def __init__(self, parameters, options_prefix):
if parameters is None:
parameters = {}
else:
parameters = parameters.copy()
if options_prefix is None:
self.options_prefix = "firedrake_%d_" % next(self.count)
self.parameters = parameters
self.to_delete = set(parameters)
else:
self.options_prefix = options_prefix
# Remove those options from the dict that were passed on
# the commandline.
self.parameters = dict(
(k, v) for k, v in parameters.iteritems()
if options_prefix + k not in self.commandline_options)
self.to_delete = set(parameters)
# Now update parameters from options, so that they're
# availabe to solver setup (for, e.g., matrix-free).
for k, v in PETSc.Options(
self.options_prefix).getAll().iteritems():
self.parameters[k] = v
self.options_object = PETSc.Options(self.options_prefix)
self._setfromoptions = False
super(ParametersMixin, self).__init__()
def get_patches(self, V):
mesh = V._mesh
mesh_dm = mesh._topology_dm
# Obtain the topological entities to use to construct the stars
depth = PETSc.Options().getInt(self.prefix + "construct_dim",
default=-1)
height = PETSc.Options().getInt(self.prefix + "construct_codim",
default=-1)
if (depth == -1 and height == -1) or (depth != -1 and height != -1):
raise ValueError(
f"Must set exactly one of {self.prefix}construct_dim or {self.prefix}construct_codim"
)
# Accessing .indices causes the allocation of a global array,
# so we need to cache these for efficiency
V_local_ises_indices = []
for (i, W) in enumerate(V):
V_local_ises_indices.append(V.dof_dset.local_ises[i].indices)
# Build index sets for the patches
ises = []
if depth != -1:
(start, end) = mesh_dm.getDepthStratum(depth)
else:
(start, end) = mesh_dm.getHeightStratum(height)
for seed in range(start, end):
# Only build patches over owned DoFs
if mesh_dm.getLabelValue("pyop2_ghost", seed) != -1:
continue
# Create point list from mesh DM
star, _ = mesh_dm.getTransitiveClosure(seed, useCone=False)
pt_array = set()
for pt in star.tolist():
closure, _ = mesh_dm.getTransitiveClosure(seed, useCone=True)
pt_array.update(closure.tolist())
# Get DoF indices for patch
indices = []
for (i, W) in enumerate(V):
section = W.dm.getDefaultSection()
for p in pt_array:
dof = section.getDof(p)
if dof <= 0:
continue
off = section.getOffset(p)
# Local indices within W
W_indices = numpy.arange(off * W.value_size,
W.value_size * (off + dof),
dtype='int32')
indices.extend(V_local_ises_indices[i][W_indices])
iset = PETSc.IS().createGeneral(indices, comm=COMM_SELF)
ises.append(iset)
return ises
def initialize(self, pc):
# Get context from pc
_, P = pc.getOperators()
dm = pc.getDM()
self.prefix = pc.getOptionsPrefix() + self._prefix
# Extract function space and mesh to obtain plex and indexing functions
V = get_function_space(dm)
# Obtain patches from user defined funtion
ises = self.get_patches(V)
# Create new PC object as ASM type and set index sets for patches
asmpc = PETSc.PC().create(comm=pc.comm)
asmpc.incrementTabLevel(1, parent=pc)
asmpc.setOptionsPrefix(self.prefix + "sub_")
asmpc.setOperators(*pc.getOperators())
backend = PETSc.Options().getString(self.prefix + "backend",
default="petscasm").lower()
