Updates for latest release of PETSc (#4181)

* Fixes for PETSc 3.23.0

* Fix that options prefixes may now be None

Introduced in https://gitlab.com/petsc/petsc/-/merge_requests/8185.

---------

Co-authored-by: David Ham <David.Ham@imperial.ac.uk>

Author: connorjward

firedrake/cython/dmcommon.pyx

@@ -2120,6 +2120,8 @@ def mark_entity_classes_using_cell_dm(PETSc.DM swarm):
         PetscInt nswarmCells, swarmCell, blocksize
         PetscInt *swarmParentCells = NULL
         PetscDataType ctype = PETSC_DATATYPE_UNKNOWN
+        const char *cellid = NULL
+        PETSc.PetscDMSwarmCellDM celldm
 
     plex = swarm.getCellDM()
     get_height_stratum(plex.dm, 0, &cStart, &cEnd)
@@ -2145,14 +2147,16 @@ def mark_entity_classes_using_cell_dm(PETSc.DM swarm):
     for ilabel, op2class in enumerate([b"pyop2_core", b"pyop2_owned", b"pyop2_ghost"]):
         CHKERR(DMCreateLabel(swarm.dm, op2class))
         CHKERR(DMGetLabel(swarm.dm, op2class, &swarm_labels[ilabel]))
-    CHKERR(DMSwarmGetField(swarm.dm, b"DMSwarm_cellid", &blocksize, &ctype, <void**>&swarmParentCells))
+    CHKERR(DMSwarmGetCellDMActive(swarm.dm, &celldm))
+    CHKERR(DMSwarmCellDMGetCellID(celldm, &cellid))
+    CHKERR(DMSwarmGetField(swarm.dm, cellid, &blocksize, &ctype, <void**> &swarmParentCells))
     assert ctype == PETSC_INT
     assert blocksize == 1
     CHKERR(DMSwarmGetLocalSize(swarm.dm, &nswarmCells))
     for swarmCell in range(nswarmCells):
         plex_cell_class = plex_cell_classes[swarmParentCells[swarmCell] - cStart]
         CHKERR(DMLabelSetValue(swarm_labels[plex_cell_class], swarmCell, label_value))
-    CHKERR(DMSwarmRestoreField(swarm.dm, b"DMSwarm_cellid", &blocksize, &ctype, <void**>&swarmParentCells))
+    CHKERR(DMSwarmRestoreField(swarm.dm, cellid, &blocksize, &ctype, <void**> &swarmParentCells))
     CHKERR(PetscFree(plex_cell_classes))
 
 

firedrake/cython/petschdr.pxi

@@ -79,6 +79,8 @@ cdef extern from "petscdm.h" nogil:
 cdef extern from "petscdmswarm.h" nogil:
     int DMSwarmGetLocalSize(PETSc.PetscDM,PetscInt*)
     int DMSwarmGetCellDM(PETSc.PetscDM, PETSc.PetscDM*)
+    int DMSwarmGetCellDMActive(PETSc.PetscDM, PETSc.PetscDMSwarmCellDM*)
+    int DMSwarmCellDMGetCellID(PETSc.PetscDMSwarmCellDM, const char *[])
     int DMSwarmGetField(PETSc.PetscDM,const char[],PetscInt*,PetscDataType*,void**)
     int DMSwarmRestoreField(PETSc.PetscDM,const char[],PetscInt*,PetscDataType*,void**)
 

firedrake/mesh.py

@@ -1966,14 +1966,15 @@ 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").ravel()
+            cell_id_name = swarm.getCellDMActive().getCellID()
+            swarm_parent_cell_nums = swarm.getField(cell_id_name).ravel()
             parent_renum = self._parent_mesh._dm_renumbering.getIndices()
             pStart, _ = parent.getChart()
             parent_renum_inv = np.empty_like(parent_renum)
             parent_renum_inv[parent_renum - pStart] = np.arange(len(parent_renum))
             # Use kind = 'stable' to make the ordering deterministic.
             perm = np.argsort(parent_renum_inv[swarm_parent_cell_nums - pStart], kind='stable').astype(IntType)
-            swarm.restoreField("DMSwarm_cellid")
+            swarm.restoreField(cell_id_name)
             perm_is = PETSc.IS().create(comm=swarm.comm)
             perm_is.setType("general")
             perm_is.setIndices(perm)
@@ -3557,11 +3558,9 @@ def _pic_swarm_in_mesh(
         #. ``parentcellextrusionheight`` which contains the extrusion height of
             the immersed vertex in the parent mesh cell.
 
