pydata / pydata/xarray

Hangs while saving netcdf file opened using xr.open_mfdataset with lock=None

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bug topic-backends topic-dask
Dominant language
Python
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Description

I am testing out code that uses xarray to process netcdf files, in particular to join multiple netcdf files into one along shared dimensions. This was working well, except sometimes when saving the netcdf file the process would hang.

I was able to whittle it down to this simple example: https://github.com/jessicaaustin/xarray_netcdf_hanging_issue

This is the code snippet at the core of the example:

 # If you set lock=False then this runs fine every time.
 # Setting lock=None causes it to intermittently hang on mfd.to_netcdf
 with xr.open_mfdataset(['dataset.nc'], combine='by_coords', lock=None) as mfd:
     p = os.path.join('tmp', 'xarray_{}.nc'.format(uuid.uuid4().hex))
     print(f"Writing data to {p}")
     mfd.to_netcdf(p)
     print("complete")

If you run this once, it's typically fine. But run it over and over again in a loop, and it'll eventually hang on mfd.to_netcdf. However if I set lock=False then it runs fine every time.

I've seen this with the following combos:

  • xarray=0.14.1
  • dask=2.9.1
  • netcdf4=1.5.3

and

  • xarray=0.15.1
  • dask=2.14.0
  • netcdf4=1.5.3

And I've tried it with different netcdf files and different computers.

Versions
Output of `xr.show_versions()`

INSTALLED VERSIONS

commit: None
python: 3.7.6 | packaged by conda-forge | (default, Mar 23 2020, 23:03:20)
[GCC 7.3.0]
python-bits: 64
OS: Linux
OS-release: 4.15.0-20-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8
libhdf5: 1.10.5
libnetcdf: 4.7.4

xarray: 0.15.1
pandas: 1.0.3
numpy: 1.18.1
scipy: None
netCDF4: 1.5.3
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: None
cftime: 1.1.1.2
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: None
dask: 2.14.0
distributed: 2.14.0
matplotlib: None
cartopy: None
seaborn: None
numbagg: None
setuptools: 46.1.3.post20200325
pip: 20.0.2
conda: None
pytest: None
IPython: None
sphinx: None

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by running the linked minimal example repeatedly with xr.open_mfdataset(..., lock=None) and mfd.to_netcdf, then compare it with lock=False using the reported xarray, dask, and netCDF4 versions. Trace the open_mfdataset and to_netcdf entry points to isolate the intermittent lock behavior. Done means repeated saves no longer hang and regression coverage preserves the working lock=False case.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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