
> > > [3]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [3]PETSC ERROR: Petsc Development HG revision:
> ebfd90d136e614e3f7e877dc536ab77f25382894  HG Date: Fri Mar 23 21:43:17 2012
> -0500
> > > [3]PETSC ERROR: See docs/changes/index.html for recent updates.
> > > [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > > [3]PETSC ERROR: See docs/index.html for manual pages.
> > > [3]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [3]PETSC ERROR: ./ex50 on a arch-gnu named
> barry-smiths-macbook-pro.local by barrysmith Fri Mar 30 20:27:34 2012
> > > [3]PETSC ERROR: Libraries linked from
> /Users/barrysmith/Src/petsc-dev/arch-gnu/lib
> > > [3]PETSC ERROR: Configure run at Fri Mar 23 22:22:13 2012
> > > [3]PETSC ERROR: Configure options --download-blacs --download-fftw
> --download-hypre --download-metis --download-mpich --download-mumps
> --download-parmetis --download-ptscotch --download-scalapack
> --download-superlu --download-superlu_dist --download-yaml
> --with-shared-libraries PETSC_ARCH=arch-gnu
> > > [3]PETSC ERROR:
> ------------------------------------------------------------------------
> > > [3]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3
> > > [cli_3]: aborting job:
> > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3
> > /Users/barrysmith/Src/petsc-dev/src/snes/examples/tutorials
> > Possible problem with ex50_6, diffs above
> >
> >
>
>
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