def test_shelve_save(mesh, casedir):
mtf = MockTupleField(dict(save=True, save_as="shelve"))
msf = MockScalarField(dict(save=True, save_as="shelve"))
pp = PostProcessor(dict(casedir=casedir))
pp.add_fields([mtf, msf])
pp.update_all({}, 0.0, 0)
pp.update_all({}, 0.1, 1)
pp.update_all({}, 0.2, 2)
pp.finalize_all()
for mf in [mtf, msf]:
assert os.path.isdir(pp.get_savedir(mf.name))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), "metadata.db"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), mf.name + ".db"))
md = shelve.open(os.path.join(pp.get_savedir(mf.name), "metadata.db"),
'r')
assert 'shelve' in md["0"]
assert md['saveformats'] == ['shelve']
md.close()
# Read back
data = shelve.open(
os.path.join(pp.get_savedir(mf.name), mf.name + ".db"), 'r')
for i in ["0", "1", "2"]:
d = data[i]
data.close()
assert d == pp.get(mf.name)
def test_pyplot():
pp = PostProcessor()
pp.add_field(MockScalarField(dict(plot=True)))
pp.update_all({}, 0.0, 0)
pp.update_all({}, 0.1, 1)
pp.update_all({}, 0.6, 2)
pp.update_all({}, 1.6, 3)
def test_default_save(mesh, casedir):
spacepool = SpacePool(mesh)
Q = spacepool.get_space(1, 0)
V = spacepool.get_space(1, 1)
mff = MockFunctionField(Q, dict(save=True))
mvff = MockVectorFunctionField(V, dict(save=True))
mtf = MockTupleField(dict(save=True))
msf = MockScalarField(dict(save=True))
pp = PostProcessor(dict(casedir=casedir))
pp.add_fields([mff, mvff, mtf, msf])
pp.update_all({}, 0.0, 0)
pp.update_all({}, 0.1, 1)
pp.update_all({}, 0.2, 2)
pp.finalize_all()
for mf in [mff, mvff]:
assert os.path.isdir(pp.get_savedir(mf.name))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), "metadata.db"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), mf.name + ".hdf5"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), mf.name + ".h5"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), mf.name + ".xdmf"))
assert len(os.listdir(pp.get_savedir(mf.name))) == 4
md = shelve.open(os.path.join(pp.get_savedir(mf.name), "metadata.db"),
'r')
assert 'hdf5' in md["0"]
assert 'hdf5' in md['saveformats']
assert 'xdmf' in md["0"]
assert 'xdmf' in md['saveformats']
assert set(md['saveformats']) == set(['hdf5', 'xdmf'])
md.close()
for mf in [mtf, msf]:
assert os.path.isdir(pp.get_savedir(mf.name))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), "metadata.db"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), mf.name + ".db"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), mf.name + ".txt"))
md = shelve.open(os.path.join(pp.get_savedir(mf.name), "metadata.db"),
'r')
assert 'txt' in md["0"]
assert 'txt' in md['saveformats']
assert 'shelve' in md["0"]
assert 'shelve' in md['saveformats']
assert set(md['saveformats']) == set(['txt', 'shelve'])
md.close()
def test_get_casedir(casedir):
pp = PostProcessor(dict(casedir=casedir))
assert os.path.isdir(pp.get_casedir())
assert os.path.samefile(pp.get_casedir(), casedir)
pp.update_all({}, 0.0, 0)
assert len(os.listdir(pp.get_casedir())) == 1
pp.clean_casedir()
assert len(os.listdir(pp.get_casedir())) == 0
def test_dolfinplot(mesh):
pp = PostProcessor()
spacepool = SpacePool(mesh)
Q = spacepool.get_space(1, 0)
V = spacepool.get_space(1, 1)
pp.add_field(MockFunctionField(Q, dict(plot=True)))
pp.add_field(MockVectorFunctionField(V, dict(plot=True)))
pp.update_all({}, 0.0, 0)
pp.update_all({}, 0.1, 1)
pp.update_all({}, 0.6, 2)
pp.update_all({}, 1.6, 3)
def test_xmlgz_save(mesh, casedir):
spacepool = SpacePool(mesh)
Q = spacepool.get_space(1, 0)
V = spacepool.get_space(1, 1)
mff = MockFunctionField(Q, dict(save=True, save_as="xml.gz"))
mvff = MockVectorFunctionField(V, dict(save=True, save_as="xml.gz"))
pp = PostProcessor(dict(casedir=casedir))
pp.add_fields([mff, mvff])
pp.update_all({}, 0.0, 0)
pp.update_all({}, 0.1, 1)
pp.update_all({}, 0.2, 2)
pp.finalize_all()
for mf, FS in [(mff, Q), (mvff, V)]:
