Merge remote-tracking branch 'origin/master' into connorjward/pyop2-f…

…ixes

docker/Dockerfile.env

@@ -13,7 +13,7 @@ RUN apt-get update \
                  cmake gfortran git libopenblas-serial-dev \
                  libtool python3-dev python3-pip python3-tk python3-venv \
                  python3-requests zlib1g-dev libboost-dev sudo gmsh \
-                 bison flex ninja-build \
+                 bison flex ninja-build pkg-config \
                  libocct-ocaf-dev libocct-data-exchange-dev \
                  swig graphviz \
                  libcurl4-openssl-dev libxml2-dev \

docs/source/download.rst

@@ -135,6 +135,7 @@ they have the system dependencies:
 * zlib
 * flex, bison
 * Ninja
+* pkg-config
 
 Firedrake has been successfully installed on Windows 10 using the
 Windows Subsystem for Linux. There are more detailed instructions for

firedrake/function.py

@@ -124,12 +124,16 @@ def split(self):
 
     @utils.cached_property
     def _components(self):
-        if self.dof_dset.cdim == 1:
-            return (self, )
+        if self.function_space().rank == 0:
+            return tuple((self, ))
         else:
-            return tuple(CoordinatelessFunction(self.function_space().sub(i), val=op2.DatView(self.dat, j),
-                                                name="view[%d](%s)" % (i, self.name()))
-                         for i, j in enumerate(np.ndindex(self.dof_dset.dim)))
+            if self.dof_dset.cdim == 1:
+                return (CoordinatelessFunction(self.function_space().sub(0), val=self.dat,
+                                               name=f"view[0]({self.name()})"),)
+            else:
+                return tuple(CoordinatelessFunction(self.function_space().sub(i), val=op2.DatView(self.dat, j),
+                                                    name=f"view[{i}]({self.name()})")
+                             for i, j in enumerate(np.ndindex(self.dof_dset.dim)))
 
     @PETSc.Log.EventDecorator()
     def sub(self, i):
@@ -143,9 +147,12 @@ def sub(self, i):
         rank-n :class:`~.FunctionSpace`, this returns a proxy object
         indexing the ith component of the space, suitable for use in
         boundary condition application."""
-        if len(self.function_space()) == 1:
-            return self._components[i]
-        return self.subfunctions[i]
+        mixed = len(self.function_space()) != 1
+        data = self.subfunctions if mixed else self._components
+        bound = len(data)
+        if i < 0 or i >= bound:
+            raise IndexError(f"Invalid component {i}, not in [0, {bound})")
+        return data[i]
 
     @property
     def cell_set(self):
@@ -327,8 +334,8 @@ def split(self):
 
     @utils.cached_property
     def _components(self):
-        if self.function_space().value_size == 1:
-            return (self, )
+        if self.function_space().rank == 0:
+            return tuple((self, ))
         else:
             return tuple(type(self)(self.function_space().sub(i), self.topological.sub(i))
                          for i in range(self.function_space().block_size))
@@ -345,9 +352,12 @@ def sub(self, i):
         :func:`~.VectorFunctionSpace` or :func:`~.TensorFunctionSpace` this returns a proxy object
         indexing the ith component of the space, suitable for use in
         boundary condition application."""
-        if len(self.function_space()) == 1:
-            return self._components[i]
-        return self.subfunctions[i]
+        mixed = len(self.function_space()) != 1
+        data = self.subfunctions if mixed else self._components
+        bound = len(data)
+        if i < 0 or i >= bound:
+            raise IndexError(f"Invalid component {i}, not in [0, {bound})")
+        return data[i]
 
     @PETSc.Log.EventDecorator()
     @FunctionMixin._ad_annotate_project

firedrake/functionspaceimpl.py

@@ -182,10 +182,12 @@ def _components(self):
 
     @PETSc.Log.EventDecorator()
     def sub(self, i):
-        bound = len(self._components)
+        mixed = len(self) != 1
+        data = self.subfunctions if mixed else self._components
+        bound = len(data)
         if i < 0 or i >= bound:
-            raise IndexError("Invalid component %d, not in [0, %d)" % (i, bound))
-        return self._components[i]
+            raise IndexError(f"Invalid component {i}, not in [0, {bound})")
+        return data[i]
 
