Add FacetSplitPC

firedrake/preconditioners/__init__.py

@@ -10,3 +10,4 @@
 from firedrake.preconditioners.hypre_ams import *  # noqa: F401
 from firedrake.preconditioners.hypre_ads import *  # noqa: F401
 from firedrake.preconditioners.fdm import *        # noqa: F401
+from firedrake.preconditioners.facet_split import *  # noqa: F401

firedrake/preconditioners/facet_split.py

@@ -0,0 +1,265 @@
+from functools import partial
+from mpi4py import MPI
+from pyop2 import op2, PermutedMap
+from firedrake.petsc import PETSc
+from firedrake.preconditioners.base import PCBase
+import firedrake.dmhooks as dmhooks
+import numpy
+
+__all__ = ['FacetSplitPC']
+
+
+class FacetSplitPC(PCBase):
+    """ A preconditioner that splits a function into interior and facet DOFs.
+
+    Internally this creates a PETSc PC object that can be controlled
+    by options using the extra options prefix ``facet_``.
+
+    This allows for statically-condensed preconditioners to be applied to
+    linear systems involving the matrix applied to the full set of DOFs. Code
+    generated for the matrix-free operator evaluation in the space with full
+    DOFs will run faster than the one with interior-facet decoposition, since
+    the full element has a simpler structure.
+    """
+
+    needs_python_pmat = False
+    _prefix = "facet_"
+
+    _permutation_cache = {}
+
+    def get_permutation(self, V, W):
+        key = (V, W)
+        if key not in self._permutation_cache:
+            indices = get_permutation_map(V, W)
+            if V._comm.allreduce(numpy.all(indices[:-1] <= indices[1:]), MPI.PROD):
+                self._permutation_cache[key] = None
+            else:
+                self._permutation_cache[key] = indices
+        return self._permutation_cache[key]
+
+    def initialize(self, pc):
+        from ufl import RestrictedElement, MixedElement, TensorElement, VectorElement
+        from firedrake import FunctionSpace, TestFunctions, TrialFunctions
+        from firedrake.assemble import allocate_matrix, TwoFormAssembler
+
+        _, P = pc.getOperators()
+        appctx = self.get_appctx(pc)
+        fcp = appctx.get("form_compiler_parameters")
+
+        prefix = pc.getOptionsPrefix()
+        options_prefix = prefix + self._prefix
+        options = PETSc.Options(options_prefix)
+        mat_type = options.getString("mat_type", "submatrix")
+
+        if P.getType() == "python":
+            ctx = P.getPythonContext()
+            a = ctx.a
+            bcs = tuple(ctx.row_bcs)
+        else:
+            ctx = dmhooks.get_appctx(pc.getDM())
+            a = ctx.Jp or ctx.J
+            bcs = tuple(ctx._problem.bcs)
+
+        V = a.arguments()[-1].function_space()
+        assert len(V) == 1, "Interior-facet decomposition of mixed elements is not supported"
+
+        def restrict(ele, restriction_domain):
+            if isinstance(ele, VectorElement):
+                return type(ele)(restrict(ele._sub_element, restriction_domain), dim=ele.num_sub_elements())
+            elif isinstance(ele, TensorElement):
+                return type(ele)(restrict(ele._sub_element, restriction_domain), shape=ele._shape, symmetry=ele._symmety)
+            else:
+                return RestrictedElement(ele, restriction_domain)
+
+        # W = V[interior] * V[facet]
+        W = FunctionSpace(V.mesh(), MixedElement([restrict(V.ufl_element(), d) for d in ("interior", "facet")]))
+        assert W.dim() == V.dim(), "Dimensions of the original and decomposed spaces do not match"
+
+        mixed_operator = a(sum(TestFunctions(W)), sum(TrialFunctions(W)), coefficients={})
+        mixed_bcs = tuple(bc.reconstruct(V=W[-1], g=0) for bc in bcs)
+
+        self.perm = None
+        self.iperm = None
+        indices = self.get_permutation(V, W)
+        if indices is not None:
+            self.perm = PETSc.IS().createGeneral(indices, comm=V._comm)
+            self.iperm = self.perm.invertPermutation()
+
+        if mat_type != "submatrix":
+            self.mixed_op = allocate_matrix(mixed_operator,
+                                            bcs=mixed_bcs,
+                                            form_compiler_parameters=fcp,
+                                            mat_type=mat_type,
+                                            options_prefix=options_prefix)
+            self._assemble_mixed_op = TwoFormAssembler(mixed_operator, tensor=self.mixed_op,
+                                                       form_compiler_parameters=fcp,
+                                                       bcs=mixed_bcs).assemble
+            self._assemble_mixed_op()
+            mixed_opmat = self.mixed_op.petscmat
+
+            def _permute_nullspace(nsp):
+                if not (nsp.handle and self.iperm):
+                    return nsp
+                vecs = [vec.duplicate() for vec in nsp.getVecs()]
+                for vec in vecs:
+                    vec.permute(self.iperm)
+                return PETSc.NullSpace().create(constant=nsp.hasConstant(), vectors=vecs, comm=nsp.getComm())
+
+            mixed_opmat.setNullSpace(_permute_nullspace(P.getNullSpace()))
+            mixed_opmat.setNearNullSpace(_permute_nullspace(P.getNearNullSpace()))
+            mixed_opmat.setTransposeNullSpace(_permute_nullspace(P.getTransposeNullSpace()))
+        elif self.perm:
+            self._permute_op = partial(PETSc.Mat().createSubMatrixVirtual, P, self.iperm, self.iperm)
+            mixed_opmat = self._permute_op()
+        else:
+            mixed_opmat = P
