remove mesh.init()

.github/workflows/core.yml

@@ -191,7 +191,7 @@ jobs:
             : # because they rely on non-PyPI versions of petsc4py.
             pip install --no-build-isolation --no-deps \
               "$PETSC_DIR"/"$PETSC_ARCH"/externalpackages/git.slepc/src/binding/slepc4py
-            pip install --no-deps ngsPETSc netgen-mesher netgen-occt
+            pip install --no-deps git+https://github.com/ksagiyam/ngsPETSc.git@ksagiyam/remove_mesh_init netgen-mesher netgen-occt
 
             : # We have to pass '--no-build-isolation' to use a custom petsc4py
             EXTRA_BUILD_ARGS='--no-isolation'

firedrake/assemble.py

@@ -981,10 +981,6 @@ def wrapper(self, *args, **kwargs):
 
     def __init__(self, form, bcs=None, form_compiler_parameters=None):
         super().__init__(form, bcs=bcs, form_compiler_parameters=form_compiler_parameters)
-        # Ensure mesh is 'initialised' as we could have got here without building a
-        # function space (e.g. if integrating a constant).
-        for mesh in form.ufl_domains():
-            mesh.init()
         if any(c.dat.dtype != ScalarType for c in form.coefficients()):
             raise ValueError("Cannot assemble a form containing coefficients where the "
                              "dtype is not the PETSc scalar type.")

firedrake/checkpointing.py

@@ -566,7 +566,6 @@ def save_mesh(self, mesh, distribution_name=None, permutation_name=None):
         :kwarg distribution_name: the name under which distribution is saved; if `None`, auto-generated name will be used.
         :kwarg permutation_name: the name under which permutation is saved; if `None`, auto-generated name will be used.
         """
-        mesh.init()
         # Handle extruded mesh
         tmesh = mesh.topology
         if mesh.extruded:
@@ -669,7 +668,6 @@ def save_mesh(self, mesh, distribution_name=None, permutation_name=None):
     @PETSc.Log.EventDecorator("SaveMeshTopology")
     def _save_mesh_topology(self, tmesh):
         # -- Save DMPlex --
-        tmesh.init()
         topology_dm = tmesh.topology_dm
         tmesh_name = topology_dm.getName()
         distribution_name = tmesh._distribution_name
@@ -1048,7 +1046,6 @@ def load_mesh(self, name=DEFAULT_MESH_NAME, reorder=None, distribution_parameter
             # -- Load mesh topology --
             base_tmesh_name = self.get_attr(path, PREFIX_EXTRUDED + "_base_mesh")
             base_tmesh = self._load_mesh_topology(base_tmesh_name, reorder, distribution_parameters)
-            base_tmesh.init()
             periodic = self.get_attr(path, PREFIX_EXTRUDED + "_periodic") if self.has_attr(path, PREFIX_EXTRUDED + "_periodic") else False
             variable_layers = self.get_attr(path, PREFIX_EXTRUDED + "_variable_layers")
             if variable_layers:
@@ -1106,9 +1103,6 @@ def load_mesh(self, name=DEFAULT_MESH_NAME, reorder=None, distribution_parameter
             # tmesh.topology_dm has already been redistributed.
             path = self._path_to_mesh(tmesh_name, name)
             # Load firedrake coordinates directly.
-            # When implementing checkpointing for MeshHierarchy in the future,
-            # we will need to postpone calling tmesh.init().
-            tmesh.init()
             coord_element = self._load_ufl_element(path, PREFIX + "_coordinate_element")
             coord_name = self.get_attr(path, PREFIX + "_coordinates")
             coordinates = self._load_function_topology(tmesh, coord_element, coord_name)
@@ -1194,7 +1188,13 @@ def _load_mesh_topology(self, tmesh_name, reorder, distribution_parameters):
         plex.distributionSetName(distribution_name)
         sfXB = plex.topologyLoad(self.viewer)
         plex.distributionSetName(None)
+        plex.labelsLoad(self.viewer, sfXB)
         self.viewer.popFormat()
+        # These labels are distribution dependent.
+        # We should be able to save/load labels selectively.
+        plex.removeLabel("pyop2_core")
+        plex.removeLabel("pyop2_owned")
+        plex.removeLabel("pyop2_ghost")
         if load_distribution_permutation:
             chart_size = np.empty(1, dtype=utils.IntType)
             chart_sizes_iset = PETSc.IS().createGeneral(chart_size, comm=self._comm)
@@ -1220,21 +1220,10 @@ def _load_mesh_topology(self, tmesh_name, reorder, distribution_parameters):
                              distribution_parameters=distribution_parameters, sfXB=sfXB, perm_is=perm_is,
                              distribution_name=distribution_name, permutation_name=permutation_name,
                              comm=self.comm)
-        self.viewer.pushFormat(format=format)
-        # tmesh.topology_dm has already been redistributed.
-        sfXCtemp = tmesh.sfXB.compose(tmesh.sfBC) if tmesh.sfBC is not None else tmesh.sfXB
-        plex.labelsLoad(self.viewer, sfXCtemp)
-        self.viewer.popFormat()
-        # These labels are distribution dependent.
-        # We should be able to save/load labels selectively.
-        plex.removeLabel("pyop2_core")
-        plex.removeLabel("pyop2_owned")
-        plex.removeLabel("pyop2_ghost")
         return tmesh
 
