def test_model_update_insert_component_on_conduit() -> None:
macro = Component('macro', 'my.macro')
micro = Component('micro', 'my.micro')
components = [macro, micro]
conduit1 = Conduit('macro.intermediate_state', 'micro.initial_state')
conduit2 = Conduit('micro.final_state', 'macro.state_update')
conduits = [conduit1, conduit2]
base = Model('test_update', components, conduits)
tee = Component('tee', 'muscle3.tee')
conduit3 = Conduit('macro.intermediate_state', 'tee.input')
conduit4 = Conduit('tee.output', 'micro.initial_state')
overlay = Model('test_update_tee', [tee], [conduit3, conduit4])
base.update(overlay)
assert len(base.components) == 3
assert macro in base.components
assert micro in base.components
assert tee in base.components
assert len(base.conduits) == 3
assert conduit2 in base.conduits
assert conduit3 in base.conduits
assert conduit4 in base.conduits
def test_model_update_set_implementation() -> None:
abstract_reaction = Component('reaction')
base = Model('test_set_impl', [abstract_reaction])
assert base.components[0].name == 'reaction'
assert base.components[0].implementation is None
reaction_python = Component('reaction', 'reaction_python')
overlay = Model('test_set_impl', [reaction_python])
base.update(overlay)
assert len(base.components) == 1
assert base.components[0].name == 'reaction'
assert base.components[0].implementation == 'reaction_python'
def test_configuration_update_model4() -> None:
component1 = Component('macro', 'my.macro')
model1 = Model('model1', [component1])
base = Configuration(model1)
component2 = Component('micro', 'my.micro')
model2 = Model('model2', [component2])
overlay = Configuration(model2)
base.update(overlay)
assert isinstance(base.model, Model)
assert base.model == model1
assert base.model.name == 'model2'
assert component1 in base.model.components
assert component2 in base.model.components
def test_config5() -> Configuration:
model = Model(
'test_model',
[
Component('ic', 'isr2d.initial_conditions'),
Component('smc', 'isr2d.smc'),
Component('bf', 'isr2d.blood_flow'),
Component('smc2bf', 'isr2d.smc2bf'),
Component('bf2smc', 'isr2d.bf2smc')],
[
Conduit('ic.out', 'smc.initial_state'),
Conduit('smc.cell_positions', 'smc2bf.in'),
Conduit('smc2bf.out', 'bf.initial_domain'),
Conduit('bf.wss_out', 'bf2smc.in'),
Conduit('bf2smc.out', 'smc.wss_in')])
implementations = [
Implementation(
Reference('isr2d.initial_conditions'), 'isr2d/bin/ic'),
Implementation(
Reference('isr2d.smc'), 'isr2d/bin/smc'),
Implementation(
Reference('isr2d.blood_flow'), 'isr2d/bin/bf'),
Implementation(
Reference('isr2d.smc2bf'), 'isr2d/bin/smc2bf.py'),
Implementation(
Reference('isr2d.bf2smc'), 'isr2d/bin/bf2smc.py')]
resources = [
Resources(Reference('isr2d.initial_conditions'), 4),
Resources(Reference('isr2d.smc'), 4),
Resources(Reference('isr2d.blood_flow'), 4),
Resources(Reference('isr2d.smc2bf'), 1),
Resources(Reference('isr2d.bf2smc'), 1)]
return Configuration(model, None, implementations, resources)
def macro_micro() -> Model:
macro = Component('macro', 'my.macro')
micro = Component('micro', 'my.micro')
components = [macro, micro]
conduit1 = Conduit('macro.intermediate_state', 'micro.initial_state')
conduit2 = Conduit('micro.final_state', 'macro.state_update')
conduits = [conduit1, conduit2]
return Model('macro_micro', components, conduits)
def test_model_update_add_component() -> None:
macro = Component('macro', 'my.macro')
base = Model('test_update', [macro])
micro = Component('micro', 'my.micro')
conduit1 = Conduit('macro.intermediate_state', 'micro.initial_state')
conduit2 = Conduit('micro.final_state', 'macro.state_update')
conduits = [conduit1, conduit2]
overlay = Model('test_update_add', [micro], conduits)
base.update(overlay)
assert len(base.components) == 2
assert macro in base.components
assert micro in base.components
assert conduit1 in base.conduits
assert conduit2 in base.conduits
def test_configuration_update_model2() -> None:
