[petsc-dev] DMCreateComposition crash in tests

Fri Mar 30 21:41:41 CDT 2012

I don't think so.

On Fri, Mar 30, 2012 at 9:39 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>  Do I have to rerun configure ?
>
> On Mar 30, 2012, at 9:35 PM, Dmitry Karpeev wrote:
>
> > 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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