Merge remote-tracking branch 'origin/master' into connorjward/avoid-c…

…omm-spawning

.github/workflows/build.yml

@@ -101,14 +101,14 @@ jobs:
         run: |
           . ../firedrake_venv/bin/activate
           parallel --line-buffer --tag \
-            pytest "$PYTEST_ARGS" --splits 12 --junit-xml=firedrake1_{#}.xml -m "parallel[1] or not parallel" tests/firedrake ::: $(seq 12)
+            "pytest $PYTEST_ARGS --splits 12 --junit-xml=firedrake1_{#}.xml -m "parallel[1] or not parallel" tests/firedrake ::: $(seq 12)"
       - name: Run tests (nprocs = 2)
         # Run even if earlier tests failed
         if: ${{ success() || steps.build.conclusion == 'success' }}
         run: |
           . ../firedrake_venv/bin/activate
           parallel --line-buffer --tag \
-            mpiexec -n 2 pytest "$PYTEST_ARGS" --splits 6 --junit-xml=firedrake2_{#}.xml -m parallel[2] tests/firedrake ::: $(seq 6)
+            "mpiexec -n 2 pytest $PYTEST_ARGS --splits 6 --junit-xml=firedrake2_{#}.xml -m parallel[2] tests/firedrake ::: $(seq 6)"
 
       # - name: Run tests (nprocs = 3)
       #   if: ${{ success() || steps.build.conclusion == 'success' }}

.github/workflows/pip-mac.yml

@@ -53,6 +53,7 @@ jobs:
             --with-shared-libraries=1 \
             --with-mpi-dir=/opt/homebrew \
             --with-zlib \
+            --with-strict-petscerrorcode \
             --download-bison \
             --download-hdf5 \
             --download-hwloc \

.github/workflows/pyop2.yml

@@ -51,6 +51,7 @@ jobs:
             --with-debugging=1 \
             --with-shared-libraries=1 \
             --with-c2html=0 \
+            --with-strict-petscerrorcode \
             --with-fortran-bindings=0
           make
 

demos/netgen/netgen_mesh.py.rst

@@ -380,8 +380,7 @@ We will now show how to solve the Poisson problem on a high-order mesh, of order
 
    bc = DirichletBC(V, 0.0, [1])
    A = assemble(a, bcs=bc)
-   b = assemble(l)
-   bc.apply(b)
+   b = assemble(l, bcs=bc)
    solve(A, sol, b, solver_parameters={"ksp_type": "cg", "pc_type": "lu"})
 
    VTKFile("output/Sphere.pvd").write(sol)

docker/Dockerfile.env

@@ -66,6 +66,7 @@ RUN bash -c 'cd petsc; \
         --download-scalapack \
         --download-suitesparse \
         --download-superlu_dist \
+        --with-strict-petscerrorcode \
         PETSC_ARCH=packages; \
         mv packages/include/petscconf.h packages/include/old_petscconf.nope; \
         rm -rf /home/firedrake/petsc/**/externalpackages; \
@@ -105,6 +106,7 @@ RUN bash -c 'export PACKAGES=/home/firedrake/petsc/packages; \
         --with-scalapack-dir=$PACKAGES \
         --with-suitesparse-dir=$PACKAGES \
         --with-superlu_dist-dir=$PACKAGES \
+        --with-strict-petscerrorcode \
         PETSC_ARCH=default; \
     make PETSC_DIR=/home/firedrake/petsc PETSC_ARCH=default all;'
 
@@ -144,6 +146,7 @@ RUN bash -c 'export PACKAGES=/home/firedrake/petsc/packages; \
         --with-scalapack-dir=$PACKAGES \
         --with-suitesparse-dir=$PACKAGES \
         --with-superlu_dist-dir=$PACKAGES \
+        --with-strict-petscerrorcode \
         PETSC_ARCH=complex; \
     make PETSC_DIR=/home/firedrake/petsc PETSC_ARCH=complex all;'
 

docs/source/firedrake_usa_25.rst

@@ -46,7 +46,7 @@ Registration
 ------------
 
 Register for the conference at
-`this link <https://pay.baylor.edu/C20024_ustores/web/product_detail.jsp?PRODUCTID=1097/>`__.  
+`this link <https://pay.baylor.edu/C20024_ustores/web/product_detail.jsp?PRODUCTID=1097>`__.  
 