     @PETSc.Log.EventDecorator("LoadFunctionSpace")
     def _load_function_space(self, mesh, name):
-        mesh.init()
         mesh_key = self._generate_mesh_key_from_names(mesh.name,
                                                       mesh.topology._distribution_name,
                                                       mesh.topology._permutation_name)
@@ -1271,7 +1260,6 @@ def _load_function_space(self, mesh, name):
 
     @PETSc.Log.EventDecorator("LoadFunctionSpaceTopology")
     def _load_function_space_topology(self, tmesh, element):
-        tmesh.init()
         if element.family() == "Real":
             return impl.RealFunctionSpace(tmesh, element, "unused_name")
         tmesh_key = self._generate_mesh_key_from_names(tmesh.name,

firedrake/cython/dmcommon.pyx

@@ -3818,7 +3818,8 @@ def create_halo_exchange_sf(PETSc.DM dm):
 def submesh_create(PETSc.DM dm,
                    PetscInt subdim,
                    label_name,
-                   PetscInt label_value):
+                   PetscInt label_value,
+                   PetscBool ignore_label_halo):
     """Create submesh.
 
     Parameters
@@ -3831,6 +3832,8 @@ def submesh_create(PETSc.DM dm,
         Name of the label
     label_value : int
         Value in the label
+    ignore_label_halo : bool
+        If labeled points in the halo are ignored.
 
     """
     cdef:
@@ -3860,7 +3863,7 @@ def submesh_create(PETSc.DM dm,
         CHKERR(ISRestoreIndices(stratum_is, &stratum_indices))
         CHKERR(ISDestroy(&stratum_is))
     # Make submesh using temp_label.
-    CHKERR(DMPlexFilter(dm.dm, temp_label.dmlabel, label_value, PETSC_FALSE, PETSC_TRUE, &ownership_transfer_sf.sf, &subdm.dm))
+    CHKERR(DMPlexFilter(dm.dm, temp_label.dmlabel, label_value, ignore_label_halo, PETSC_TRUE, &ownership_transfer_sf.sf, &subdm.dm))
     # Destroy temp_label.
     dm.removeLabel(temp_label_name)
     subdm.removeLabel(temp_label_name)
@@ -4112,3 +4115,36 @@ def submesh_create_cell_closure(
     CHKERR(PetscFree(subpoint_indices_inv))
     CHKERR(ISRestoreIndices(subpoint_is.iset, &subpoint_indices))
     return subcell_closure
+
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+def get_dm_cell_types(PETSc.DM dm):
+    """Return all cell types in the mesh.
+
+    Parameters
+    ----------
+    dm : PETSc.DM
+        The parent dm.
+
+    Returns
+    -------
+    tuple
+        Tuple of all cell types in the mesh.
+
+    """
+    cdef:
+        PetscInt cStart, cEnd, c
+        np.ndarray found, found_all
+        PetscDMPolytopeType celltype
+
+    cStart, cEnd = dm.getHeightStratum(0)
+    found = np.zeros((DM_NUM_POLYTOPES, ), dtype=IntType)
+    found_all = np.zeros((DM_NUM_POLYTOPES, ), dtype=IntType)
+    for c in range(cStart, cEnd):
+        CHKERR(DMPlexGetCellType(dm.dm, c, &celltype))
+        found[celltype] = 1
+    dm.comm.tompi4py().Allreduce(found, found_all, op=MPI.MAX)
+    return tuple(
+        polytope_type_enum for polytope_type_enum, found in enumerate(found_all) if found
+    )

