[petsc-dev] Issues with DMComplexGetTransitiveClosure in Fortran

Tue Aug 28 17:01:08 CDT 2012

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.

> 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