 The registration fees are as follows:
 
@@ -60,6 +60,8 @@ The registration fees are as follows:
      - $200
 
 The `SIAM Texas-Louisiana Section <https://www.siam.org/get-involved/connect-with-a-community/sections/siam-texas-louisiana-section/>`__ is providing some support for students currently attending universities in Texas or Louisiana to attend.
+Students may submit an application to be considered for funding `here <https://docs.google.com/forms/d/e/1FAIpQLSdXKsGE3D18BhvRpfcGD_gSdDmmXGRQ4l47k4Aj4SKJ2c6DZg/viewform?usp=sharing>`__.
+
 
 
 Abstract submission

firedrake/adjoint_utils/blocks/dirichlet_bc.py

@@ -51,7 +51,7 @@ def evaluate_adj_component(self, inputs, adj_inputs, block_variable, idx,
         adj_output = None
         for adj_input in adj_inputs:
             if isconstant(c):
-                adj_value = firedrake.Function(self.parent_space.dual())
+                adj_value = firedrake.Function(self.parent_space)
                 adj_input.apply(adj_value)
                 if self.function_space != self.parent_space:
                     vec = extract_bc_subvector(
@@ -88,11 +88,11 @@ def evaluate_adj_component(self, inputs, adj_inputs, block_variable, idx,
                 #       you can even use the Function outside its domain.
                 # For now we will just assume the FunctionSpace is the same for
                 # the BC and the Function.
-                adj_value = firedrake.Function(self.parent_space.dual())
+                adj_value = firedrake.Function(self.parent_space)
                 adj_input.apply(adj_value)
                 r = extract_bc_subvector(
                     adj_value, c.function_space(), bc
-                )
+                ).riesz_representation("l2")
             if adj_output is None:
                 adj_output = r
             else:

firedrake/adjoint_utils/blocks/function.py

@@ -79,6 +79,7 @@ def evaluate_adj_component(self, inputs, adj_inputs, block_variable, idx,
                 )
                 diff_expr_assembled = firedrake.Function(adj_input_func.function_space())
                 diff_expr_assembled.interpolate(ufl.conj(diff_expr))
+                diff_expr_assembled = diff_expr_assembled.riesz_representation(riesz_map="l2")
                 adj_output = firedrake.Function(
                     R, val=firedrake.assemble(ufl.Action(diff_expr_assembled, adj_input_func))
                 )

firedrake/adjoint_utils/blocks/solving.py

@@ -197,14 +197,12 @@ def _assemble_dFdu_adj(self, dFdu_adj_form, **kwargs):
 
     def _assemble_and_solve_adj_eq(self, dFdu_adj_form, dJdu, compute_bdy):
         dJdu_copy = dJdu.copy()
-        kwargs = self.assemble_kwargs.copy()
         # Homogenize and apply boundary conditions on adj_dFdu and dJdu.
         bcs = self._homogenize_bcs()
-        kwargs["bcs"] = bcs
-        dFdu = self._assemble_dFdu_adj(dFdu_adj_form, **kwargs)
+        dFdu = firedrake.assemble(dFdu_adj_form, bcs=bcs, **self.assemble_kwargs)
 
         for bc in bcs:
-            bc.apply(dJdu)
+            bc.zero(dJdu)
 
         adj_sol = firedrake.Function(self.function_space)
         firedrake.solve(
@@ -219,10 +217,8 @@ def _assemble_and_solve_adj_eq(self, dFdu_adj_form, dJdu, compute_bdy):
         return adj_sol, adj_sol_bdy
 
     def _compute_adj_bdy(self, adj_sol, adj_sol_bdy, dFdu_adj_form, dJdu):
-        adj_sol_bdy = firedrake.Function(
-            self.function_space.dual(), dJdu.dat - firedrake.assemble(
-                firedrake.action(dFdu_adj_form, adj_sol)).dat)
-        return adj_sol_bdy
+        adj_sol_bdy = firedrake.assemble(dJdu - firedrake.action(dFdu_adj_form, adj_sol))
+        return adj_sol_bdy.riesz_representation("l2")
 