     @utils.cached_property
     def dm(self):
@@ -654,13 +656,16 @@ def __getitem__(self, i):
 
     @utils.cached_property
     def _components(self):
-        return tuple(ComponentFunctionSpace(self, i) for i in range(self.block_size))
+        if self.rank == 0:
+            return self.subfunctions
+        else:
+            return tuple(ComponentFunctionSpace(self, i) for i in range(self.block_size))
 
     def sub(self, i):
         r"""Return a view into the ith component."""
-        if self.rank == 0:
-            assert i == 0
-            return self
+        bound = len(self._components)
+        if i < 0 or i >= bound:
+            raise IndexError(f"Invalid component {i}, not in [0, {bound})")
         return self._components[i]
 
     def __mul__(self, other):

firedrake/mesh.py

@@ -66,10 +66,10 @@
 }
 
 
-_supported_embedded_cell_types_and_gdims = [(ufl.Cell('interval'), 2),
-                                            (ufl.Cell('triangle'), 3),
-                                            (ufl.Cell("quadrilateral"), 3),
-                                            (ufl.TensorProductCell(ufl.Cell('interval'), ufl.Cell('interval')), 3)]
+_supported_embedded_cell_types_and_gdims = [('interval', 2),
+                                            ('triangle', 3),
+                                            ("quadrilateral", 3),
+                                            ("interval * interval", 3)]
 
 
 unmarked = -1
@@ -1966,7 +1966,7 @@ def _renumber_entities(self, reorder):
         if reorder:
             swarm = self.topology_dm
             parent = self._parent_mesh.topology_dm
-            swarm_parent_cell_nums = swarm.getField("DMSwarm_cellid")
+            swarm_parent_cell_nums = swarm.getField("DMSwarm_cellid").ravel()
             parent_renum = self._parent_mesh._dm_renumbering.getIndices()
             pStart, _ = parent.getChart()
             parent_renum_inv = np.empty_like(parent_renum)
@@ -2063,7 +2063,7 @@ def cell_parent_cell_list(self):
         """Return a list of parent mesh cells numbers in vertex only
         mesh cell order.
         """
-        cell_parent_cell_list = np.copy(self.topology_dm.getField("parentcellnum"))
+        cell_parent_cell_list = np.copy(self.topology_dm.getField("parentcellnum").ravel())
         self.topology_dm.restoreField("parentcellnum")
         return cell_parent_cell_list[self.cell_closure[:, -1]]
 
@@ -2082,7 +2082,7 @@ def cell_parent_base_cell_list(self):
         """
         if not isinstance(self._parent_mesh, ExtrudedMeshTopology):
             raise AttributeError("Parent mesh is not extruded")
-        cell_parent_base_cell_list = np.copy(self.topology_dm.getField("parentcellbasenum"))
+        cell_parent_base_cell_list = np.copy(self.topology_dm.getField("parentcellbasenum").ravel())
         self.topology_dm.restoreField("parentcellbasenum")
         return cell_parent_base_cell_list[self.cell_closure[:, -1]]
 
@@ -2103,7 +2103,7 @@ def cell_parent_extrusion_height_list(self):
         """
         if not isinstance(self._parent_mesh, ExtrudedMeshTopology):
             raise AttributeError("Parent mesh is not extruded.")
-        cell_parent_extrusion_height_list = np.copy(self.topology_dm.getField("parentcellextrusionheight"))
+        cell_parent_extrusion_height_list = np.copy(self.topology_dm.getField("parentcellextrusionheight").ravel())
         self.topology_dm.restoreField("parentcellextrusionheight")
         return cell_parent_extrusion_height_list[self.cell_closure[:, -1]]
 
@@ -2123,7 +2123,7 @@ def mark_entities(self, tf, label_value, label_name=None):
     @utils.cached_property  # TODO: Recalculate if mesh moves
     def cell_global_index(self):
         """Return a list of unique cell IDs in vertex only mesh cell order."""
-        cell_global_index = np.copy(self.topology_dm.getField("globalindex"))
+        cell_global_index = np.copy(self.topology_dm.getField("globalindex").ravel())
         self.topology_dm.restoreField("globalindex")
         return cell_global_index
 
