def execute(self):
# compile submission arguments
kwargs = self.build_args[1]
source_me_id = kwargs.pop("source_me_id")
target_me_id = kwargs.pop("target_me_id")
# make server directory
directory = "{root}/{proc}".format(root=root, proc=self.identity)
if not os.path.exists(directory):
os.makedirs(directory)
else:
shutil.rmtree(directory)
os.makedirs(directory)
west_params = [
"--source_me_id", source_me_id, "--target_me_id", target_me_id
]
q = qmaster.MonitoredQ(directory, request_timeout=30000) # monitor
try:
q.qsub(runfile="{root}/infertility/westrom.py".format(root=root),
jobname=self.identity,
parameters=west_params,
slots=10,
memory=20,
project="proj_custom_models")
q.qblock(poll_interval=60) # monitor them
fail = q.manager.query(
"select count(*) as num from job where current_status != 5;"
)[1]["num"].item()
if fail > 0:
raise Exception("Not all jobs finished")
finally:
q.stop_monitor() # stop monitor
def launch_squeeze(log_dir='FILEPATH', squeeze=True, save=True):
try:
jm = CentralJobMonitor(log_dir, persistent=False)
time.sleep(5)
except MonitorAlreadyRunning:
pass
else:
err = glob('/FILEPATH')
out = glob('/FILEPATH')
ps = glob('/FILEPATH')
for log in err + out + ps:
os.remove(log)
conda_dir = '/FILEPATH'
execute = sge_exec.SGEExecutor(jm.out_dir, 3, 30000, conda_dir, 'epic')
q = qmaster.MonitoredQ(execute)
if squeeze:
squeezer(q, log_dir)
dirs = glob("/FILEPATH")
save_func = "save_custom_results"
if save:
saver(q, dirs, save_func, log_dir)
finally:
jm.generate_report()
jm.stop_responder()
def get_qmaster(self):
execute = sge_exec.SGEExecutor(
log_dir, 3, 30000, conda_bin_dir, conda_env)
return qmaster.MonitoredQ(execute)
def execute(self):
# compile submission arguments
kwargs = self.build_args[1]
male_prop_id = kwargs.pop("male_prop_id")
female_prop_id = kwargs.pop("female_prop_id")
exp_id = kwargs.pop("exp_id")
env_id = kwargs.pop("env_id")
male_env_id = kwargs.pop("male_env_id")
female_env_id = kwargs.pop("female_env_id")
# make server directory
directory = "{root}/{proc}".format(root=root, proc=self.identity)
if not os.path.exists(directory):
os.makedirs(directory)
else:
shutil.rmtree(directory)
os.makedirs(directory)
# make output directories
for _id in [male_env_id, female_env_id]:
sub_dir = os.path.join(directory, str(_id))
if not os.path.exists(sub_dir):
os.makedirs(sub_dir)
else:
shutil.rmtree(sub_dir)
os.makedirs(sub_dir)
env_params = [
"--male_prop_id", male_prop_id, "--female_prop_id", female_prop_id,
"--exp_id", exp_id, "--env_id", env_id, "--male_env_id",
male_env_id, "--female_env_id", female_env_id, "--out_dir",
directory, "--year_id"
]
q = qmaster.MonitoredQ(directory, request_timeout=30000) # monitor
try:
# parallelize by location
for i in [i for i in range(1990, 2016, 5)]:
q.qsub(
runfile="{root}/infertility/calc_env.py".format(root=root),
jobname="{proc}_{loc}".format(proc=self.identity, loc=i),
parameters=env_params + [i],
slots=7,
memory=14,
project="proj_custom_models")
q.qblock(poll_interval=60) # monitor them
fail = q.manager.query(
"select count(*) as num from job where current_status != 5;"
)[1]["num"].item()
if fail > 0:
raise Exception("Not all jobs finished")
# save the results
for save_id in [male_env_id, female_env_id]:
save_params = [
save_id, env_description,
os.path.join(directory, str(save_id)), "--best",
"--file_pattern", "{year_id}.h5", "--h5_tablename", "data"
]
q.qsub(runfile=("/home/j/WORK/10_gbd/00_library/adding_machine"
"/bin/save_custom_results"),
jobname="save_" + str(save_id),
parameters=save_params,
slots=20,
memory=40,
project="proj_custom_models")
q.qblock(poll_interval=60) # monitor them
fail = q.manager.query(
"select count(*) as num from job where current_status != 5;"
)[1]["num"].item()
if fail > 0:
raise Exception("Not all jobs finished")
finally:
q.stop_monitor() # stop monitor
def execute(self):
kwargs = self.build_args[1]
excess_id = kwargs.pop("excess")
redist_map = kwargs.pop("redist")
# make server directory
directory = "{root}/{proc}".format(root=root, proc=self.identity)
if not os.path.exists(directory):
os.makedirs(directory)
else:
shutil.rmtree(directory)
os.makedirs(directory)
# make output directories
for me_id in redist_map.values():
sub_dir = os.path.join(directory, str(me_id))
if not os.path.exists(sub_dir):
os.makedirs(sub_dir)
else:
shutil.rmtree(sub_dir)
os.makedirs(sub_dir)
exs_params = [
"--excess_id", excess_id, "--redist_map",
json.dumps(redist_map), "--out_dir", directory, "--year_id"
]
q = qmaster.MonitoredQ(directory, request_timeout=120000) # monitor
try:
# attribution jobs by location_id
for i in [i for i in range(1990, 2016, 5)]:
q.qsub(
runfile="{root}/infertility/excess.py".format(root=root),
jobname="{proc}_{loc}".format(proc=self.identity, loc=i),
