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

[Patrick Sanan]

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).

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/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20180429/a5ed187f/attachment.html>