HDF5-DIAG warnings calling `open_mfdataset` with more than `file_cache_maxsize` datasets (hdf5 1.12.2) #7549

mx-moth · 2023-02-23T02:28:23Z

What happened?

Using ds = open_mfdataset(...) to open more than file_cache_maxsize files, then saving the combined dataset with ds.to_netcdf() prints many HDF5-DIAG warnings. This happens when using hdf5==1.12.2 as bundled with netcdf4~=1.6.0. Downgrading to netcdf4~=1.5.8 which bundles hdf5==1.12.0 stops the warnings being printed. The output file appears to be correct in either case.

What did you expect to happen?

No warnings from HDF5-DIAG. Either raise an error because of the number of files being opened at once, or behaving as open_mfdataset() normally does.

Minimal Complete Verifiable Example

import argparse
import pathlib
import tempfile
from typing import List

import netCDF4
import xarray

HERE = pathlib.Path(__file__).parent


def add_arguments(parser: argparse.ArgumentParser):
    parser.add_argument('count', type=int, default=200, nargs='?')
    parser.add_argument('--file-cache-maxsize', type=int, required=False)


def main():
    parser = argparse.ArgumentParser()
    add_arguments(parser)
    opts = parser.parse_args()

    if opts.file_cache_maxsize is not None:
        xarray.set_options(file_cache_maxsize=opts.file_cache_maxsize)

    temp_dir = tempfile.mkdtemp(dir=HERE, prefix='work-dir-')
    work_dir = pathlib.Path(temp_dir)
    print("Working in", work_dir.name)

    print("Making", opts.count, "datasets")
    dataset_paths = make_many_datasets(work_dir, count=opts.count)

    print("Combining", len(dataset_paths), "datasets")
    dataset = xarray.open_mfdataset(dataset_paths, lock=False)
    dataset.to_netcdf(work_dir / 'combined.nc')


def make_many_datasets(
    work_dir: pathlib.Path,
    count: int = 200
) -> List[pathlib.Path]:
    dataset_paths = []
    for i in range(count):
        variable = f'var_{i}'
        path = work_dir / f'{variable}.nc'
        dataset_paths.append(path)
        make_dataset(path, variable)

    return dataset_paths


def make_dataset(
    path: pathlib.Path,
    variable: str,
) -> None:
    ds = netCDF4.Dataset(path, "w", format="NETCDF4")
    ds.createDimension("x", 1)
    var = ds.createVariable(variable, "i8", ("x",))
    var[:] = 1
    ds.close()


if __name__ == '__main__':
    main()

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.

Relevant log output

Working in work-dir-yi3jp5ly
Making 128 datasets
Combining 128 datasets
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 1:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitGroomNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 1:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeGranularBitRoundNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 1:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitRoundNumberOfSignificantBits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 1:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitGroomNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 1:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeGranularBitRoundNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 1:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitRoundNumberOfSignificantBits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 2:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitGroomNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 2:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeGranularBitRoundNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 2:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitRoundNumberOfSignificantBits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 3:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitGroomNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 3:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeGranularBitRoundNumberOfSignificantDigits'
    major: Attribute
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 3:
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
    major: Attribute
    minor: Can't open object
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
    major: Virtual Object Layer
    minor: Can't open object
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
    major: Attribute
    minor: Can't open object
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitRoundNumberOfSignificantBits'
    major: Attribute
    minor: Object not found

Anything else we need to know?

The example is a script to run on the command line. Assuming the file is named test.py, invoke as:

# This will show the error. Defaults to making 200 files
$ python3 ./test.py
# This will not show the error - the number of files is less than file_cache_maxsize:
$ python3 ./test.py 127
# This will adjust file_cache_maxsize to show the error again, despite the lower number of files
$ python3 ./test.py 11 --file-cache-maxsize=10

The log output is from python3 ./test.py 128. The length of the log output depends on the number of files opened - the more files the longer the log. The log output from python3 ./test.py using the default of 200 datasets was too long to include in this issue!

All output files are restricted to directories created in the current working directory named work-dir-XXXXXXX, and are retained after the program exits. 200 datasets take up a total of 1.7MB.

