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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
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topic-backendsupstream issue
@mx-moth

Description

@mx-moth
mx-moth
opened on Feb 23, 2023

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:

Details

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:

Details

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

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