assert os.path.isdir(pp.get_savedir(mf.name))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), "metadata.db"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), "mesh.hdf5"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), mf.name + "0.xml.gz"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), mf.name + "1.xml.gz"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), mf.name + "2.xml.gz"))
md = shelve.open(os.path.join(pp.get_savedir(mf.name), "metadata.db"),
'r')
assert 'xml.gz' in md["0"]
assert 'xml.gz' in md["1"]
assert 'xml.gz' in md["2"]
assert 'xml.gz' in md['saveformats']
assert md['saveformats'] == ['xml.gz']
md.close()
assert len(os.listdir(pp.get_savedir(mf.name))) == 1 + 1 + 3
# Read back
for i in ["0", "1", "2"]:
f = Function(
FS,
os.path.join(pp.get_savedir(mf.name), mf.name + i + ".xml.gz"))
assert norm(f) == norm(pp.get(mf.name))
def test_hdf5_save(mesh, casedir):
spacepool = SpacePool(mesh)
Q = spacepool.get_space(1, 0)
V = spacepool.get_space(1, 1)
mff = MockFunctionField(Q, dict(save=True, save_as="hdf5"))
mvff = MockVectorFunctionField(V, dict(save=True, save_as="hdf5"))
pp = PostProcessor(dict(casedir=casedir))
pp.add_fields([mff, mvff])
pp.update_all({}, 0.0, 0)
pp.update_all({}, 0.1, 1)
pp.update_all({}, 0.2, 2)
pp.finalize_all()
for mf, FS in [(mff, Q), (mvff, V)]:
assert os.path.isdir(pp.get_savedir(mf.name))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), "metadata.db"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), mf.name + ".hdf5"))
md = shelve.open(os.path.join(pp.get_savedir(mf.name), "metadata.db"),
'r')
assert 'hdf5' in md["0"]
assert 'hdf5' in md["1"]
assert 'hdf5' in md["2"]
assert 'hdf5' in md['saveformats']
assert md['saveformats'] == ['hdf5']
md.close()
assert len(os.listdir(pp.get_savedir(mf.name))) == 2
# Read back
hdf5file = HDF5File(
mpi_comm_world(),
os.path.join(pp.get_savedir(mf.name), mf.name + ".hdf5"), 'r')
f = Function(FS)
for i in ["0", "1", "2"]:
hdf5file.read(f, mf.name + i)
assert norm(f) == norm(pp.get(mf.name))
def test_playlog(casedir):
pp = PostProcessor(dict(casedir=casedir))
# Test playlog
assert not os.path.isfile(os.path.join(casedir, 'play.db'))
MPI.barrier(mpi_comm_world())
pp.update_all({}, 0.0, 0)
pp.finalize_all()
playlog = pp.get_playlog('r')
assert playlog == {"0": {"t": 0.0}}
playlog.close()
pp.update_all({}, 0.1, 1)
pp.finalize_all()
playlog = pp.get_playlog('r')
assert playlog == {"0": {"t": 0.0}, "1": {"t": 0.1}}
playlog.close()
def test_update_all():
pressure = SolutionField("MockPressure") #MockPressure()
velocity = SolutionField("MockVelocity") #MockVelocity()
Du = MockVelocityGradient()
epsilon = MockStrain(dict(start_timestep=3))
sigma = MockStress(dict(start_time=0.5, end_time=0.8))
# Add fields to postprocessor
pp = PostProcessor()
pp.add_fields([pressure, velocity, Du, epsilon, sigma])
N = 11
T = [(i, float(i) / (N - 1)) for i in xrange(N)]
for timestep, t in T:
pp.update_all(
{
"MockPressure": lambda: "p" + str(timestep),
"MockVelocity": lambda: "u" + str(timestep)
}, t, timestep)
assert Du.touched == timestep + 1
assert pp._cache[0]["MockPressure"] == "p%d" % timestep
assert pp._cache[0]["MockVelocity"] == "u%d" % timestep
assert pp._cache[0]["MockVelocityGradient"] == "grad(u%d)" % timestep
if timestep >= 3:
assert pp._cache[0][
"MockStrain"] == "epsilon(grad(u%d))" % timestep
else:
assert "MockStrain" not in pp._cache[0]
if 0.5 <= t <= 0.8:
assert pp._cache[0][
"MockStress"] == "sigma(epsilon(grad(u%d)), p%d)" % (timestep,
timestep)
else:
assert "MockStress" not in pp._cache[0]
def test_basic_replay(mesh, casedir):
spacepool = SpacePool(mesh)
Q = spacepool.get_space(1,0)
V = spacepool.get_space(1,1)
pp = PostProcessor(dict(casedir=casedir))
pp.add_fields([
MockFunctionField(Q, dict(save=True)),
MockVectorFunctionField(V, dict(save=True))
])
replay_fields = lambda save: [Norm("MockFunctionField", dict(save=save)),
Norm("MockVectorFunctionField", dict(save=save)),
TimeIntegral("Norm_MockFunctionField", dict(save=save)),]
rf_names = [f.name for f in replay_fields(False)]
# Add fields, but don't save (for testing)
pp.add_fields(replay_fields(False))
# Solutions to check against
checks = {}
pp.update_all({}, 0.0, 0)
