def build_ldl_thresholds(location: str, draws: str, concat_only: bool,
verbose: int):
output_dir = paths.LDL_C_THRESHOLD_DIR
locations = project_globals.LOCATIONS if location == 'all' else [location]
if not concat_only:
from vivarium_cluster_tools.psimulate.utilities import get_drmaa
drmaa = get_drmaa()
jobs = {}
draw_list = range(1000) if draws == 'all' else draws.split(',')
with drmaa.Session() as session:
for location in locations:
build_ldl_thresholds_single_location(drmaa, jobs, location,
draw_list, output_dir,
session)
if verbose:
logger.info('Entering monitoring loop.')
logger.info('-------------------------')
logger.info('')
while any([
job[1]
not in [drmaa.JobState.DONE, drmaa.JobState.FAILED]
for job in jobs.values()
]):
for location, (job_id, status) in jobs.items():
jobs[location] = (job_id, session.jobStatus(job_id))
logger.info(
f'{location:<35}: {decode_status(drmaa, jobs[location][1]):>15}'
)
logger.info('')
time.sleep(project_globals.MAKE_ARTIFACT_SLEEP)
logger.info('Checking status again')
logger.info('---------------------')
logger.info('')
for location in locations:
sanitized_location = f'{sanitize_location(location)}'
path = output_dir / sanitized_location
existing_data_path = output_dir / f'{sanitized_location}.hdf'
existing_data = []
if existing_data_path.exists():
existing_data.append(
pd.read_hdf(output_dir / f'{sanitized_location}.hdf'))
existing_data[0].to_hdf(
output_dir / f'{sanitized_location}-old.hdf', 'data')
threshold_data = pd.concat(
existing_data + [pd.read_hdf(file) for file in path.iterdir()],
axis=1)
threshold_data = threshold_data[[f'draw_{d}' for d in range(1000)
]] # sort the columns
threshold_data = utilities.sort_hierarchical_data(
threshold_data).convert_objects()
threshold_data.to_hdf(output_dir / f'{sanitized_location}.hdf', 'data')
shutil.rmtree(path)
logger.info('**Done**')
def pcalculate_ckd_rr(location):
drmaa = get_drmaa()
num_draws = 1000
data_file = ckd_rr.RR_DATA_FOLDER / f'{location}.hdf'
if data_file.exists():
# I don't want to write over b/c of issue where writing to same hdf key makes the files huge
logger.info(
f'Existing data found for {location}. Removing and re-calculating.'
)
data_file.unlink()
output_path = ckd_rr.RR_DATA_FOLDER / location
output_path.mkdir(parents=True, exist_ok=True)
logger.info('Submitting jobs.')
with drmaa.Session() as s:
jt = s.createJobTemplate()
jt.remoteCommand = sys.executable
jt.nativeSpecification = '-l m_mem_free=1.5G,fthread=1,h_rt=02:00:00 -q all.q -P proj_csu'
jt.args = [ckd_rr.__file__, location, 'draw']
jt.jobName = f'{location}_ckd_rr_draw'
draw_jids = s.runBulkJobs(jt, 1, num_draws, 1)
draw_jid_base = draw_jids[0].split('.')[0]
jt.nativeSpecification = f'-l m_mem_free=3G,fthread=1,h_rt=00:45:00 ' \
f'-q all.q -P proj_csu -hold_jid {draw_jid_base}'
jt.args = [ckd_rr.__file__, location, 'aggregate']
jt.jobName = f'{location}_ckd_rr_aggregate'
agg_jid = s.runJob(jt)
logger.info(
f'Draws for {location} have been submitted with jid {draw_jid_base}. '
f'They will be aggregated by jid {agg_jid}.')
def build_sample_histories(locations: str, scenarios: str, verbose: int, queue: str):
output_dir = paths.SAMPLE_HISTORY_ROOT
locations = project_globals.LOCATIONS if locations == 'all' else locations.split(',')
scenarios = project_globals.SCENARIOS if scenarios == 'all' else scenarios.split(',')
from vivarium_cluster_tools.psimulate.utilities import get_drmaa
drmaa = get_drmaa()
jobs = {}
with drmaa.Session() as session:
for location in locations:
make_sample_history_single_location(drmaa, queue, jobs, location, scenarios, output_dir, session)
if verbose:
logger.info('Entering monitoring loop.')
