def _init_local(self):
# Set up temp folder in shared directory (trim to max filename length)
base_tmp_dir = self.shared_tmp_dir
random_id = '%016x' % random.getrandbits(64)
folder_name = self.task_id + '-' + random_id
self.tmp_dir = os.path.join(base_tmp_dir, folder_name)
max_filename_length = os.fstatvfs(0).f_namemax
self.tmp_dir = self.tmp_dir[:max_filename_length]
logger.info("Tmp dir: %s", self.tmp_dir)
os.makedirs(self.tmp_dir)
# Dump the code to be run into a pickle file
logging.debug("Dumping pickled class")
self._dump(self.tmp_dir)
if not self.no_tarball:
# Make sure that all the class's dependencies are tarred and available
# This is not necessary if luigi is importable from the cluster node
logging.debug("Tarballing dependencies")
# Grab luigi and the module containing the code to be run
packages = [luigi
] + [__import__(self.__module__, None, None, 'dummy')]
create_packages_archive(packages,
os.path.join(self.tmp_dir, "packages.tar"))
def _init_local(self):
base_tmp_dir = self.shared_tmp_dir
random_id = '%016x' % random.getrandbits(64)
task_name = random_id + self.task_id
# If any parameters are directories, if we don't
# replace the separators on *nix, it'll create a weird nested directory
task_name = task_name.replace("/", "::")
# Max filename length
max_filename_length = os.fstatvfs(0).f_namemax
self.tmp_dir = os.path.join(base_tmp_dir, task_name[:max_filename_length])
LOGGER.info("Tmp dir: %s", self.tmp_dir)
os.makedirs(self.tmp_dir)
# Dump the code to be run into a pickle file
LOGGER.debug("Dumping pickled class")
self._dump(self.tmp_dir)
# Make sure that all the class's dependencies are tarred and available
LOGGER.debug("Tarballing dependencies")
# Grab luigi and the module containing the code to be run
packages = [luigi, __import__(self.__module__, None, None, 'dummy')]
create_packages_archive(packages, os.path.join(self.tmp_dir, "packages.tar"))
# Now, pass onto the class's specified init_local() method.
self.init_local()
def _init_local(self):
# Set up temp folder in shared directory (trim to max filename length)
base_tmp_dir = self.shared_tmp_dir
random_id = '%016x' % random.getrandbits(64)
folder_name = self.task_id + '-' + random_id
self.tmp_dir = os.path.join(base_tmp_dir, folder_name)
max_filename_length = os.fstatvfs(0).f_namemax
self.tmp_dir = self.tmp_dir[:max_filename_length]
logger.info("Tmp dir: %s", self.tmp_dir)
os.makedirs(self.tmp_dir)
# Dump the code to be run into a pickle file
logging.debug("Dumping pickled class")
self._dump(self.tmp_dir)
if not self.no_tarball:
# Make sure that all the class's dependencies are tarred and available
# This is not necessary if luigi is importable from the cluster node
logging.debug("Tarballing dependencies")
# Grab luigi and the module containing the code to be run
packages = [luigi] + [__import__(self.__module__, None, None, 'dummy')]
create_packages_archive(packages, os.path.join(self.tmp_dir, "packages.tar"))
def run(self):
if self.run_locally == 1:
return self.work()
else:
# Set up temp folder in shared directory (trim to max filename length)
base_tmp_dir = self.shared_tmp_dir
random_id = '%016x' % random.getrandbits(64)
folder_name = self.task_id + '-' + random_id
self.tmp_dir = os.path.join(base_tmp_dir, folder_name)
max_filename_length = os.fstatvfs(0).f_namemax
self.tmp_dir = self.tmp_dir[:max_filename_length]
logger.info("Tmp dir: %s", self.tmp_dir)
to_copy = [d for d in os.listdir() if d != ".git"]
if not os.path.exists(self.tmp_dir):
os.makedirs(self.tmp_dir)
for f in to_copy:
if os.path.isfile(f):
copyfile(f, os.path.join(self.tmp_dir, f))
else:
copytree(f, os.path.join(self.tmp_dir, f))
# Dump the code to be run into a pickle file
logging.debug("Dumping pickled class")
self._dump(self.tmp_dir)
if not self.no_tarball:
# Make sure that all the class's dependencies are tarred and available
# This is not necessary if luigi is importable from the cluster node
logging.debug("Tarballing dependencies")
# Grab luigi and the module containing the code to be run
packages = [luigi] + [
__import__(self.__module__, None, None, 'dummy')
]
create_packages_archive(
packages, os.path.join(self.tmp_dir, "packages.tar"))
# make a stamp indicator in the folder
# generate unique descriptive stamp for current commit
get_commit_property = lambda s: subprocess.check_output(
"git --no-pager log -1 --format=%{}".format(
s), shell=True).decode("utf-8").strip()
commit_time = get_commit_property("ci")[:16] \
.replace(" ", "-") \
.replace(":", "-")
commit_author = get_commit_property("ce").split("@")[0]
commit_hash = get_commit_property("h")
stamp = "{}-{}-{}".format(commit_time, commit_author, commit_hash)
# write out stamp to temp folder
with open(os.path.join(self.tmp_dir, "stamp"), "w") as stamp_file:
stamp_file.write(stamp)
# Build a qsub argument that will run sge_runner.py on the directory
# we've specified
runner_path = os.path.join("utility", "sge_runner.py")
if runner_path.endswith("pyc"):
runner_path = runner_path[:-3] + "py"
# enclose tmp_dir in quotes to protect from special escape chars
job_str = 'python {0} "{1}" "{2}"'.format(runner_path,
self.tmp_dir,
os.getcwd())
if self.no_tarball:
job_str += ' "--no-tarball"'
qsub_template = """echo {cmd} | {qsub_command} -V -r y -pe {pe} {n_cpu} -N {job_name} -l m_mem_free={mem_free} -sync y"""
submit_cmd = qsub_template.format(cmd=job_str,
job_name=self.job_name,
pe=self.parallel_env,
n_cpu=self.n_cpu,
mem_free=self.mem_free,
qsub_command=self.qsub_command)
logger.debug('qsub command: \n' + submit_cmd)
# Submit the job and grab job ID
try:
output = subprocess.check_output(submit_cmd,
shell=True,
stderr=subprocess.STDOUT)
logger.debug("qsub job complete with output:\n" +
output.decode('utf-8'))
except subprocess.CalledProcessError as e:
logger.error("qsub submission failed with output:\n" +
e.output.decode('utf-8'))
if os.path.exists(os.path.join(self.tmp_dir, "job.err")):
with open(os.path.join(self.tmp_dir, "job.err"),
"r") as err:
logger.error(err.read())
# wait a beat, to give things a chance to settle
time.sleep(2)
# check whether the file exists
if not self.output().exists():
raise Exception("qsub failed to produce output")
else:
# delete the temporaries, if they're there.
if self.tmp_dir and os.path.exists(self.tmp_dir):
logger.info('Removing temporary directory %s',
self.tmp_dir)
subprocess.call(["rm", "-rf", self.tmp_dir])