Re: [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 <knep...@gmail.com> wrote:

On Sat, Apr 28, 2018 at 2:08 AM, Danyang Su <danyang...@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/