class SimulatorAdapterTest(TransactionalTestCase):
"""
Basic testing that Simulator is still working from UI.
"""
CONNECTIVITY_NODES = 74
def setUp(self):
"""
Reset the database before each test.
"""
initialize_storage()
self.datatypes_factory = DatatypesFactory()
self.test_user = self.datatypes_factory.get_user()
self.test_project = self.datatypes_factory.get_project()
self.connectivity = self.datatypes_factory.create_connectivity(
self.CONNECTIVITY_NODES)[1]
algo_group = dao.find_group(SIMULATOR_MODULE, SIMULATOR_CLASS)
algorithm = dao.get_algorithm_by_group(algo_group.id)
self.simulator_adapter = FlowService().build_adapter_instance(
algo_group)
self.operation = TestFactory.create_operation(
algorithm, self.test_user, self.test_project, model.STATUS_STARTED,
json.dumps(SIMULATOR_PARAMETERS))
SIMULATOR_PARAMETERS['connectivity'] = self.connectivity.gid
def test_happy_flow_launch(self):
"""
Test that launching a simulation from UI works.
"""
OperationService().initiate_prelaunch(self.operation,
self.simulator_adapter, {},
**SIMULATOR_PARAMETERS)
sim_result = dao.get_generic_entity(TimeSeriesRegion,
'TimeSeriesRegion', 'type')[0]
self.assertEquals(sim_result.read_data_shape(),
(32, 1, self.CONNECTIVITY_NODES, 1))
def _estimate_hdd(self, new_parameters_dict):
""" Private method, to return HDD estimation for a given set of input parameters"""
filtered_params = self.simulator_adapter.prepare_ui_inputs(
new_parameters_dict)
self.simulator_adapter.configure(**filtered_params)
return self.simulator_adapter.get_required_disk_size(**filtered_params)
def test_estimate_hdd(self):
"""
Test that occupied HDD estimation for simulation results considers simulation length.
"""
factor = 5
simulation_parameters = copy(SIMULATOR_PARAMETERS)
## Estimate HDD with default simulation parameters
estimate1 = self._estimate_hdd(simulation_parameters)
self.assertTrue(estimate1 > 1)
## Change simulation length and monitor period, we expect a direct proportial increase in estimated HDD
simulation_parameters['simulation_length'] = float(
simulation_parameters['simulation_length']) * factor
period = float(simulation_parameters[
'monitors_parameters_option_TemporalAverage_period'])
simulation_parameters[
'monitors_parameters_option_TemporalAverage_period'] = period / factor
estimate2 = self._estimate_hdd(simulation_parameters)
self.assertEqual(estimate1, estimate2 / factor / factor)
## Change number of nodes in connectivity. Expect HDD estimation increase.
large_conn_gid = self.datatypes_factory.create_connectivity(
self.CONNECTIVITY_NODES * factor)[1].gid
simulation_parameters['connectivity'] = large_conn_gid
estimate3 = self._estimate_hdd(simulation_parameters)
self.assertEqual(estimate2, estimate3 / factor)
def test_estimate_execution_time(self):
"""
Test that get_execution_time_approximation considers the correct params
"""
## Compute reference estimation
params = self.simulator_adapter.prepare_ui_inputs(SIMULATOR_PARAMETERS)
estimation1 = self.simulator_adapter.get_execution_time_approximation(
**params)
## Estimation when the surface input parameter is set
params['surface'] = "GID_surface"
estimation2 = self.simulator_adapter.get_execution_time_approximation(
**params)
self.assertEqual(estimation1, estimation2 / 500)
params['surface'] = ""
## Modify integration step and simulation length:
initial_simulation_length = float(params['simulation_length'])
initial_integration_step = float(params['integrator_parameters']['dt'])
for factor in (2, 4, 10):
params['simulation_length'] = initial_simulation_length * factor
params['integrator_parameters'][
'dt'] = initial_integration_step / factor
estimation3 = self.simulator_adapter.get_execution_time_approximation(
**params)
self.assertEqual(estimation1, estimation3 / factor / factor)
## Check that no division by zero happens
params['integrator_parameters']['dt'] = 0
estimation4 = self.simulator_adapter.get_execution_time_approximation(
**params)
self.assertTrue(estimation4 > 0)
## even with length zero, still a positive estimation should be returned
params['simulation_length'] = 0
estimation5 = self.simulator_adapter.get_execution_time_approximation(
**params)
self.assertTrue(estimation5 > 0)
def test_noise_2d_bad_shape(self):
"""
Test a simulation with noise. Pass a wrong shape and expect exception to be raised.