-        Another three are required for proper functioning of the DMSwarm:
+        Another two are required for proper functioning of the DMSwarm:
 
         #. ``DMSwarmPIC_coor`` which contains the coordinates of the point.
-        #. ``DMSwarm_cellid`` the DMPlex cell within which the DMSwarm point is
-           located.
         #. ``DMSwarm_rank``: the MPI rank which owns the DMSwarm point.
 
     .. note::
@@ -3794,7 +3793,6 @@ def _dmswarm_create(
     # These are created by default for a PIC DMSwarm
     default_fields = [
         ("DMSwarmPIC_coor", gdim, RealType),
-        ("DMSwarm_cellid", 1, IntType),
         ("DMSwarm_rank", 1, IntType),
     ]
 
@@ -3853,12 +3851,6 @@ def _dmswarm_create(
     # Set to Particle In Cell (PIC) type
     if not isinstance(plex, PETSc.DMSwarm):
         swarm.setType(PETSc.DMSwarm.Type.PIC)
-    else:
-        # This doesn't work where we embed a DMSwarm in a DMSwarm, instead
-        # we register some default fields manually
-        for name, size, dtype in default_fields:
-            if name == "DMSwarmPIC_coor" or name == "DMSwarm_cellid":
-                swarm.registerField(name, size, dtype=dtype)
 
     # Register any fields
     for name, size, dtype in swarm.default_extra_fields + swarm.other_fields:
@@ -3872,14 +3864,15 @@ def _dmswarm_create(
     # Add point coordinates. This amounts to our own implementation of
     # DMSwarmSetPointCoordinates because Firedrake's mesh coordinate model
     # doesn't always exactly coincide with that of DMPlex: in most cases the
-    # plex_parent_cell_nums (DMSwarm_cellid field) and parent_cell_nums
-    # (parentcellnum field), the latter being the numbering used by firedrake,
-    # refer fundamentally to the same cells. For extruded meshes the DMPlex
-    # dimension is based on the topological dimension of the base mesh.
+    # plex_parent_cell_nums and parent_cell_nums (parentcellnum field), the
+    # latter being the numbering used by firedrake, refer fundamentally to the
+    # same cells. For extruded meshes the DMPlex dimension is based on the
+    # topological dimension of the base mesh.
 
     # 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").ravel()
+    cell_id_name = swarm.getCellDMActive().getCellID()
+    swarm_parent_cell_nums = swarm.getField(cell_id_name).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").ravel()
@@ -3903,7 +3896,7 @@ def _dmswarm_create(
     swarm.restoreField("refcoord")
     swarm.restoreField("parentcellnum")
     swarm.restoreField("DMSwarmPIC_coor")
-    swarm.restoreField("DMSwarm_cellid")
+    swarm.restoreField(cell_id_name)
 
     if extruded:
         field_base_parent_cell_nums = swarm.getField("parentcellbasenum").ravel()

firedrake/preconditioners/asm.py

@@ -29,7 +29,7 @@ def initialize(self, pc):
         # Get context from pc
         _, P = pc.getOperators()
         dm = pc.getDM()
-        self.prefix = pc.getOptionsPrefix() + self._prefix
+        self.prefix = (pc.getOptionsPrefix() or "") + self._prefix
 
         # Extract function space and mesh to obtain plex and indexing functions
         V = get_function_space(dm)

firedrake/preconditioners/assembled.py

@@ -37,7 +37,7 @@ def initialize(self, pc):
             if not context.on_diag:
                 raise ValueError("Only makes sense to invert diagonal block")
 