# Either use PETSc's ASM PC or use TinyASM (as simple ASM
# implementation designed to be fast for small block sizes).
if backend == "petscasm":
asmpc.setType(asmpc.Type.ASM)
# Set default solver parameters
asmpc.setASMType(PETSc.PC.ASMType.BASIC)
opts = PETSc.Options(asmpc.getOptionsPrefix())
if "sub_pc_type" not in opts:
opts["sub_pc_type"] = "lu"
if "sub_pc_factor_shift_type" not in opts:
opts["sub_pc_factor_shift_type"] = "NONE"
lgmap = V.dof_dset.lgmap
# Translate to global numbers
ises = tuple(lgmap.applyIS(iset) for iset in ises)
asmpc.setASMLocalSubdomains(len(ises), ises)
elif backend == "tinyasm":
if not have_tinyasm:
raise ValueError(
"To use the TinyASM backend you need to install firedrake with TinyASM (firedrake-update --tinyasm)"
)
_, P = asmpc.getOperators()
lgmap = V.dof_dset.lgmap
P.setLGMap(rmap=lgmap, cmap=lgmap)
asmpc.setType("tinyasm")
# TinyASM wants local numbers, no need to translate
tinyasm.SetASMLocalSubdomains(
asmpc, ises, [W.dm.getDefaultSF() for W in V],
[W.value_size for W in V],
sum(W.value_size * W.dof_dset.total_size for W in V))
asmpc.setUp()
else:
raise ValueError(f"Unknown backend type f{backend}")
asmpc.setFromOptions()
self.asmpc = asmpc
def configure_pmg(self, snes, pdm):
odm = snes.getDM()
psnes = PETSc.SNES().create(comm=snes.comm)
psnes.setOptionsPrefix(snes.getOptionsPrefix() + "pfas_")
psnes.setType("fas")
psnes.setDM(pdm)
psnes.incrementTabLevel(1, parent=snes)
(f, residual) = snes.getFunction()
assert residual is not None
(fun, args, kargs) = residual
psnes.setFunction(fun, f.duplicate(), args=args, kargs=kargs)
pdm.setGlobalVector(f.duplicate())
self.dummy = f.duplicate()
psnes.setSolution(f.duplicate())
# PETSc unfortunately requires us to make an ugly hack.
# We would like to use GMG for the coarse solve, at least
# sometimes. But PETSc will use this p-DM's getRefineLevels()
# instead of the getRefineLevels() of the MeshHierarchy to
# decide how many levels it should use for PCMG applied to
# the p-MG's coarse problem. So we need to set an option
# for the user, if they haven't already; I don't know any
# other way to get PETSc to know this at the right time.
opts = PETSc.Options(snes.getOptionsPrefix() + "pfas_")
if "fas_coarse_pc_mg_levels" not in opts:
opts["fas_coarse_pc_mg_levels"] = odm.getRefineLevel() + 1
if "fas_coarse_snes_fas_levels" not in opts:
opts["fas_coarse_snes_fas_levels"] = odm.getRefineLevel() + 1
return psnes
def initialize(self, obj):
if complex_mode:
raise NotImplementedError("HypreAMS preconditioner not yet implemented in complex mode")
Citations().register("Kolev2009")
A, P = obj.getOperators()
prefix = obj.getOptionsPrefix()
V = get_function_space(obj.getDM())
mesh = V.mesh()
family = str(V.ufl_element().family())
degree = V.ufl_element().degree()
if family != 'Nedelec 1st kind H(curl)' or degree != 1:
raise ValueError("Hypre AMS requires lowest order Nedelec elements! (not %s of degree %d)" % (family, degree))
P1 = FunctionSpace(mesh, "Lagrange", 1)
G = Interpolator(grad(TestFunction(P1)), V).callable().handle
pc = PETSc.PC().create(comm=obj.comm)
pc.incrementTabLevel(1, parent=obj)
pc.setOptionsPrefix(prefix + "hypre_ams_")
pc.setOperators(A, P)
pc.setType('hypre')
pc.setHYPREType('ams')
pc.setHYPREDiscreteGradient(G)
zero_beta = PETSc.Options(prefix).getBool("pc_hypre_ams_zero_beta_poisson", default=False)
if zero_beta:
pc.setHYPRESetBetaPoissonMatrix(None)
VectorP1 = VectorFunctionSpace(mesh, "Lagrange", 1)
pc.setCoordinates(interpolate(SpatialCoordinate(mesh), VectorP1).dat.data_ro.copy())
pc.setUp()
self.pc = pc
def __call__(self, pc):
dm = pc.getDM()
prefix = pc.getOptionsPrefix()
sentinel = object()