logger.info('-------------------------')
logger.info('')
while any([job[1] not in [drmaa.JobState.DONE, drmaa.JobState.FAILED] for job in jobs.values()]):
for location, (job_id, status) in jobs.items():
jobs[location] = (job_id, session.jobStatus(job_id))
logger.info(f'{location:<35}: {decode_status(drmaa, jobs[location][1]):>15}')
logger.info('')
time.sleep(project_globals.MAKE_ARTIFACT_SLEEP)
logger.info('Checking status again')
logger.info('---------------------')
logger.info('')
logger.info('**Done**')
def build_all_artifacts(output_dir, verbose):
from vivarium_cluster_tools.psimulate.utilities import get_drmaa
drmaa = get_drmaa()
jobs = {}
with drmaa.Session() as session:
for location in project_globals.LOCATIONS:
path = output_dir / f'{sanitize_location(location)}.hdf'
job_template = session.createJobTemplate()
job_template.remoteCommand = shutil.which("python")
job_template.args = [__file__, str(path), f'"{location}"']
job_template.nativeSpecification = (
f'-V -b y -P {project_globals.CLUSTER_PROJECT} -q all.q '
f'-l fmem=3G -l fthread=1 -l h_rt=3:00:00 -l archive=TRUE '
f'-N {sanitize_location(location)}_artifact')
jobs[location] = (session.runJob(job_template),
drmaa.JobState.UNDETERMINED)
logger.info(
f'Submitted job {jobs[location][0]} to build artifact for {location}.'
)
session.deleteJobTemplate(job_template)
decodestatus = {
drmaa.JobState.UNDETERMINED: 'undetermined',
drmaa.JobState.QUEUED_ACTIVE: 'queued_active',
drmaa.JobState.SYSTEM_ON_HOLD: 'system_hold',
drmaa.JobState.USER_ON_HOLD: 'user_hold',
drmaa.JobState.USER_SYSTEM_ON_HOLD: 'user_system_hold',
drmaa.JobState.RUNNING: 'running',
drmaa.JobState.SYSTEM_SUSPENDED: 'system_suspended',
drmaa.JobState.USER_SUSPENDED: 'user_suspended',
drmaa.JobState.DONE: 'finished',
drmaa.JobState.FAILED: 'failed'
}
if verbose:
logger.info('Entering monitoring loop.')
logger.info('-------------------------')
logger.info('')
while any([
job[1] not in [drmaa.JobState.DONE, drmaa.JobState.FAILED]
for job in jobs.values()
]):
for location, (job_id, status) in jobs.items():
jobs[location] = (job_id, session.jobStatus(job_id))
logger.info(
f'{location:<35}: {decodestatus[jobs[location][1]]:>15}'
)
logger.info('')
time.sleep(10)
logger.info('Checking status again')
logger.info('---------------------')
logger.info('')
logger.info('**Done**')
def build_all_artifacts(output_dir: Path, verbose: int):
"""Builds artifacts for all locations in parallel.
Parameters
----------
output_dir
The directory where the artifacts will be built.
verbose
How noisy the logger should be.
Note
----
This function should not be called directly. It is intended to be
called by the :func:`build_artifacts` function located in the same
module.
"""
from vivarium_cluster_tools.psimulate.utilities import get_drmaa
drmaa = get_drmaa()
jobs = {}
with drmaa.Session() as session:
for location in project_globals.LOCATIONS:
path = output_dir / f'{sanitize_location(location)}.hdf'
job_template = session.createJobTemplate()
job_template.remoteCommand = shutil.which("python")
job_template.args = [__file__, str(path), f'"{location}"']
job_template.nativeSpecification = (f'-V ' # Export all environment variables
f'-b y ' # Command is a binary (python)
f'-P {project_globals.CLUSTER_PROJECT} '
f'-q {project_globals.CLUSTER_QUEUE} '
f'-l fmem={project_globals.MAKE_ARTIFACT_MEM} '
f'-l fthread={project_globals.MAKE_ARTIFACT_CPU} '
f'-l h_rt={project_globals.MAKE_ARTIFACT_RUNTIME} '
f'-l archive=TRUE ' # Need J-drive access for data
f'-N {sanitize_location(location)}_artifact') # Name of the job
jobs[location] = (session.runJob(job_template), drmaa.JobState.UNDETERMINED)
logger.info(f'Submitted job {jobs[location][0]} to build artifact for {location}.')
