help debugging `minor: Can't open object` related to attributes?

To assist reproducing bugs, please include the following:

• Operating System (e.g. Windows 10, MacOS 10.11, Ubuntu 16.04.2 LTS, CentOS 7)
• Python version (e.g. 2.7, 3.5)
• Where Python was acquired (e.g. system Python on MacOS or Linux, Anaconda on Windows)
• h5py version (e.g. 2.6)
• HDF5 version (e.g. 1.8.17)
• The full traceback/stack trace shown (if it appears)

h5py.version.info contains the needed versions, which can be displayed by

python -c 'import h5py; print(h5py.version.info)'

where python should be substituted for the path to python used to install h5py with.

–

I get the following warnings when I open files and I am not really sure how to debug this or even narrow down where in my lengthy code it is taking place. Could someone offer some insights on debugging something like this?

minor: Can't open object
9265
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
9266
    major: Attribute
9267
    minor: Unable to initialize object
9268
  #005: H5Oattribute.c line 476 in H5O__attr_open_by_name(): can't open attribute
9269
    major: Attribute
9270
    minor: Can't open object
9271
  #006: H5Adense.c line 394 in H5A__dense_open(): can't locate attribute in name index
9272
    major: Attribute
9273
    minor: Object not found
9274
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 1:
9275
  #000: H5A.c line 528 in H5Aopen_by_name(): can't open attribute
9276
    major: Attribute
9277
    minor: Can't open object
9278
  #001: H5VLcallback.c line 1091 in H5VL_attr_open(): attribute open failed
9279
    major: Virtual Object Layer
9280
    minor: Can't open object
9281
  #002: H5VLcallback.c line 1058 in H5VL__attr_open(): attribute open failed
9282
    major: Virtual Object Layer
9283
    minor: Can't open object
9284
  #003: H5VLnative_attr.c line 130 in H5VL__native_attr_open(): can't open attribute
9285
    major: Attribute
9286
    minor: Can't open object
9287
  #004: H5Aint.c line 545 in H5A__open_by_name(): unable to load attribute info from object header
9288
    major: Attribute
9289
    minor: Unable to initialize object
9290
  #005: H5Oattribute.c line 476 in H5O__attr_open_by_name(): can't open attribute
9291
    major: Attribute
9292
    minor: Can't open object
9293
  #006: H5Adense.c line 394 in H5A__dense_open(): can't locate attribute in name index
9294

This is on hosted github runner (ubuntu 20.04), using h5py.File through fsspec.filesystem to access files on Google Cloud buckets. All pieces of software are current (latest). Any suggestions? I could come back with a more verbose bug report if necessary. I will also try to narrow it down enough to make a small repro… but the tests do pass (i.e. the expected results are produced/extracted).

Observation, this so far only happens if h5py is installed via a PyPI wheel. It doesn’t happen if the tests are run in a conda env with the h5py conda package.

[tacaswell]

I mean if there are functions in libhdf5 that we do not expose we will definitely expose them (we tend to wait for a request / need rather than just exposing everything. There can be some work / thought required on how to expose it to Python “right”), we try to make Group work as much like dict as is technicallly possible and Dataset look as much like a numpy array as is technically possible (one of our tests is “does slicing do exactly the same thing”).

Anything beyond that, including domain specific functions, anything about the semantics of the data is out of scope for h5py, or API elaborations above those core abstractions are (in my view) out of scope.

[tacaswell]

This is very likely an issue with multiple wheels having copies of libhdf5 which are conflicting.