Hi Matt,To test the Segmentation Violation problem in my code, I modified the example ex1f90.F to reproduce the problem I have in my own code.
If use DMPlexCreateBoxMesh to generate the mesh, the code works fine. However, if I use DMPlexCreateGmshFromFile, using the same mesh exported from "DMPlexCreateBoxMesh", it gives Segmentation Violation error.
Did I miss something in the input mesh file? My first guess is the label "marker" used in the code, but I couldn't find any place to set this label.
Would you please let me know how to solve this problem. My code is done in a similar way as ex1f90, it reads mesh from external file or creates from cell list, distributes the mesh (these already work), and then creates sections and sets ndof to the nodes.
Thanks, Danyang On 18-02-20 10:07 AM, Danyang Su wrote:
On 18-02-20 09:52 AM, Matthew Knepley wrote:On Tue, Feb 20, 2018 at 12:30 PM, Danyang Su <danyang...@gmail.com <mailto:danyang...@gmail.com>> wrote:Hi All, I tried to compile the DMPlexCreateSection code but got error information as shown below. Error: Symbol 'petsc_null_is' at (1) has no IMPLICIT type I tried to use PETSC_NULL_OBJECT instead of PETSC_NULL_IS, then the code can be compiled but run into Segmentation Violation error in DMPlexCreateSection. From the webpagehttp://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMPLEX/DMPlexCreateSection.htmlThe F90 version is DMPlexCreateSectionF90. Doing this with F77 arrays would have been too painful.Hi Matt,Sorry, I still cannot compile the code if use DMPlexCreateSectionF90 instead of DMPlexCreateSection. Would you please tell me in more details?undefined reference to `dmplexcreatesectionf90_'then I #include <petsc/finclude/petscdmplex.h90>, but this throws more error during compilation.Included at /home/dsu/Soft/PETSc/petsc-3.7.5/include/petsc/finclude/petscdmplex.h90:6:Included at ../../solver/solver_ddmethod.F90:62: PETSCSECTION_HIDE section 1 Error: Unclassifiable statement at (1) /home/dsu/Soft/PETSc/petsc-3.7.5/include/petsc/finclude/ftn-custom/petscdmplex.h90:167.10:Included at /home/dsu/Soft/PETSc/petsc-3.7.5/include/petsc/finclude/petscdmplex.h90:6:Included at ../../solver/solver_ddmethod.F90:62: PETSCSECTION_HIDE section 1 Error: Unclassifiable statement at (1) /home/dsu/Soft/PETSc/petsc-3.7.5/include/petsc/finclude/ftn-custom/petscdmplex.h90:179.10:Included at /home/dsu/Soft/PETSc/petsc-3.7.5/include/petsc/finclude/petscdmplex.h90:6:Included at ../../solver/solver_ddmethod.F90:62:Thanks, Matt dmda_flow%da is distributed dm object that works fine. The fortran example I follow is http://www.mcs.anl.gov/petsc/petsc-dev/src/dm/impls/plex/examples/tutorials/ex1f90.F90 <http://www.mcs.anl.gov/petsc/petsc-dev/src/dm/impls/plex/examples/tutorials/ex1f90.F90>. What parameters should I use if passing null to bcField, bcComps, bcPoints and perm. PetscErrorCode <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscErrorCode.html#PetscErrorCode> DMPlexCreateSection <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/DMPLEX/DMPlexCreateSection.html#DMPlexCreateSection>(DM <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/DM/DM.html#DM> dm,PetscInt <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt> dim,PetscInt <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt> numFields,constPetscInt <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt> numComp[],constPetscInt <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt> numDof[],PetscInt <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt> numBC,constPetscInt <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt> bcField[], constIS <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/IS/IS.html#IS> bcComps[], constIS <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/IS/IS.html#IS> bcPoints[],IS <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/IS/IS.html#IS> perm,PetscSection <https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/IS/PetscSection.html#PetscSection> *section) #include <petsc/finclude/petscis.h> #include <petsc/finclude/petscis.h90> #include <petsc/finclude/petscdmplex.h> ... #ifdef USG numFields = 1 numComp(1) = 1 pNumComp => numComp do i = 1, numFields*(dmda_flow%dim+1) numDof(i) = 0 end do numDof(0*(dmda_flow%dim+1)+1) = dmda_flow%dof pNumDof => numDof numBC = 0 call DMPlexCreateSection(dmda_flow%da,dmda_flow%dim, & numFields,pNumComp,pNumDof, & numBC,PETSC_NULL_INTEGER, & PETSC_NULL_IS,PETSC_NULL_IS, & !Error here PETSC_NULL_IS,section,ierr) CHKERRQ(ierr) call PetscSectionSetFieldName(section,0,'flow',ierr) CHKERRQ(ierr) call DMSetDefaultSection(dmda_flow%da,section,ierr) CHKERRQ(ierr) call PetscSectionDestroy(section,ierr) CHKERRQ(ierr) #endif Thanks, Danyang --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 https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/%7Emk51/>