"""
params = copy(SIMULATOR_PARAMETERS)
params['integrator'] = u'HeunStochastic'
noise_4d_config = [[1 for _ in xrange(self.CONNECTIVITY_NODES)]
for _ in xrange(4)]
params[
'integrator_parameters_option_HeunStochastic_dt'] = u'0.01220703125'
params[
'integrator_parameters_option_HeunStochastic_noise'] = u'Additive'
params[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = str(
noise_4d_config)
params[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_ntau'] = u'0.0'
params[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream'] = u'RandomStream'
params[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream_parameters_option_RandomStream_init_seed'] = u'42'
filtered_params = self.simulator_adapter.prepare_ui_inputs(params)
self.simulator_adapter.configure(**filtered_params)
if hasattr(self.simulator_adapter, 'algorithm'):
self.assertEqual(
(4, 74),
self.simulator_adapter.algorithm.integrator.noise.nsig.shape)
else:
self.fail("Simulator adapter was not initialized properly")
self.assertRaises(Exception,
OperationService().initiate_prelaunch,
self.operation, self.simulator_adapter, {}, **params)
def test_noise_2d_happy_flow(self):
"""
Test a simulation with noise.
"""
params = copy(SIMULATOR_PARAMETERS)
params['integrator'] = u'HeunStochastic'
noise_2d_config = [[1 for _ in xrange(self.CONNECTIVITY_NODES)]
for _ in xrange(2)]
params[
'integrator_parameters_option_HeunStochastic_dt'] = u'0.01220703125'
params[
'integrator_parameters_option_HeunStochastic_noise'] = u'Additive'
params[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = str(
noise_2d_config)
params[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_ntau'] = u'0.0'
params[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream'] = u'RandomStream'
params[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream_parameters_option_RandomStream_init_seed'] = u'42'
self._launch_and_check_noise(params, (2, 74))
sim_result = dao.get_generic_entity(TimeSeriesRegion,
'TimeSeriesRegion', 'type')[0]
self.assertEquals(sim_result.read_data_shape(),
(32, 1, self.CONNECTIVITY_NODES, 1))
params[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = '[1]'
self._launch_and_check_noise(params, (1, ))
def _launch_and_check_noise(self, params, expected_noise_shape):
filtered_params = self.simulator_adapter.prepare_ui_inputs(params)
self.simulator_adapter.configure(**filtered_params)
if hasattr(self.simulator_adapter, 'algorithm'):
self.assertEqual(
expected_noise_shape,
self.simulator_adapter.algorithm.integrator.noise.nsig.shape)
else:
self.fail("Simulator adapter was not initialized properly")
OperationService().initiate_prelaunch(self.operation,
self.simulator_adapter, {},
**params)
def test_simulation_with_stimulus(self):
"""
Test a simulation with noise.
"""
params = copy(SIMULATOR_PARAMETERS)
params["stimulus"] = self.datatypes_factory.create_stimulus(
self.connectivity).gid
filtered_params = self.simulator_adapter.prepare_ui_inputs(params)
self.simulator_adapter.configure(**filtered_params)
OperationService().initiate_prelaunch(self.operation,
self.simulator_adapter, {},
**params)
class SimulatorAdapterTest(TransactionalTestCase):
"""
Basic testing that Simulator is still working from UI.
"""
CONNECTIVITY_NODES = 74
def setUp(self):
"""
Reset the database before each test.