-        prefix = pc.getOptionsPrefix()
+        prefix = pc.getOptionsPrefix() or ""
         options_prefix = prefix + self._prefix
 
         mat_type = PETSc.Options().getString(options_prefix + "mat_type", "aij")

firedrake/preconditioners/bddc.py

@@ -42,7 +42,7 @@ def initialize(self, pc):
         # Get context from pc
         _, P = pc.getOperators()
         dm = pc.getDM()
-        self.prefix = pc.getOptionsPrefix() + self._prefix
+        self.prefix = (pc.getOptionsPrefix() or "") + self._prefix
 
         V = get_function_space(dm)
 

firedrake/preconditioners/facet_split.py

@@ -41,7 +41,7 @@ def get_indices(self, V, W):
     def initialize(self, pc):
         from firedrake import FunctionSpace, TestFunction, TrialFunction, split
 
-        prefix = pc.getOptionsPrefix()
+        prefix = pc.getOptionsPrefix() or ""
         options_prefix = prefix + self._prefix
         options = PETSc.Options(options_prefix)
         mat_type = options.getString("mat_type", "submatrix")

firedrake/preconditioners/fdm.py

@@ -121,7 +121,7 @@ def initialize(self, pc):
         Citations().register(self._citation)
         self.comm = pc.comm
         Amat, Pmat = pc.getOperators()
-        prefix = pc.getOptionsPrefix()
+        prefix = pc.getOptionsPrefix() or ""
         options_prefix = prefix + self._prefix
         options = PETSc.Options(options_prefix)
 

firedrake/preconditioners/gtmg.py

@@ -31,7 +31,7 @@ def initialize(self, pc):
         if not isinstance(ctx, _SNESContext):
             raise ValueError("Don't know how to get form from %r" % ctx)
 
-        prefix = pc.getOptionsPrefix()
+        prefix = pc.getOptionsPrefix() or ""
         options_prefix = prefix + self._prefix
         opts = PETSc.Options()
 

firedrake/preconditioners/hiptmair.py

@@ -41,7 +41,7 @@ def initialize(self, pc):
         appctx = self.get_appctx(pc)
         fcp = appctx.get("form_compiler_parameters")
 
-        prefix = pc.getOptionsPrefix()
+        prefix = pc.getOptionsPrefix() or ""
         options_prefix = prefix + self._prefix
         opts = PETSc.Options()
 
@@ -156,7 +156,7 @@ def coarsen(self, pc):
         else:
             raise ValueError("Hiptmair decomposition not available for", element)
 
-        prefix = pc.getOptionsPrefix()
+        prefix = pc.getOptionsPrefix() or ""
         options_prefix = prefix + self._prefix
         opts = PETSc.Options(options_prefix)
         domain = opts.getString("mg_coarse_restriction_domain", "")

firedrake/preconditioners/hypre_ads.py

@@ -16,7 +16,7 @@ class HypreADS(PCBase):
     def initialize(self, obj):
         A, P = obj.getOperators()
         appctx = self.get_appctx(obj)
-        prefix = obj.getOptionsPrefix()
+        prefix = obj.getOptionsPrefix() or ""
         V = get_function_space(obj.getDM())
         mesh = V.mesh()
 

firedrake/preconditioners/hypre_ams.py

@@ -37,7 +37,7 @@ def initialize(self, obj):
         Citations().register("Kolev2009")
         A, P = obj.getOperators()
         appctx = self.get_appctx(obj)
-        prefix = obj.getOptionsPrefix()
+        prefix = obj.getOptionsPrefix() or ""
         V = get_function_space(obj.getDM())
         mesh = V.mesh()
 

firedrake/preconditioners/patch.py

@@ -715,7 +715,7 @@ def __call__(self, pc):
             raise NotImplementedError("Sorry, plane smoothers not yet implemented in complex mode")
         dm = pc.getDM()
         context = dm.getAttr("__firedrake_ctx__")
-        prefix = pc.getOptionsPrefix()
+        prefix = pc.getOptionsPrefix() or ""
         sentinel = object()
         sweeps = PETSc.Options(prefix).getString("pc_patch_construct_ps_sweeps", default=sentinel)
         if sweeps == sentinel:
@@ -789,7 +789,7 @@ def initialize(self, obj):
                 PETSc.Sys.Print("Warning: you almost surely want to set an overlap_type in your mesh's distribution_parameters.")
 