+
+        # Internally, we just set up a PC object that the user can configure
+        # however from the PETSc command line.  Since PC allows the user to specify
+        # a KSP, we can do iterative by -facet_pc_type ksp.
+        scpc = PETSc.PC().create(comm=pc.comm)
+        scpc.incrementTabLevel(1, parent=pc)
+
+        # We set a DM and an appropriate SNESContext on the constructed PC so one
+        # can do e.g. fieldsplit.
+        mixed_dm = W.dm
+        self._dm = mixed_dm
+
+        # Create new appctx
+        self._ctx_ref = self.new_snes_ctx(pc,
+                                          mixed_operator,
+                                          mixed_bcs,
+                                          mat_type,
+                                          fcp,
+                                          options_prefix=options_prefix)
+
+        scpc.setDM(mixed_dm)
+        scpc.setOptionsPrefix(options_prefix)
+        scpc.setOperators(A=mixed_opmat, P=mixed_opmat)
+        with dmhooks.add_hooks(mixed_dm, self, appctx=self._ctx_ref, save=False):
+            scpc.setFromOptions()
+        self.pc = scpc
+
+    def update(self, pc):
+        if hasattr(self, "mixed_op"):
+            self._assemble_mixed_op()
+        elif hasattr(self, "_permute_op"):
+            for mat in self.pc.getOperators():
+                mat.destroy()
+            P = self._permute_op()
+            self.pc.setOperators(A=P, P=P)
+        self.pc.setUp()
+
+    def apply(self, pc, x, y):
+        if self.perm:
+            x.permute(self.iperm)
+        dm = self._dm
+        with dmhooks.add_hooks(dm, self, appctx=self._ctx_ref):
+            self.pc.apply(x, y)
+        if self.perm:
+            x.permute(self.perm)
+            y.permute(self.perm)
+
+    def applyTranspose(self, pc, x, y):
+        if self.perm:
+            x.permute(self.iperm)
+        dm = self._dm
+        with dmhooks.add_hooks(dm, self, appctx=self._ctx_ref):
+            self.pc.applyTranspose(x, y)
+        if self.perm:
+            x.permute(self.perm)
+            y.permute(self.perm)
+
+    def view(self, pc, viewer=None):
+        super(FacetSplitPC, self).view(pc, viewer)
+        if hasattr(self, "pc"):
+            viewer.printfASCII("PC using interior-facet decomposition\n")
+            self.pc.view(viewer)
+
+    def destroy(self, pc):
+        if hasattr(self, "pc"):
+            if hasattr(self, "_permute_op"):
+                for mat in self.pc.getOperators():
+                    mat.destroy()
+            self.pc.destroy()
+        if hasattr(self, "iperm"):
+            if self.iperm:
+                self.iperm.destroy()
+        if hasattr(self, "perm"):
+            if self.perm:
+                self.perm.destroy()
+
+
+def split_dofs(elem):
+    """ Split DOFs into interior and facet DOF, where facets are sorted by entity.
+    """
+    entity_dofs = elem.entity_dofs()
+    ndim = elem.cell.get_spatial_dimension()
+    edofs = [[], []]
+    for key in sorted(entity_dofs.keys()):
+        vals = entity_dofs[key]
+        edim = key
+        try:
+            edim = sum(edim)
+        except TypeError:
+            pass
+        for k in sorted(vals.keys()):
+            edofs[edim < ndim].extend(sorted(vals[k]))
+    return tuple(numpy.array(e, dtype=PETSc.IntType) for e in edofs)
+
+
+def restricted_dofs(celem, felem):
+    """ Find which DOFs from felem are on celem
+    :arg celem: the restricted :class:`finat.FiniteElement`
+    :arg felem: the unrestricted :class:`finat.FiniteElement`
+    :returns: :class:`numpy.array` with indices of felem that correspond to celem
+    """
+    csplit = split_dofs(celem)
+    fsplit = split_dofs(felem)
+    if len(csplit[0]) and len(csplit[1]):
+        csplit = [numpy.concatenate(csplit)]
+        fsplit = [numpy.concatenate(fsplit)]
+
+    k = len(csplit[0]) == 0
+    if len(csplit[k]) != len(fsplit[k]):
+        raise ValueError("Finite elements have different DOFs")
+    perm = numpy.empty_like(csplit[k])
+    perm[csplit[k]] = numpy.arange(len(perm), dtype=perm.dtype)
+    return fsplit[k][perm]
+
+
+def get_permutation_map(V, W):
+    perm = numpy.empty((V.dof_count, ), dtype=PETSc.IntType)
+    perm.fill(-1)
+    vdat = V.make_dat(val=perm)
+
+    offset = 0
+    wdats = []
+    for Wsub in W:
+        val = numpy.arange(offset, offset + Wsub.dof_count, dtype=PETSc.IntType)
+        wdats.append(Wsub.make_dat(val=val))
+        offset += Wsub.dof_dset.layout_vec.sizes[0]
+
+    sizes = [Wsub.finat_element.space_dimension() * Wsub.value_size for Wsub in W]
+    eperm = numpy.concatenate([restricted_dofs(Wsub.finat_element, V.finat_element) for Wsub in W])
+    pmap = PermutedMap(V.cell_node_map(), eperm)
+
+    kernel_code = f"""
+    void permutation(PetscInt *restrict x,
+                     const PetscInt *restrict xi,
+                     const PetscInt *restrict xf){{
+        for(PetscInt i=0; i<{sizes[0]}; i++) x[i] = xi[i];
+        for(PetscInt i=0; i<{sizes[1]}; i++) x[i+{sizes[0]}] = xf[i];
+        return;
+    }}
+    """
+    kernel = op2.Kernel(kernel_code, "permutation", requires_zeroed_output_arguments=False)
+    op2.par_loop(kernel, V.mesh().cell_set,
+                 vdat(op2.WRITE, pmap),
+                 wdats[0](op2.READ, W[0].cell_node_map()),
+                 wdats[1](op2.READ, W[1].cell_node_map()))
+
+    own = V.dof_dset.layout_vec.sizes[0]
+    perm = perm.reshape((-1, ))
+    perm = V.dof_dset.lgmap.apply(perm, result=perm)
+    return perm[:own]