"""
initialize_storage()
user = model.User("test_user", "test_pass", "*****@*****.**", True,
"user")
self.test_user = dao.store_entity(user)
data = dict(name='test_proj', description='desc', users=[])
self.test_project = ProjectService().store_project(
self.test_user, True, None, **data)
meta = {
DataTypeMetaData.KEY_SUBJECT: "John Doe",
DataTypeMetaData.KEY_STATE: "INTERMEDIATE"
}
algo_group = dao.find_group(SIMULATOR_MODULE, SIMULATOR_CLASS)
self.simulator_adapter = FlowService().build_adapter_instance(
algo_group)
self.operation = model.Operation(self.test_user.id,
self.test_project.id,
algo_group.id,
json.dumps(SIMULATOR_PARAMETERS),
meta=json.dumps(meta),
status=model.STATUS_STARTED,
method_name=ABCAdapter.LAUNCH_METHOD)
self.operation = dao.store_entity(self.operation)
SIMULATOR_PARAMETERS['connectivity'] = self._create_connectivity(
self.CONNECTIVITY_NODES)
def _create_connectivity(self, nodes_number):
"""
Create a connectivity entity and return its GID
"""
storage_path = FilesHelper().get_project_folder(
self.test_project, str(self.operation.id))
connectivity = Connectivity(storage_path=storage_path)
connectivity.weights = numpy.ones((nodes_number, nodes_number))
connectivity.centres = numpy.ones((nodes_number, 3))
adapter_instance = StoreAdapter([connectivity])
OperationService().initiate_prelaunch(self.operation, adapter_instance,
{})
return dao.get_datatype_by_id(connectivity.id).gid
def test_happy_flow_launch(self):
"""
Test that launching a simulation from UI works.
"""
OperationService().initiate_prelaunch(self.operation,
self.simulator_adapter, {},
**SIMULATOR_PARAMETERS)
sim_result = dao.get_generic_entity(TimeSeriesRegion,
'TimeSeriesRegion', 'type')[0]
self.assertEquals(sim_result.read_data_shape(),
(32, 1, self.CONNECTIVITY_NODES, 1))
def _estimate_hdd(self, new_parameters_dict):
""" Private method, to return HDD estimation for a given set of input parameters"""
filtered_params = self.simulator_adapter.prepare_ui_inputs(
new_parameters_dict)
self.simulator_adapter.configure(**filtered_params)
return self.simulator_adapter.get_required_disk_size(**filtered_params)
def test_estimate_hdd(self):
"""
Test that occupied HDD estimation for simulation results considers simulation length.
"""
factor = 5
simulation_parameters = copy(SIMULATOR_PARAMETERS)
## Estimate HDD with default simulation parameters
estimate1 = self._estimate_hdd(simulation_parameters)
self.assertTrue(estimate1 > 1)
## Change simulation length and monitor period, we expect a direct proportial increase in estimated HDD
simulation_parameters['simulation_length'] = float(
simulation_parameters['simulation_length']) * factor
period = float(simulation_parameters[
'monitors_parameters_option_TemporalAverage_period'])
simulation_parameters[
'monitors_parameters_option_TemporalAverage_period'] = period / factor
estimate2 = self._estimate_hdd(simulation_parameters)
self.assertEqual(estimate1, estimate2 / factor / factor)
