[petsc-dev] Error in PetscSectionCreate using Fortran

[Matthew Knepley]

On Tue, Aug 28, 2012 at 4:49 PM, Chris Eldred <chris.eldred at gmail.com>wrote:

> I am getting a segmentation fault when calling PetscSectionCreate. The
> error is:
> [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]PETSC
> ERROR: 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] PetscTrMallocDefault line 183
> /home/user/Desktop/LIBRARIES/petsc-dev/src/sys/memory/mtr.c
> [0]PETSC ERROR: [0] PetscSectionCreate line 37
> /home/user/Desktop/LIBRARIES/petsc-dev/src/vec/vec/impls/seq/vsection.c
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development HG revision:
> b6fe82991deee4a0d3f9a20654bc7750a6b1fe0f  HG Date: Mon Aug 27 13:17:10
> 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: ./test on a arch-linu named Puget-101334 by user Tue
> Aug 28 15:47:36 2012
> [0]PETSC ERROR: Libraries linked from
> /home/user/Desktop/LIBRARIES/petsc-dev/arch-linux2-cxx-debug/lib
> [0]PETSC ERROR: Configure run at Mon Aug 27 12:55:14 2012
> [0]PETSC ERROR: Configure options --download-boost --download-chaco
> --download-ctetgen --download-f-blas-lapack --download-fiat
> --download-generator --download-metis --download-ml --download-mpich
> --download-parmetis --download-scientificpython --download-triangle
> --with-clanguage=cxx --with-dynamic-loading --with-shared-libraries
> --with-sieve PETSC_ARCH=arch-linux2-cxx-debug
> [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
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
> The relevant code section is:
>

>From a recent petsc-users reply:

Okay, there was a bug in the Fortran stub generation for this type. I have
pushed a fix for this. In order to
get these to rebuild, you need to

  rm $PETSC_DIR/$PETSC_ARCH/bin/bfort
  rm -rf $PETSC_DIR/externalpackages/sowing*
  cd $PETSC_DIR
  cd externalpackages
  hg clone http://petsc.cs.iit.edu/petsc/externalpackages/sowing-1.1.16/
  ./$PETSC_ARCH/conf/reconfigure-$PETSC_ARCH.py

Then you can run src/vec/vec/examples/tests/ex40f90.F

  Thanks

    Matt


> call PetscSectionCreate(PETSC_COMM_WORLD, section, ierr)
> CHKERRQ(ierr)
>
> call PetscSectionSetChart(section, 0, 11, ierr)
> CHKERRQ(ierr)
> do p=0,10
>  call PetscSectionSetDof(section, p, 3, ierr)
>  CHKERRQ(ierr)
> end do
> call PetscSectionSetUp(section, ierr)
> CHKERRQ(ierr)
>
> call PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD, ierr)
> CHKERRQ(ierr)
>
> call PetscSectionDestroy(section, ierr)
> CHKERRQ(ierr)
>
> Ideas?
>
> --
> Chris Eldred
> DOE Computational Science Graduate Fellow
> Graduate Student, Atmospheric Science, Colorado State University
> B.S. Applied Computational Physics, Carnegie Mellon University, 2009
> chris.eldred at gmail.com
>



-- 
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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