Environment

Failing environment:

INSTALLED VERSIONS

commit: None
python: 3.8.10 (default, Nov 14 2022, 12:59:47)
[GCC 9.4.0]
python-bits: 64
OS: Linux
OS-release: 5.15.0-58-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_AU.UTF-8
LOCALE: ('en_AU', 'UTF-8')
libhdf5: 1.12.2
libnetcdf: 4.9.0

xarray: 2023.1.0
pandas: 1.5.3
numpy: 1.24.2
scipy: None
netCDF4: 1.6.2
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: None
cftime: 1.6.2
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: None
dask: 2023.2.0
distributed: None
matplotlib: None
cartopy: None
seaborn: None
numbagg: None
fsspec: 2023.1.0
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 44.0.0
pip: 23.0.1
conda: None
pytest: None
mypy: None
IPython: None
sphinx: None

Working environment:

INSTALLED VERSIONS

commit: None
python: 3.8.10 (default, Nov 14 2022, 12:59:47)
[GCC 9.4.0]
python-bits: 64
OS: Linux
OS-release: 5.15.0-58-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_AU.UTF-8
LOCALE: ('en_AU', 'UTF-8')
libhdf5: 1.12.0
libnetcdf: 4.7.4

xarray: 2023.1.0
pandas: 1.5.3
numpy: 1.24.2
scipy: None
netCDF4: 1.5.8
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: None
cftime: 1.6.2
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: None
dask: 2023.2.0
distributed: None
matplotlib: None
cartopy: None
seaborn: None
numbagg: None
fsspec: 2023.1.0
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 44.0.0
pip: 23.0.1
conda: None
pytest: None
mypy: None
IPython: None
sphinx: None

The text was updated successfully, but these errors were encountered:

dcherian · 2023-02-28T23:14:44Z

Not clear to me if this is a bug or just some verbose warnings.

@kmuehlbauer do you have any thoughts?

kmuehlbauer · 2023-03-01T07:01:40Z

@dcherian Thanks for the ping.

I can reproduce in a fresh conda-forge env with pip installed netcdf4, xarray and dask.

@mx-moth A search brought up this likely related issue over at netcdf-c, Unidata/netcdf-c#2458. The according PR with a fix Unidata/netcdf-c#2461 is milestoned for netcdf-c 4.9.1.

kmuehlbauer · 2023-03-01T09:19:26Z

I just tested this with netcdf-c 4.9.1 but still these errors show up, also using conda-forge only install.

To make this even weirder I've checked creation/reading with only hdf5/h5py/h5netcdf in the environment. Seems everything is working well.

import argparse
import pathlib
import tempfile
from typing import List

import h5netcdf.legacyapi as nc
import xarray

HERE = pathlib.Path(__file__).parent


def add_arguments(parser: argparse.ArgumentParser):
    parser.add_argument('count', type=int, default=200, nargs='?')
    parser.add_argument('--file-cache-maxsize', type=int, required=False)


def main():
    parser = argparse.ArgumentParser()
    add_arguments(parser)
    opts = parser.parse_args()

    if opts.file_cache_maxsize is not None:
        xarray.set_options(file_cache_maxsize=opts.file_cache_maxsize)

    temp_dir = tempfile.mkdtemp(dir=HERE, prefix='work-dir-')
    work_dir = pathlib.Path(temp_dir)
    print("Working in", work_dir.name)

    print("Making", opts.count, "datasets")
    dataset_paths = make_many_datasets(work_dir, count=opts.count)

    print("Combining", len(dataset_paths), "datasets")
    dataset = xarray.open_mfdataset(dataset_paths, lock=False, engine="h5netcdf")
    dataset.to_netcdf(work_dir / 'combined.nc', engine="h5netcdf")


def make_many_datasets(
    work_dir: pathlib.Path,
    count: int = 200
) -> List[pathlib.Path]:
    dataset_paths = []
    for i in range(count):
        variable = f'var_{i}'
        path = work_dir / f'{variable}.nc'
        dataset_paths.append(path)
        make_dataset(path, variable)

    return dataset_paths


def make_dataset(
    path: pathlib.Path,
    variable: str,
) -> None:
    ds = nc.Dataset(path, "w")
    ds.createDimension("x", 1)
    var = ds.createVariable(variable, "i8", ("x",))
    var[:] = 1
    ds.close()


if __name__ == '__main__':
    main()