## Change number of nodes in connectivity. Expect HDD estimation increase.
simulation_parameters['connectivity'] = self._create_connectivity(
self.CONNECTIVITY_NODES * factor)
estimate3 = self._estimate_hdd(simulation_parameters)
self.assertEqual(estimate2, estimate3 / factor)
def test_estimate_execution_time(self):
"""
Test that get_execution_time_approximation considers the correct params
"""
## Compute reference estimation
simulation_parameters = self.simulator_adapter.prepare_ui_inputs(
SIMULATOR_PARAMETERS)
estimation1 = self.simulator_adapter.get_execution_time_approximation(
**simulation_parameters)
## Estimation when the surface input parameter is set
simulation_parameters['surface'] = "GID_surface"
estimation2 = self.simulator_adapter.get_execution_time_approximation(
**simulation_parameters)
self.assertEqual(estimation1, estimation2 / 500)
simulation_parameters['surface'] = ""
## Modify integration step and simulation length:
initial_simulation_length = float(
simulation_parameters['simulation_length'])
initial_integration_step = float(
simulation_parameters['integrator_parameters']['dt'])
for factor in (2, 4, 10):
simulation_parameters[
'simulation_length'] = initial_simulation_length * factor
simulation_parameters['integrator_parameters'][
'dt'] = initial_integration_step / factor
estimation3 = self.simulator_adapter.get_execution_time_approximation(
**simulation_parameters)
self.assertEqual(estimation1, estimation3 / factor / factor)
## Check that no division by zero happens
simulation_parameters['integrator_parameters']['dt'] = 0
estimation4 = self.simulator_adapter.get_execution_time_approximation(
**simulation_parameters)
self.assertTrue(estimation4 > 0)
## even with length zero, still a positive estimation should be returned
simulation_parameters['simulation_length'] = 0
estimation5 = self.simulator_adapter.get_execution_time_approximation(
**simulation_parameters)
self.assertTrue(estimation5 > 0)
def test_noise_2d_bad_shape(self):
"""
Test a simulation with noise. Pass a wrong shape and expect exception to be raised.
"""
SIMULATOR_PARAMETERS['integrator'] = u'HeunStochastic'
noise_4d_config = [[1 for _ in xrange(self.CONNECTIVITY_NODES)]
for _ in xrange(4)]
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_dt'] = u'0.01220703125'
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_noise'] = u'Additive'
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = str(
noise_4d_config)
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_ntau'] = u'0.0'
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream'] = u'RandomStream'
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream_parameters_option_RandomStream_init_seed'] = u'42'
filtered_params = self.simulator_adapter.prepare_ui_inputs(
SIMULATOR_PARAMETERS)
self.simulator_adapter.configure(**filtered_params)
if hasattr(self.simulator_adapter, 'algorithm'):
self.assertEqual(
(4, 74),
self.simulator_adapter.algorithm.integrator.noise.nsig.shape)
else:
self.fail("Simulator adapter was not initialized properly")
self.assertRaises(Exception,
OperationService().initiate_prelaunch,
self.operation, self.simulator_adapter, {},
**SIMULATOR_PARAMETERS)
def test_noise_2d_happy_flow(self):
"""
Test a simulation with noise.
"""
SIMULATOR_PARAMETERS['integrator'] = u'HeunStochastic'
noise_2d_config = [[1 for _ in xrange(self.CONNECTIVITY_NODES)]
for _ in xrange(2)]
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_dt'] = u'0.01220703125'
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_noise'] = u'Additive'
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = str(
noise_2d_config)
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_ntau'] = u'0.0'
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream'] = u'RandomStream'
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream_parameters_option_RandomStream_init_seed'] = u'42'
filtered_params = self.simulator_adapter.prepare_ui_inputs(
SIMULATOR_PARAMETERS)
self.simulator_adapter.configure(**filtered_params)
if hasattr(self.simulator_adapter, 'algorithm'):
self.assertEqual(
(2, 74, 1),
self.simulator_adapter.algorithm.integrator.noise.nsig.shape)
else:
self.fail("Simulator adapter was not initialized properly")
OperationService().initiate_prelaunch(self.operation,
self.simulator_adapter, {},
**SIMULATOR_PARAMETERS)
sim_result = dao.get_generic_entity(TimeSeriesRegion,
'TimeSeriesRegion', 'type')[0]
self.assertEquals(sim_result.read_data_shape(),
(32, 1, self.CONNECTIVITY_NODES, 1))
SIMULATOR_PARAMETERS[
'integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = '[1]'
filtered_params = self.simulator_adapter.prepare_ui_inputs(
SIMULATOR_PARAMETERS)
self.simulator_adapter.configure(**filtered_params)
if hasattr(self.simulator_adapter, 'algorithm'):
self.assertEqual(
(1, ),
self.simulator_adapter.algorithm.integrator.noise.nsig.shape)
else:
self.fail("Simulator adapter was not initialized properly")
OperationService().initiate_prelaunch(self.operation,
self.simulator_adapter, {},
**SIMULATOR_PARAMETERS)
class SimulatorAdapterTest(TransactionalTestCase):
"""
Basic testing that Simulator is still working from UI.