sweeps = PETSc.Options(prefix).getString(
"pc_patch_construct_ps_sweeps", default=sentinel)
if sweeps == sentinel:
raise ValueError("Must set %spc_patch_construct_ps_sweeps" %
prefix)
patches = []
for sweep in sweeps.split(':'):
axis = int(sweep[0])
dir = {'+': +1, '-': -1}[sweep[1]]
ndiv = int(sweep[2:])
entities = self.sort_entities(dm, axis, dir, ndiv)
for patch in entities:
iset = PETSc.IS().createGeneral(patch, comm=PETSc.COMM_SELF)
patches.append(iset)
iterationSet = PETSc.IS().createStride(size=len(patches),
first=0,
step=1,
comm=PETSc.COMM_SELF)
return (patches, iterationSet)
def create_interpolation(self, dmc, dmf):
prefix = dmc.getOptionsPrefix()
mat_type = PETSc.Options(prefix).getString(
"mg_levels_transfer_mat_type", default="matfree")
I = self.create_transfer(get_appctx(dmc), get_appctx(dmf), mat_type,
True, False)
return I, None
def get_patches(self, V):
mesh = V._mesh
assert mesh.cell_set._extruded
dm = mesh._topology_dm
section = V.dm.getDefaultSection()
# Obtain the codimensions to loop over from options, if present
codim_list = PETSc.Options().getString(self.prefix + "codims", "0, 1")
codim_list = [int(ii) for ii in codim_list.split(",")]
# Build index sets for the patches
ises = []
for codim in codim_list:
for p in range(*dm.getHeightStratum(codim)):
# Only want to build patches over owned faces
if dm.getLabelValue("pyop2_ghost", p) != -1:
continue
dof = section.getDof(p)
if dof <= 0:
continue
off = section.getOffset(p)
indices = numpy.arange(off * V.value_size,
V.value_size * (off + dof),
dtype='int32')
iset = PETSc.IS().createGeneral(indices, comm=COMM_SELF)
ises.append(iset)
return ises
def create_injection(self, dmc, dmf):
prefix = dmc.getOptionsPrefix()
mat_type = PETSc.Options(prefix).getString(
"mg_levels_transfer_mat_type", default="matfree")
I = self.create_transfer(get_appctx(dmf), get_appctx(dmc), mat_type,
False, False)
return PETSc.Mat().createTranspose(I)
def __call__(self, pc):
dm = pc.getDM()
prefix = pc.getOptionsPrefix()
opts = PETSc.Options(prefix)
select = partial(self.select_entity, dm=dm, exclude="pyop2_ghost")
(pStart, pEnd) = dm.getChart()
owned_entities = set(filter(select, range(pStart, pEnd)))
overlap = 1 # FIXME: get from options
all_entities = set(owned_entities)
for i in range(overlap):
tmp_entities = set(all_entities)
for entity in tmp_entities:
for s in self.star(dm, entity):
for c in self.closure(dm, s):
all_entities.add(c)
overlap_entities = list(all_entities.difference(owned_entities))
iset = PETSc.IS().createGeneral(overlap_entities, comm=PETSc.COMM_SELF)
patches = [iset]
iterset = PETSc.IS().createStride(size=len(patches),
first=0,
step=1,
comm=PETSc.COMM_SELF)
#print("owned_entities: ", owned_entities)
#print("all_entities: ", all_entities)
#print("overlap_entities: ", overlap_entities)
return (patches, iterset)
def __del__(self):
# Remove stuff from the options database
# It's fixed size, so if we don't it gets too big.
if self._auto_prefix and hasattr(self, '_opt_prefix'):
opts = PETSc.Options()
for k in self.parameters.iterkeys():
del opts[self._opt_prefix + k]
delattr(self, '_opt_prefix')
def _check_options(self, valid):
default = object()
opts = PETSc.Options(self.prefix)
for key, supported in valid:
value = opts.getString(key, default=default)
if value is not default and value not in supported:
raise ValueError(
f"Unsupported value ({value}) for '{self.prefix + key}'. "
f"Should be one of {supported}")
def test_petsc_options_cleared(a_L_out):
a, L, out = a_L_out
opts = PETSc.Options()
original = {}
original.update(opts.getAll())
solve(a == L, out, solver_parameters={'foo': 'bar'})
assert original == opts.getAll()
def initialize(self, pc):