parameters=exs_params + [i],
slots=5,
memory=10,
project="proj_custom_models")
time.sleep(1.5)
q.qblock(poll_interval=60) # monitor them
fail = q.manager.query(
"select count(*) as num from job where current_status != 5;"
)[1]["num"].item()
if fail > 0:
raise Exception("Not all attr jobs finished")
# save the results
for save_id in redist_map.values():
save_params = [
save_id, excess_description,
os.path.join(directory,
str(save_id)), "--best", "--sexes", "2",
"--file_pattern", "{year_id}.h5", "--h5_tablename", "data"
]
q.qsub(runfile=("/home/j/WORK/10_gbd/00_library/adding_machine"
"/bin/save_custom_results"),
jobname="save_" + str(save_id),
parameters=save_params,
slots=20,
memory=40,
project="proj_custom_models")
q.qblock(poll_interval=60) # monitor them
fail = q.manager.query(
"select count(*) as num from job where current_status != 5;"
)[1]["num"].item()
if fail > 0:
raise Exception("Not all save jobs finished")
finally:
q.stop_monitor() # stop monitor
def execute(self):
# compile submission arguments
me_map = self.build_args[0][0]
# make server directory
directory = "{root}/{proc}".format(root=root, proc=self.identity)
if not os.path.exists(directory):
os.makedirs(directory)
else:
shutil.rmtree(directory)
os.makedirs(directory)
# make output directories
save_ids = []
for mapper in me_map.values():
outputs = mapper.get("trgs", {})
for me_id in outputs.values():
os.makedirs(os.path.join(directory, str(me_id)))
save_ids.append(me_id)
attr_params = [
"--me_map",
json.dumps(me_map), "--out_dir", directory, "--year_id"
]
q = qmaster.MonitoredQ(directory, request_timeout=30000) # monitor
try:
# attribution jobs by year_id
for i in [i for i in range(1990, 2016, 5)]:
q.qsub(runfile="{root}/infertility/male_attr.py".format(
root=root),
jobname="{proc}_{year}".format(proc=self.identity,
year=i),
parameters=attr_params + [i],
slots=3,
memory=6,
project="proj_custom_models")
q.qblock(poll_interval=60) # monitor them
fail = q.manager.query(
"select count(*) as num from job where current_status != 5;"
)[1]["num"].item()
if fail > 0:
raise Exception("Not all attr jobs finished")
# save the results
for save_id in save_ids:
save_params = [
save_id, male_attr_description,
os.path.join(directory,
str(save_id)), "--best", "--sexes", "1",
"--file_pattern", "{year_id}.h5", "--h5_tablename", "data"
]
q.qsub(runfile=("/home/j/WORK/10_gbd/00_library/adding_machine"
"/bin/save_custom_results"),
jobname="save_" + str(save_id),
parameters=save_params,
slots=20,
memory=40,
project="proj_custom_models")
q.qblock(poll_interval=60) # monitor them
fail = q.manager.query(
"select count(*) as num from job where current_status != 5;"
)[1]["num"].item()
if fail > 0:
raise Exception("Not all save jobs finished")
finally:
q.stop_monitor() # stop monitor
def execute(self):
# compile submission arguments
kwargs = self.build_args[1]
pid_env_id = kwargs.pop("pid_env_id")
chlam_prop_id = kwargs.pop("chlam_prop_id")
gono_prop_id = kwargs.pop("gono_prop_id")
other_prop_id = kwargs.pop("other_prop_id")
chlam_id = kwargs.pop("chlam_id")
gono_id = kwargs.pop("gono_id")
other_id = kwargs.pop("other_id")
# make server directory
directory = "{root}/{proc}".format(root=root, proc=self.identity)
if not os.path.exists(directory):
os.makedirs(directory)
else:
shutil.rmtree(directory)
os.makedirs(directory)
split_params = [
pid_env_id, "--target_meids", chlam_id, gono_id, other_id,
"--prop_meids", chlam_prop_id, gono_prop_id, other_prop_id,
"--split_meas_ids", 5, 6, "--prop_meas_id", 18, "--output_dir",
directory
]
q = qmaster.MonitoredQ(directory, request_timeout=30000) # monitor
try:
q.qsub(runfile=("/home/j/WORK/10_gbd/00_library/transmogrifier"
"/transmogrifier/epi.py"),
jobname=self.identity,
parameters=split_params,
slots=40,
memory=60,
project="proj_custom_models")
q.qblock(poll_interval=60) # monitor them
fail = q.manager.query(
"select count(*) as num from job where current_status != 5;"
)[1]["num"].item()
if fail > 0:
raise Exception("Not all jobs finished")
# save the results
for save_id in [chlam_id, gono_id, other_id]:
save_params = [
save_id, pid_split_description,
os.path.join(directory, str(save_id)), "--best", "--sexes",
"2", "--file_pattern", "{location_id}.h5",
"--h5_tablename", "draws"
]
q.qsub(runfile=("/home/j/WORK/10_gbd/00_library/adding_machine"
"/bin/save_custom_results"),
jobname="save_" + str(save_id),
parameters=save_params,
slots=20,
memory=40,
project="proj_custom_models")
q.qblock(poll_interval=60) # monitor them
fail = q.manager.query(
"select count(*) as num from job where current_status != 5;"
)[1]["num"].item()
if fail > 0:
raise Exception("Not all jobs finished")
finally:
q.stop_monitor() # stop monitor