session.deleteJobTemplate(job_template)
if verbose:
logger.info('Entering monitoring loop.')
logger.info('-------------------------')
logger.info('')
while any([job[1] not in [drmaa.JobState.DONE, drmaa.JobState.FAILED] for job in jobs.values()]):
for location, (job_id, status) in jobs.items():
jobs[location] = (job_id, session.jobStatus(job_id))
logger.info(f'{location:<35}: {decode_status(drmaa, jobs[location][1]):>15}')
logger.info('')
time.sleep(project_globals.MAKE_ARTIFACT_SLEEP)
logger.info('Checking status again')
logger.info('---------------------')
logger.info('')
logger.info('**Done**')
def pcalculate_proportion_hypertensive(location):
"""Calculate 1000 draws of the proportion of the population that has a SBP
above the hypertensive threshold (SBP of 140) in parallel and aggregate
to a single hdf file saved in the central vivarium artifact store as
``proportion_hypertensive/location.hdf``. This should be run once for each
location to generate the data that the artifact builder will look for.
LOCATION should be specified as all lower-case, with underscores replacing
spaces (i.e., the same way the model artifacts are named),
e.g., russian_federation
"""
drmaa = get_drmaa()
num_draws = 1000
data_file = proportion_hypertensive.HYPERTENSION_DATA_FOLDER / f'{location}.hdf'
if data_file.exists():
# I don't want to write over b/c of issue where writing to same hdf key makes the files huge
logger.info(
f'Existing data found for {location}. Removing and re-calculating.'
)
data_file.unlink()
output_path = proportion_hypertensive.HYPERTENSION_DATA_FOLDER / location
output_path.mkdir(parents=True)
proportion_hypertensive.prep_input_data(output_path, location)
logger.info('Submitting jobs.')
with drmaa.Session() as s:
jt = s.createJobTemplate()
jt.remoteCommand = sys.executable
jt.nativeSpecification = '-l m_mem_free=1G,fthread=1,h_rt=00:05:00 -q all.q -P proj_cost_effect'
jt.args = [proportion_hypertensive.__file__, location, 'draw']
jt.jobName = f'{location}_prop_hypertensive_draw'
draw_jids = s.runBulkJobs(jt, 1, num_draws, 1)
draw_jid_base = draw_jids[0].split('.')[0]
jt.nativeSpecification = f'-l m_mem_free=3G,fthread=1,h_rt=00:15:00 ' \
f'-q all.q -P proj_cost_effect -hold_jid {draw_jid_base}'
jt.args = [proportion_hypertensive.__file__, location, 'aggregate']
jt.jobName = f'{location}_prop_hypertensive_aggregate'
agg_jid = s.runJob(jt)
logger.info(
f'Draws for {location} have been submitted with jid {draw_jid_base}. '
f'They will be aggregated by jid {agg_jid}.')
def kill_jobs():
if "drmaa" not in dir():
# FIXME: The global drmaa should be available here.
# This is maybe a holdover from old code?
# Maybe something to do with atexit?
drmaa = utilities.get_drmaa()
try:
s.control(array_job_id, drmaa.JobControlAction.TERMINATE)
# FIXME: Hack around issue where drmaa.errors sometimes doesn't
# exist.
except Exception as e:
if 'There are no jobs registered' in str(e):
# This is the case where all our workers have already shut down
# on their own, which isn't actually an error.
pass
elif 'Discontinued delete' in str(e):
# sge has already cleaned up some of the jobs.
pass
else:
raise
def build_joint_pafs(location: str, draws: str, verbose: int, queue: str):
# Local import to avoid data dependencies
from vivarium_inputs import globals as vi_globals, utilities
output_dir = paths.JOINT_PAF_DIR
locations = project_globals.LOCATIONS if location == 'all' else [location]
from vivarium_cluster_tools.psimulate.utilities import get_drmaa
drmaa = get_drmaa()
jobs = {}
draw_list = {'all': range(1000), 'none': []}.get(draws, draws.split(','))
with drmaa.Session() as session:
for location in locations:
build_joint_pafs_single_location(drmaa, queue, jobs, location,
draw_list, output_dir, session)
if verbose:
logger.info('Entering monitoring loop.')