     def evaluate_adj_component(self, inputs, adj_inputs, block_variable, idx,
                                prepared=None):
@@ -264,8 +260,11 @@ def evaluate_adj_component(self, inputs, adj_inputs, block_variable, idx,
             return dFdm
 
         dFdm = -firedrake.derivative(F_form, c_rep, trial_function)
-        dFdm = firedrake.adjoint(dFdm)
-        dFdm = dFdm * adj_sol
+        if isinstance(dFdm, ufl.Form):
+            dFdm = firedrake.adjoint(dFdm)
+            dFdm = firedrake.action(dFdm, adj_sol)
+        else:
+            dFdm = dFdm(adj_sol)
         dFdm = firedrake.assemble(dFdm, **self.assemble_kwargs)
         return dFdm
 
@@ -654,9 +653,8 @@ def _forward_solve(self, lhs, rhs, func, bcs, **kwargs):
     def _adjoint_solve(self, dJdu, compute_bdy):
         dJdu_copy = dJdu.copy()
         # Homogenize and apply boundary conditions on adj_dFdu and dJdu.
-        bcs = self._homogenize_bcs()
-        for bc in bcs:
-            bc.apply(dJdu)
+        for bc in self.bcs:
+            bc.zero(dJdu)
 
         if (
             self._ad_solvers["forward_nlvs"]._problem._constant_jacobian
@@ -876,7 +874,7 @@ def __init__(self, source, target_space, target, bcs=[], **kwargs):
             self.add_dependency(bc, no_duplicates=True)
 
     def apply_mixedmass(self, a):
-        b = firedrake.Function(self.target_space)
+        b = firedrake.Function(self.target_space.dual())
         with a.dat.vec_ro as vsrc, b.dat.vec_wo as vrhs:
             self.mixed_mass.mult(vsrc, vrhs)
         return b

firedrake/adjoint_utils/variational_solver.py

@@ -2,6 +2,7 @@
 from functools import wraps
 from pyadjoint.tape import get_working_tape, stop_annotating, annotate_tape, no_annotations
 from firedrake.adjoint_utils.blocks import NonlinearVariationalSolveBlock
+from firedrake.ufl_expr import derivative, adjoint
 from ufl import replace
 
 
@@ -11,7 +12,6 @@ def _ad_annotate_init(init):
         @no_annotations
         @wraps(init)
         def wrapper(self, *args, **kwargs):
-            from firedrake import derivative, adjoint, TrialFunction
             init(self, *args, **kwargs)
             self._ad_F = self.F
             self._ad_u = self.u_restrict
@@ -20,10 +20,13 @@ def wrapper(self, *args, **kwargs):
             try:
                 # Some forms (e.g. SLATE tensors) are not currently
                 # differentiable.
-                dFdu = derivative(self.F,
-                                  self.u_restrict,
-                                  TrialFunction(self.u_restrict.function_space()))
-                self._ad_adj_F = adjoint(dFdu)
+                dFdu = derivative(self.F, self.u_restrict)
+                try:
+                    self._ad_adj_F = adjoint(dFdu)
+                except ValueError:
+                    # Try again without expanding derivatives,
+                    # as dFdu might have been simplied to an empty Form
+                    self._ad_adj_F = adjoint(dFdu, derivatives_expanded=True)
             except (TypeError, NotImplementedError):
                 self._ad_adj_F = None
             self._ad_kwargs = {'Jp': self.Jp, 'form_compiler_parameters': self.form_compiler_parameters, 'is_linear': self.is_linear}

firedrake/assemble.py

@@ -83,7 +83,7 @@ def assemble(expr, *args, **kwargs):
     zero_bc_nodes : bool
         If `True`, set the boundary condition nodes in the
         output tensor to zero rather than to the values prescribed by the
-        boundary condition. Default is `False`.
+        boundary condition. Default is `True`.
     diagonal : bool
         If assembling a matrix is it diagonal?
     weight : float
@@ -143,7 +143,6 @@ def get_assembler(form, *args, **kwargs):
 