# Make a new DM.
# Hook up a (new) coarsen routine on that DM.
# Make a new PC, of type MG.
# Assign the DM to that PC.
odm = pc.getDM()
ctx = get_appctx(odm)
test, trial = ctx.J.arguments()
if test.function_space() != trial.function_space():
raise NotImplementedError("test and trial spaces must be the same")
prefix = pc.getOptionsPrefix()
options_prefix = prefix + "pmg_"
pdm = PETSc.DMShell().create(comm=pc.comm)
pdm.setOptionsPrefix(options_prefix)
# Get the coarse degree from PETSc options
self.coarse_degree = PETSc.Options(options_prefix).getInt("mg_coarse_degree", default=1)
# Construct a list with the elements we'll be using
V = test.function_space()
ele = V.ufl_element()
elements = [ele]
while True:
try:
ele_ = self.coarsen_element(ele)
assert ele_.value_shape() == ele.value_shape()
ele = ele_
except ValueError:
break
elements.append(ele)
sf = odm.getPointSF()
section = odm.getDefaultSection()
attach_hooks(pdm, level=len(elements)-1, sf=sf, section=section)
# Now overwrite some routines on the DM
pdm.setRefine(None)
pdm.setCoarsen(self.coarsen)
pdm.setCreateInterpolation(self.create_interpolation)
# We need this for p-FAS
pdm.setCreateInjection(self.create_injection)
pdm.setSNESJacobian(_SNESContext.form_jacobian)
pdm.setSNESFunction(_SNESContext.form_function)
pdm.setKSPComputeOperators(_SNESContext.compute_operators)
set_function_space(pdm, get_function_space(odm))
parent = get_parent(odm)
assert parent is not None
add_hook(parent, setup=partial(push_parent, pdm, parent), teardown=partial(pop_parent, pdm, parent), call_setup=True)
add_hook(parent, setup=partial(push_appctx, pdm, ctx), teardown=partial(pop_appctx, pdm, ctx), call_setup=True)
self.ppc = self.configure_pmg(pc, pdm)
self.ppc.setFromOptions()
self.ppc.setUp()
def __init__(self, Q, free_bids=["on_boundary"]):
(V, I_interp) = Q.get_space_for_inner()
self.free_bids = free_bids
u = fd.TrialFunction(V)
v = fd.TestFunction(V)
n = fd.FacetNormal(V.mesh())
def surf_grad(u):
return fd.sym(fd.grad(u) - fd.outer(fd.grad(u) * n, n))
a = (fd.inner(surf_grad(u), surf_grad(v)) + fd.inner(u, v)) * fd.ds
# petsc doesn't like matrices with zero rows
a += 1e-10 * fd.inner(u, v) * fd.dx
A = fd.assemble(a, mat_type="aij")
A = A.petscmat
tdim = V.mesh().topological_dimension()
lsize = fd.Function(V).vector().local_size()
def get_nodes_bc(bc):
nodes = bc.nodes
return nodes[nodes < lsize]
def get_nodes_bid(bid):
bc = fd.DirichletBC(V, fd.Constant(tdim * (0, )), bid)
return get_nodes_bc(bc)
free_nodes = np.concatenate(
[get_nodes_bid(bid) for bid in self.free_bids])
free_dofs = np.concatenate(
[tdim * free_nodes + i for i in range(tdim)])
free_dofs = np.unique(np.sort(free_dofs))
self.free_is = PETSc.IS().createGeneral(free_dofs)
lgr, lgc = A.getLGMap()
self.global_free_is_row = lgr.applyIS(self.free_is)
self.global_free_is_col = lgc.applyIS(self.free_is)
A = A.createSubMatrix(self.global_free_is_row, self.global_free_is_col)
# A.view()
A.assemble()
self.A = A
Aksp = PETSc.KSP().create()
Aksp.setOperators(self.A)
Aksp.setOptionsPrefix("A_")
opts = PETSc.Options()
opts["A_ksp_type"] = "cg"
opts["A_pc_type"] = "hypre"
opts["A_ksp_atol"] = 1e-10
opts["A_ksp_rtol"] = 1e-10
Aksp.setUp()
Aksp.setFromOptions()
self.Aksp = Aksp
def opts(request, prefix, global_parameters):
opts = PETSc.Options()
if prefix is None:
prefix = ""
for k, v in global_parameters.iteritems():
opts["%s%s" % (prefix, k)] = v
def finalize():
for k in global_parameters.keys():
del opts["%s%s" % (prefix, k)]
request.addfinalizer(finalize)
def user_construction_op(self, obj, *args, **kwargs):
prefix = obj.getOptionsPrefix()
sentinel = object()
usercode = PETSc.Options(prefix).getString("%s_patch_construct_python_type" % self._objectname, default=sentinel)
if usercode == sentinel:
raise ValueError("Must set %s%s_patch_construct_python_type" % (prefix, self._objectname))
(modname, funname) = usercode.rsplit('.', 1)
mod = __import__(modname)
fun = getattr(mod, funname)
if isinstance(fun, type):
fun = fun()
return fun(obj, *args, **kwargs)
def initialize(self, pc):
from firedrake import TrialFunction, TestFunction, dx, assemble, inner, parameters
if pc.getType() != "python":
raise ValueError("Expecting PC type python")
prefix = pc.getOptionsPrefix()
options_prefix = prefix + "Mp_"
# we assume P has things stuffed inside of it
_, P = pc.getOperators()
context = P.getPythonContext()
test, trial = context.a.arguments()
if test.function_space() != trial.function_space():
raise ValueError(
"MassInvPC only makes sense if test and trial space are the same"
)
V = test.function_space()
mu = context.appctx.get("mu", 1.0)
u = TrialFunction(V)
v = TestFunction(V)
