[petsc-dev] DMPlexComputeCellGeometryFVM from fortran

[Matthew Knepley]

On Wed, Mar 19, 2014 at 7:35 PM, Adrian Croucher
<a.croucher at auckland.ac.nz>wrote:

>
> On 19/03/14 02:14, Matthew Knepley wrote:
>
>
> hi, I'm trying to use the DMPlexComputeCellGeometryFVM() function from a
>> fortran program, but when I compile and link it complains:
>>
>> undefined reference to `dmplexcomputecellgeometryfvm_'
>>
>> I am running the 'next' branch of PETSc (having previously tried the
>> master branch) and configured with --with-fortran-interfaces=1. At the top
>> of my code I have #include <finclude/petsc.h90>.
>>
>> I noticed the fortran interfaces to some other functions (e.g.
>> DMPlexCreateFromDAG) also seemed to be missing in older versions (e.g. the
>> 'maint' branch)- is this one perhaps still to be added too?
>>
>
>  This is my fault. I will push it to 'next' today.
>
>
> Thanks for doing that. I can access DMPlexComputeCellGeometryFVM() from
> fortran now.
>
> However at runtime it is giving me a segfault- perhaps I am not declaring
> the centroid and normal arrays properly? I also tried declaring them as
> ordinary fortran arrays instead of pointers, but that also segfaulted. It
> works OK when I call it from C. My fortran code is below- any clues much
> appreciated. The error it gives is:
>

They need to be F90 pointers and they need to be associated with an
allocated array. Take
a look at how I do it for the arguments to DMPlexCreateSection() in DMPlex
ex1f90.F

  Thanks

     Matt


> [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 G
> NU/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] F90Array1dAccess line 70
> /home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See
> http://http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.4.4-4938-g89a3bfc  GIT
> Date: 2014-03-19 17:00:11 +0000
> [0]PETSC ERROR: testdag on a linux-gnu-c-opt named des108 by acro018 Thu
> Mar 20 13:22:15 2014
> [0]PETSC ERROR: Configure options --download-netcdf --download-exodusii
> --with-hdf5-dir=/usr/lib --with-numpy-dir=
> [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>
> - Adrian
>
> --
> program main
>
> ! setting up 3-D DMPlex using DMPlexCreateFromDAG(), DMPlexInterpolate()
> and
> ! DMPlexComputeCellGeometryFVM()
>
>   implicit none
>
> #include <finclude/petsc.h90>
>
>   DM :: dm, dmi
>   PetscInt :: dim = 3
>   PetscInt :: depth = 1
>   PetscErrorCode :: ierr
>   PetscInt, allocatable :: numPoints(:)
>   PetscInt, allocatable :: coneSize(:)
>   PetscInt, allocatable :: cones(:)
>   PetscInt, allocatable :: coneOrientations(:)
>   PetscScalar, allocatable :: vertexCoords(:)
>   PetscReal ::  vol
>   PetscReal, pointer :: centroid(:), normal(:)
>   PetscInt :: i
>
>   numPoints = [12, 2]
>   coneSize  = [8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
>   cones = [2,5,4,3,6,7,8,9,  3,4,11,10,7,12,13,8]
>   coneOrientations = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
>   vertexCoords = [ &
>        -0.5,0.0,0.0, 0.0,0.0,0.0, 0.0,1.0,0.0, -0.5,1.0,0.0, &
>        -0.5,0.0,1.0, 0.0,0.0,1.0, 0.0,1.0,1.0, -0.5,1.0,1.0, &
>         0.5,0.0,0.0, 0.5,1.0,0.0, 0.5,0.0,1.0,  0.5,1.0,1.0 ]
>
>   call PetscInitialize(PETSC_NULL_CHARACTER,ierr); CHKERRQ(ierr)
>
>   call DMPlexCreate(PETSC_COMM_WORLD, dm, ierr); CHKERRQ(ierr)
>   call PetscObjectSetName(dm, "testplex", ierr); CHKERRQ(ierr)
>   call DMPlexSetDimension(dm, dim, ierr); CHKERRQ(ierr)
>
>   call DMPlexCreateFromDAG(dm, depth, numPoints, coneSize, cones, &
>        coneOrientations, vertexCoords, ierr); CHKERRQ(ierr)
>
>   call DMPlexInterpolate(dm, dmi, ierr); CHKERRQ(ierr)
>   call DMPlexCopyCoordinates(dm, dmi, ierr); CHKERRQ(ierr)
>   call DMDestroy(dm, ierr); CHKERRQ(ierr)
>   dm = dmi
>
>   call DMView(dm, PETSC_VIEWER_STDOUT_WORLD, ierr); CHKERRQ(ierr)
>
>   do i = 0, 1
>      call DMPlexComputeCellGeometryFVM(dm, i, vol, centroid, normal, ierr)
>      CHKERRQ(ierr)
>      write(*, '(a, i2, a, f8.4, a, 3(f8.4, 1x))'), &
>           'cell:', i, 'volume:', vol, 'centroid:', centroid(1),
> centroid(2), centroid(3)
>   end do
>
>   call DMDestroy(dm, ierr); CHKERRQ(ierr)
>   call PetscFinalize(ierr); CHKERRQ(ierr)
>   deallocate(numPoints, coneSize, cones, coneOrientations, vertexCoords)
>
> end program main
>
> --
> Dr Adrian Croucher
> Department of Engineering Science
> University of Auckland
> New Zealand
> tel 64-9-373-7599 ext 84611
>
>


-- 
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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