     """
     is_base_form_preprocessed = kwargs.pop('is_base_form_preprocessed', False)
-    bcs = kwargs.get('bcs', None)
     fc_params = kwargs.get('form_compiler_parameters', None)
     if isinstance(form, ufl.form.BaseForm) and not is_base_form_preprocessed:
         mat_type = kwargs.get('mat_type', None)
@@ -155,8 +154,13 @@ def get_assembler(form, *args, **kwargs):
         if len(form.arguments()) == 0:
             return ZeroFormAssembler(form, form_compiler_parameters=fc_params)
         elif len(form.arguments()) == 1 or diagonal:
-            return OneFormAssembler(form, *args, bcs=bcs, form_compiler_parameters=fc_params, needs_zeroing=kwargs.get('needs_zeroing', True),
-                                    zero_bc_nodes=kwargs.get('zero_bc_nodes', False), diagonal=diagonal)
+            return OneFormAssembler(form, *args,
+                                    bcs=kwargs.get("bcs", None),
+                                    form_compiler_parameters=fc_params,
+                                    needs_zeroing=kwargs.get("needs_zeroing", True),
+                                    zero_bc_nodes=kwargs.get("zero_bc_nodes", True),
+                                    diagonal=diagonal,
+                                    weight=kwargs.get("weight", 1.0))
         elif len(form.arguments()) == 2:
             return TwoFormAssembler(form, *args, **kwargs)
         else:
@@ -308,7 +312,7 @@ def __init__(self,
                  sub_mat_type=None,
                  options_prefix=None,
                  appctx=None,
-                 zero_bc_nodes=False,
+                 zero_bc_nodes=True,
                  diagonal=False,
                  weight=1.0,
                  allocation_integral_types=None):
@@ -381,6 +385,12 @@ def visitor(e, *operands):
         visited = {}
         result = BaseFormAssembler.base_form_postorder_traversal(self._form, visitor, visited)
 
+        # Apply BCs after assembly
+        rank = len(self._form.arguments())
+        if rank == 1 and not isinstance(result, ufl.ZeroBaseForm):
+            for bc in self._bcs:
+                bc.zero(result)
+
         if tensor:
             BaseFormAssembler.update_tensor(result, tensor)
             return tensor
@@ -405,8 +415,8 @@ def base_form_assembly_visitor(self, expr, tensor, *args):
             if rank == 0:
                 assembler = ZeroFormAssembler(form, form_compiler_parameters=self._form_compiler_params)
             elif rank == 1 or (rank == 2 and self._diagonal):
-                assembler = OneFormAssembler(form, bcs=self._bcs, form_compiler_parameters=self._form_compiler_params,
-                                             zero_bc_nodes=self._zero_bc_nodes, diagonal=self._diagonal)
+                assembler = OneFormAssembler(form, form_compiler_parameters=self._form_compiler_params,
+                                             zero_bc_nodes=self._zero_bc_nodes, diagonal=self._diagonal, weight=self._weight)
             elif rank == 2:
                 assembler = TwoFormAssembler(form, bcs=self._bcs, form_compiler_parameters=self._form_compiler_params,
                                              mat_type=self._mat_type, sub_mat_type=self._sub_mat_type,
@@ -577,10 +587,15 @@ def base_form_assembly_visitor(self, expr, tensor, *args):
     @staticmethod
     def update_tensor(assembled_base_form, tensor):
         if isinstance(tensor, (firedrake.Function, firedrake.Cofunction)):
-            assembled_base_form.dat.copy(tensor.dat)
+            if isinstance(assembled_base_form, ufl.ZeroBaseForm):
+                tensor.dat.zero()
+            else:
+                assembled_base_form.dat.copy(tensor.dat)
         elif isinstance(tensor, matrix.MatrixBase):
-            # Uses the PETSc copy method.
-            assembled_base_form.petscmat.copy(tensor.petscmat)
+            if isinstance(assembled_base_form, ufl.ZeroBaseForm):
+                tensor.petscmat.zeroEntries()
+            else:
+                assembled_base_form.petscmat.copy(tensor.petscmat)
         else:
             raise NotImplementedError("Cannot update tensor of type %s" % type(tensor))
 
@@ -807,9 +822,9 @@ def restructure_base_form(expr, visited=None):
             return ufl.action(expr, ustar)
 
