[petsc-dev] Issues with DMComplexGetTransitiveClosure in Fortran
Chris Eldred
chris.eldred at gmail.com
Wed Aug 29 13:35:36 CDT 2012
DMComplexGetTransitiveClosure (and Restore) work fine now. What are
the new restrictions on numbering mentioned in
src/dm/impls/complex/examples/tests/ex2f90.F?
On Tue, Aug 28, 2012 at 8:16 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Tue, Aug 28, 2012 at 5:01 PM, Chris Eldred <chris.eldred at gmail.com>
> wrote:
>>
>> On Tue, Aug 28, 2012 at 3:49 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>> > On Tue, Aug 28, 2012 at 4:39 PM, Chris Eldred <chris.eldred at gmail.com>
>> > wrote:
>> >>
>> >> DMComplexGetTransitiveClosure does not appear to have the calling
>> >> sequence (DM dm, PetscInt p, PetscBool useCone, PetscInt *numPoints,
>> >> PetscInt *points[]) indicated in the documentation- instead it has DM
>> >> dm, PetscInt p, PetscBool useCone, PetscInt *points[]. In addition, it
>> >> does not appear to be returning the full closure- instead it just
>> >> gives cone + the point.
>> >
>> >
>> > 1) I will turn this code into a running example
>> >
>>
>> Awesome! I have been using the Doublet mesh to test DMComplex routines
>> and my own functions, so that is great.
>
>
> Okay, there was a bug in the array handling. The test is
>
> src/dm/impls/complex/examples/tests/ex2f90.F
>
> Thanks,
>
> Matt
>
>>
>> > 2) I will fix the documentation. The interface change for Fortran comes
>> > because the size
>> > is embedded in the array pointer. If you think I should still return
>> > the
>> > size in Fortran,
>> > let me know.
>>
>> I can get the size from the array pointer so just returning that works.
>>
>> >
>> > 3) I will also check to make sure the documentation is clear that this
>> > thing
>> > returns each
>> > point AND its orientation.
>> >
>> > Will write again when I have your thing running. It could be an error
>> > with
>> > the Fortran array
>> > processing I put in.
>> >
>> > Thanks,
>> >
>> > Matt
>> >
>> >>
>> >> Sample code is below:
>> >>
>> >> program main
>> >> implicit none
>> >> !
>> >> ! #echo '#include <finclude/petscsys.h>\n'
>> >> #echo '#include <finclude/petsc.h90>'
>> >> #echo '#include <finclude/petscdmcomplex.h>\n'
>> >> #echo '#include <finclude/petscdmcomplex.h90>'
>> >> ! #echo '#include <finclude/petscdm.h>\n'
>> >> ! #echo '#include <finclude/petscdm.h90>\n'
>> >>
>> >> !
>> >> DM dm
>> >> PetscInt, target, dimension(3) :: EC
>> >> PetscInt, target, dimension(2) :: VE
>> >> PetscInt, pointer :: pEC(:), pVE(:)
>> >> PetscInt, pointer :: nClosure(:)
>> >> PetscInt, pointer :: pClosure(:), pCone(:), pCone2(:)
>> >> PetscErrorCode ierr
>> >>
>> >> call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
>> >> CHKERRQ(ierr)
>> >> call DMComplexCreate(PETSC_COMM_WORLD, dm, ierr)
>> >> CHKERRQ(ierr)
>> >>
>> >> !Make Doublet Mesh from Fig 2 of Flexible Representation of
>> >> Computational Meshes (except indexing is from 0 instead of 1)
>> >> call DMComplexSetChart(dm, 0, 11, ierr)
>> >> CHKERRQ(ierr)
>> >>
>> >> call DMComplexSetConeSize(dm, 9, 3,ierr)
>> >> CHKERRQ(ierr)
>> >> call DMComplexSetConeSize(dm, 10, 3,ierr)
>> >> CHKERRQ(ierr)
>> >> call DMComplexSetConeSize(dm, 4, 2,ierr)
>> >> CHKERRQ(ierr)
>> >> call DMComplexSetConeSize(dm, 5, 2,ierr)
>> >> CHKERRQ(ierr)
>> >> call DMComplexSetConeSize(dm, 6, 2,ierr)
>> >> CHKERRQ(ierr)
>> >> call DMComplexSetConeSize(dm, 7, 2,ierr)
>> >> CHKERRQ(ierr)
>> >> call DMComplexSetConeSize(dm, 8, 2,ierr)
>> >> CHKERRQ(ierr)
>> >>
>> >> call DMSetUp(dm, ierr)
>> >> CHKERRQ(ierr)
>> >>
>> >> EC(1) = 4
>> >> EC(2) = 5
>> >> EC(3) = 6
>> >> pEC => EC
>> >> call DMComplexSetCone(dm, 9 , pEC, ierr)
>> >> CHKERRQ(ierr)
>> >> EC(1) = 6
>> >> EC(2) = 7
>> >> EC(3) = 8
>> >> pEC => EC
>> >> call DMComplexSetCone(dm, 10 , pEC, ierr)
>> >> CHKERRQ(ierr)
>> >>
>> >> VE(1) = 0
>> >> VE(2) = 1
>> >> pVE => VE
>> >> call DMComplexSetCone(dm, 4 , pVE, ierr)
>> >> CHKERRQ(ierr)
>> >> VE(1) = 0
>> >> VE(2) = 2
>> >> pVE => VE
>> >> call DMComplexSetCone(dm, 5 , pVE, ierr)
>> >> CHKERRQ(ierr)
>> >> VE(1) = 1
>> >> VE(2) = 2
>> >> pVE => VE
>> >> call DMComplexSetCone(dm, 6 , pVE, ierr)
>> >> CHKERRQ(ierr)
>> >> VE(1) = 2
>> >> VE(2) = 3
>> >> pVE => VE
>> >> call DMComplexSetCone(dm, 7 , pVE, ierr)
>> >> CHKERRQ(ierr)
>> >> VE(1) = 1
>> >> VE(2) = 3
>> >> pVE => VE
>> >> call DMComplexSetCone(dm, 8 , pVE, ierr)
>> >> CHKERRQ(ierr)
>> >>
>> >> call DMComplexSymmetrize(dm,ierr)
>> >> CHKERRQ(ierr)
>> >> call DMComplexStratify(dm,ierr)
>> >> CHKERRQ(ierr)
>> >>
>> >> !Test Stuff
>> >>
>> >> call DMComplexGetTransitiveClosure(dm,10,PETSC_TRUE,nClosure,ierr)
>> >> !pClosure,ierr)
>> >> CHKERRQ(ierr)
>> >> write(*,*) nClosure
>> >> write(*,*) pClosure
>> >>
>> >> call DMDestroy(dm,ierr)
>> >> CHKERRQ(ierr)
>> >> call PetscFinalize(ierr)
>> >> CHKERRQ(ierr)
>> >> end
>> >>
>> >>
>> >> The output is:
>> >> 10 0 6 0 7
>> >> 0 8
>> >>
>> >> and then there is an error in DMDestroy
>> >>
>> >> [0]PETSC ERROR: --------------------- Error Message
>> >> ------------------------------------
>> >> [0]PETSC ERROR: Object is in wrong state!
>> >> [0]PETSC ERROR: Work array still checked out!
>> >> [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 15:31:06 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: DMDestroy() line 234 in
>> >> /home/user/Desktop/LIBRARIES/petsc-dev/src/dm/interface/dm.c
>> >> application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0
>> >> [unset]: aborting job:
>> >> application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0
>> >>
>> >> 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
>
>
>
>
> --
> 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
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