tests/regression/test_facet_split.py

@@ -0,0 +1,63 @@
+import pytest
+from firedrake import *
+
+
+@pytest.mark.parametrize(['quadrilateral', 'ptype'],
+                         [(q, p)
+                          for q in [True, False]
+                          for p in ["lu", "jacobi"]])
+def test_facet_split(quadrilateral, ptype):
+    if ptype == "lu":
+        parameters = {
+            "mat_type": "matfree",
+            "ksp_type": "preonly",
+            "pc_type": "python",
+            "pc_python_type": "firedrake.FacetSplitPC",
+            "facet": {
+                "mat_type": "aij",
+                "pc_type": "fieldsplit",
+                "pc_fieldsplit_type": "schur",
+                "pc_fieldsplit_schur_fact_type": "full",
+                "pc_fieldsplit_schur_precondition": "selfp",
+                "fieldsplit_0_pc_type": "jacobi",
+                "fieldsplit_1_pc_type": "lu",
+            },
+        }
+    elif ptype == "jacobi":
+        parameters = {
+            "mat_type": "matfree",
+            "ksp_type": "preonly",
+            "pc_type": "python",
+            "pc_python_type": "firedrake.FacetSplitPC",
+            "facet": {
+                "mat_type": "submatrix",
+                "pc_type": "fieldsplit",
+                "pc_fieldsplit_type": "schur",
+                "pc_fieldsplit_schur_fact_type": "full",
+                "pc_fieldsplit_schur_precondition": "a11",
+                "fieldsplit_0_pc_type": "jacobi",
+                "fieldsplit_1_pc_type": "jacobi",
+                "fieldsplit_1_ksp_type": "cg",
+                "fieldsplit_1_ksp_rtol": 1E-12,
+                "fieldsplit_1_ksp_atol": 1E-10,
+            },
+        }
+
+    r = 2
+    variant = "fdm" if quadrilateral else None
+    mesh = UnitSquareMesh(2 ** r, 2 ** r, quadrilateral=quadrilateral)
+
+    V = FunctionSpace(mesh, FiniteElement("Lagrange", degree=3, variant=variant))
+    u = TrialFunction(V)
+    v = TestFunction(V)
+    uh = Function(V)
+
+    a = inner(grad(u), grad(v)) * dx
+    L = inner(Constant(0), v) * dx
+    x = SpatialCoordinate(mesh)
+    u_exact = 42 * x[1]
+    bcs = [DirichletBC(V, Constant(0), 3),
+           DirichletBC(V, Constant(42), 4)]
+
+    solve(a == L, uh, bcs=bcs, solver_parameters=parameters)
+    assert sqrt(assemble(inner(uh - u_exact, uh - u_exact) * dx)) < 1E-10