# This will show no error. Defaults to making 200 files
$ python3 ./test.py
# This will also not show the error - the number of files is less than file_cache_maxsize:
$ python3 ./test.py 127
# This will adjust file_cache_maxsize to show the error again, despite the lower number of files, here we see another error issued by h5py
$ python3 ./test.py 11 --file-cache-maxsize=10

Working in work-dir-40mwn69y
Making 11 datasets
Combining 11 datasets
Traceback (most recent call last):
  File "/home/kai/python/gists/xarray/7549.py", line 65, in <module>
    main()
  File "/home/kai/python/gists/xarray/7549.py", line 36, in main
    dataset.to_netcdf(work_dir / 'combined.nc', engine="h5netcdf")
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/xarray/core/dataset.py", line 1911, in to_netcdf
    return to_netcdf(  # type: ignore  # mypy cannot resolve the overloads:(
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/xarray/backends/api.py", line 1226, in to_netcdf
    writes = writer.sync(compute=compute)
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/xarray/backends/common.py", line 172, in sync
    delayed_store = da.store(
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/dask/array/core.py", line 1236, in store
    compute_as_if_collection(Array, store_dsk, map_keys, **kwargs)
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/dask/base.py", line 341, in compute_as_if_collection
    return schedule(dsk2, keys, **kwargs)
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/dask/threaded.py", line 89, in get
    results = get_async(
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/dask/local.py", line 511, in get_async
    raise_exception(exc, tb)
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/dask/local.py", line 319, in reraise
    raise exc
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/dask/local.py", line 224, in execute_task
    result = _execute_task(task, data)
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/dask/core.py", line 119, in _execute_task
    return func(*(_execute_task(a, cache) for a in args))
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/dask/array/core.py", line 126, in getter
    c = np.asarray(c)
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/xarray/core/indexing.py", line 459, in __array__
    return np.asarray(self.array, dtype=dtype)
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/xarray/core/indexing.py", line 623, in __array__
    return np.asarray(self.array, dtype=dtype)
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/xarray/core/indexing.py", line 524, in __array__
    return np.asarray(array[self.key], dtype=None)
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/xarray/backends/h5netcdf_.py", line 43, in __getitem__
    return indexing.explicit_indexing_adapter(
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/xarray/core/indexing.py", line 815, in explicit_indexing_adapter
    result = raw_indexing_method(raw_key.tuple)
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/xarray/backends/h5netcdf_.py", line 50, in _getitem
    return array[key]
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/h5netcdf/core.py", line 337, in __getitem__
    padding = self._get_padding(key)
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/h5netcdf/core.py", line 291, in _get_padding
    shape = self.shape
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/h5netcdf/core.py", line 268, in shape
    return tuple([self._parent._all_dimensions[d].size for d in self.dimensions])
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/h5netcdf/core.py", line 268, in <listcomp>
    return tuple([self._parent._all_dimensions[d].size for d in self.dimensions])
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/h5netcdf/dimensions.py", line 113, in size
    if self.isunlimited():
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/h5netcdf/dimensions.py", line 133, in isunlimited
    return self._h5ds.maxshape == (None,)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/home/kai/miniconda/envs/test-netcdf4/lib/python3.9/site-packages/h5py/_hl/dataset.py", line 588, in maxshape
    space = self.id.get_space()
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5d.pyx", line 299, in h5py.h5d.DatasetID.get_space
ValueError: Invalid dataset identifier (invalid dataset identifier)

INSTALLED VERSIONS ------------------ commit: None python: 3.9.16 | packaged by conda-forge | (main, Feb 1 2023, 21:39:03) [GCC 11.3.0] python-bits: 64 OS: Linux OS-release: 5.14.21-150400.24.46-default machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: de_DE.UTF-8 LOCALE: ('de_DE', 'UTF-8') libhdf5: 1.12.2 libnetcdf: None

xarray: 2023.2.0
pandas: 1.5.3
numpy: 1.24.2
scipy: None
netCDF4: None
pydap: None
h5netcdf: 1.1.0
h5py: 3.7.0
Nio: None
zarr: None
cftime: None
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: None
dask: 2023.2.1
distributed: 2023.2.1
matplotlib: None
cartopy: None
seaborn: None
numbagg: None
fsspec: 2023.1.0
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 67.4.0
pip: 23.0.1
conda: None
pytest: None
mypy: None
IPython: None
sphinx: None