         patch = obj.__class__().create(comm=mesh.comm)
-        patch.setOptionsPrefix(obj.getOptionsPrefix() + "patch_")
+        patch.setOptionsPrefix((obj.getOptionsPrefix() or "") + "patch_")
         self.configure_patch(patch, obj)
         patch.setType("patch")
 
@@ -924,7 +924,7 @@ def destroy(self, obj):
             self.patch.destroy()
 
     def user_construction_op(self, obj, *args, **kwargs):
-        prefix = obj.getOptionsPrefix()
+        prefix = obj.getOptionsPrefix() or ""
         sentinel = object()
         usercode = PETSc.Options(prefix).getString("%s_patch_construct_python_type" % self._objectname, default=sentinel)
         if usercode == sentinel:

firedrake/preconditioners/pcd.py

@@ -45,7 +45,7 @@ def initialize(self, pc):
         from firedrake.assemble import assemble, get_assembler
         if pc.getType() != "python":
             raise ValueError("Expecting PC type python")
-        prefix = pc.getOptionsPrefix() + "pcd_"
+        prefix = (pc.getOptionsPrefix() or "") + "pcd_"
 
         # we assume P has things stuffed inside of it
         _, P = pc.getOperators()

firedrake/preconditioners/pmg.py

@@ -106,7 +106,7 @@ def initialize(self, obj):
         if test.function_space() != trial.function_space():
             raise NotImplementedError("test and trial spaces must be the same")
 
-        prefix = obj.getOptionsPrefix()
+        prefix = obj.getOptionsPrefix() or ""
         options_prefix = prefix + self._prefix
         pdm = PETSc.DMShell().create(comm=obj.comm)
         pdm.setOptionsPrefix(options_prefix)
@@ -119,7 +119,7 @@ def initialize(self, obj):
             default_mat_type = "matfree"
 
         # Get the coarse degree from PETSc options
-        copts = PETSc.Options(ppc.getOptionsPrefix() + ppc.getType() + "_coarse_")
+        copts = PETSc.Options((ppc.getOptionsPrefix() or "") + ppc.getType() + "_coarse_")
         self.coarse_degree = copts.getInt("degree", default=1)
         self.coarse_mat_type = copts.getString("mat_type", default=default_mat_type)
         self.coarse_pmat_type = copts.getString("pmat_type", default=self.coarse_mat_type)
@@ -443,7 +443,7 @@ class PMGPC(PCBase, PMGBase):
     def configure_pmg(self, pc, pdm):
         odm = pc.getDM()
         ppc = PETSc.PC().create(comm=pc.comm)
-        ppc.setOptionsPrefix(pc.getOptionsPrefix() + self._prefix)
+        ppc.setOptionsPrefix((pc.getOptionsPrefix() or "") + self._prefix)
         ppc.setType("mg")
         ppc.setOperators(*pc.getOperators())
         ppc.setDM(pdm)
@@ -458,7 +458,7 @@ def configure_pmg(self, pc, pdm):
         # other way to get PETSc to know this at the right time.
         max_levels = odm.getRefineLevel() + 1
         if max_levels > 1:
-            opts = PETSc.Options(pc.getOptionsPrefix() + "pmg_")
+            opts = PETSc.Options((pc.getOptionsPrefix() or "") + "pmg_")
             if opts.getString("mg_coarse_pc_type") == "mg":
                 opts["mg_coarse_pc_mg_levels"] = min(opts.getInt("mg_coarse_pc_mg_levels", max_levels), max_levels)
         return ppc
@@ -479,7 +479,7 @@ class PMGSNES(SNESBase, PMGBase):
     def configure_pmg(self, snes, pdm):
         odm = snes.getDM()
         psnes = PETSc.SNES().create(comm=snes.comm)
-        psnes.setOptionsPrefix(snes.getOptionsPrefix() + self._prefix)
+        psnes.setOptionsPrefix((snes.getOptionsPrefix() or "") + self._prefix)
         psnes.setType("fas")
         psnes.setDM(pdm)
         psnes.setTolerances(max_it=1)
@@ -503,7 +503,7 @@ def configure_pmg(self, snes, pdm):
         # other way to get PETSc to know this at the right time.
         max_levels = odm.getRefineLevel() + 1
         if max_levels > 1:
-            opts = PETSc.Options(snes.getOptionsPrefix() + "pfas_")
+            opts = PETSc.Options((snes.getOptionsPrefix() or "") + "pfas_")
             if opts.getString("fas_coarse_pc_type") == "mg":
                 opts["fas_coarse_pc_mg_levels"] = min(opts.getInt("fas_coarse_pc_mg_levels", max_levels), max_levels)
             if opts.getString("fas_coarse_snes_type") == "fas":

