[petsc-users] Question on DMPlexCreateSection for Fortran

Thu Feb 22 17:10:15 CST 2018

Hi Matt,

Just to let you know that after updating to PETSc 3.8.3 version, the 
DMPlexCreateSection in my code now works.

One more question, what is the PETSC_NULL_XXX for IS pointer, as shown 
below, in C code, it just pass NULL, but in fortran, what is the name of 
null object for pBcCompIS and pBcPointIS.

         call DMPlexCreateSection(dmda_flow%da,dmda_flow%dim,           &
numFields,pNumComp,pNumDof,           &
numBC,pBcField,                       &
pBcCompIS,pBcPointIS,                 &
                                  PETSC_NULL_IS,section,ierr)
         CHKERRQ(ierr)

Thanks,

Danyang

On 18-02-21 09:22 AM, Danyang Su wrote:
>
> 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.su at gmail.com 
>>> <mailto:danyang.su at 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 webpage
>>>
>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMPLEX/DMPlexCreateSection.html 
>>>
>>>
>>> The 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/>
>>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20180222/0d1623b3/attachment.html>