# Handle vector and tensor-valued spaces.
# 1/mu goes into the inner product in case it varies spatially.
a = inner(1 / mu * u, v) * dx
opts = PETSc.Options()
mat_type = opts.getString(options_prefix + "mat_type",
parameters["default_matrix_type"])
A = assemble(a,
form_compiler_parameters=context.fc_params,
mat_type=mat_type,
options_prefix=options_prefix)
A.force_evaluation()
Pmat = A.petscmat
Pmat.setNullSpace(P.getNullSpace())
tnullsp = P.getTransposeNullSpace()
if tnullsp.handle != 0:
Pmat.setTransposeNullSpace(tnullsp)
ksp = PETSc.KSP().create(comm=pc.comm)
ksp.incrementTabLevel(1, parent=pc)
ksp.setOperators(Pmat)
ksp.setOptionsPrefix(options_prefix)
ksp.setFromOptions()
ksp.setUp()
self.ksp = ksp
def initialize(self, pc):
from firedrake.assemble import allocate_matrix, create_assembly_callable
_, P = pc.getOperators()
if pc.getType() != "python":
raise ValueError("Expecting PC type python")
opc = pc
context = P.getPythonContext()
prefix = pc.getOptionsPrefix()
options_prefix = prefix + "assembled_"
# It only makes sense to preconditioner/invert a diagonal
# block in general. That's all we're going to allow.
if not context.on_diag:
raise ValueError("Only makes sense to invert diagonal block")
mat_type = PETSc.Options().getString(options_prefix + "mat_type",
"aij")
self.P = allocate_matrix(context.a,
bcs=context.row_bcs,
form_compiler_parameters=context.fc_params,
mat_type=mat_type,
options_prefix=options_prefix)
self._assemble_P = create_assembly_callable(
context.a,
tensor=self.P,
bcs=context.row_bcs,
form_compiler_parameters=context.fc_params,
mat_type=mat_type)
self._assemble_P()
self.P.force_evaluation()
# Transfer nullspace over
Pmat = self.P.petscmat
Pmat.setNullSpace(P.getNullSpace())
tnullsp = P.getTransposeNullSpace()
if tnullsp.handle != 0:
Pmat.setTransposeNullSpace(tnullsp)