checks[0] = dict([(name, pp.get(name)) for name in rf_names])
pp.update_all({}, 0.1, 1)
checks[1] = dict([(name, pp.get(name)) for name in rf_names])
pp.update_all({}, 0.2, 2)
pp.finalize_all()
checks[2] = dict([(name, pp.get(name)) for name in rf_names])
# Make sure that nothing is saved yet
for name in rf_names:
assert not os.path.isfile(os.path.join(pp.get_savedir(name), name+".db"))
# ----------- Replay -----------------
pp = PostProcessor(dict(casedir=casedir))
pp.add_fields([
MockFunctionField(Q),
MockVectorFunctionField(V),
])
# This time, save the fields
pp.add_fields(replay_fields(True))
replayer = Replay(pp)
replayer.replay()
# Test that replayed solution is the same as computed in the original "solve"
for name in rf_names:
data = shelve.open(os.path.join(pp.get_savedir(name), name+".db"), 'r')
for i in range(3):
assert data.get(str(i), None) == checks[i][name] or abs(data.get(str(i), None) - checks[i][name]) < 1e-8
data.close()
def replay(self):
"Replay problem with given postprocessor."
# Backup play log
self.backup_playlog()
# Set up for replay
replay_plan = self._fetch_history()
postprocessors = []
for fieldname, field in self.postproc._fields.items():
if not (field.params.save or field.params.plot):
continue
# Check timesteps covered by current field
keys = self._check_field_coverage(replay_plan, fieldname)
# Get the time dependency for the field
t_dep = min(
[dep[1]
for dep in self.postproc._dependencies[fieldname]] + [0])
dep_fields = []
for dep in self.postproc._full_dependencies[fieldname]:
if dep[0] in ["t", "timestep"]:
continue
if dep[0] in dep_fields:
continue
# Copy dependency and set save/plot to False. If dependency should be
# plotted/saved, this field will be added separately.
dependency = self.postproc._fields[dep[0]]
dependency = copy.copy(dependency)
dependency.params.save = False
dependency.params.plot = False
dependency.params.safe = False
dep_fields.append(dependency)
added_to_postprocessor = False
for i, (ppkeys, ppt_dep, pp) in enumerate(postprocessors):
if t_dep == ppt_dep and set(keys) == set(ppkeys):
pp.add_fields(dep_fields, exists_reaction="ignore")
pp.add_field(field, exists_reaction="replace")
added_to_postprocessor = True
break
else:
continue
# Create new postprocessor if no suitable postprocessor found
if not added_to_postprocessor:
pp = PostProcessor(self.postproc.params, self.postproc._timer)
pp.add_fields(dep_fields, exists_reaction="ignore")
pp.add_field(field, exists_reaction="replace")
postprocessors.append([keys, t_dep, pp])
postprocessors = sorted(postprocessors,
key=itemgetter(1),
reverse=True)
t_independent_fields = []
for fieldname in self.postproc._fields:
if self.postproc._full_dependencies[fieldname] == []:
t_independent_fields.append(fieldname)
elif min(t for dep, t in
self.postproc._full_dependencies[fieldname]) == 0:
t_independent_fields.append(fieldname)
# Run replay
sorted_keys = sorted(replay_plan.keys())
N = max(sorted_keys)
for timestep in sorted_keys:
cbc_print("Processing timestep %d of %d. %.3f%% complete." %
(timestep, N, 100.0 * (timestep) / N))
# Load solution at this timestep (all available fields)
solution = replay_plan[timestep]
t = solution.pop("t")
# Cycle through postprocessors and update if required
for ppkeys, ppt_dep, pp in postprocessors:
if timestep in ppkeys:
# Add dummy solutions to avoid error when handling dependencies
# We know this should work, because it has already been established that
# the fields to be computed at this timestep can be computed from stored
# solutions.
for field in pp._sorted_fields_keys:
for dep in reversed(pp._dependencies[field]):
if not have_necessary_deps(solution, pp, dep[0]):
solution[dep[0]] = lambda: None
pp.update_all(solution, t, timestep)
# Clear None-objects from solution
[
solution.pop(k) for k in solution.keys()
if not solution[k]
]
# Update solution to avoid re-computing data
for fieldname, value in pp._cache[0].items():
if fieldname in t_independent_fields:
value = pp._cache[0][fieldname]
#solution[fieldname] = lambda value=value: value # Memory leak!
