[petsc-dev] Error in PetscSectionCreate using Fortran

[Chris Eldred]

That fixed it- thanks!

On Tue, Aug 28, 2012 at 4:01 PM, Matthew Knepley <knepley at gmail.com> wrote:
> 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



-- 
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