@@ -2158,8 +2158,8 @@ def _make_input_ordering_sf(swarm, nroots, ilocal):
         # ilocal = None -> leaves are swarm points [0, 1, 2, ...).
         # ilocal can also be Firedrake cell numbers.
         sf = PETSc.SF().create(comm=swarm.comm)
-        input_ranks = swarm.getField("inputrank")
-        input_indices = swarm.getField("inputindex")
+        input_ranks = swarm.getField("inputrank").ravel()
+        input_indices = swarm.getField("inputindex").ravel()
         nleaves = len(input_ranks)
         if ilocal is not None and nleaves != len(ilocal):
             swarm.restoreField("inputrank")
@@ -2765,7 +2765,7 @@ def init_cell_orientations(self, expr):
         import firedrake.function as function
         import firedrake.functionspace as functionspace
 
-        if (self.ufl_cell(), self.geometric_dimension()) not in _supported_embedded_cell_types_and_gdims:
+        if (self.ufl_cell().cellname(), self.geometric_dimension()) not in _supported_embedded_cell_types_and_gdims:
             raise NotImplementedError('Only implemented for intervals embedded in 2d and triangles and quadrilaterals embedded in 3d')
 
         if hasattr(self, '_cell_orientations'):
@@ -3652,7 +3652,7 @@ def _pic_swarm_in_mesh(
     # local_points[halo_indices] (it also updates local_points[~halo_indices]`, not changing any values there).
     # If some index of local_points_reduced corresponds to a missing point, local_points_reduced[index] is not updated
     # when we reduce and it does not update any leaf data, i.e., local_points, when we bcast.
-    owners = swarm.getField("DMSwarm_rank")
+    owners = swarm.getField("DMSwarm_rank").ravel()
     halo_indices, = np.where(owners != parent_mesh.comm.rank)
     halo_indices = halo_indices.astype(IntType)
     n = coords.shape[0]
@@ -3868,13 +3868,13 @@ def _dmswarm_create(
 
     # NOTE ensure that swarm.restoreField is called for each field too!
     swarm_coords = swarm.getField("DMSwarmPIC_coor").reshape((num_vertices, gdim))
-    swarm_parent_cell_nums = swarm.getField("DMSwarm_cellid")
-    field_parent_cell_nums = swarm.getField("parentcellnum")
+    swarm_parent_cell_nums = swarm.getField("DMSwarm_cellid").ravel()
+    field_parent_cell_nums = swarm.getField("parentcellnum").ravel()
     field_reference_coords = swarm.getField("refcoord").reshape((num_vertices, tdim))
-    field_global_index = swarm.getField("globalindex")
-    field_rank = swarm.getField("DMSwarm_rank")
-    field_input_rank = swarm.getField("inputrank")
-    field_input_index = swarm.getField("inputindex")
+    field_global_index = swarm.getField("globalindex").ravel()
+    field_rank = swarm.getField("DMSwarm_rank").ravel()
+    field_input_rank = swarm.getField("inputrank").ravel()
+    field_input_index = swarm.getField("inputindex").ravel()
     swarm_coords[...] = coords
     swarm_parent_cell_nums[...] = plex_parent_cell_nums
     field_parent_cell_nums[...] = parent_cell_nums
@@ -3895,8 +3895,8 @@ def _dmswarm_create(
     swarm.restoreField("DMSwarm_cellid")
 
     if extruded:
-        field_base_parent_cell_nums = swarm.getField("parentcellbasenum")
-        field_extrusion_heights = swarm.getField("parentcellextrusionheight")
+        field_base_parent_cell_nums = swarm.getField("parentcellbasenum").ravel()
+        field_extrusion_heights = swarm.getField("parentcellextrusionheight").ravel()
         field_base_parent_cell_nums[...] = base_parent_cell_nums
         field_extrusion_heights[...] = extrusion_heights
         swarm.restoreField("parentcellbasenum")