"""
CONNECTIVITY_NODES = 74
def setUp(self):
"""
Reset the database before each test.
"""
initialize_storage()
user = model.User("test_user", "test_pass", "*****@*****.**", True, "user")
self.test_user = dao.store_entity(user)
data = dict(name='test_proj', description='desc', users=[])
self.test_project = ProjectService().store_project(self.test_user, True, None, **data)
meta = {DataTypeMetaData.KEY_SUBJECT: "John Doe",
DataTypeMetaData.KEY_STATE: "INTERMEDIATE"}
algo_group = dao.find_group(SIMULATOR_MODULE, SIMULATOR_CLASS)
self.simulator_adapter = FlowService().build_adapter_instance(algo_group)
self.operation = model.Operation(self.test_user.id, self.test_project.id, algo_group.id,
json.dumps(SIMULATOR_PARAMETERS),
meta=json.dumps(meta), status=model.STATUS_STARTED,
method_name=ABCAdapter.LAUNCH_METHOD)
self.operation = dao.store_entity(self.operation)
SIMULATOR_PARAMETERS['connectivity'] = self._create_connectivity(self.CONNECTIVITY_NODES)
def _create_connectivity(self, nodes_number):
"""
Create a connectivity entity and return its GID
"""
storage_path = FilesHelper().get_project_folder(self.test_project, str(self.operation.id))
connectivity = Connectivity(storage_path=storage_path)
connectivity.weights = numpy.ones((nodes_number, nodes_number))
connectivity.centres = numpy.ones((nodes_number, 3))
adapter_instance = StoreAdapter([connectivity])
OperationService().initiate_prelaunch(self.operation, adapter_instance, {})
return dao.get_datatype_by_id(connectivity.id).gid
def test_happy_flow_launch(self):
"""
Test that launching a simulation from UI works.
"""
OperationService().initiate_prelaunch(self.operation, self.simulator_adapter, {}, **SIMULATOR_PARAMETERS)
sim_result = dao.get_generic_entity(TimeSeriesRegion, 'TimeSeriesRegion', 'type')[0]
self.assertEquals(sim_result.read_data_shape(), (32, 1, self.CONNECTIVITY_NODES, 1))
def _estimate_hdd(self, new_parameters_dict):
""" Private method, to return HDD estimation for a given set of input parameters"""
filtered_params = self.simulator_adapter.prepare_ui_inputs(new_parameters_dict)
self.simulator_adapter.configure(**filtered_params)
return self.simulator_adapter.get_required_disk_size(**filtered_params)
def test_estimate_hdd(self):
"""
Test that occupied HDD estimation for simulation results considers simulation length.
"""
factor = 5
simulation_parameters = copy(SIMULATOR_PARAMETERS)
## Estimate HDD with default simulation parameters
estimate1 = self._estimate_hdd(simulation_parameters)
self.assertTrue(estimate1 > 1)
## Change simulation length and monitor period, we expect a direct proportial increase in estimated HDD
simulation_parameters['simulation_length'] = float(simulation_parameters['simulation_length']) * factor
period = float(simulation_parameters['monitors_parameters_option_TemporalAverage_period'])
simulation_parameters['monitors_parameters_option_TemporalAverage_period'] = period / factor
estimate2 = self._estimate_hdd(simulation_parameters)
self.assertEqual(estimate1, estimate2 / factor / factor)
## Change number of nodes in connectivity. Expect HDD estimation increase.
simulation_parameters['connectivity'] = self._create_connectivity(self.CONNECTIVITY_NODES * factor)
estimate3 = self._estimate_hdd(simulation_parameters)
self.assertEqual(estimate2, estimate3 / factor)
def test_estimate_execution_time(self):
"""
Test that get_execution_time_approximation considers the correct params
"""
## Compute reference estimation
simulation_parameters = self.simulator_adapter.prepare_ui_inputs(SIMULATOR_PARAMETERS)
estimation1 = self.simulator_adapter.get_execution_time_approximation(**simulation_parameters)
## Estimation when the surface input parameter is set
simulation_parameters['surface'] = "GID_surface"
estimation2 = self.simulator_adapter.get_execution_time_approximation(**simulation_parameters)
self.assertEqual(estimation1, estimation2 / 500)
simulation_parameters['surface'] = ""
## Modify integration step and simulation length:
initial_simulation_length = float(simulation_parameters['simulation_length'])
initial_integration_step = float(simulation_parameters['integrator_parameters']['dt'])
for factor in (2, 4, 10):
simulation_parameters['simulation_length'] = initial_simulation_length * factor
simulation_parameters['integrator_parameters']['dt'] = initial_integration_step / factor
estimation3 = self.simulator_adapter.get_execution_time_approximation(**simulation_parameters)
self.assertEqual(estimation1, estimation3 / factor / factor)
## Check that no division by zero happens
simulation_parameters['integrator_parameters']['dt'] = 0
estimation4 = self.simulator_adapter.get_execution_time_approximation(**simulation_parameters)
self.assertTrue(estimation4 > 0)
## even with length zero, still a positive estimation should be returned
simulation_parameters['simulation_length'] = 0
estimation5 = self.simulator_adapter.get_execution_time_approximation(**simulation_parameters)
self.assertTrue(estimation5 > 0)
def test_noise_2d_bad_shape(self):
"""
Test a simulation with noise. Pass a wrong shape and expect exception to be raised.
"""
SIMULATOR_PARAMETERS['integrator'] = u'HeunStochastic'
noise_4d_config = [[1 for _ in xrange(self.CONNECTIVITY_NODES)] for _ in xrange(4)]
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_dt'] = u'0.01220703125'
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_noise'] = u'Additive'
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = str(noise_4d_config)
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_ntau'] = u'0.0'
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream'] = u'RandomStream'
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream_parameters_option_RandomStream_init_seed'] = u'42'
filtered_params = self.simulator_adapter.prepare_ui_inputs(SIMULATOR_PARAMETERS)
self.simulator_adapter.configure(**filtered_params)
if hasattr(self.simulator_adapter, 'algorithm'):
self.assertEqual((4, 74), self.simulator_adapter.algorithm.integrator.noise.nsig.shape)
else:
self.fail("Simulator adapter was not initialized properly")
self.assertRaises(Exception, OperationService().initiate_prelaunch, self.operation, self.simulator_adapter, {}, **SIMULATOR_PARAMETERS)
def test_noise_2d_happy_flow(self):
"""
Test a simulation with noise.
"""
SIMULATOR_PARAMETERS['integrator'] = u'HeunStochastic'
noise_2d_config = [[1 for _ in xrange(self.CONNECTIVITY_NODES)] for _ in xrange(2)]
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_dt'] = u'0.01220703125'
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_noise'] = u'Additive'
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = str(noise_2d_config)
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_ntau'] = u'0.0'
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream'] = u'RandomStream'
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream_parameters_option_RandomStream_init_seed'] = u'42'
filtered_params = self.simulator_adapter.prepare_ui_inputs(SIMULATOR_PARAMETERS)
self.simulator_adapter.configure(**filtered_params)
if hasattr(self.simulator_adapter, 'algorithm'):
self.assertEqual((2, 74, 1), self.simulator_adapter.algorithm.integrator.noise.nsig.shape)
else:
self.fail("Simulator adapter was not initialized properly")
OperationService().initiate_prelaunch(self.operation, self.simulator_adapter, {}, **SIMULATOR_PARAMETERS)
sim_result = dao.get_generic_entity(TimeSeriesRegion, 'TimeSeriesRegion', 'type')[0]
self.assertEquals(sim_result.read_data_shape(), (32, 1, self.CONNECTIVITY_NODES, 1))
SIMULATOR_PARAMETERS['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = '[1]'
filtered_params = self.simulator_adapter.prepare_ui_inputs(SIMULATOR_PARAMETERS)
self.simulator_adapter.configure(**filtered_params)
if hasattr(self.simulator_adapter, 'algorithm'):
self.assertEqual((1,), self.simulator_adapter.algorithm.integrator.noise.nsig.shape)
else:
self.fail("Simulator adapter was not initialized properly")
OperationService().initiate_prelaunch(self.operation, self.simulator_adapter, {}, **SIMULATOR_PARAMETERS)
class SimulatorAdapterTest(TransactionalTestCase):
"""
Basic testing that Simulator is still working from UI.
"""
CONNECTIVITY_NODES = 74
def setUp(self):
"""
Reset the database before each test.
"""
initialize_storage()
self.datatypes_factory = DatatypesFactory()
self.test_user = self.datatypes_factory.get_user()
self.test_project = self.datatypes_factory.get_project()
self.connectivity = self.datatypes_factory.create_connectivity(self.CONNECTIVITY_NODES)[1]
algo_group = dao.find_group(SIMULATOR_MODULE, SIMULATOR_CLASS)
algorithm = dao.get_algorithm_by_group(algo_group.id)
self.simulator_adapter = FlowService().build_adapter_instance(algo_group)
self.operation = TestFactory.create_operation(algorithm, self.test_user, self.test_project,
model.STATUS_STARTED, json.dumps(SIMULATOR_PARAMETERS))
SIMULATOR_PARAMETERS['connectivity'] = self.connectivity.gid
def test_happy_flow_launch(self):
"""
Test that launching a simulation from UI works.
"""
OperationService().initiate_prelaunch(self.operation, self.simulator_adapter, {}, **SIMULATOR_PARAMETERS)
sim_result = dao.get_generic_entity(TimeSeriesRegion, 'TimeSeriesRegion', 'type')[0]
self.assertEquals(sim_result.read_data_shape(), (32, 1, self.CONNECTIVITY_NODES, 1))
def _estimate_hdd(self, new_parameters_dict):
""" Private method, to return HDD estimation for a given set of input parameters"""
filtered_params = self.simulator_adapter.prepare_ui_inputs(new_parameters_dict)
self.simulator_adapter.configure(**filtered_params)
return self.simulator_adapter.get_required_disk_size(**filtered_params)
def test_estimate_hdd(self):
"""
Test that occupied HDD estimation for simulation results considers simulation length.
"""
factor = 5
simulation_parameters = copy(SIMULATOR_PARAMETERS)
## Estimate HDD with default simulation parameters
estimate1 = self._estimate_hdd(simulation_parameters)
self.assertTrue(estimate1 > 1)
## Change simulation length and monitor period, we expect a direct proportial increase in estimated HDD
simulation_parameters['simulation_length'] = float(simulation_parameters['simulation_length']) * factor
period = float(simulation_parameters['monitors_parameters_option_TemporalAverage_period'])
simulation_parameters['monitors_parameters_option_TemporalAverage_period'] = period / factor
estimate2 = self._estimate_hdd(simulation_parameters)
self.assertEqual(estimate1, estimate2 / factor / factor)
## Change number of nodes in connectivity. Expect HDD estimation increase.
large_conn_gid = self.datatypes_factory.create_connectivity(self.CONNECTIVITY_NODES * factor)[1].gid
simulation_parameters['connectivity'] = large_conn_gid
estimate3 = self._estimate_hdd(simulation_parameters)
self.assertEqual(estimate2, estimate3 / factor)
def test_estimate_execution_time(self):
"""
Test that get_execution_time_approximation considers the correct params
"""
## Compute reference estimation
params = self.simulator_adapter.prepare_ui_inputs(SIMULATOR_PARAMETERS)
estimation1 = self.simulator_adapter.get_execution_time_approximation(**params)
## Estimation when the surface input parameter is set
params['surface'] = "GID_surface"
estimation2 = self.simulator_adapter.get_execution_time_approximation(**params)
self.assertEqual(estimation1, estimation2 / 500)
params['surface'] = ""
## Modify integration step and simulation length:
initial_simulation_length = float(params['simulation_length'])
initial_integration_step = float(params['integrator_parameters']['dt'])
for factor in (2, 4, 10):
params['simulation_length'] = initial_simulation_length * factor
params['integrator_parameters']['dt'] = initial_integration_step / factor
estimation3 = self.simulator_adapter.get_execution_time_approximation(**params)
self.assertEqual(estimation1, estimation3 / factor / factor)
## Check that no division by zero happens
params['integrator_parameters']['dt'] = 0
estimation4 = self.simulator_adapter.get_execution_time_approximation(**params)
self.assertTrue(estimation4 > 0)
## even with length zero, still a positive estimation should be returned
params['simulation_length'] = 0
estimation5 = self.simulator_adapter.get_execution_time_approximation(**params)
self.assertTrue(estimation5 > 0)
def test_noise_2d_bad_shape(self):
"""
Test a simulation with noise. Pass a wrong shape and expect exception to be raised.
"""
params = copy(SIMULATOR_PARAMETERS)
params['integrator'] = u'HeunStochastic'
noise_4d_config = [[1 for _ in xrange(self.CONNECTIVITY_NODES)] for _ in xrange(4)]
params['integrator_parameters_option_HeunStochastic_dt'] = u'0.01220703125'
params['integrator_parameters_option_HeunStochastic_noise'] = u'Additive'
params['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = str(noise_4d_config)
params['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_ntau'] = u'0.0'
params['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream'] = u'RandomStream'
params['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream_parameters_option_RandomStream_init_seed'] = u'42'
filtered_params = self.simulator_adapter.prepare_ui_inputs(params)
self.simulator_adapter.configure(**filtered_params)
if hasattr(self.simulator_adapter, 'algorithm'):
self.assertEqual((4, 74), self.simulator_adapter.algorithm.integrator.noise.nsig.shape)
else:
self.fail("Simulator adapter was not initialized properly")
self.assertRaises(Exception, OperationService().initiate_prelaunch, self.operation,
self.simulator_adapter, {}, **params)
def test_noise_2d_happy_flow(self):
"""
Test a simulation with noise.
"""
params = copy(SIMULATOR_PARAMETERS)
params['integrator'] = u'HeunStochastic'
noise_2d_config = [[1 for _ in xrange(self.CONNECTIVITY_NODES)] for _ in xrange(2)]
params['integrator_parameters_option_HeunStochastic_dt'] = u'0.01220703125'
params['integrator_parameters_option_HeunStochastic_noise'] = u'Additive'
params['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = str(noise_2d_config)
params['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_ntau'] = u'0.0'
params['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream'] = u'RandomStream'
params['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_random_stream_parameters_option_RandomStream_init_seed'] = u'42'
self._launch_and_check_noise(params, (2, 74))
sim_result = dao.get_generic_entity(TimeSeriesRegion, 'TimeSeriesRegion', 'type')[0]
self.assertEquals(sim_result.read_data_shape(), (32, 1, self.CONNECTIVITY_NODES, 1))
params['integrator_parameters_option_HeunStochastic_noise_parameters_option_Additive_nsig'] = '[1]'
self._launch_and_check_noise(params, (1,))
def _launch_and_check_noise(self, params, expected_noise_shape):
filtered_params = self.simulator_adapter.prepare_ui_inputs(params)
self.simulator_adapter.configure(**filtered_params)
if hasattr(self.simulator_adapter, 'algorithm'):
self.assertEqual(expected_noise_shape, self.simulator_adapter.algorithm.integrator.noise.nsig.shape)
else:
self.fail("Simulator adapter was not initialized properly")
OperationService().initiate_prelaunch(self.operation, self.simulator_adapter, {}, **params)
def test_simulation_with_stimulus(self):
"""
Test a simulation with noise.
"""
params = copy(SIMULATOR_PARAMETERS)
params["stimulus"] = self.datatypes_factory.create_stimulus(self.connectivity).gid
filtered_params = self.simulator_adapter.prepare_ui_inputs(params)
self.simulator_adapter.configure(**filtered_params)
OperationService().initiate_prelaunch(self.operation, self.simulator_adapter, {}, **params)
