[petsc-dev] [petsc-users] Segmentation Violation in getting DMPlex coordinates

[Smith, Barry F.]

> On Apr 29, 2018, at 6:19 AM, Patrick Sanan <patrick.sanan at gmail.com> wrote:
> 
> For functions like this (only for one impl), should this new check be considered new best practices (as opposed to the composition approach, defining things with names like DMDASetUniformCoordinates_DMDA())? It seems like less boilerplate, as well as avoiding a function on the stack (and the check itself if it's turned off in optimized mode).

    No, it is just error checking for incorrectly written code that is too much hassle to change. 

   Barry

> 
> 2018-04-28 22:38 GMT+02:00 Smith, Barry F. <bsmith at mcs.anl.gov>:
> 
>   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/
> 
>