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brtnfld avatar brtnfld commented on May 29, 2024

Indeed, I see the same issue, and I don’t see in the tests that we actually test the value returned for the number of bases.

I think there might be a bug in cg_open. For some reason, ADFH_Number_of_Children is not calling the callback count_children.

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brtnfld avatar brtnfld commented on May 29, 2024

H5Literate2 is failing with:

HDF5-DIAG: Error detected in HDF5 (1.15.0) thread 0:
  #000: ../../src/H5L.c line 1698 in H5Literate2(): synchronous link iteration failed
    major: Links
    minor: Iteration failed
  #001: ../../src/H5L.c line 1663 in H5L__iterate_api_common(): link iteration failed
    major: Links
    minor: Iteration failed
  #002: ../../src/H5VLcallback.c line 5517 in H5VL_link_specific(): unable to execute link specific callback
    major: Virtual Object Layer
    minor: Can't operate on object
  #003: ../../src/H5VLcallback.c line 5483 in H5VL__link_specific(): unable to execute link specific callback
    major: Virtual Object Layer
    minor: Can't operate on object
  #004: ../../src/H5VLnative_link.c line 368 in H5VL__native_link_specific(): error iterating over links
    major: Links
    minor: Iteration failed
  #005: ../../src/H5Lint.c line 2247 in H5L_iterate(): link iteration failed
    major: Links
    minor: Iteration failed
  #006: ../../src/H5Gint.c line 922 in H5G_iterate(): error iterating over links
    major: Symbol table
    minor: Iteration failed
  #007: ../../src/H5Gobj.c line 649 in H5G__obj_iterate(): creation order not tracked for links in group
    major: Symbol table
    minor: Object not found

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brtnfld avatar brtnfld commented on May 29, 2024

It looks to me that the file was created with a version of HDF5 < 1.8 (1.6?) because the creation order was not set and that only happens in CGNS if,

#if H5_VERS_MAJOR < 2 && H5_VERS_MINOR < 8
#define HDF5_PRE_1_8 1
#endif

This is not an issue in 3.3.1 because it uses H5Giterate, which does not have a creation order argument. But CGNS now uses H5Literate instead, which assumes the creation order is (mistakenly) always set.

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brtnfld avatar brtnfld commented on May 29, 2024

Creation order was introduced in CGNS 3.1.3, so the file is most likely from an older version of CGNS.

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brtnfld avatar brtnfld commented on May 29, 2024

A think this is fixed now with #690, re-open if that is not the case.

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