[Bug]: OSError: [Errno 5] Unable to synchronously open file

[nwatters01]

What happened?

I tried validating an .nwb file with and ran into an error in h5py (see below).

Steps to Reproduce

python -m pynwb.validate ses-2022-05-31_processed.nwb

Traceback

Traceback (most recent call last):
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/site-packages/pynwb/validate.py", line 238, in <module>
    validate_cli()
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/site-packages/pynwb/validate.py", line 227, in validate_cli
    validation_errors, validation_status = validate(
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/site-packages/hdmf/utils.py", line 668, in func_call
    return func(**pargs)
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/site-packages/pynwb/validate.py", line 143, in validate
    cached_namespaces, manager, namespace_dependencies = _get_cached_namespaces_to_validate(
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/site-packages/pynwb/validate.py", line 61, in _get_cached_namespaces_to_validate
    namespace_dependencies = NWBHDF5IO.load_namespaces(namespace_catalog=catalog, path=path, driver=driver)
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/site-packages/hdmf/utils.py", line 664, in func_call
    return func(args[0], **pargs)
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/site-packages/hdmf/backends/hdf5/h5tools.py", line 169, in load_namespaces
    open_file_obj = cls.__resolve_file_obj(path, file_obj, driver)
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/site-packages/hdmf/backends/hdf5/h5tools.py", line 144, in __resolve_file_obj
    file_obj = File(path, 'r', **file_kwargs)
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/site-packages/h5py/_hl/files.py", line 562, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
  File "/om/user/nwatters/venvs/catalystneuro/lib/python3.10/site-packages/h5py/_hl/files.py", line 235, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
  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/h5f.pyx", line 102, in h5py.h5f.open
OSError: [Errno 5] Unable to synchronously open file (unable to lock file, errno = 5, error message = 'Input/output error')

Operating System

Linux

Python Executable

Conda

Python Version

3.10

Package Versions

aiobotocore==2.7.0
aiohttp==3.8.6
aioitertools==0.11.0
aiosignal==1.3.1
appdirs==1.4.4
arrow==1.3.0
asciitree==0.3.3
asttokens==2.4.1
async-timeout==4.0.3
attrs==23.1.0
backcall==0.2.0
bidsschematools==0.7.2
blessed==1.20.0
boto3==1.28.64
botocore==1.31.64
bqplot==0.12.42
certifi==2023.7.22
cffi==1.16.0
cfgv==3.4.0
charset-normalizer==3.3.1
ci-info==0.3.0
click==8.1.7
click-didyoumean==0.3.0
comm==0.1.4
contourpy==1.1.1
cryptography==41.0.5
cycler==0.12.1
dandi==0.56.2
dandischema==0.8.4
decorator==5.1.1
dill==0.3.7
distlib==0.3.7
dnspython==2.4.2
email-validator==2.1.0.post1
etelemetry==0.3.1
exceptiongroup==1.1.3
executing==2.0.0
fasteners==0.19
filelock==3.12.4
fonttools==4.43.1
fparse==1.20.1
fqdn==1.5.1
frozenlist==1.4.0
fscacher==0.4.0
fsspec==2023.10.0
gast==0.4.0
h5py==3.10.0
hdmf==3.10.0
humanize==4.8.0
identify==2.5.30
idna==3.4
imageio==2.31.6
importlib-metadata==4.13.0
interleave==0.2.1
ipydatagrid==1.2.0
ipydatawidgets==4.3.2
ipyfilechooser==0.6.0
ipympl==0.9.3
ipython==8.16.1
ipython-genutils==0.2.0
ipyvolume==0.6.3
ipyvue==1.10.1
ipyvuetify==1.8.10
ipywebrtc==0.6.0
ipywidgets==8.1.1
isodate==0.6.1
isoduration==20.11.0
jaraco.classes==3.3.0
-e git+https://github.com/catalystneuro/jazayeri-lab-to-nwb@a72dd8cf14cfea8e2e9f8fff837ae56970c6e471#egg=jazayeri_lab_to_nwb
jedi==0.19.1
jeepney==0.8.0
jmespath==1.0.1
joblib==1.3.2
jsonpointer==2.4
jsonschema==4.19.1
jsonschema-specifications==2023.7.1
jupyterlab-widgets==3.0.9
keyring==24.2.0
keyrings.alt==5.0.0
kiwisolver==1.4.5
lazy-ops==0.2.0
lazy_loader==0.3
lxml==4.9.3
matplotlib==3.8.0
matplotlib-inline==0.1.6
more-itertools==10.1.0
multidict==6.0.4
natsort==8.4.0
ndx-grayscalevolume==0.0.2
ndx-icephys-meta==0.1.0
ndx-spectrum==0.2.2
neo==0.12.0
networkx==3.2
neuroconv==0.4.4
nodeenv==1.8.0
numcodecs==0.12.1
numpy==1.26.1
nwb-conversion-tools==0.11.1
nwbinspector==0.4.30
nwbwidgets==0.11.3
packaging==23.2
pandas==2.1.1
parso==0.8.3
pexpect==4.8.0
pickleshare==0.7.5
Pillow==10.0.1
platformdirs==3.11.0
plotly==5.13.1
pre-commit==3.5.0
probeinterface==0.2.17
prompt-toolkit==3.0.39
psutil==5.9.6
ptyprocess==0.7.0
pure-eval==0.2.2
py2vega==0.6.1
pycparser==2.21
pycryptodomex==3.19.0
pydantic==1.10.13
Pygments==2.16.1
pynwb==2.5.0
pyout==0.7.3
pyparsing==3.1.1
python-dateutil==2.8.2
pythreejs==2.4.2
pytz==2023.3.post1
PyYAML==6.0.1
quantities==0.14.1
referencing==0.30.2
requests==2.31.0
rfc3339-validator==0.1.4
rfc3987==1.3.8
roiextractors @ git+https://github.com/catalystneuro/roiextractors.git@8db5f9cb3a7ee5efee49b7fd0b694c7a8105519a
rpds-py==0.10.6
ruamel.yaml==0.18.2
ruamel.yaml.clib==0.2.8
s3fs==2023.10.0
s3transfer==0.7.0
scikit-image==0.22.0
scipy==1.11.3
SecretStorage==3.3.3
semantic-version==2.10.0
six==1.16.0
spikeextractors==0.9.11
spikeinterface==0.98.2
stack-data==0.6.3
tenacity==8.2.3
threadpoolctl==3.2.0
tifffile==2023.9.26
tqdm==4.66.1
traitlets==5.12.0
traittypes==0.2.1
trimesh==4.0.1
types-python-dateutil==2.8.19.14
typing_extensions==4.8.0
tzdata==2023.3
uri-template==1.3.0
urllib3==2.0.7
virtualenv==20.24.6
wcwidth==0.2.8
webcolors==1.13
widgetsnbextension==4.0.9
wrapt==1.15.0
yarl==1.9.2
zarr==2.16.1
zarr-checksum==0.2.9
zipp==3.17.0

Code of Conduct

• I agree to follow this project's Code of Conduct
• Have you checked the Contributing document?
• Have you ensured this bug was not already reported?

[rly]

Can you check that you have permissions to read the file? For example, use head ses-2022-05-31_processed.nwb to try reading part of the file.

Also what kind of file system is the file stored in?
Depending on the file system, running export HDF5_USE_FILE_LOCKING="FALSE"
before the validate command may be helpful.

[nwatters01]

Oh, the export HDF5_USE_FILE_LOCKING="FALSE" command worked! Everything is good now, thank you very much!