program DMPlexTestField
implicit none
#include "petsc/finclude/petsc.h90"
DM :: dm, dmDist
DMLabel :: label
Vec :: u
PetscViewer :: viewer
PetscSection :: section
PetscInt :: dim,numFields,numBC,i,val
PetscInt, target, dimension(3) :: &
& numComp
PetscInt, pointer :: pNumComp(:)
PetscInt, target, dimension(12) :: &
& numDof
PetscInt, pointer :: pNumDof(:)
PetscInt, target, dimension(1) :: &
& bcField
PetscInt, pointer :: pBcField(:)
IS, target, dimension(1) :: &
& bcCompIS
IS, target, dimension(1) :: &
& bcPointIS
IS, pointer :: pBcCompIS(:)
IS, pointer :: pBcPointIS(:)
PetscBool :: interpolate
PetscErrorCode :: ierr
call PetscInitialize(PETSC_NULL_CHARACTER, ierr)
CHKERRQ(ierr)
dim = 2
call PetscOptionsGetInt(PETSC_NULL_OBJECT,PETSC_NULL_CHARACTER, &
& '-dim', dim,PETSC_NULL_BOOL, ierr)
CHKERRQ(ierr)
interpolate = PETSC_TRUE
! Create a mesh
! call DMPlexCreateBoxMesh(PETSC_COMM_WORLD, dim, interpolate, dm,
! & ierr)
call DMPlexCreateGmshFromFile(PETSC_COMM_WORLD,'./sol.msh', &
& interpolate,dm)
CHKERRQ(ierr)
call DMPlexDistribute(dm, 0, PETSC_NULL_OBJECT, dmDist,ierr)
CHKERRQ(ierr)
if (dmDist /= PETSC_NULL_OBJECT) then
call DMDestroy(dm,ierr)
CHKERRQ(ierr)
dm = dmDist
end if
! Create a scalar field u, a vector field v, and a surface vector field w
numFields = 3
numComp(1) = 1
numComp(2) = dim
numComp(3) = dim-1
pNumComp => numComp
do i = 1, numFields*(dim+1)
numDof(i) = 0
end do
! Let u be defined on vertices
numDof(0*(dim+1)+1) = 1
! Let v be defined on cells
numDof(1*(dim+1)+dim+1) = dim
! Let v be defined on faces
numDof(2*(dim+1)+dim) = dim-1
pNumDof => numDof
! Setup boundary conditions
numBC = 1
! Test label retrieval
call DMGetLabel(dm, 'marker', label, ierr)
CHKERRQ(ierr)
call DMLabelGetValue(label, 0, val, ierr)
CHKERRQ(ierr)
if (val .ne. -1) then
CHKERRQ(1)
endif
call DMLabelGetValue(label, 8, val, ierr)
CHKERRQ(ierr)
if (val .ne. 1) then
CHKERRQ(1)
endif
! Prescribe a Dirichlet condition on u on the boundary
! Label "marker" is made by the mesh creation routine
bcField(1) = 0
pBcField => bcField
call ISCreateStride(PETSC_COMM_WORLD, 1, 0, 1, bcCompIS(1), ierr)
CHKERRQ(ierr)
pBcCompIS => bcCompIS
call DMGetStratumIS(dm, 'marker', 1, bcPointIS(1),
& ierr)
CHKERRQ(ierr)
pBcPointIS => bcPointIS
! Create a PetscSection with this data layout
call DMPlexCreateSection(dm, dim, numFields, pNumComp,
& pNumDof, numBC, pBcField, pBcCompIS, pBcPointIS,
& PETSC_NULL_OBJECT, section, ierr)
CHKERRQ(ierr)
call ISDestroy(bcCompIS(1), ierr)
CHKERRQ(ierr)
call ISDestroy(bcPointIS(1), ierr)
CHKERRQ(ierr)
! Name the Field variables
call PetscSectionSetFieldName(section, 0, 'u', ierr)
CHKERRQ(ierr)
call PetscSectionSetFieldName(section, 1, 'v', ierr)
CHKERRQ(ierr)
call PetscSectionSetFieldName(section, 2, 'w', ierr)
CHKERRQ(ierr)
call PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD, ierr)
CHKERRQ(ierr)
! Tell the DM to use this data layout
call DMSetDefaultSection(dm, section, ierr)
CHKERRQ(ierr)
! Create a Vec with this layout and view it
call DMGetGlobalVector(dm, u, ierr)
CHKERRQ(ierr)
call PetscViewerCreate(PETSC_COMM_WORLD, viewer, ierr)
CHKERRQ(ierr)
call PetscViewerSetType(viewer, PETSCVIEWERVTK, ierr)
CHKERRQ(ierr)
call PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_VTK, ierr)
CHKERRQ(ierr)
call PetscViewerFileSetName(viewer, 'sol.vtk', ierr)
CHKERRQ(ierr)
call VecView(u, viewer, ierr)
CHKERRQ(ierr)
call PetscViewerDestroy(viewer, ierr)
CHKERRQ(ierr)
call DMRestoreGlobalVector(dm, u, ierr)
CHKERRQ(ierr)
! Cleanup
call PetscSectionDestroy(section, ierr)
CHKERRQ(ierr)
call DMDestroy(dm, ierr)
CHKERRQ(ierr)
call PetscFinalize(ierr)
end program DMPlexTestField
sol.msh
Description: Mesh model
