Update code to work with v1.14.5 of the HDF5 library #745

abensonca · 2024-11-26T19:29:27Z

This requires some changes to our HDF5 interface module, and fixes to file locking.

`h5py` is more reliable.

…mpting to lock the files We do our own locking as necessary.

…s writing to the output file `Parameters` group

…5 library attempting to lock them

github-actions · 2024-11-26T19:44:05Z

⚠️ Possible misspelled word 'nadler' in file 'source/output.analyses.Local_Group.occupation_fraction.F90'
⚠️ Possible misspelled word 'ctypes' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'vlen' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'vlen' (2 instances) in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'vlen' (2 instances) in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'vlen' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'integer8' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'vlen' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'

github-actions · 2024-11-27T08:01:04Z

⚠️ Possible misspelled word 'nadler' in file 'source/output.analyses.Local_Group.occupation_fraction.F90'
⚠️ Possible misspelled word 'ctypes' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'datatypes' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'datatypes' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'h5dread' (4 instances) in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'h5' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'h5' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 's1' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'datatypes' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'datatypes' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'vlen' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'vlen' (2 instances) in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'vlen' (2 instances) in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'vlen' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'integer8' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'vlen' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'

github-actions · 2024-12-01T22:08:15Z

⚠️ Possible misspelled word 'nadler' in file 'source/output.analyses.Local_Group.occupation_fraction.F90'
⚠️ Possible misspelled word 'ctypes' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'datatypes' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'datatypes' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'h5dread' (4 instances) in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'h5' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 's1' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'h5' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 's1' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'datatypes' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'vlen' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'datatypes' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
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⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'integer8' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'vlen' in file 'source/utility.IO.HDF5.F90'
⚠️ Possible misspelled word 'pre' in file 'source/utility.IO.HDF5.F90'

abensonca added 9 commits November 21, 2024 15:27

fix: Temporarily switch to using the HDF1.14.5 build environment

c42c43f

feat: Update for compatibility with HDF v1.14.5

49594d6

fix: Update comment section in HDF5 test file

5ad2f9b

fix: Switch to HDF5 v1.14.5 for MacOS builds

da153d0

fix: Port test codes to Python so that they work with HDF5 file reads

dc0f8be

`h5py` is more reliable.

fix: Open files in read-only mode to avoid the HDF5 library from atte…

c6c93ad

…mpting to lock the files We do our own locking as necessary.

fix: Use a pointer to parameters instead of a copy to avoid problem…

69ac047

…s writing to the output file `Parameters` group

fix: Ensure HDF5 file is closed

7929e4e

fix: Ensure HDF5 files are opened in read-only mode to avoid the LHDF…

5a9ca4f

…5 library attempting to lock them

abensonca added IO Input/output dependencies Pull requests that update a dependency file hdf5 labels Nov 26, 2024

abensonca self-assigned this Nov 26, 2024

fix: Adjust test tolerance

a2232d4

fix: Switch back to latest build environment

59a239b

abensonca added this pull request to the merge queue Dec 2, 2024

Merged via the queue into master with commit a6a5c8c Dec 2, 2024
290 of 291 checks passed

abensonca deleted the featHDF1.14.5 branch December 2, 2024 02:11

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Update code to work with v1.14.5 of the HDF5 library #745

Update code to work with v1.14.5 of the HDF5 library #745

abensonca commented Nov 26, 2024

github-actions bot commented Nov 26, 2024

github-actions bot commented Nov 27, 2024

github-actions bot commented Dec 1, 2024

Update code to work with v1.14.5 of the HDF5 library #745

Update code to work with v1.14.5 of the HDF5 library #745

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abensonca commented Nov 26, 2024

github-actions bot commented Nov 26, 2024

github-actions bot commented Nov 27, 2024

github-actions bot commented Dec 1, 2024