firedrake/slate/static_condensation/hybridization.py

@@ -43,7 +43,7 @@ def initialize(self, pc):
         from ufl.algorithms.replace import replace
 
         # Extract the problem context
-        prefix = pc.getOptionsPrefix() + "hybridization_"
+        prefix = (pc.getOptionsPrefix() or "") + "hybridization_"
         _, P = pc.getOperators()
         self.ctx = P.getPythonContext()
 

firedrake/slate/static_condensation/scpc.py

@@ -36,7 +36,7 @@ def initialize(self, pc):
         from firedrake.parloops import par_loop, INC
         from ufl import dx
 
-        prefix = pc.getOptionsPrefix() + "condensed_field_"
+        prefix = (pc.getOptionsPrefix() or "") + "condensed_field_"
         A, P = pc.getOperators()
         self.cxt = A.getPythonContext()
         if not isinstance(self.cxt, ImplicitMatrixContext):
@@ -49,7 +49,7 @@ def initialize(self, pc):
         if len(W) > 3:
             raise NotImplementedError("Only supports up to three function spaces.")
 
-        elim_fields = PETSc.Options().getString(pc.getOptionsPrefix()
+        elim_fields = PETSc.Options().getString((pc.getOptionsPrefix() or "")
                                                 + "pc_sc_eliminate_fields",
                                                 None)
         if elim_fields:

pyproject.toml

@@ -22,7 +22,7 @@ dependencies = [
   "libsupermesh",
   # NOTE: If changing the PETSc/SLEPc version then firedrake-configure also needs
   # changing (as well as other references to petsc4py and slepc4py here)
-  "petsc4py==3.22.2",
+  "petsc4py==3.23.0",
   "numpy",
   "packaging",
   "pkgconfig",
@@ -119,7 +119,7 @@ ci = [
   "pytest-split",  # needed for firedrake-run-split-tests
   "pytest-timeout",
   "pytest-xdist",
-  "slepc4py==3.22.2",
+  "slepc4py==3.23.0",
   "torch",  # requires passing '--extra-index-url' to work
   "vtk",
 ]
@@ -133,7 +133,7 @@ docker = [  # Used in firedrake-vanilla container
   "pytest-split",  # needed for firedrake-run-split-tests
   "pytest-timeout",
   "pytest-xdist",
-  "slepc4py==3.22.2",
+  "slepc4py==3.23.0",
 ]
 
 [build-system]
@@ -146,7 +146,7 @@ requires = [
   "pkgconfig",
   "pybind11",
   "setuptools>61.2",
-  "petsc4py==3.22.2",
+  "petsc4py==3.23.0",
   "rtree>=1.2",
 ]
 build-backend = "setuptools.build_meta"

scripts/firedrake-configure

@@ -41,7 +41,7 @@ ARCH_COMPLEX = FiredrakeArch.COMPLEX
 
 # NOTE: When updating this variable corresponding changes must be made inside
 # pyproject.toml
-SUPPORTED_PETSC_VERSION = "v3.22.2"
+SUPPORTED_PETSC_VERSION = "v3.23.0"
 
 
 def main():

tests/firedrake/regression/test_matrix_prefix.py

@@ -32,9 +32,7 @@ def test_matrix_prefix_solver(options_prefix):
     assert factor.getType() == DEFAULT_DIRECT_SOLVER
 
     for A in pc.getOperators():
-        pfx = A.getOptionsPrefix()
-        if pfx is None:
-            pfx = ""
+        pfx = A.getOptionsPrefix() or ""
         assert pfx == solver.options_prefix