def general_sim(erad_path, ep4_scripts):
"""
This function is designed to be a parameterized version of the sequence of things we do
every time we run an emod experiment.
"""
print_params()
# Create a platform
# Show how to dynamically set priority and node_group
platform = Platform("SLURM")
pl = RequirementsToAssetCollection(platform,
requirements_path=manifest.requirements)
# create EMODTask
print("Creating EMODTask (from files)...")
camp_path = build_camp()
params.base_infectivity = 0.2
task = EMODTask.from_default2(config_path="my_config.json",
eradication_path=manifest.eradication_path,
campaign_path=camp_path,
schema_path=manifest.schema_file,
param_custom_cb=set_param_fn,
ep4_custom_cb=None,
demog_builder=build_demog)
print("Adding asset dir...")
task.common_assets.add_directory(
assets_directory=manifest.assets_input_dir)
# Set task.campaign to None to not send any campaign to comps since we are going to override it later with
# dtk-pre-process.
print("Adding local assets (py scripts mainly)...")
if ep4_scripts is not None:
for asset in ep4_scripts:
pathed_asset = Asset(pathlib.PurePath.joinpath(
manifest.ep4_path, asset),
relative_path="python")
task.common_assets.add_asset(pathed_asset)
# Create simulation sweep with builder
builder = SimulationBuilder()
builder.add_sweep_definition(update_sim_random_seed, range(params.nSims))
# create experiment from builder
experiment = Experiment.from_builder(builder, task, name=params.exp_name)
# The last step is to call run() on the ExperimentManager to run the simulations.
experiment.run(wait_until_done=True, platform=platform)
#other_assets = AssetCollection.from_id(pl.run())
#experiment.assets.add_assets(other_assets)
# Check result
if not experiment.succeeded:
print(f"Experiment {experiment.uid} failed.\n")
exit()
print(f"Experiment {experiment.uid} succeeded.")
# Save experiment id to file
with open("COMPS_ID", "w") as fd:
fd.write(experiment.uid.hex)
print()
print(experiment.uid.hex)
from emodpy.bamboo import get_model_files
from emodpy.emod_task import EMODTask
from emodpy.utils import EradicationBambooBuilds
from idmtools.builders import SimulationBuilder
from idmtools.core.platform_factory import Platform
import manifest
import params
from idmtools.entities.experiment import Experiment
from interventions import build_campaign_with_standard_events
from setup_sim import build_project_config
from sweeps import update_sim_bic, update_sim_random_seed
platform = Platform("SLURM") #, num_cores=params.num_cores)
print("Creating EMODTask (from files)...")
def build_demographics():
import emod_api.demographics.Demographics as Demographics
demo = Demographics.from_file(manifest.demographics_file_path)
return demo
def create_and_submit_experiment():
task = EMODTask.from_default2(
config_path="config.json",
eradication_path=manifest.eradication_path,
campaign_builder=build_campaign_with_standard_events,
import os
from COMPS import Client, AuthManager
from idmtools.assets import Asset
from idmtools.core.platform_factory import Platform
from idmtools.managers import ExperimentManager
from idmtools_models.python.python_experiment import PythonExperiment
# This provisions a script runs a pip install on a requirements.txt file to a temp direcorty on COMPS and then creates
# an asset collection from the output. This helps avoid target the COMPS python binary that is currently available and
# also avoid the need for the user to upload a large set of files to COMPS
experiment = PythonExperiment(
name="fractals asset bootstrap",
model_path=os.path.join("requirements_to_asset_collection.py"))
experiment.add_asset(Asset('model_requirements.txt'))
platform = Platform('COMPS2')
am = AuthManager(platform.endpoint)
with open('token.txt', 'w') as of:
of.write(am.get_auth_token()[1])
experiment.base_simulation.add_asset(Asset("token.txt"))
em = ExperimentManager(experiment=experiment, platform=platform)
em.run()
em.wait_till_done()
def general_sim( erad_path ):
# Function specially set parameter Run_Number
set_Run_Number = partial(param_update, param="Run_Number")
# Get experiment parameters from json file
with open(manifest.PARAM_PATH) as f:
param_dict = json.load(f)
exp_name = param_dict['expName']
nSims = param_dict['nSims']
# Display exp_name and nSims
print('exp_name: ', exp_name)
print('nSims: ', nSims)
# Create a platform
# Show how to dynamically set priority and node_group
platform = Platform('SLURM')
pl = RequirementsToAssetCollection( platform, requirements_path=manifest.requirements )
# create EMODTask from default
#task = EMODTask.from_default( default=EMODSir(), eradication_path=erad_path )
#task = EMODTask.from_default2(config_path="ignore_my_config.json", eradication_path=manifest.eradication_path, campaign_path=None, param_custom_cb=None, ep4_custom_cb=manifest.ep4_path)
task = EMODTask.from_files(config_path=None, eradication_path=manifest.eradication_path, ep4_path=manifest.ep4_path, demographics_paths=None)
# Add the parameters dictionary as an asset
param_asset = Asset(absolute_path=manifest.PARAM_PATH)
task.common_assets.add_asset(param_asset)
# Add more asset from a directory
assets_dir = 'measles_kurt/Assets'
task.common_assets.add_directory(assets_directory=assets_dir)
#task.is_linux = True
# set campaign to None to not sending any campaign to comps since we are going to override it later with
# dtk-pre-process, This is import step in COMPS2
task.campaign = None
# Load campaign_template.json to simulation which used by dtk_pre_process.py
campaign_template_asset = Asset(os.path.join(manifest.assets_input_dir, "campaign_template.json"))
task.transient_assets.add_asset(campaign_template_asset)
# Create simulation sweep with builder
builder = SimulationBuilder()
builder.add_sweep_definition(set_Run_Number, range(nSims))
# Create an experiment from builder
experiment = Experiment.from_builder(builder, task, name=exp_name)
other_assets = AssetCollection.from_id(pl.run())
experiment.assets.add_assets(other_assets)
# Run experiment
platform.run_items(experiment)
# Wait experiment to finish
platform.wait_till_done(experiment)
# Check result
if not experiment.succeeded:
print(f"Experiment {experiment.uid} failed.\n")
exit()
print(f"Experiment {experiment.uid} succeeded.")
# Save experiment id to file
with open('COMPS_ID', 'w') as fd:
fd.write(experiment.uid.hex)
print()
print(experiment.uid.hex)
covid_config_filename = emodpy_covid.build_covid_config(schema_filename)
covid_demographics_filename = emodpy_covid.covid.get_demographics_json()
seed_campaign_filename = emodpy_covid.covid.get_seed_campaign()
dtk_pre_process_filename = emodpy_covid.write_pre_process_py()
dtk_in_process_filename = emodpy_covid.write_in_process_py()
local_assets_dict = {
'config': covid_config_filename,
'demog': covid_demographics_filename,
'campaign': seed_campaign_filename,
'pre_proc': dtk_pre_process_filename,
'in_proc': dtk_in_process_filename
}
if __name__ == "__main__":
local_assets = build_emod_assets(schema_filename)
platform = Platform('COMPS2')
contact_tracing_task = EMODTask.from_files(
eradication_path=Eradication_filename,
config_path=local_assets['config'],
campaign_path=local_assets['campaign'],
demographics_paths=[
local_assets['demog']
]
)
dtk_in_process_asset = Asset(local_assets['in_proc'],
relative_path='python')
contact_tracing_task.common_assets.add_asset(dtk_in_process_asset)
dtk_pre_process_asset = Asset(local_assets['pre_proc'],