That fixed it- thanks! On Tue, Aug 28, 2012 at 4:01 PM, Matthew Knepley <[email protected]> wrote:
On Tue, Aug 28, 2012 at 4:49 PM, Chris Eldred <[email protected]> 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 [email protected]
-- 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 [email protected]