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fix: work around segfault with >100 jobs in google life sciences backend #1451

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merged 7 commits into from Mar 4, 2022
Merged

fix: work around segfault with >100 jobs in google life sciences backend #1451

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d802477
refactor _retry_request to avoid segfault
cademirch Mar 2, 2022
bf5fdfe
fmt
johanneskoester Mar 3, 2022
4ae4df8
Merge branch 'main' into gls-segfault
johanneskoester Mar 3, 2022
9728ada
reworking _get_services to use auth_http
cademirch Mar 3, 2022
344f8d4
Merge branch 'gls-segfault' of https://github.com/cademirch/snakemake…
cademirch Mar 3, 2022
9a7815b
fix mistake in retry_request
cademirch Mar 3, 2022
d8fa333
remove imports outside of func
cademirch Mar 3, 2022
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27 changes: 22 additions & 5 deletions snakemake/executors/google_lifesciences.py
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Expand Up @@ -22,6 +22,8 @@
from snakemake.executors import ClusterExecutor, sleep
from snakemake.common import get_container_image, get_file_hash
from snakemake.resources import DefaultResources
import httplib2
import google_auth_httplib2
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# https://github.com/googleapis/google-api-python-client/issues/299#issuecomment-343255309
logging.getLogger("googleapiclient.discovery_cache").setLevel(logging.ERROR)
Expand Down Expand Up @@ -148,6 +150,7 @@ def _get_services(self):
# Credentials must be exported to environment
try:
creds = GoogleCredentials.get_application_default()
self.creds = creds
except ApplicationDefaultCredentialsError as ex:
log_verbose_traceback(ex)
raise ex
Expand Down Expand Up @@ -885,7 +888,7 @@ def _job_was_successful(self, status):

return success

def _retry_request(self, request, timeout=2, attempts=3):
def _retry_request(self, request, http=None, timeout=2, attempts=3):
"""The Google Python API client frequently has BrokenPipe errors. This
function takes a request, and executes it up to number of retry,
each time with a 2* increase in timeout.
Expand All @@ -897,24 +900,38 @@ def _retry_request(self, request, timeout=2, attempts=3):
attempts: remaining attempts, throw error when hit 0
"""
import googleapiclient
import google.auth

credentials, project_id = google.auth.default(
scopes=["https://www.googleapis.com/auth/cloud-platform"]
)
if http is None:
http = google_auth_httplib2.AuthorizedHttp(
credentials=credentials, http=httplib2.Http()
)
try:
return request.execute()
return request.execute(http=http)
except BrokenPipeError as ex:
if attempts > 0:
time.sleep(timeout)
return self._retry_request(request, timeout * 2, attempts - 1)
return self._retry_request(
request, http=http, timeout=timeout * 2, attempts=attempts - 1
)
raise ex
except googleapiclient.errors.HttpError as ex:
if attempts > 0:
time.sleep(timeout)
return self._retry_request(request, timeout * 2, attempts - 1)
return self._retry_request(
request, http=http, timeout=timeout * 2, attempts=attempts - 1
)
log_verbose_traceback(ex)
raise ex
except Exception as ex:
if attempts > 0:
time.sleep(timeout)
return self._retry_request(request, timeout * 2, attempts - 1)
return self._retry_request(
request, http=http, timeout=timeout * 2, attempts=attempts - 1
)
log_verbose_traceback(ex)
raise ex

Expand Down