firedrake/output/vtk_output.py

@@ -452,7 +452,7 @@ def __init__(self, filename, project_output=False, comm=None, mode="w",
     @no_annotations
     def _prepare_output(self, function, max_elem):
         from firedrake import FunctionSpace, VectorFunctionSpace, \
-            TensorFunctionSpace, Function
+            TensorFunctionSpace, Function, Cofunction
 
         name = function.name()
         # Need to project/interpolate?
@@ -477,16 +477,23 @@ def _prepare_output(self, function, max_elem):
                                     shape=shape)
         else:
             raise ValueError("Unsupported shape %s" % (shape, ))
-        output = Function(V)
+        if isinstance(function, Function):
+            output = Function(V)
+        else:
+            assert isinstance(function, Cofunction)
+            output = Function(V.dual())
+
         if self.project:
+            if isinstance(function, Cofunction):
+                raise ValueError("Can not project Cofunctions")
             output.project(function)
         else:
             output.interpolate(function)
 
         return OFunction(array=get_array(output), name=name, function=output)
 
     def _write_vtu(self, *functions):
-        from firedrake.function import Function
+        from firedrake import Function, Cofunction
 
         # Check if the user has requested to write out a plain mesh
         if len(functions) == 1 and isinstance(functions[0], ufl.Mesh):
@@ -496,8 +503,8 @@ def _write_vtu(self, *functions):
             functions = [Function(V)]
 
         for f in functions:
-            if not isinstance(f, Function):
-                raise ValueError("Can only output Functions or a single mesh, not %r" % type(f))
+            if not isinstance(f, (Function, Cofunction)):
+                raise ValueError(f"Can only output Functions, Cofunctions or a single mesh, not {type(f).__name__}")
         meshes = tuple(extract_unique_domain(f) for f in functions)
         if not all(m == meshes[0] for m in meshes):
             raise ValueError("All functions must be on same mesh")

scripts/firedrake-install

@@ -742,7 +742,7 @@ def get_petsc_options(minimal=False):
         petsc_options.add("--download-suitesparse")
         petsc_options.add("--download-pastix")
         # Required by pastix
-        petsc_options.add("--download-hwloc")
+        petsc_options.update({"--download-hwloc", "--download-netlib-lapack", "--with-netlib-lapack-c-bindings"})
         if osname == "Darwin":
             petsc_options.add("--download-hwloc-configure-arguments=--disable-opencl")
         # Serial mesh partitioner
@@ -1517,6 +1517,7 @@ if mode == "install" or not args.update_script:
     if osname == "Darwin":
         package_manager = "brew"
         required_packages = ["gcc",
+                             "pkg-config",
                              "autoconf",
                              "make",
                              "automake",
@@ -1535,6 +1536,7 @@ if mode == "install" or not args.update_script:
                              "flex",   # for ptscotch
                              "cmake",
                              "gfortran",
+                             "pkg-config",
                              "git",
                              "libcurl4-openssl-dev",
                              "pkgconf",  # for p4est

tests/firedrake/output/test_pvd_output.py

@@ -79,11 +79,16 @@ def test_bad_file_name(tmpdir):
         VTKFile(str(tmpdir.join("foo.vtu")))
 
 
-def test_different_functions(mesh, pvd):
+@pytest.mark.parametrize("space",
+                         ["primal", "dual"])
+def test_different_functions(mesh, pvd, space):
     V = FunctionSpace(mesh, "DG", 0)
-
-    f = Function(V, name="foo")
-    g = Function(V, name="bar")
+    if space == "primal":
+        f = Function(V, name="foo")
+        g = Function(V, name="bar")
+    else:
+        f = Cofunction(V.dual(), name="foo")
+        g = Cofunction(V.dual(), name="bar")
 
     pvd.write(f)
 
@@ -136,9 +141,14 @@ def test_not_function(mesh, pvd):
         pvd.write(grad(f))
 
 
-def test_append(mesh, tmpdir):
+@pytest.mark.parametrize("space",
+                         ["primal", "dual"])
+def test_append(mesh, tmpdir, space):
     V = FunctionSpace(mesh, "DG", 0)
-    g = Function(V)
+    if space == "primal":
+        g = Function(V)
+    else:
+        g = Cofunction(V.dual())
 
     outfile = VTKFile(str(tmpdir.join("restart_test.pvd")))
     outfile.write(g)