Skip to content

Enh/wait #3089

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
oesteban merged 7 commits into from
Nov 8, 2019
Merged

Enh/wait #3089

Changes from 1 commit
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
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
e97b7f9
add delay to read results
satra Nov 5, 2019
ead9032
fix: config call and gzipped write
satra Nov 6, 2019
78f03e9
Update nipype/utils/filemanip.py
satra Nov 6, 2019
c956c8d
fix: replace glob with file exists check
satra Nov 6, 2019
e572991
enh: refactor saving based on feedback
satra Nov 7, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
fix: config call and gzipped write
  • Loading branch information
@satra
satra committed Nov 6, 2019
commit ead903262f9a5aa772039500b37ca33425831b13
11 changes: 6 additions & 5 deletions nipype/utils/filemanip.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -720,7 +720,7 @@ def loadpkl(infile):
pklopen = gzip.open if infile.suffix == ".pklz" else open

t = time()
timeout = float(config["execution"]["job_finished_timeout"])
timeout = float(config.get("execution", "job_finished_timeout"))
timed_out = True
while (time() - t) < timeout:
try:
Expand Down Expand Up @@ -826,8 +826,8 @@ def read_stream(stream, logger=None, encoding=None):


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
pkl_open = gzip.open if filename.endswith(".pklz") else open
with pkl_open(filename, "wb") as pkl_file:
if versioning:
from nipype import __version__ as version

Expand All @@ -837,9 +837,10 @@ def savepkl(filename, record, versioning=False, sync=False):
pkl_file.write("\n".encode("utf-8"))

pickle.dump(record, pkl_file)
fmlogger.info("Finished saving: {}".format(filename))
if sync:
fobj.flush()
os.fsync(fobj.fileno())
pkl_file.flush()
os.fsync(pkl_file.fileno())


rst_levels = ["=", "-", "~", "+"]
Expand Down