sampler = uq.sampling.SCSampler(vary=vary, polynomial_order=4)
# Associate the sampler with the campaign
campaign.set_sampler(sampler)
###############################
# execute the defined actions #
###############################
campaign.execute().collate()
###############################################
# run the UQ ensemble using FabSim3 interface #
###############################################
fab.run_uq_ensemble(CONFIG, campaign.campaign_dir, script='ade',
machine=MACHINE, PJ=PILOT_JOB)
# wait for job to complete
fab.wait(machine=MACHINE)
# check if all output files are retrieved from the remote machine, returns a Boolean flag
all_good = fab.verify(CONFIG, campaign.campaign_dir,
TARGET_FILENAME,
machine=MACHINE)
if all_good:
# copy the results from the FabSim results dir to the EasyVVUQ results dir
fab.get_uq_samples(CONFIG, campaign.campaign_dir, sampler.n_samples, machine=MACHINE)
else:
print("Not all samples executed correctly")
import sys
sampler = uq.sampling.MCSampler(vary=vary, n_mc_samples=2000)
# Associate the sampler with the campaign
campaign.set_sampler(sampler)
# Will draw all (of the finite set of samples)
campaign.draw_samples()
campaign.populate_runs_dir()
#Save the Campaign
campaign.save_state("campaign_state_PO.json")
# run the UQ ensemble
fab.run_uq_ensemble(config,
campaign.campaign_dir,
script=script,
machine=machine,
PJ=True)
#wait for job to complete
# fab.wait(machine=machine)
# #wait for jobs to complete and check if all output files are retrieved
# #from the remote machine
# fab.verify(config, campaign.campaign_dir,
# campaign._active_app_decoder.target_filename,
# machine=machine, PilotJob=True)
# #run the UQ ensemble
# fab.get_uq_samples(config, campaign.campaign_dir, sampler._n_samples,
# skip=0, machine='eagle_vecma')
def run_sc_samples(work_dir):
# Set up a fresh campaign called "sc"
my_campaign = uq.Campaign(name='ocean', work_dir=work_dir)
# Define parameter space
params = {
"decay_time_nu": {
"type": "float",
"min": 0.0,
"max": 1000.0,
"default": 5.0},
"decay_time_mu": {
"type": "float",
"min": 0.0,
"max": 1000.0,
"default": 90.0},
"out_file": {
"type": "string",
"default": "output.csv"}}
output_filename = params["out_file"]["default"]
output_columns = ["E_mean", "Z_mean", "E_std", "Z_std"]
# Create an encoder, decoder and collation element for PCE test app
encoder = uq.encoders.GenericEncoder(
template_fname= HOME + '/sc/ocean.template',
delimiter='$',
target_filename='ocean_in.json')
decoder = uq.decoders.SimpleCSV(target_filename=output_filename,
output_columns=output_columns,
header=0)
collater = uq.collate.AggregateSamples(average=False)
# Add the SC app (automatically set as current app)
my_campaign.add_app(name="sc",
params=params,
encoder=encoder,
decoder=decoder,
collater=collater)
# Create the sampler
vary = {
"decay_time_nu": cp.Uniform(1.0, 5.0),
"decay_time_mu": cp.Uniform(85.0, 95.0)
}
my_sampler = uq.sampling.SCSampler(vary=vary, polynomial_order=2)
# Associate the sampler with the campaign
my_campaign.set_sampler(my_sampler)
# Will draw all (of the finite set of samples)
my_campaign.draw_samples()
my_campaign.populate_runs_dir()
#Run execution using Fabsim
fab.run_uq_ensemble(my_campaign.campaign_dir, 'ocean', machine='localhost')
#Save the Campaign
my_campaign.save_state("campaign_state.json")
delimiter='$',
target_filename='theta_initial_conditions.csv')
decoder = uq.decoders.SimpleCSV(target_filename=output_filename,
output_columns=output_columns,
header=0)
collater = uq.collate.AggregateSamples(average=False)
# Add the SC app (automatically set as current app)
my_campaign.add_app(name="sc",
params=params,
encoder=encoder,
decoder=decoder,
collater=collater)
# Create the sampler
vary = {"incubation": cp.Normal(5.2, 0.1), "r0": cp.Normal(2.5, 0.1)}
my_sampler = uq.sampling.SCSampler(vary=vary, polynomial_order=2)
# Associate the sampler with the campaign
my_campaign.set_sampler(my_sampler)
# Will draw all (of the finite set of samples)
my_campaign.draw_samples()
my_campaign.populate_runs_dir()
#Run execution using Fabsim
fab.run_uq_ensemble(my_campaign.campaign_dir, 'corona', machine='localhost')
#Save the Campaign
my_campaign.save_state("campaign_state.json")
my_sampler = uq.sampling.SCSampler(vary=vary, polynomial_order=2,