# 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 -assembled_pc_type ksp.
pc = PETSc.PC().create(comm=opc.comm)
pc.incrementTabLevel(1, parent=opc)
pc.setOptionsPrefix(options_prefix)
pc.setOperators(Pmat, Pmat)
pc.setFromOptions()
pc.setUp()
self.pc = pc
def GetPETScBFBTApproximateToSchurInverse():
Fass = assemble(lhs(F))
Gass = assemble(inner(u, v) * dx)
# bcin.apply(Fass)
# bcnoslip.apply(Fass)
# bcin.apply(Gass)
# bcnoslip.apply(Gass)
A = Fass.M[0,0].handle
BT = Fass.M[0,1].handle
B = Fass.M[1,0].handle
D = Fass.M[1,1].handle
VM = Gass.M[0, 0].handle
# Adiag = A.getDiagonal()
Adiag = VM.getRowSum()
invAdiag = Adiag.duplicate()
Adiag.copy(invAdiag)
invAdiag.reciprocal()
Einv = A.duplicate()
Einv.setDiagonal(invAdiag)
# Einv.convert(PETSc.Mat.Type.SEQAIJ)
BEBT = B.matMult(Einv.matMult(BT))
BEBT_ksp = PETSc.KSP().create()
BEBT_ksp.setOperators(BEBT)
opts = PETSc.Options()
BEBT_ksp.setOptionsPrefix("bebt_")
opts['bebt_ksp_type'] = 'richardson'
opts['bebt_pc_type'] = 'hypre'
opts['bebt_ksp_max_it'] = 1
opts['bebt_ksp_atol'] = 1.0e-9
opts['bebt_ksp_rtol'] = 1.0e-9
BEBT_ksp.setUp()
BEBT_ksp.setFromOptions()
MIDDLE = B.matMult(Einv.matMult(A.matMult(Einv.matMult(BT))))
MIDDLE.scale(-1)
class SchurInvApprox(object):
def mult(self, mat, x, y):
y1 = y.duplicate()
BEBT_ksp.solve(x, y1)
y2 = y.duplicate()
MIDDLE.mult(y1, y2)
BEBT_ksp.solve(y2, y)
schur = PETSc.Mat()
schur.createPython(D.getSizes(), SchurInvApprox())
schur.setUp()
return schur
def __call__(self, pc):
dm = pc.getDM()
prefix = pc.getOptionsPrefix()
sentinel = object()
opts = PETSc.Options(prefix)
name = self.name
assert self.name is not None
self.set_options(dm, opts, name)
select = partial(select_entity, dm=dm, exclude="pyop2_ghost")
entities = list(filter(select, self.get_entities(opts, name, dm)))
nclosure = opts.getInt("pc_patch_construction_%s_nclosures" % name, default=1)
patches = []
for entity in entities:
subentities = self.callback(dm, entity, nclosure)
iset = PETSc.IS().createGeneral(subentities, comm=PETSc.COMM_SELF)
patches.append(iset)
# Now make the iteration set.
iterset = []
sortorders = opts.getString("pc_patch_construction_%s_sort_order" % name, default=sentinel)
if sortorders == sentinel:
sortorders = "None"
if sortorders == "None":
piterset = PETSc.IS().createStride(size=len(patches), first=0, step=1, comm=PETSc.COMM_SELF)
return (patches, piterset)
coords = list(enumerate(self.coords(dm, p) for p in entities))
for sortorder in sortorders.split("|"):
sortdata = []
for axis in sortorder.split(':'):
ax = int(axis[0])
if len(axis) > 1:
sgn = {'+': 1, '-': -1}[axis[1]]
else:
sgn = 1
sortdata.append((ax, sgn))
def keyfunc(z):
return tuple(sgn*z[1][ax] for (ax, sgn) in sortdata)
iterset += [x[0] for x in sorted(coords, key=keyfunc)]
piterset = PETSc.IS().createGeneral(iterset, comm=PETSc.COMM_SELF)
return (patches, piterset)
def initialize(self, obj):
if complex_mode:
raise NotImplementedError(
"HypreAMS preconditioner not yet implemented in complex mode")
Citations().register("Kolev2009")
A, P = obj.getOperators()
prefix = obj.getOptionsPrefix()
V = get_function_space(obj.getDM())
mesh = V.mesh()
family = str(V.ufl_element().family())
degree = V.ufl_element().degree()
if family != 'Nedelec 1st kind H(curl)' or degree != 1:
raise ValueError(
"Hypre AMS requires lowest order Nedelec elements! (not %s of degree %d)"
% (family, degree))
P1 = FunctionSpace(mesh, "Lagrange", 1)
G = Interpolator(grad(TestFunction(P1)), V).callable().handle
pc = PETSc.PC().create(comm=obj.comm)
pc.incrementTabLevel(1, parent=obj)
pc.setOptionsPrefix(prefix + "hypre_ams_")
pc.setOperators(A, P)
pc.setType('hypre')
pc.setHYPREType('ams')
pc.setHYPREDiscreteGradient(G)
zero_beta = PETSc.Options(prefix).getBool(
"pc_hypre_ams_zero_beta_poisson", default=False)
if zero_beta:
pc.setHYPRESetBetaPoissonMatrix(None)
# Build constants basis for the Nedelec space
cvecs = []
for i in range(mesh.cell_dimension()):
direction = [
1.0 if i == j else 0.0 for j in range(mesh.cell_dimension())
]
c = project(Constant(direction), V)
with c.vector().dat.vec_ro as cvec:
cvecs.append(cvec)
pc.setHYPRESetEdgeConstantVectors(*cvecs)
pc.setUp()
self.pc = pc
def opts(request, prefix, global_parameters):
opts = PETSc.Options()
if prefix is None:
prefix = ""
for k, v in global_parameters.items():
opts[prefix + k] = v
# Pretend these came from the commandline
OptionsManager.commandline_options = frozenset(opts.getAll())
def finalize():
for k in global_parameters.keys():
del opts[prefix + k]
# And remove again
OptionsManager.commandline_options = frozenset(opts.getAll())
request.addfinalizer(finalize)
def update_parameters(obj, petsc_obj):
"""Update parameters on a petsc object
:arg obj: An object with a parameters dict (mapping to petsc options).
