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Attempt to parallelize FileByFileTask #4

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Attempt to parallelize FileByFileTask #4

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36 changes: 14 additions & 22 deletions src/romitask/task.py
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Original file line number Diff line number Diff line change
Expand Up @@ -458,7 +458,7 @@ class FileByFileTask(RomiTask):
and applies some function to it and saves it back to the target.
"""
query = luigi.DictParameter(default={})
# n_jobs = luigi.IntParameter(default=-1) # control number of parallel jobs
n_jobs = luigi.IntParameter(default=-1) # control number of parallel jobs
type = None

reader = None
Expand All @@ -485,31 +485,23 @@ def run(self):
"""Run the task on every file in the fileset."""
input_fileset = self.input().get()
output_fileset = self.output().get()
for fi in tqdm(input_fileset.get_files(query=self.query), unit="file"):
outfi = self.f(fi, output_fileset)

def apply_f(f, fi, output_fileset):
outfi = f(fi, output_fileset)
return fi, outfi

from joblib import Parallel
from joblib import delayed
files = Parallel(n_jobs=self.n_jobs)(
delayed(apply_f)(self.f, fi, output_fileset) for fi in
tqdm(input_fileset.get_files(query=self.query), unit="file"))

for (infi, outfi) in files:
if outfi is not None:
m = fi.get_metadata()
m = infi.get_metadata()
outm = outfi.get_metadata()
outfi.set_metadata({**m, **outm})

# ATTEMPT to parallelize:
# def apply_f(f, fi, output_fileset):
# outfi = f(fi, output_fileset)
# return fi, outfi
#
# from joblib import Parallel
# from joblib import delayed
# files = Parallel(n_jobs=self.n_jobs)(
# delayed(apply_f)(self.f, fi, output_fileset) for fi in
# tqdm(input_fileset.get_files(query=self.query), unit="file"))
#
# for (infi, outfi) in files:
# if outfi is not None:
# m = infi.get_metadata()
# outm = outfi.get_metadata()
# outfi.set_metadata({**m, **outm})



@RomiTask.event_handler(luigi.Event.FAILURE)
def mourn_failure(task, exception):
Expand Down