[petsc-users] Segmentation Violation in getting DMPlex coordinates

[Danyang Su]

Hi Matt and Barry,

Thanks for your quick response. After changing DMDAVecGetArrayF90 to 
VecGetArrayF90, everything works now.

Thanks,

Danyang


On 18-04-28 01:38 PM, Smith, Barry F. wrote:
>    Added runtime error checking for such incorrect calls in barry/dmda-calls-type-check
>
>
>> On Apr 28, 2018, at 9:19 AM, Matthew Knepley <knepley at gmail.com> wrote:
>>
>> On Sat, Apr 28, 2018 at 2:08 AM, Danyang Su <danyang.su at gmail.com> wrote:
>> Hi All,
>>
>> I use DMPlex and need to get coordinates back after distribution. However, I always get segmentation violation in getting coords values in the following codes if using multiple processors. If only one processor is used, it works fine.
>>
>> For each processors, the off value starts from 0 which looks good. I also tried 0-based index, which gives the same error. Would any one help to check what is wrong here?
>>
>>   idof           1 off           0
>>   idof           2 off           0
>>   idof           1 off           2
>>   idof           2 off           2
>>   idof           1 off           4
>>   idof           2 off           4
>>   idof           1 off           6
>>   idof           2 off           6
>>   idof           1 off           8
>>   idof           2 off           8
>>
>>
>>        DM :: distributedMesh, cda
>>        Vec :: gc
>>        PetscScalar, pointer :: coords(:)
>>        PetscSection ::  cs
>>
>>        ...
>>
>>        call DMGetCoordinatesLocal(dmda_flow%da,gc,ierr)
>>        CHKERRQ(ierr)
>>
>>        call DMGetCoordinateDM(dmda_flow%da,cda,ierr)
>>        CHKERRQ(ierr)
>>
>>        call DMGetDefaultSection(cda,cs,ierr)
>>        CHKERRQ(ierr)
>>
>>        call PetscSectionGetChart(cs,istart,iend,ierr)
>>        CHKERRQ(ierr)
>>
>>        !c get coordinates array
>>        call DMDAVecGetArrayF90(cda,gc,coords,ierr)
>>
>> You cannot call DMDA function if you have a DMPlex. You jsut call VecGetArrayF90()
>>
>>     Matt
>>   
>>        CHKERRQ(ierr)
>>
>>        do ipoint = istart, iend-1
>>
>>          call PetscSectionGetDof(cs,ipoint,dof,ierr)
>>          CHKERRQ(ierr)
>>
>>          call PetscSectionGetOffset(cs,ipoint,off,ierr)
>>          CHKERRQ(ierr)
>>
>>          inode = ipoint-istart+1
>>
>>          if (cell_coords == coords_xyz) then
>>            nodes(inode)%x = coords(off+1)
>>            nodes(inode)%y = coords(off+2)
>>            nodes(inode)%z = coords(off+3)
>>          else if (cell_coords == coords_xy) then
>>            nodes(inode)%x = coords(off+1)
>>            nodes(inode)%y = coords(off+2)
>>            nodes(inode)%z = 0.0d0
>>          else if (cell_coords == coords_yz) then
>>            nodes(inode)%x = 0.0d0
>>            nodes(inode)%y = coords(off+1)
>>            nodes(inode)%z = coords(off+2)
>>          else if (cell_coords ==coords_xz) then
>>            nodes(inode)%x = coords(off+1)
>>            nodes(inode)%y = 0.0d0
>>            nodes(inode)%z = coords(off+2)
>>          end if
>>        end do
>>
>>        call DMDAVecRestoreArrayF90(cda,gc,coords,ierr)
>>        CHKERRQ(ierr)
>>
>> 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/