:arg petsc_obj: The PETSc object to set parameters on."""
# Skip if parameters haven't changed
if hasattr(obj,
'_set_parameters') and obj.parameters == obj._set_parameters:
return
opts = PETSc.Options(obj._opt_prefix)
for k, v in obj.parameters.iteritems():
if type(v) is bool:
if v:
opts[k] = None
else:
opts[k] = v
petsc_obj.setFromOptions()
obj._set_parameters = obj.parameters.copy()
def solve(ctx, state):
out_file = File(solution_out) if solution_out else None
mass = state["mass"]
hats = state["hats"]
u = ctx[2]["u"]
u0 = ctx[2]["u0"]
solver = ctx[1]
from firedrake.petsc import PETSc
ksp_hats = PETSc.KSP()
ksp_hats.create()
ksp_hats.setOperators(hats)
opts = PETSc.Options()
opts['ksp_type'] = inner_ksp
opts['ksp_max_it'] = max_iterations
opts['pc_type'] = 'hypre'
ksp_hats.setFromOptions()
class SchurInv(object):
def mult(self, mat, x, y):
tmp1 = y.duplicate()
tmp2 = y.duplicate()
ksp_hats.solve(x, tmp1)
mass.mult(tmp1, tmp2)
ksp_hats.solve(tmp2, y)
pc_schur = PETSc.Mat()
pc_schur.createPython(mass.getSizes(), SchurInv())
pc_schur.setUp()
pc = solver.snes.ksp.pc
pc.setFieldSplitSchurPreType(PETSc.PC.SchurPreType.USER, pc_schur)
for step in range(steps):
casper.invoke_task(ctx, "assign", state)
solver.solve()
if out_file is not None:
out_file.write(u.split()[0], time=step)
if compute_norms:
nu = norm(u)
if comm.rank == 0:
print(step, 'L2(u):', nu)
def get_patches(self, V):
mesh = V._mesh
mesh_dm = mesh.topology_dm
if mesh.layers:
warning("applying ASMStarPC on an extruded mesh")
# Obtain the topological entities to use to construct the stars
depth = PETSc.Options().getInt(self.prefix+"construct_dim", default=0)
# Accessing .indices causes the allocation of a global array,
# so we need to cache these for efficiency
V_local_ises_indices = []
for (i, W) in enumerate(V):
V_local_ises_indices.append(V.dof_dset.local_ises[i].indices)
# Build index sets for the patches
ises = []
(start, end) = mesh_dm.getDepthStratum(depth)
for seed in range(start, end):
# Only build patches over owned DoFs
if mesh_dm.getLabelValue("pyop2_ghost", seed) != -1:
continue
# Create point list from mesh DM
pt_array, _ = mesh_dm.getTransitiveClosure(seed, useCone=False)
# Get DoF indices for patch
indices = []
for (i, W) in enumerate(V):
section = W.dm.getDefaultSection()
for p in pt_array.tolist():
dof = section.getDof(p)
if dof <= 0:
continue
off = section.getOffset(p)
# Local indices within W
W_indices = numpy.arange(off*W.value_size, W.value_size * (off + dof), dtype=IntType)
indices.extend(V_local_ises_indices[i][W_indices])
iset = PETSc.IS().createGeneral(indices, comm=COMM_SELF)
ises.append(iset)
return ises
def test_options_database_cleared():
opts = PETSc.Options()
expect = len(opts.getAll())
mesh = UnitIntervalMesh(1)
V = FunctionSpace(mesh, "DG", 0)
u = TrialFunction(V)
v = TestFunction(V)
A = assemble(inner(u, v) * dx)
b = assemble(conj(v) * dx)
u = Function(V)
solvers = []
for i in range(100):
solver = LinearSolver(A,
solver_parameters={
"ksp_type": "preonly",
"pc_type": "lu"
})
solver.solve(u, b)
solvers.append(solver)
assert expect == len(opts.getAll())
def assembleK(self):
ctx = self.ctx
mat_type = PETSc.Options().getString(