Update: added engine="h5netcdf" to call of open_mfdataset.

kmuehlbauer · 2023-03-01T09:37:43Z

This as far I can get for the moment. @mx-moth I'd suggest to go upstream (netCDF4/netcdf-c) with details about this issue. At least we can rule out an issue only related to hdf5=1.12.2.

Maybe @DennisHeimbigner can shed more light here?

( #005: H5Oattribute.c line 494 in H5O__attr_open_by_name(): can't locate attribute: '_QuantizeBitRoundNumberOfSignificantBits'
    major: Attribute
    minor: Object not found

trexfeathers · 2023-03-08T18:00:35Z

@pp-mo 👀

pp-mo · 2023-03-09T10:28:24Z

@pp-mo 👀

See our issues here : SciTools/iris#5187
It does look a lot like the "same" problem.
It is specifically related to the use of dask and multi-threading.
Here in python-netCDF4 land, we were protected from all of that before netCDF4 v1.6.1, since before that all netcdf operations held the Python GIL so could not be re-entered by threads.

trexfeathers · 2023-03-09T10:30:28Z

before netCDF4 v1.6.2

Before v1.6.1, I believe

pp-mo · 2023-03-09T10:43:50Z

@trexfeathers Before v1.6.1, I believe

Oops, fixed.

gewitterblitz · 2023-03-24T21:58:38Z

Thanks, @trexfeathers. I had the same problem of HDF5 DIAG warnings after upgrading to xarray v2023.3.0 yesterday. Your diagnosis in SciTools/iris#5187 helped isolate the issue with libnetcdf v4.9.1. Downgrading libnetcdf to v4.8.1 resulted in no HDF5 warnings.

Mikejmnez · 2023-03-26T00:41:10Z

Thanks everybody. Similar to @gewitterblitz and based on SciTools/iris#5187 , pinning libnetcdf to v4.8.1 did the trick

mx-moth added bug needs triage Issue that has not been reviewed by xarray team member labels Feb 23, 2023

dcherian added topic-backends and removed needs triage Issue that has not been reviewed by xarray team member bug labels Feb 28, 2023

trexfeathers mentioned this issue Mar 8, 2023

HDF5-DIAG warnings from libnetcdf v4.9.1 SciTools/iris#5187

Closed

malmans2 mentioned this issue Mar 16, 2023

IGPwinter opening bug hainegroup/oceanspy#330

Closed

nbud mentioned this issue Mar 31, 2023

Many HDF5-DIAG warnings when used with xarray and dask Unidata/netcdf4-python#1242

Open

trexfeathers mentioned this issue Apr 17, 2023

Xarray does not support full range of netcdf-python compression options #7388

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ekatef mentioned this issue May 5, 2023

Error in build_cutout for Ukraine pypsa-meets-earth/pypsa-earth#669

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keewis mentioned this issue Nov 3, 2023

Segmentation fault 139 (SIGSEGV) #8410

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HDF5-DIAG warnings calling `open_mfdataset` with more than `file_cache_maxsize` datasets (hdf5 1.12.2) #7549

HDF5-DIAG warnings calling `open_mfdataset` with more than `file_cache_maxsize` datasets (hdf5 1.12.2) #7549

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HDF5-DIAG warnings calling open_mfdataset with more than file_cache_maxsize datasets (hdf5 1.12.2) #7549

HDF5-DIAG warnings calling open_mfdataset with more than file_cache_maxsize datasets (hdf5 1.12.2) #7549

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mx-moth commented Feb 23, 2023 • edited Loading

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HDF5-DIAG warnings calling `open_mfdataset` with more than `file_cache_maxsize` datasets (hdf5 1.12.2) #7549

HDF5-DIAG warnings calling `open_mfdataset` with more than `file_cache_maxsize` datasets (hdf5 1.12.2) #7549

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