         # -- Case (6) -- #
-        if isinstance(expr, ufl.FormSum) and all(isinstance(c, ufl.core.base_form_operator.BaseFormOperator) for c in expr.components()):
-            # Return ufl.Sum
-            return sum([c for c in expr.components()])
+        if isinstance(expr, ufl.FormSum) and all(ufl.duals.is_dual(a.function_space()) for a in expr.arguments()):
+            # Return ufl.Sum if we are assembling a FormSum with Coarguments (a primal expression)
+            return sum(w*c for w, c in zip(expr.weights(), expr.components()))
         return expr
 
     @staticmethod
@@ -1138,7 +1153,7 @@ class OneFormAssembler(ParloopFormAssembler):
 
     Parameters
     ----------
-    form : ufl.Form or slate.TensorBasehe
+    form : ufl.Form or slate.TensorBase
         1-form.
 
     Notes
@@ -1149,14 +1164,15 @@ class OneFormAssembler(ParloopFormAssembler):
 
     @classmethod
     def _cache_key(cls, form, bcs=None, form_compiler_parameters=None, needs_zeroing=True,
-                   zero_bc_nodes=False, diagonal=False):
+                   zero_bc_nodes=True, diagonal=False, weight=1.0):
         bcs = solving._extract_bcs(bcs)
-        return tuple(bcs), tuplify(form_compiler_parameters), needs_zeroing, zero_bc_nodes, diagonal
+        return tuple(bcs), tuplify(form_compiler_parameters), needs_zeroing, zero_bc_nodes, diagonal, weight
 
     @FormAssembler._skip_if_initialised
     def __init__(self, form, bcs=None, form_compiler_parameters=None, needs_zeroing=True,
-                 zero_bc_nodes=False, diagonal=False):
+                 zero_bc_nodes=True, diagonal=False, weight=1.0):
         super().__init__(form, bcs=bcs, form_compiler_parameters=form_compiler_parameters, needs_zeroing=needs_zeroing)
+        self._weight = weight
         self._diagonal = diagonal
         self._zero_bc_nodes = zero_bc_nodes
         if self._diagonal and any(isinstance(bc, EquationBCSplit) for bc in self._bcs):
@@ -1185,23 +1201,21 @@ def _apply_bc(self, tensor, bc):
         elif isinstance(bc, EquationBCSplit):
             bc.zero(tensor)
             type(self)(bc.f, bcs=bc.bcs, form_compiler_parameters=self._form_compiler_params, needs_zeroing=False,
-                       zero_bc_nodes=self._zero_bc_nodes, diagonal=self._diagonal).assemble(tensor=tensor)
+                       zero_bc_nodes=self._zero_bc_nodes, diagonal=self._diagonal, weight=self._weight).assemble(tensor=tensor)
         else:
             raise AssertionError
 
     def _apply_dirichlet_bc(self, tensor, bc):
-        if not self._zero_bc_nodes:
-            tensor_func = tensor.riesz_representation(riesz_map="l2")
-            if self._diagonal:
-                bc.set(tensor_func, 1)
-            else:
-                bc.apply(tensor_func)
-            tensor.assign(tensor_func.riesz_representation(riesz_map="l2"))
+        if self._diagonal:
+            bc.set(tensor, self._weight)
+        elif not self._zero_bc_nodes:
+            # NOTE this only works if tensor is a Function and not a Cofunction
+            bc.apply(tensor)
         else:
             bc.zero(tensor)
 
     def _check_tensor(self, tensor):
-        if tensor.function_space() != self._form.arguments()[0].function_space():
+        if tensor.function_space() != self._form.arguments()[0].function_space().dual():
             raise ValueError("Form's argument does not match provided result tensor")
 
     @staticmethod
@@ -2127,14 +2141,13 @@ def iter_active_coefficients(form, kinfo):
 
     @staticmethod
     def iter_constants(form, kinfo):
-        """Yield the form constants"""
+        """Yield the form constants referenced in ``kinfo``."""
         if isinstance(form, slate.TensorBase):
-            for const in form.constants():
-                yield const
+            all_constants = form.constants()
         else:
             all_constants = extract_firedrake_constants(form)
-            for constant_index in kinfo.constant_numbers:
-                yield all_constants[constant_index]
+        for constant_index in kinfo.constant_numbers:
+            yield all_constants[constant_index]
 
     @staticmethod
     def index_function_spaces(form, indices):