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ENH: Always fsync pickle files #3083

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d5d22be
ENH: Always fsync pickle files
effigies Oct 26, 2019
a07c138
ENH: Add sync option to savepkl, sync when saving result file
effigies Oct 29, 2019
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8 changes: 4 additions & 4 deletions nipype/pipeline/engine/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -236,17 +236,17 @@ def save_resultfile(result, cwd, name, rebase=None):

if result.outputs is None:
logger.warning('Storing result file without outputs')
savepkl(resultsfile, result)
savepkl(resultsfile, result, sync=True)
return
try:
output_names = result.outputs.copyable_trait_names()
except AttributeError:
logger.debug('Storing non-traited results, skipping rebase of paths')
savepkl(resultsfile, result)
savepkl(resultsfile, result, sync=True)
return

if not rebase:
savepkl(resultsfile, result)
savepkl(resultsfile, result, sync=True)
return

backup_traits = {}
Expand All @@ -262,7 +262,7 @@ def save_resultfile(result, cwd, name, rebase=None):
backup_traits[key] = old
val = rebase_path_traits(result.outputs.trait(key), old, cwd)
setattr(result.outputs, key, val)
savepkl(resultsfile, result)
savepkl(resultsfile, result, sync=True)
finally:
# Restore resolved paths from the outputs dict no matter what
for key, val in list(backup_traits.items()):
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26 changes: 14 additions & 12 deletions nipype/utils/filemanip.py
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Original file line number Diff line number Diff line change
Expand Up @@ -789,18 +789,20 @@ def read_stream(stream, logger=None, encoding=None):
return out.splitlines()


def savepkl(filename, record, versioning=False):
pklopen = gzip.open if filename.endswith('.pklz') else open
with SoftFileLock('%s.lock' % filename):
with pklopen(filename, 'wb') as pkl_file:
if versioning:
from nipype import __version__ as version
metadata = json.dumps({'version': version})

pkl_file.write(metadata.encode('utf-8'))
pkl_file.write('\n'.encode('utf-8'))

pickle.dump(record, pkl_file)
def savepkl(filename, record, versioning=False, sync=False):
with open(filename, 'wb') as fobj:
pkl_file = gzip.GzipFile(fileobj=fobj) if filename.endswith('.pklz') else fobj
if versioning:
from nipype import __version__ as version
metadata = json.dumps({'version': version})

pkl_file.write(metadata.encode('utf-8'))
pkl_file.write('\n'.encode('utf-8'))

pickle.dump(record, pkl_file)
if sync:
fobj.flush()
os.fsync(fobj.fileno())


rst_levels = ['=', '-', '~', '+']
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