model_ref1 = ModelReference('model1')
base = PartialConfiguration(model_ref1)
component1 = Component('macro', 'my.macro')
model2 = Model('model2', [component1])
overlay = PartialConfiguration(model2)
base.update(overlay)
assert base.model == model2
def test_model_update_replace_component() -> None:
macro = Component('macro', 'my.macro')
micro = Component('micro', 'my.micro')
components = [macro, micro]
conduit1 = Conduit('macro.intermediate_state', 'micro.initial_state')
conduit2 = Conduit('micro.final_state', 'macro.state_update')
conduits = [conduit1, conduit2]
base = Model('test_update', components, conduits)
surrogate = Component('micro', 'my.surrogate')
overlay = Model('test_update_surrogate', [surrogate])
base.update(overlay)
assert len(base.components) == 2
assert macro in base.components
assert surrogate in base.components
assert len(base.conduits) == 2
assert conduit1 in base.conduits
assert conduit2 in base.conduits
def test_configuration_update_model3() -> None:
component1 = Component('macro', 'my.macro')
model1 = Model('model1', [component1])
base = Configuration(model1)
model_ref2 = ModelReference('model2')
overlay = PartialConfiguration(model_ref2)
base.update(overlay)
assert base.model == model1
assert model1.name == 'model2'
assert model1.components == [component1]
def topology_store() -> TopologyStore:
config = Configuration(
Model(
'test_model',
[
ComputeElement('macro', 'macro_implementation'),
ComputeElement(
'micro', 'micro_implementation', [10, 10])],
[
Conduit('macro.out', 'micro.in'),
Conduit('micro.out', 'macro.in')
]))
return TopologyStore(config)
def test_dump_model(dump_model: Callable) -> None:
ce1 = Component('ce1', 'test.impl1')
ce2 = Component('ce2', 'test.impl2')
cd1 = Conduit('ce1.state_out', 'ce2.init_in')
cd2 = Conduit('ce2.fini_out', 'ce1.boundary_in')
model = Model('test_model', [ce1, ce2], [cd1, cd2])
text = dump_model(model)
assert text == ('name: test_model\n'
'components:\n'
' ce1: test.impl1\n'
' ce2: test.impl2\n'
'conduits:\n'
' ce1.state_out: ce2.init_in\n'
' ce2.fini_out: ce1.boundary_in\n')
def test_config2() -> PartialConfiguration:
model = Model(
'test_model',
[
Component('ic', 'isr2d.initial_conditions'),
Component('smc', 'isr2d.smc'),
Component('bf', 'isr2d.blood_flow'),
Component('smc2bf', 'isr2d.smc2bf'),
Component('bf2smc', 'isr2d.bf2smc')],
[
Conduit('ic.out', 'smc.initial_state'),
Conduit('smc.cell_positions', 'smc2bf.in'),
Conduit('smc2bf.out', 'bf.initial_domain'),
Conduit('bf.wss_out', 'bf2smc.in'),
Conduit('bf2smc.out', 'smc.wss_in')])
return PartialConfiguration(model)
def test_duplication_mapper(log_file_in_tmpdir):
"""A positive all-up test of duplication mappers.
This is an acyclic workflow.
"""
elements = [
ComputeElement('dm', 'muscle.duplication_mapper'),
ComputeElement('first', 'receiver'),
ComputeElement('second', 'receiver')
]
conduits = [Conduit('dm.out', 'first.in'), Conduit('dm.out2', 'second.in')]
model = Model('test_model', elements, conduits)
settings = Settings()
configuration = Configuration(model, settings)
implementations = {
'muscle.duplication_mapper': duplication_mapper,
'receiver': receiver
}
run_simulation(configuration, implementations)
def test_all(log_file_in_tmpdir):
"""A positive all-up test of everything.
"""
elements = [
ComputeElement('macro', 'macro_impl'),
ComputeElement('micro', 'micro_impl', [10])
]
conduits = [
Conduit('macro.out', 'micro.in'),
Conduit('micro.out', 'macro.in')
]
model = Model('test_model', elements, conduits)
settings = Settings(
OrderedDict([('test1', 13), ('test2', 13.3), ('test3', 'testing'),
('test4', True), ('test5', [2.3, 5.6]),
('test6', [[1.0, 2.0], [3.0, 1.0]])]))
configuration = Configuration(model, settings)
implementations = {'macro_impl': macro, 'micro_impl': micro}
run_simulation(configuration, implementations)
def test_settings_overlays(log_file_in_tmpdir):
"""A positive all-up test of settings overlays.
