Dear all,

I am playing around with creating DMPlex from a periodic Gmsh mesh (still in the same finite volume code that solves the Euler equations) because I want to run some classical periodic test cases from the literature (like convecting a vortex and so on).

I got from the mailing list and the examples that I gotta use -dm_plex_gmsh_periodic for the reader and the DM creator to do their job properly and read the $Periodic section from the Gmsh mesh. That works fine, I can write the DM in HDF5 format afterwards and the periodicity is clearly there (i can see in Paraview that opposite sides are "attached" to each other).

Now, in the context of the finite volume solver, I wrote my one right-hand side term computing routine, and I rely heavily on routines such as DMPlexGetFaceFields. Those routines, in turn rely on the ghost cells and ... I am having an issue with DMPlexConstructGhostCells. When I use -dm_plex_gmsh_periodic, DMPlexCreateFromFile works fine, DMSetBasicAdjacency(dm, true, false) works fine, DMPlexDistribute works fine, but when I get to DMPlexConstructGhostCells, I get

 "DM has boundary face 2048 with 2 support cells"

I understand the DM begin periodic, even the "boundary" faces have two neighbors because of the topological folding, so ... yeah, the ghost cells cannot really exist. But then how can I proceed ? Because I need that "ghost" label for all the routines I call from the RHS computing routine ...

I attach to this email the periodic Gmsh mesh I am playing with, and the routine from my code where I create the DM and so on:

subroutine initmesh

PetscErrorCode :: ierr

DM :: dmDist, dmGhost

integer :: overlap

PetscViewer :: vtkViewer

call PetscLogEventBegin(timer_initmesh, ierr); CHKERRA(ierr)

! Number of neighbours taken into account in MP communications(1 - Order 1; 2 - Order 2)

overlap = 1

call PetscPrintf(PETSC_COMM_WORLD, "Initializing mesh...\n", ierr) ; CHKERRA(ierr)

! Force DMPlex to use gmsh marker

! call PetscOptionsSetValue(PETSC_NULL_OPTIONS, "-dm_plex_gmsh_use_marker", "true", ierr); CHKERRA(ierr)

! Read mesh from file name 'meshname'

call DMPlexCreateFromFile(PETSC_COMM_WORLD, meshname, PETSC_TRUE, dm, ierr); CHKERRA(ierr)

! Distribute on processors

! Start with connectivity

call DMSetBasicAdjacency(dm, PETSC_TRUE, PETSC_FALSE, ierr) ; CHKERRA(ierr)

! Distribute on processors

call DMPlexDistribute(dm, overlap, PETSC_NULL_SF, dmDist, ierr) ; CHKERRA(ierr)

! Security check

if (dmDist /= PETSC_NULL_DM) then

! Destroy previous dm

call DMDestroy(dm, ierr) ; CHKERRA(ierr)

! Replace with dmDist

dm = dmDist

end if

! Finalize setup of the object

call DMSetFromOptions(dm, ierr) ; CHKERRA(ierr)

! Boundary condition with ghost cells

call DMPlexConstructGhostCells(dm, PETSC_NULL_CHARACTER, PETSC_NULL_INTEGER, dmGhost, ierr); CHKERRA(ierr)

! Security check

if (dmGhost /= PETSC_NULL_DM) then

! Destroy previous dm

call DMDestroy(dm, ierr) ; CHKERRA(ierr)

! Replace with dmGhost

dm = dmGhost

end if

if (debug) then

! Show in terminal

call PetscPrintf(PETSC_COMM_WORLD, ":: [DEBUG] Visualizing DM in console ::\n", ierr); CHKERRA(ierr)

call DMView(dm, PETSC_VIEWER_STDOUT_WORLD, ierr) ; CHKERRA(ierr)

! VTK viewer

call PetscViewerCreate(PETSC_COMM_WORLD, vtkViewer, ierr) ; CHKERRA(ierr)

call PetscViewerSetType(vtkViewer, PETSCVIEWERHDF5, ierr) ; CHKERRA(ierr)

call PetscViewerFileSetMode(vtkViewer, FILE_MODE_WRITE, ierr) ; CHKERRA(ierr)

call PetscViewerFileSetName(vtkViewer, "debug_initmesh.h5", ierr) ; CHKERRA(ierr)

call DMView(dm, vtkViewer, ierr) ; CHKERRA(ierr)

call PetscViewerDestroy(vtkViewer, ierr) ; CHKERRA(ierr)

end if

call PetscPrintf(PETSC_COMM_WORLD, "Done !\n", ierr) ; CHKERRA(ierr)

call PetscLogEventEnd(timer_initmesh, ierr); CHKERRA(ierr)

end subroutine initmesh

Thank you very much for your help !

Best regards, 

Thibault Bridel-Bertomeu