logger.info('-------------------------')
logger.info('')
while any([
job[1] not in [drmaa.JobState.DONE, drmaa.JobState.FAILED]
for job in jobs.values()
]):
for location, (job_id, status) in jobs.items():
jobs[location] = (job_id, session.jobStatus(job_id))
logger.info(
f'{location:<35}: {decode_status(drmaa, jobs[location][1]):>15}'
)
logger.info('')
time.sleep(project_globals.MAKE_ARTIFACT_SLEEP)
logger.info('Checking status again')
logger.info('---------------------')
logger.info('')
for location in locations:
logger.info(f'Merging data for location - {location}')
sanitized_location = sanitize_location(location)
location_dir = paths.JOINT_PAF_DIR / sanitized_location
existing_data_path = output_dir / f'{sanitized_location}.hdf'
joint_pafs = []
if existing_data_path.exists():
joint_pafs.append(
pd.read_hdf(output_dir / f'{sanitized_location}.hdf'))
joint_pafs[0].to_hdf(output_dir / f'{sanitized_location}-old.hdf',
'data')
for file_path in location_dir.iterdir():
draw = file_path.parts[-1].split('.')[0]
draw_joint_paf = pd.read_hdf(file_path).rename(columns={0: draw})
draw_joint_paf['affected_measure'] = 'incidence_rate'
draw_joint_paf = draw_joint_paf.set_index(
list(draw_joint_paf.columns.drop(draw)))
joint_pafs.append(draw_joint_paf)
joint_paf_data = pd.concat(joint_pafs, axis=1)
joint_paf_data = joint_paf_data[
vi_globals.DRAW_COLUMNS] # sort the columns
joint_paf_data = utilities.sort_hierarchical_data(
joint_paf_data).convert_objects()
joint_paf_data.to_hdf(output_dir / f'{sanitized_location}.hdf', 'data')
shutil.rmtree(location_dir)
logger.info('**Done**')
from pathlib import Path
from time import sleep, time
import numpy as np
import pandas as pd
from loguru import logger
from vivarium.framework.configuration import build_model_specification
from vivarium.framework.utilities import collapse_nested_dict
from vivarium.framework.artifact import parse_artifact_path_config
from vivarium_cluster_tools.psimulate.branches import Keyspace
from vivarium_cluster_tools.psimulate import globals as vct_globals, utilities
from vivarium_cluster_tools.psimulate.registry import RegistryManager
drmaa = utilities.get_drmaa()
class RunContext:
def __init__(self, model_specification_file: str,
branch_configuration_file: str, output_directory: Path,
logging_directories: Dict[str, Path], num_input_draws: int,
num_random_seeds: int, restart: bool, expand: Dict[str, int],
no_batch: bool):
self.number_already_completed = 0
self.output_directory = output_directory
self.no_batch = no_batch
self.sge_log_directory = logging_directories['sge']
self.worker_log_directory = logging_directories['worker']
if restart:
from pathlib import Path
from jinja2 import Template
import click
from vivarium_gbd_access.gbd import ARTIFACT_FOLDER
from vivarium_cluster_tools.psimulate.utilities import get_drmaa
JOB_MEMORY_NEEDED = 50
JOB_TIME_NEEDED = '24:00:00'
drmaa = get_drmaa() # safe if not on cluster
def create_and_run_job(model_spec_path: Path, output_root: Path):
with drmaa.Session() as s:
jt = s.createJobTemplate()
jt.remoteCommand = "build_artifact"
jt.nativeSpecification = '-V -l m_mem_free={}G,fthread=1,h_rt={} -q all.q -P proj_cost_effect'.format(
JOB_MEMORY_NEEDED, JOB_TIME_NEEDED)
jt.args = [model_spec_path, '-o', output_root]
jt.jobName = f'build_artifact_{model_spec_path.name}'
result = s.runJob(jt)
print(f"Submitted job for {model_spec_path.name}. Job id: {result}")
@click.command()
@click.option(
'--model_spec',
'-m',
multiple=True,