self.prefix + "assembled_mat_type", "aij")
self.K = allocate_matrix(ctx.a,
bcs=ctx.row_bcs,
form_compiler_parameters=ctx.fc_params,
mat_type=mat_type)
self._assemble_K = create_assembly_callable(
ctx.a,
tensor=self.K,
bcs=ctx.row_bcs,
form_compiler_parameters=ctx.fc_params,
mat_type=mat_type)
self._assemble_K()
self.mat_type = mat_type
self.K.force_evaluation()
def _retrieve_options(self, pc):
get_option = lambda key: PETSc.Options(self.prefix).getString(
key, default="")
# Get options for Schur complement decomposition
self._check_options([("ksp_type", {"preonly"}),
("pc_type", {"fieldsplit"}),
("pc_fieldsplit_type", {"schur"})])
self.nested = (get_option("ksp_type") == "preonly"
and get_option("pc_type") == "fieldsplit"
and get_option("pc_fieldsplit_type") == "schur")
# Get preconditioning options for A00
fs0, fs1 = ("fieldsplit_" + str(idx) for idx in (self.vidx, self.pidx))
self._check_options([(fs0 + "ksp_type", {"preonly", "default"}),
(fs0 + "pc_type", {"jacobi"})])
self.preonly_A00 = get_option(fs0 + "_ksp_type") == "preonly"
self.jacobi_A00 = get_option(fs0 + "_pc_type") == "jacobi"
# Get preconditioning options for the Schur complement
self._check_options([(fs1 + "ksp_type", {"preonly", "default"}),
(fs1 + "pc_type", {"jacobi", "python"})])
self.preonly_S = get_option(fs1 + "_ksp_type") == "preonly"
self.jacobi_S = get_option(fs1 + "_pc_type") == "jacobi"
# Get user supplied operator and its options
self.schur_approx = (self.retrieve_user_S_approx(
pc, get_option(fs1 + "_pc_python_type"))
if get_option(fs1 +
"_pc_type") == "python" else None)
self._check_options([(fs1 + "aux_ksp_type", {"preonly", "default"}),
(fs1 + "aux_pc_type", {"jacobi"})])
self.preonly_Shat = get_option(fs1 + "_aux_ksp_type") == "preonly"
self.jacobi_Shat = get_option(fs1 + "_aux_pc_type") == "jacobi"
if self.jacobi_Shat or self.jacobi_A00:
assert parameters["slate_compiler"]["optimise"], (
"Local systems should only get preconditioned with "
"a preconditioning matrix if the Slate optimiser replaces "
"inverses by solves.")
def transfer_manager(self):
"""This allows the transfer manager to be set from options, e.g.
solver_parameters = {"ksp_type": "cg",
"pc_type": "mg",
"mg_transfer_manager": __name__ + ".manager"}
The value for "mg_transfer_manager" can either be a specific instantiated
object, or a function or class name. In the latter case it will be invoked
with no arguments to instantiate the object.
If "snes_type": "fas" is used, the relevant option is "fas_transfer_manager",
with the same semantics.
"""
if self._transfer_manager is None:
opts = PETSc.Options()
prefix = self.options_prefix or ""
if opts.hasName(prefix + "mg_transfer_manager"):
managername = opts[prefix + "mg_transfer_manager"]
elif opts.hasName(prefix + "fas_transfer_manager"):
managername = opts[prefix + "fas_transfer_manager"]
else:
managername = None
if managername is None:
from firedrake import TransferManager
transfer = TransferManager(use_averaging=True)
else:
(modname, objname) = managername.rsplit(".", 1)
mod = __import__(modname)
obj = getattr(mod, objname)
if isinstance(obj, type):
transfer = obj()
else:
transfer = obj
self._transfer_manager = transfer
return self._transfer_manager