solution[fieldname] = MiniCallable(value)
self.timer.increment()
if self.params.check_memory_frequency != 0 and timestep % self.params.check_memory_frequency == 0:
cbc_print('Memory usage is: %s' %
MPI.sum(mpi_comm_world(), get_memory_usage()))
# Clean up solution: Required to avoid memory leak for some reason...
for f, v in solution.items():
if isinstance(v, MiniCallable):
v.value = None
del v
solution.pop(f)
for ppkeys, ppt_dep, pp in postprocessors:
pp.finalize_all()
def run_splitting_solver(domain, dt, T):
# Create cardiac model problem description
cell_model = Tentusscher_panfilov_2006_epi_cell()
heart = setup_model(cell_model, domain)
# Customize and create monodomain solver
ps = SplittingSolver.default_parameters()
ps["pde_solver"] = "monodomain"
ps["apply_stimulus_current_to_pde"] = True
# 2nd order splitting scheme
ps["theta"] = 0.5
# Use explicit first-order Rush-Larsen scheme for the ODEs
ps["ode_solver_choice"] = "CardiacODESolver"
ps["CardiacODESolver"]["scheme"] = "RL1"
# Crank-Nicolson discretization for PDEs in time:
ps["MonodomainSolver"]["theta"] = 0.5
ps["MonodomainSolver"]["linear_solver_type"] = "iterative"
ps["MonodomainSolver"]["algorithm"] = "cg"
ps["MonodomainSolver"]["preconditioner"] = "petsc_amg"
# Create solver
solver = SplittingSolver(heart, params=ps)
# Extract the solution fields and set the initial conditions
(vs_, vs, vur) = solver.solution_fields()
vs_.assign(cell_model.initial_conditions())
solutions = solver.solve((0, T), dt)
postprocessor = PostProcessor(dict(casedir="test", clean_casedir=True))
postprocessor.store_mesh(heart.domain())
field_params = dict(
save=True,
save_as=["hdf5", "xdmf"],
plot=False,
start_timestep=-1,
stride_timestep=1
)
postprocessor.add_field(SolutionField("v", field_params))
theta = ps["theta"]
# Solve
total = Timer("XXX Total cbcbeat solver time")
for i, (timestep, (vs_, vs, vur)) in enumerate(solutions):
t0, t1 = timestep
current_t = t0 + theta*(t1 - t0)
postprocessor.update_all({"v": lambda: vur}, current_t, i)
print("Solving on %s" % str(timestep))
# Print memory usage (just for the fun of it)
print(memory_usage())
total.stop()
# Plot result (as sanity check)
#plot(vs[0], interactive=True)
# Stop timer and list timings
if MPI.rank(mpi_comm_world()) == 0:
list_timings(TimingClear_keep, [TimingType_wall])
def test_pvd_save(mesh, casedir):
spacepool = SpacePool(mesh)
Q = spacepool.get_space(1, 0)
V = spacepool.get_space(1, 1)
mff = MockFunctionField(Q, dict(save=True, save_as="pvd"))
mvff = MockVectorFunctionField(V, dict(save=True, save_as="pvd"))
pp = PostProcessor(dict(casedir=casedir))
pp.add_fields([mff, mvff])
pp.update_all({}, 0.0, 0)
pp.update_all({}, 0.1, 1)
pp.update_all({}, 0.2, 2)
pp.finalize_all()
for mf, FS in [(mff, Q), (mvff, V)]:
assert os.path.isdir(pp.get_savedir(mf.name))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), "metadata.db"))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name), mf.name + ".pvd"))
if MPI.size(mpi_comm_world()) == 1:
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name),
mf.name + "%0.6d.vtu" % 0))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name),
mf.name + "%0.6d.vtu" % 1))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name),
mf.name + "%0.6d.vtu" % 2))
else:
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name),
mf.name + "%0.6d.pvtu" % 0))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name),
mf.name + "%0.6d.pvtu" % 1))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name),
mf.name + "%0.6d.pvtu" % 2))
for i in range(MPI.size(mpi_comm_world())):
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name),
mf.name + "_p%d_%0.6d.vtu" % (i, 0)))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name),
mf.name + "_p%d_%0.6d.vtu" % (i, 1)))
assert os.path.isfile(
os.path.join(pp.get_savedir(mf.name),
mf.name + "_p%d_%0.6d.vtu" % (i, 2)))
md = shelve.open(os.path.join(pp.get_savedir(mf.name), "metadata.db"),
'r')
assert 'pvd' in md["0"]
assert 'pvd' in md["1"]
assert 'pvd' in md["2"]
assert md['saveformats'] == ['pvd']
md.close()
assert len(os.listdir(pp.get_savedir(mf.name))) == 1 + 1 + 3 + int(
MPI.size(mpi_comm_world()) != 1) * MPI.size(mpi_comm_world()) * 3
