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issues: 1399324758

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id node_id number title user state locked assignee milestone comments created_at updated_at closed_at author_association active_lock_reason draft pull_request body reactions performed_via_github_app state_reason repo type
1399324758 I_kwDOAMm_X85TaABW 7136 import xarray causes fatal python crash on windows when h5netcdf and netcdf4 are installed 21100296 closed 0     3 2022-10-06T10:38:59Z 2023-01-30T14:41:52Z 2023-01-30T14:41:52Z NONE      

What happened?

On Windows with python (3.9 and 3.10) the command import xarray results in a crash of python, if I have the packages netcdf4 and h5netcdf installed.

What did you expect to happen?

I expected that xarray would import normally, without a fatal python error.

Minimal Complete Verifiable Example

```Python

On windows:

pip install xarray pip install h5netcdf pip install netcdf4

This results in a crash

python -c "import xarray"

The crash does not occur when I first import h5netcdf and then import xarray, so the next line does not result in a crash:

python -c "import h5netcdf;import xarray"

The crash does not occur on linux.

The crash does not occur when I have only h5netcdf or netcdf4 installed.

```

MVCE confirmation

  • [X] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • [X] 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.
  • [X] New issue — a search of GitHub Issues suggests this is not a duplicate.

Relevant log output

```Python command: python -c "import xarray" C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\h5py__init__.py:36: UserWarning: h5py is running against HDF5 1.12.1 when it was built against 1.12.2, this may cause problems _warn(("h5py is running against HDF5 {0} when it was built against {1}, " Warning! HDF5 library version mismatched error The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.12.2, library is 1.12.1 SUMMARY OF THE HDF5 CONFIGURATION =================================

General Information:

               HDF5 Version: 1.12.1
              Configured on: 2022-03-04
              Configured by: Ninja
                Host system: Windows-10.0.17763
          Uname information: Windows
                   Byte sex: little-endian
         Installation point: D:/bld/hdf5_split_1646412547396/_h_env/Library

Compiling Options:

                 Build Mode: RELEASE
          Debugging Symbols: OFF
                    Asserts: OFF
                  Profiling: OFF
         Optimization Level: OFF

Linking Options:

                  Libraries:

Statically Linked Executables: OFF LDFLAGS: /machine:x64 H5_LDFLAGS: AM_LDFLAGS: Extra libraries: D:/bld/hdf5_split_1646412547396/_h_env/Library/lib/libcurl.lib;D:/bld/hdf5_split_1646412547396/_h_env/Library/lib/libssl.lib;D:/bld/hdf5_split_1646412547396/_h_env/Library/lib/libcrypto.lib Archiver: C:/Program Files (x86)/Microsoft Visual Studio/2019/Enterprise/VC/Tools/MSVC/14.16.27023/bin/HostX64/x64/lib.exe Ranlib: :

Languages:

                          C: YES
                 C Compiler: C:/Program Files (x86)/Microsoft Visual Studio/2019/Enterprise/VC/Tools/MSVC/14.16.27023/bin/HostX64/x64/cl.exe 19.16.27045.0
                   CPPFLAGS: 
                H5_CPPFLAGS: 
                AM_CPPFLAGS: 
                     CFLAGS:   /DWIN32 /D_WINDOWS 
                  H5_CFLAGS: /W3;/wd4100;/wd4706;/wd4127
                  AM_CFLAGS: 
           Shared C Library: YES
           Static C Library: YES

                    Fortran: OFF
           Fortran Compiler:  
              Fortran Flags: 
           H5 Fortran Flags: 
           AM Fortran Flags: 
     Shared Fortran Library: YES
     Static Fortran Library: YES

                        C++: ON
               C++ Compiler: C:/Program Files (x86)/Microsoft Visual Studio/2019/Enterprise/VC/Tools/MSVC/14.16.27023/bin/HostX64/x64/cl.exe 19.16.27045.0
                  C++ Flags:   
               H5 C++ Flags: /W3;/wd4100;/wd4706;/wd4127
               AM C++ Flags: 
         Shared C++ Library: YES
         Static C++ Library: YES

                        JAVA: OFF
             JAVA Compiler:

Features:

               Parallel HDF5: OFF

Parallel Filtered Dataset Writes: Large Parallel I/O: High-level library: ON Build HDF5 Tests: ON Build HDF5 Tools: ON Threadsafety: ON (recursive RW locks: ) Default API mapping: v112 With deprecated public symbols: ON I/O filters (external): DEFLATE MPE: Direct VFD: Mirror VFD: (Read-Only) S3 VFD: 1 (Read-Only) HDFS VFD: dmalloc: Packages w/ extra debug output: API Tracing: OFF Using memory checker: OFF Memory allocation sanity checks: OFF Function Stack Tracing: OFF Use file locking: best-effort Strict File Format Checks: OFF Optimization Instrumentation: Bye... Error: Process completed with exit code 1. ```

Anything else we need to know?

This bug is reproduced by the github action runner: https://github.com/daanscheltens/test-netcdf4/actions/runs/3196339371/jobs/5218135577

This action is part of a dedicated empty repository that just contains this action workflow: https://github.com/daanscheltens/test-netcdf4/blob/main/.github/workflows/action.yml

Environment

python -c "import h5netcdf; import xarray as xr;xr.show_versions()"

INSTALLED VERSIONS ------------------ commit: None python: 3.9.13 (tags/v3.9.13:6de2ca5, May 17 2022, 16:36:42) [MSC v.1929 64 bit (AMD64)] python-bits: 64 OS: Windows OS-release: 10 machine: AMD64 processor: Intel64 Family 6 Model 106 Stepping 6, GenuineIntel byteorder: little LC_ALL: None LANG: None LOCALE: ('English_United States', '1252') libhdf5: 1.12.2 libnetcdf: None xarray: 2022.9.0 pandas: 1.5.0 numpy: 1.23.3 scipy: None netCDF4: None pydap: None h5netcdf: 1.0.2 h5py: 3.7.0 Nio: None zarr: None cftime: 1.6.2 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: None distributed: None matplotlib: None cartopy: None seaborn: None numbagg: None fsspec: None cupy: None pint: None sparse: None flox: None numpy_groupies: None setuptools: 5[8](https://github.com/daanscheltens/test-netcdf4/actions/runs/3196339371/jobs/5218135408#step:15:9).1.0 pip: [22](https://github.com/daanscheltens/test-netcdf4/actions/runs/3196339371/jobs/5218135408#step:15:23).2.2 conda: None pytest: None IPython: None sphinx: None
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  completed 13221727 issue

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