def run_como(
como_dir=None,
root_dir="FILEPATH",
gbd_round_id=5,
location_set_id=35,
year_id=list(range(1990, 2018)),
measure_id=[3, 5, 6],
n_draws=1000,
n_simulants=20000,
components=["cause", "sequela", "injuries", "impairment"],
change_years=[(1990, 2007), (2007, 2017), (1990, 2017)],
agg_loc_sets=[35, 83],
project="proj_como"):
special_sets = set(agg_loc_sets) - set([location_set_id])
all_sets = set(agg_loc_sets) | set([location_set_id])
if como_dir is not None:
cv = ComoVersion(como_dir)
cv.load_cache()
else:
cv = ComoVersion.new(
root_dir, gbd_round_id, location_set_id, year_id, measure_id,
n_draws, components, change_years, special_sets)
cwf = ComoWorkFlow(cv)
cwf.add_tasks_to_dag(n_simulants=n_simulants, agg_loc_sets=all_sets)
if cwf.run_workflow(project=project):
all_locs = []
for location_set_id in all_sets:
loc_tree = loctree(location_set_id=location_set_id,
gbd_round_id=cv.gbd_round_id)
all_locs.extend(loc_tree.node_ids)
all_locs = list(set(all_locs))
run_upload(cv, all_locs)
else:
raise RuntimeError("como unsuccessful")
def run_pipeline_como(
root_dir,
gbd_round_id=4,
location_id=[],
year_id=[],
sex_id=[],
age_group_id=[],
measure_id=[],
n_draws=1000,
n_simulants=20000,
components=["sequela", "cause", "impairment", "injuries"]):
cv = ComoVersion.new(root_dir, gbd_round_id, location_id, year_id, sex_id,
age_group_id, measure_id, n_draws, components)
try:
cjm = CentralJobMonitor(cv.como_dir, persistent=False)
time.sleep(5)
except Exception as e:
raise e
else:
executor_params = {"request_timeout": 10000}
jobq = JobQueue(cv.como_dir,
scheduler=RetryScheduler,
executor=SGEExecutor,
executor_params=executor_params)
# run nonfatal pipeline by location/year/sex
parallelism = ["location_id", "sex_id"]
for slices in cv.dimensions.index_slices(parallelism):
jobname = "como_e_sim_{location_id}_{sex_id}".format(
location_id=slices[0], sex_id=slices[1])
job = jobq.create_job(
jobname=jobname,
runfile=true_path(executable="compute_nonfatal"),
parameters=[
"--como_dir", cv.como_dir, "--location_id",
str(slices[0]), "--sex_id",
str(slices[1]), "--n_processes", "23", "--n_simulants",
str(n_simulants)
])
jobq.queue_job(job,
slots=50,
memory=400,
project="proj_como",
process_timeout=(60 * 180))
jobq.block_till_done(stop_scheduler_when_done=False)
# run aggregation by year/sex/measure
parallelism = ["year_id", "sex_id", "measure_id"]
for slices in cv.dimensions.index_slices(parallelism):
for component in cv.components:
if component != "sequela":
loc_sets = [35, 40]
else:
loc_sets = [35]
for location_set_id in loc_sets:
jobname = ("como_e_agg_{component}_{year_id}_{sex_id}"
"_{measure_id}_{location_set_id}").format(
component=component,
year_id=slices[0],
sex_id=slices[1],
measure_id=slices[2],
location_set_id=location_set_id)
job = jobq.create_job(
jobname=jobname,
runfile=true_path(executable="aggregate_nonfatal"),
parameters=[
"--como_dir", cv.como_dir, "--component",
component, "--year_id",
str(slices[0]), "--sex_id",
str(slices[1]), "--measure_id",
str(slices[2]), "--location_set_id",
str(location_set_id)
])
jobq.queue_job(job,
slots=25,
memory=200,
project="proj_como",
process_timeout=(60 * 600))
jobq.block_till_done(stop_scheduler_when_done=False)
# run summaries by component/location
lt = dbtrees.loctree(None, 35)
sdi_lts = dbtrees.loctree(None, 40, return_many=True)
locs = [l.id for l in lt.nodes]
sdi_locs = [l.root.id for l in sdi_lts]
for component in cv.components:
if component != "sequela":
summ_locs = locs + sdi_locs
else:
summ_locs = locs[:]
for location_id in summ_locs:
jobname = "como_e_summ_{component}_{location_id}".format(
component=component, location_id=location_id)
job = jobq.create_job(
jobname=jobname,
runfile=true_path(executable="summarize_nonfatal"),
parameters=[
"--como_dir", cv.como_dir, "--component", component,
"--location_id",
str(location_id)
])
jobq.queue_job(job,
slots=48,
memory=96,
project="proj_como",
process_timeout=(60 * 240))
jobq.block_till_done(stop_scheduler_when_done=False)
for component in cv.components:
jobname = "como_e_upload_{component}".format(component=component)
job = jobq.create_job(
jobname=jobname,
runfile=true_path(executable="upload_nonfatal"),
parameters=[
"--como_dir", cv.como_dir, "--component", component,
"--location_id",
" ".join([str(l) for l in locs + sdi_locs])
])
jobq.queue_job(job,
slots=20,
memory=40,
project="proj_como",
process_timeout=(60 * 720))
jobq.block_till_done()
finally:
cjm.generate_report()
cjm.stop_responder()
cjm.stop_publisher()