"""
elements = [
ComputeElement('qmc', 'qmc'),
ComputeElement('macro', 'macro', [10]),
ComputeElement('relay', 'explicit_relay'),
ComputeElement('relay2', 'explicit_relay'),
ComputeElement('micro', 'micro', [10])]
conduits = [
Conduit('qmc.settings_out', 'macro.muscle_settings_in'),
Conduit('macro.out', 'relay.in'),
Conduit('relay.out', 'micro.in'),
Conduit('micro.out', 'relay2.in'),
Conduit('relay2.out', 'macro.in')]
model = Model('test_model', elements, conduits)
settings = Settings(OrderedDict([
('test1', 13),
('test2', 13.3),
('test3', 'testing'),
('test4', True),
('test5', [2.3, 5.6]),
('test6', [[1.0, 2.0], [3.0, 1.0]])]))
configuration = Configuration(model, settings)
implementations = {
'qmc': qmc,
'macro': macro,
'explicit_relay': explicit_relay,
'micro': micro}
run_simulation(configuration, implementations)
def test_model_check_consistent1(macro_micro: Model) -> None:
macro_micro.check_consistent()
def test_model_check_consistent2(macro_micro: Model) -> None:
macro_micro.conduits[0].sender = Reference('marco.intermediate_state')
with pytest.raises(RuntimeError):
macro_micro.check_consistent()
def test_model_check_consistent3(macro_micro: Model) -> None:
macro_micro.conduits[1].receiver = Reference('Macro.state_update')
with pytest.raises(RuntimeError):
macro_micro.check_consistent()
for i in range(n_samples):
feed.append(float(inputs['feed' + str(i)]))
kill.append(float(inputs['kill' + str(i)]))
feed = np.array(feed)
kill = np.array(kill)
# Compute elements for the macro and micro model: specify the name of the python file here
elements = [ComputeElement('macro', 'macro', [n_samples]),
ComputeElement('micro', 'micro', [n_samples])]
# connect the submodels
conduits = [Conduit('macro.state_out', 'micro.state'),
Conduit('micro.sgs', 'macro.state_in')]
# create model instance
model = Model('gray_scott_reduced', elements, conduits)
# common settings
settings_dict = {'micro.t_max': 0.1, 'micro.dt': 0.1, 'N_Q': 2, 'N_LF': 128}
# parameter value settings, differs per run
for i in range(n_samples):
settings_dict['macro[%d].feed' % i] = feed[i]
settings_dict['macro[%d].kill' % i] = kill[i]
settings = Settings(settings_dict)
configuration = Configuration(model, settings)
# actual subroutines to run, imported from macro.py and micro.py
implementations = {'macro': gray_scott_macro, 'micro': reduced_sgs}
elements = [
ComputeElement('qmc', 'qmc_driver'),
ComputeElement('rr', 'load_balancer'),
ComputeElement('macro', 'diffusion', [10]),
ComputeElement('micro', 'reaction', [10])]
conduits = [
Conduit('qmc.parameters_out', 'rr.front_in'),
Conduit('rr.front_out', 'qmc.states_in'),
Conduit('rr.back_out', 'macro.muscle_settings_in'),
Conduit('macro.final_state_out', 'rr.back_in'),
Conduit('macro.state_out', 'micro.initial_state'),
Conduit('micro.final_state', 'macro.state_in')
]
model = Model('reaction_diffusion_qmc', elements, conduits)
settings = Settings(OrderedDict([
('micro.t_max', 2.469136e-6),
('micro.dt', 2.469136e-8),
('macro.t_max', 1.234568e-4),
('macro.dt', 2.469136e-6),
('qmc.t_max', 1.234568e-4),
('qmc.dt', 2.469136e-6),
('x_max', 1.01),
('dx', 0.01),
('k_min', -4.455e4),
('k_max', -3.645e4),
('d_min', 0.03645),
('d_max', 0.04455),
('n_samples', 100)
]))
def test_dump_no_conduits(dump_model: Callable) -> None:
ce1 = Component('ce1', 'test.impl1')
model = Model('test_model', [ce1])
text = dump_model(model)
assert text == ('name: test_model\n' 'components:\n' ' ce1: test.impl1\n')