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ComparativeGenomicsToolkit / hal

Hierarchical Alignment Format
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HDF5 1.8.16 apparent problem. #158

Open diekhans opened 4 years ago

diekhans commented 4 years ago

https://github.com/ComparativeGenomicsToolkit/cactus/issues/103 is getting a failure from halSetMetadata

halSetMetadata tmp_alignment.hal CACTUS_COMMIT c087fe129d8c337c7eab961cebd49c80bcc20ef3 

HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
  #000: H5A.c line 249 in H5Acreate2(): no write intent on file
    major: Invalid arguments to routine
    minor: Write failed
terminate called after throwing an instance of 'H5::AttributeIException'
Aborted

this doesn't happen with HDF5 1.8.12\, so probably an API chance that needs to be tracked.

glennhickey commented 4 years ago

Hmm, could be the logic here:

https://github.com/ComparativeGenomicsToolkit/hal/blob/master/api/hdf5_impl/hdf5ExternalArray.h#L17-L25

needs fixing to handle 1.8.16 either as a special case, or maybe treating it like 1.10.