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issues: 1574694462

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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
1574694462 I_kwDOAMm_X85d2-4- 7513 intermittent failures with h5netcdf, h5py on macos 2448579 closed 0     5 2023-02-07T16:58:43Z 2024-04-28T23:35:21Z 2024-04-28T23:35:21Z MEMBER      

What is your issue?

cc @hmaarrfk @kmuehlbauer

Passed: https://github.com/pydata/xarray/actions/runs/4115923717/jobs/7105298426 Failed: https://github.com/pydata/xarray/actions/runs/4115946392/jobs/7105345290

Versions: h5netcdf 1.1.0 pyhd8ed1ab_0 conda-forge h5py 3.8.0 nompi_py310h5555e59_100 conda-forge hdf4 4.2.15 h7aa5921_5 conda-forge hdf5 1.12.2 nompi_h48135f9_101 conda-forge

``` =================================== FAILURES =================================== ___ test_open_mfdataset_manyfiles[h5netcdf-20-True-5-5] ______ [gw1] darwin -- Python 3.10.9 /Users/runner/micromamba-root/envs/xarray-tests/bin/python

readengine = 'h5netcdf', nfiles = 20, parallel = True, chunks = 5 file_cache_maxsize = 5

@requires_dask
@pytest.mark.filterwarnings("ignore:use make_scale(name) instead")
def test_open_mfdataset_manyfiles(
    readengine, nfiles, parallel, chunks, file_cache_maxsize
):
    # skip certain combinations
    skip_if_not_engine(readengine)

    if ON_WINDOWS:
        pytest.skip("Skipping on Windows")

    randdata = np.random.randn(nfiles)
    original = Dataset({"foo": ("x", randdata)})
    # test standard open_mfdataset approach with too many files
    with create_tmp_files(nfiles) as tmpfiles:
        writeengine = readengine if readengine != "pynio" else "netcdf4"
        # split into multiple sets of temp files
        for ii in original.x.values:
            subds = original.isel(x=slice(ii, ii + 1))
            if writeengine != "zarr":
                subds.to_netcdf(tmpfiles[ii], engine=writeengine)
            else:  # if writeengine == "zarr":
                subds.to_zarr(store=tmpfiles[ii])

        # check that calculation on opened datasets works properly
      with open_mfdataset(
            tmpfiles,
            combine="nested",
            concat_dim="x",
            engine=readengine,
            parallel=parallel,
            chunks=chunks if (not chunks and readengine != "zarr") else "auto",
        ) as actual:

/Users/runner/work/xarray/xarray/xarray/tests/test_backends.py:3267:


/Users/runner/work/xarray/xarray/xarray/backends/api.py:991: in open_mfdataset datasets, closers = dask.compute(datasets, closers) /Users/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/base.py:599: in compute results = schedule(dsk, keys, kwargs) /Users/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/threaded.py:89: in get results = get_async( /Users/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/local.py:511: in get_async raise_exception(exc, tb) /Users/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/local.py:319: in reraise raise exc /Users/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/local.py:224: in execute_task result = _execute_task(task, data) /Users/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/core.py:119: in _execute_task return func((_execute_task(a, cache) for a in args)) /Users/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/dask/utils.py:72: in apply return func(args, kwargs) /Users/runner/work/xarray/xarray/xarray/backends/api.py:526: in open_dataset backend_ds = backend.open_dataset( /Users/runner/work/xarray/xarray/xarray/backends/h5netcdf_.py:417: in open_dataset ds = store_entrypoint.open_dataset( /Users/runner/work/xarray/xarray/xarray/backends/store.py:32: in open_dataset vars, attrs = store.load() /Users/runner/work/xarray/xarray/xarray/backends/common.py:129: in load (decode_variable_name(k), v) for k, v in self.get_variables().items() /Users/runner/work/xarray/xarray/xarray/backends/h5netcdf.py:220: in get_variables return FrozenDict( /Users/runner/work/xarray/xarray/xarray/core/utils.py:471: in FrozenDict return Frozen(dict(args, *kwargs)) /Users/runner/work/xarray/xarray/xarray/backends/h5netcdf_.py:221: in <genexpr> (k, self.open_store_variable(k, v)) for k, v in self.ds.variables.items() /Users/runner/work/xarray/xarray/xarray/backends/h5netcdf_.py:200: in open_store_variable elif var.compression is not None: /Users/runner/micromamba-root/envs/xarray-tests/lib/python3.10/site-packages/h5netcdf/core.py:394: in compression return self._h5ds.compression


self = <[AttributeError("'NoneType' object has no attribute '_root'") raised in repr()] Variable object at 0x151378970>

@property
def _h5ds(self):
    # Always refer to the root file and store not h5py object
    # subclasses:
  return self._root._h5file[self._h5path]

E AttributeError: 'NoneType' object has no attribute '_h5file'

```

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