pydata / pydata/xarray

open_mfdataset segfaults when using engine="netcdf4" and Prallel=Tru

Open
#11,088 2 comments 1 reaction 0 assignees View on GitHub

Nobody has claimed this yet.

bug
Dominant language
Python
Stars
4.2k
Forks
1.4k
Avg merge
2d 15h
Merged PRs (30d)
14

Description

What happened?

When opening a mf_dataset using netcdf4 engine and parallel=True a segmentation fault arises. The whole open_mfdataset and all operations are wrapped in a class inheriting from xr.Dataset. I would like to know whether netcdf4 engine is compatible with parallel=True, or if there are other ways of doing this. Don't mind the preprocess steps, it changes a dimension name.

PS : Using h5netcdf engine with parallel=True increases the reading time compared to using the serial netcdf4 engine

What did you expect to happen?

No segmentation fault.

Minimal Complete Verifiable Example
import os

os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"

import re
from typing import List, Optional, Any

import numpy as np
import xarray as xr
import dask

mf_dataset = xr.open_mfdataset(
  self.data_paths, engine="netcdf4", preprocess=preprocess, combine="by_coords", mask_and_scale=False, decode_cf=False, parallel=False,
)
Steps to reproduce

No response

MVCE confirmation
  • Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • Complete example — the example is self-contained, including all data and the text of any traceback.
  • Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • New issue — a search of GitHub Issues suggests this is not a duplicate.
  • Recent environment — the issue occurs with the latest version of xarray and its dependencies.
Relevant log output

Anything else we need to know?

No response

Environment

commit: None
python: 3.13.8 (main, Dec 11 2025, 09:26:20) [GCC 11.5.0 20240719 (Red Hat 11.5.0-5)]
python-bits: 64
OS: Linux
OS-release: 5.14.0-611.13.1.el9_7.x86_64
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: fr_FR.UTF-8
LOCALE: ('fr_FR', 'UTF-8')
libhdf5: 1.14.6
libnetcdf: 4.9.3

xarray: 2025.7.1
pandas: 2.3.3
numpy: 2.3.4
scipy: 1.16.3
netCDF4: 1.7.2
pydap: None
h5netcdf: 1.6.1
h5py: 3.14.0
zarr: None
cftime: 1.6.4
nc_time_axis: None
iris: None
bottleneck: 1.5.0
dask: 2025.7.0
distributed: 2025.7.0
matplotlib: 3.10.7
cartopy: None
seaborn: None
numbagg: None
fsspec: 2025.9.0
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 80.9.0
pip: 25.1.1
conda: None
pytest: 9.0.2
mypy: None
IPython: 9.8.0
sphinx: 8.1.3

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 with xr.open_mfdataset using engine="netcdf4" and parallel=True, then verify the behavior against the reported Python, xarray, netCDF4, HDF5, and Dask environment. The report does not include a complete verifiable example, traceback, or test location, so first establish a reproducible case and compare serial and parallel opening. Done means the reproducible case no longer segfaults or the incompatibility is clearly documented.

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
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.