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fix: implement lock-free source file caching. This avoids hangs on network file systems like NFS. #1464

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merged 4 commits into from Mar 11, 2022
Merged

fix: implement lock-free source file caching. This avoids hangs on network file systems like NFS. #1464

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67db58f
fix: implement lock-free source file caching. This avoids hangs on ne…
johanneskoester Mar 8, 2022
9291fef
convert prefix path to str
johanneskoester Mar 8, 2022
7fa28dd
fix superfluous tempfile deletion
johanneskoester Mar 11, 2022
5a0b801
close tmp file before moving
johanneskoester Mar 11, 2022
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1 change: 0 additions & 1 deletion setup.py
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Expand Up @@ -74,7 +74,6 @@
"connection_pool >=0.0.3",
"pulp >=2.0",
"smart_open >=3.0",
"filelock",
"stopit",
"tabulate",
"yte >=1.0,<2.0",
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25 changes: 13 additions & 12 deletions snakemake/sourcecache.py
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Expand Up @@ -7,6 +7,7 @@
from pathlib import Path
import re
import os
import shutil
from snakemake import utils
import tempfile
import io
Expand Down Expand Up @@ -308,11 +309,6 @@ def __init__(self, runtime_cache_path=None):
def runtime_cache_path(self):
return self._runtime_cache_path or self.runtime_cache.name

def lock_cache(self, entry):
from filelock import FileLock

return FileLock(entry.with_suffix(".lock"))

def open(self, source_file, mode="r"):
cache_entry = self._cache(source_file)
return self._open(cache_entry, mode)
Expand Down Expand Up @@ -341,17 +337,22 @@ def _cache_entry(self, source_file):

def _cache(self, source_file):
cache_entry = self._cache_entry(source_file)
with self.lock_cache(cache_entry):
if not cache_entry.exists():
self._do_cache(source_file, cache_entry)
if not cache_entry.exists():
self._do_cache(source_file, cache_entry)
return cache_entry

def _do_cache(self, source_file, cache_entry):
# open from origin
with self._open(source_file.get_path_or_uri(), "rb") as source, open(
cache_entry, "wb"
) as cache_source:
cache_source.write(source.read())
with self._open(source_file.get_path_or_uri(), "rb") as source:
tmp_source = tempfile.NamedTemporaryFile(
prefix=str(cache_entry),
delete=False, # no need to delete since we move it below
)
tmp_source.write(source.read())
tmp_source.close()
# Atomic move to right name.
# This way we avoid the need to lock.
shutil.move(tmp_source.name, cache_entry)

mtime = source_file.mtime()
if mtime is not None:
Expand Down