google-deepmind / google-deepmind/torch-hdf5

H5Iget_name(): can't retrieve object location

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Description

In upgrading to hdf5 807187e2f200e63, I am running into a bunch of failures with torch-hdf5 at head built with bazel on linux. `hdf5_test_reference` passes, but the rest fail.

hdf5_test_data:

```
1/7 testDoubleTensor .................................................... [WAIT]HDF5-DIAG: Error detected in HDF5 (1.9.234) thread 140294485233664:
#000: third_party/hdf5/src/H5I.c line 2049 in H5Iget_name(): can't retrieve object location
major: Object atom
minor: Can't get value
#001: third_party/hdf5/src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
1/7 testDoubleTensor .................................................... [ERROR]
2/7 testLongTensor ...................................................... [WAIT]HDF5-DIAG: Error detected in HDF5 (1.9.234) thread 140294485233664:
#000: third_party/hdf5/src/H5I.c line 2049 in H5Iget_name(): can't retrieve object location
major: Object atom
minor: Can't get value
#001: third_party/hdf5/src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
2/7 testLongTensor ...................................................... [ERROR]
3/7 testShortTensor ..................................................... [WAIT]HDF5-DIAG: Error detected in HDF5 (1.9.234) thread 140294485233664:
#000: third_party/hdf5/src/H5I.c line 2049 in H5Iget_name(): can't retrieve object location
major: Object atom
minor: Can't get value
#001: third_party/hdf5/src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
3/7 testShortTensor ..................................................... [ERROR]
4/7 testIntTensor ....................................................... [WAIT]HDF5-DIAG: Error detected in HDF5 (1.9.234) thread 140294485233664:
#000: third_party/hdf5/src/H5I.c line 2049 in H5Iget_name(): can't retrieve object location
major: Object atom
minor: Can't get value
#001: third_party/hdf5/src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
4/7 testIntTensor ....................................................... [ERROR]
5/7 testFloatTensor ..................................................... [WAIT]HDF5-DIAG: Error detected in HDF5 (1.9.234) thread 140294485233664:
#000: third_party/hdf5/src/H5I.c line 2049 in H5Iget_name(): can't retrieve object location
major: Object atom
minor: Can't get value
#001: third_party/hdf5/src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
5/7 testFloatTensor ..................................................... [ERROR]
6/7 testByteTensor ...................................................... [WAIT]HDF5-DIAG: Error detected in HDF5 (1.9.234) thread 140294485233664:
#000: third_party/hdf5/src/H5I.c line 2049 in H5Iget_name(): can't retrieve object location
major: Object atom
minor: Can't get value
#001: third_party/hdf5/src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
6/7 testByteTensor ...................................................... [ERROR]
7/7 testNonContiguous ................................................... [WAIT]HDF5-DIAG: Error detected in HDF5 (1.9.234) thread 140294485233664:
#000: third_party/hdf5/src/H5I.c line 2049 in H5Iget_name(): can't retrieve object location
major: Object atom
minor: Can't get value
#001: third_party/hdf5/src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
7/7 testNonContiguous ................................................... [ERROR]
Completed 0 asserts in 7 tests with 0 failures and 7 errors and 1 warning
```

and

```
third_party/lua/hdf5/hdf5/ffi.lua:353: in function '_getObjectType'
third_party/lua/hdf5/hdf5/ffi.lua:368: in function '_describeObject'
third_party/lua/hdf5/hdf5/file.lua:45: in function 'tostring'
third_party/lua/hdf5/hdf5/file.lua:17: in function '__init'
```

Looks to be the same as:

https://stackoverflow.com/questions/39220312/use-torch-hdf5-to-save-tensor-to-hdf5/

Contributor guide

Open the contributing guide

Research direction

Start with third_party/lua/hdf5/hdf5/ffi.lua at _getObjectType and _describeObject, then follow the calls from third_party/lua/hdf5/hdf5/file.lua. Reproduce the failure by running hdf5_test_data under the reported HDF5 revision and Bazel-on-Linux setup. Done means the tensor tests complete without the H5Iget_name invalid object ID errors.

Written by the indexing model from the issue text.

Assessment

Tech stack
lua
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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