quadrature_rule="G",
sparse=False, growth=False)
# Associate the sampler with the campaign
my_campaign.set_sampler(my_sampler)
# Will draw all (of the finite set of samples)
my_campaign.draw_samples()
my_campaign.populate_runs_dir()
## Use this instead to run the samples using EasyVVUQ on the localhost
#my_campaign.apply_for_each_run_dir(uq.actions.ExecuteLocal(
# "sc_model.py ade_in.json"))
fab.run_uq_ensemble(my_campaign.campaign_dir, script_name='ade', machine='localhost')
fab.get_uq_samples(my_campaign.campaign_dir, machine='localhost')
my_campaign.collate()
# Post-processing analysis
analysis = uq.analysis.SCAnalysis(sampler=my_sampler, qoi_cols=output_columns)
my_campaign.apply_analysis(analysis)
results = my_campaign.get_last_analysis()
###################################
# Plot the moments and SC samples #
###################################
# Associate the sampler with the campaign
campaign.set_sampler(sampler)
###############################
# execute the defined actions #
###############################
campaign.execute().collate()
####################################
# Ensemble execution using FabSim3 #
####################################
fab.run_uq_ensemble(CONFIG,
campaign.campaign_dir,
script='ohagan',
machine=MACHINE,
PJ=PILOT_JOB)
# wait for job to complete
fab.wait(machine=MACHINE)
# check if all output files are retrieved from the remote machine, returns a Boolean flag
all_good = fab.verify(CONFIG,
campaign.campaign_dir,
TARGET_FILENAME,
machine=MACHINE)
if all_good:
# copy the results from the FabSim results dir to the EasyVVUQ results dir
fab.get_uq_samples(CONFIG,
def run_campaign(poly_order, work_dir='/tmp'):
# Set up a fresh campaign called "sc"
my_campaign = uq.Campaign(name='sc', work_dir=work_dir)
# Define parameter space
params = {
"x1": {
"type": "float",
"min": 0.0,
"max": 1.0,
"default": 0.5
},
"x2": {
"type": "float",
"min": 0.0,
"max": 1.0,
"default": 0.5
},
"out_file": {
"type": "string",
"default": "output.csv"
}
}
output_filename = params["out_file"]["default"]
output_columns = ["f"]
# Create an encoder, decoder and collation element
encoder = uq.encoders.GenericEncoder(template_fname=HOME +
'/sc/sobol.template',
delimiter='$',
target_filename='sobol_in.json')
decoder = uq.decoders.SimpleCSV(target_filename=output_filename,
output_columns=output_columns,
header=0)
collater = uq.collate.AggregateSamples(average=False)
# Add the SC app (automatically set as current app)
my_campaign.add_app(name="sc",
params=params,
encoder=encoder,
decoder=decoder,
collater=collater)
# Create the sampler
vary = {"x1": cp.Uniform(0.0, 1.0), "x2": cp.Uniform(0.0, 1.0)}
"""
SPARSE GRID PARAMETERS
----------------------
- sparse = True: use a Smolyak sparse grid
- growth = True: use an exponential rule for the growth of the number
of 1D collocation points per level. Used to make e.g. clenshaw-curtis
quadrature nested.
"""
my_sampler = uq.sampling.SCSampler(vary=vary,
polynomial_order=poly_order,
quadrature_rule="G",
sparse=False,
growth=False)
# Associate the sampler with the campaign
my_campaign.set_sampler(my_sampler)
print('Number of samples:', my_sampler.xi_d.shape[0])
# Will draw all (of the finite set of samples)
my_campaign.draw_samples()
my_campaign.populate_runs_dir()
# Use this instead to run the samples using EasyVVUQ on the localhost
# my_campaign.apply_for_each_run_dir(uq.actions.ExecuteLocal(
# "sc/sobol_model.py sobol_in.json"))
#Run execution using Fabsim
fab.run_uq_ensemble(my_campaign.campaign_dir,
'sobol_test',
machine='localhost')
fab.get_uq_samples(my_campaign.campaign_dir, machine='localhost')
my_campaign.collate()
# Post-processing analysis
analysis = uq.analysis.SCAnalysis(sampler=my_sampler,
qoi_cols=output_columns)
my_campaign.apply_analysis(analysis)
results = my_campaign.get_last_analysis()
#the unique ID of this Campaign
ID = my_campaign.campaign_dir.split('/')[-1]
#store the sobol indices of each campaign to the same results directory
results_dir = work_dir + '/sobols/' + ID
if os.path.exists(results_dir) == False:
os.makedirs(results_dir)
#store the 1st order sobols indices to a CSV file
sobols = pd.DataFrame(results['sobols_first']['f'])
sobols.to_csv(results_dir + '/sobols.csv')
return results, ID