firedrake/cython/petschdr.pxi

@@ -29,6 +29,27 @@ cdef extern from "petscsys.h" nogil:
     int PetscFree2(void*,void*)
     int PetscSortIntWithArray(PetscInt,PetscInt[],PetscInt[])
 
+cdef extern from "petscdmtypes.h" nogil:
+    ctypedef enum PetscDMPolytopeType "DMPolytopeType":
+        DM_POLYTOPE_POINT
+        DM_POLYTOPE_SEGMENT
+        DM_POLYTOPE_POINT_PRISM_TENSOR
+        DM_POLYTOPE_TRIANGLE
+        DM_POLYTOPE_QUADRILATERAL
+        DM_POLYTOPE_SEG_PRISM_TENSOR
+        DM_POLYTOPE_TETRAHEDRON
+        DM_POLYTOPE_HEXAHEDRON
+        DM_POLYTOPE_TRI_PRISM
+        DM_POLYTOPE_TRI_PRISM_TENSOR
+        DM_POLYTOPE_QUAD_PRISM_TENSOR
+        DM_POLYTOPE_PYRAMID
+        DM_POLYTOPE_FV_GHOST
+        DM_POLYTOPE_INTERIOR_GHOST
+        DM_POLYTOPE_UNKNOWN
+        DM_POLYTOPE_UNKNOWN_CELL
+        DM_POLYTOPE_UNKNOWN_FACE
+        DM_NUM_POLYTOPES
+
 cdef extern from "petscdmplex.h" nogil:
     int DMPlexGetHeightStratum(PETSc.PetscDM,PetscInt,PetscInt*,PetscInt*)
     int DMPlexGetDepthStratum(PETSc.PetscDM,PetscInt,PetscInt*,PetscInt*)
@@ -56,6 +77,9 @@ cdef extern from "petscdmplex.h" nogil:
     int DMPlexGetSubpointMap(PETSc.PetscDM,PETSc.PetscDMLabel*)
     int DMPlexSetSubpointMap(PETSc.PetscDM,PETSc.PetscDMLabel)
 
+    int DMPlexSetCellType(PETSc.PetscDM,PetscInt,PetscDMPolytopeType)
+    int DMPlexGetCellType(PETSc.PetscDM,PetscInt,PetscDMPolytopeType*)
+
 cdef extern from "petscdmlabel.h" nogil:
     struct _n_DMLabel
     ctypedef _n_DMLabel* DMLabel "DMLabel"

firedrake/functionspaceimpl.py

@@ -359,7 +359,6 @@ def collapse(self):
     @classmethod
     def make_function_space(cls, mesh, element, name=None):
         r"""Factory method for :class:`.WithGeometryBase`."""
-        mesh.init()
         topology = mesh.topology
         # Create a new abstract (Mixed/Real)FunctionSpace, these are neither primal nor dual.
         if type(element) is finat.ufl.MixedElement: