"Enable_Vital_Dynamics": 1,
"Enable_Birth": 1,
'Enable_Default_Reporting': 1,
'Enable_Demographics_Other': 1,
'logLevel_default': 'ERROR',
# 'Enable_Property_Output': 1,
'x_Temporary_Larval_Habitat': 1,
"Simulation_Duration": sim_duration,
"Run_Number": 0,
"Vector_Species_Names": ['gambiae']
})
add_SerializationTimesteps(cb, [sim_duration], end_at_final=True)
#
# add_health_seeking(cb,
# targets=[{'trigger': 'NewClinicalCase', 'coverage': 0.3, 'agemin': 5, 'agemax': 70, 'seek': 1.0,
# 'rate': 0.3},
# {'trigger': 'NewClinicalCase', 'coverage': 0.5, 'agemin': 0, 'agemax': 5,
# 'seek': 1.0, 'rate': 0.3},
# {'trigger': 'NewSevereCase', 'coverage': 0.5, 'seek': 1.0, 'rate': 0.5}],
# drug=['Artemether', 'Lumefantrine'],
# dosing='FullTreatmentNewDetectionTech',
# nodes={"class": "NodeSetAll"},
# repetitions=1,
# start_day=sim_duration-10*365,
# tsteps_btwn_repetitions=365,
# broadcast_event_name='Received_Treatment'
# )
cb_serializing = DTKConfigBuilder.from_defaults('VECTOR_SIM')
configure_site(cb_serializing, 'Namawala')
cb_reloading = DTKConfigBuilder.from_defaults('VECTOR_SIM')
configure_site(cb_reloading, 'Namawala')
if __name__ == "__main__":
SetupParser.init()
exp_manager = ExperimentManagerFactory.from_setup()
timesteps_to_serialize = [5, 10, 50]
old_simulation_duration = cb_serializing.params["Simulation_Duration"]
serialized_last_timestep = timesteps_to_serialize[-1]
serialization.add_SerializationTimesteps(config_builder=cb_serializing,
timesteps=timesteps_to_serialize,
end_at_final=True)
serialized_builder = SingleSimulationBuilder()
exp_manager.run_simulations(config_builder=cb_serializing,
exp_builder=serialized_builder,
exp_name="Sample serialization test")
exp_manager.wait_for_finished()
serialized_sim = exp_manager.experiment.simulations[0]
serialized_output_path = path.join(serialized_sim.get_path(), 'output')
s_pop_filename = "state-00050.dtk"
reloaded_builder = SingleSimulationBuilder()
cb_reloading.params["Start_Time"] = serialized_last_timestep
cb_reloading.params[
def run_test(self):
SetupParser.init()
self.exp_manager = ExperimentManagerFactory.init()
exp_manager = self.exp_manager
for tag in self.exp_tags:
exp_manager.experiment_tags[tag] = self.exp_tags[tag]
cfg_builder = self.cb
cfg_builder.set_param("Config_Name", "Full run sim")
fullrun_builder = SingleSimulationBuilder()
fullrun_builder.tags['role'] = 'fullrun'
exp_manager.run_simulations(config_builder=cfg_builder,
exp_builder=fullrun_builder,
exp_name=self.exp_name)
old_sim_duration = cfg_builder.params["Simulation_Duration"]
for ts in self.timesteps_to_serialize:
ts_string = str(ts)
serialization.add_SerializationTimesteps(
config_builder=cfg_builder, timesteps=[ts], end_at_final=True)
cfg_builder.set_param("Config_Name",
"Serializing sim at {0}".format(ts_string))
serialized_builder = SingleSimulationBuilder()
serialized_builder.tags['role'] = 'serializer'
serialized_builder.tags[self.s_timestep_tagname] = ts_string
exp_manager.run_simulations(config_builder=cfg_builder,
exp_builder=serialized_builder,
exp_name=self.exp_name)
exp_manager.wait_for_finished()
self.baseline_sim = exp_manager.experiment.get_simulations_with_tag(
'role', 'fullrun')[0]
cfg_builder.params.pop("Serialization_Time_Steps")
for ts in self.timesteps_to_serialize:
ts_string = str(ts)
serialized_sim = exp_manager.experiment.get_simulations_with_tag(
self.s_timestep_tagname, ts_string)[0]
serialized_output_path = path.join(serialized_sim.get_path(),
'output')
# build s_pop_filename
prefix_len = 5 - len(ts_string)
prefix = '0' * prefix_len
s_pop_filename = 'state-{0}{1}.dtk'.format(prefix, ts_string)
cfg_builder.set_param("Config_Name",
"Reloading sim at {0}".format(ts_string))
reloaded_builder = SingleSimulationBuilder()
reloaded_builder.tags['role'] = 'reloader'
reloaded_builder.tags[self.s_timestep_tagname] = ts_string
cfg_builder.params["Start_Time"] = ts
cfg_builder.params["Simulation_Duration"] = old_sim_duration - ts
serialization.load_Serialized_Population(
config_builder=cfg_builder,
population_filenames=[s_pop_filename],
population_path=serialized_output_path)
exp_manager.run_simulations(config_builder=cfg_builder,
exp_builder=reloaded_builder,
exp_name=self.exp_name)
exp_manager.wait_for_finished()
self.create_combined_charts()
if self.inset_channels:
self.test_channels(self.inset_channels,
original_report_name='InsetChart.json')
if __name__ == "__main__":
# Initialize the SetupParser
SetupParser.init()
# Create a configbuilder for the simulation to serialize
cb_serializing = DTKConfigBuilder.from_defaults('VECTOR_SIM')
configure_site(cb_serializing, 'Namawala')
cb_serializing.set_param("Simulation_Duration", 365)
# Create an experiment manager
exp_manager = ExperimentManagerFactory.init()
# Set the serialization
add_SerializationTimesteps(config_builder=cb_serializing,
timesteps=[timestep_to_reload],
end_at_final=True)
s_pop_filename = "state-{0:05d}.dtk".format(timestep_to_reload)
# Run the simulation
exp_manager.run_simulations(config_builder=cb_serializing,
exp_name="Sample serialization test")
exp_manager.wait_for_finished(verbose=True)
# Download the state file
simulation = exp_manager.experiment.simulations[0]
da = DownloadAnalyzer(filenames=["output\\{}".format(s_pop_filename)],
output_path="temp")
am = AnalyzeManager(sim_list=[simulation], analyzers=[da])
am.analyze()
if __name__ == "__main__":
dir = './'
geography = 'Burkina Faso'
prefix = 'single_node_simulations'
exp = 8.60
exp_name = "insecticide_resistance_single_node_serialization"
num_years = 40
num_seeds = 1
cb = DTKConfigBuilder.from_defaults('MALARIA_SIM',
Simulation_Duration=int(365 *
num_years))
update_config_params(cb, direc=dir, geography=geography)
add_SerializationTimesteps(cb, [num_years * 365], end_at_final=True)
########################## VECTOR GENETICS ####################################################
builder = ModBuilder.from_list([
[
ModFn(DTKConfigBuilder.set_param, 'Run_Number', seed),
ModFn(change_vector_params,
species='gambiae',
mutation_rate1=mutation_rate,
mutation_rate2=mutation_rate,
serialization_seed=seed)
] for seed in range(num_seeds)
for mutation_rate in [0] # pow(10, x) for x in range(-5, 0)
])
from simtools.SetupParser import SetupParser
from examples.simple_1node_drug_interventions.configure_sahel_intervention_system import configure_sahel_intervention_system
from dtk.generic.serialization import add_SerializationTimesteps
sim_duration = 1 # in years
num_seeds = 1
serialization_path = './input'
expname = 'single_node_example_with_interventions_serialized_file'
# Initialize and setup config builder
cb = configure_sahel_intervention_system(sim_duration)
builder = GenericSweepBuilder.from_dict({'Run_Number': range(1)})
add_SerializationTimesteps(cb, [60 * 365], end_at_final=True)
run_sim_args = {
'config_builder': cb,
'exp_name': expname,
'exp_builder': builder
}
if __name__ == "__main__":
SetupParser.default_block = 'HPC'
SetupParser.init()
exp_manager = ExperimentManagerFactory.init()
exp_manager.run_simulations(**run_sim_args)
# Wait for the simulations to be done