Sync develop changes May 6 - May 20 to hdf5_1_14 #4503
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…#4453) All calls to the H5I routines are now made in API routines (sometimes in FUNC_ENTER/LEAVE_* macros), except for some calls to H5E_clear_stack() within the library, but I'm planning to remove those over time. Also, made all the library internal error messages into static const variables, instead of malloc'ing them, which means that they can just be referenced and not copied. Several new and updated auto-generated header files were necessary to enable this.
…conversion (HDFGroup#4459) Also fixes issues with handling of partially initialized datatypes during library shutdown
…t sentence alias (HDFGroup#4474)
…up#4477) * Properly clean up cache when failing to load an object header * Don't check message type a second time in H5G__open_oid if the first attempt returns error * Add more asserts to H5O__assert() to avoid segfaults --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Fixes a race condition where the reader opens the file and sets its EOF from the file's size (from the stat() call in the driver open callback). Then, before the reader can read the file's superblock, a SWMR writer races in, extends the file, and closes the file, writing an updated superblock with the 'writer' and 'SWMR writer' flags in the superblock off (appropriately). Then the reader proceeds to read the superblock, and flags the EOF as wrong. Taking out the check for the 'writer' and 'SWMR writer' flags will cause SWMR readers to avoid flagging the file as incorrect.
Document the limitation in the Passthrough Conncector section of the VOL Connector Author Guide. The limitation is posted by Neil in the github issue on Dec 22, 2022.
…ze (HDFGroup#4491) * Improve spec. reading superblock into cache (a little) by using v2 size Instead of reading the absolute minimal possible, use the likely value of a v2+ superblock w/8-byte addresses & lengths.
…te with corder tracking enabled (HDFGroup#4462) * Fix for github issue HDFGroup#1388: can't delete renamed dense attribute with corder tracking enabled The problem occurs in step 3(b) below which will delete the attribute with corder x from the creation order index v2 B-tree. The rename sequence in H5A__dense_rename() occurs in the following order: 1) The old attribute with corder x was removed from the creation order index v2 B-tree 2) The new renamed attribute was inserted via H5A__dense_insert(): (a) insert the attribute with new name j into the name index v2 B-tree (b) insert the attribute with corder x into the creation order index v2 B-tree 3) The old attribute was removed via H5A__dense_remove(): (a) remove the attribute with old name k from the name index v2 B-tree (b) remove the attribute with coorder x from the creation order index v2 B-tree Fix: deactivate the "corder_bt2_addr" field so that H5A__dense_remove() won't delete the attribute with corder x from the creation order index v2 B-tree.
* Revert "Remove Autotools sed hack (HDFGroup#3848)" This reverts commit 8b3ffde. * Fix libtool sed cleanup on MacOS Convert sed -i line to sed > libtool.bak && mv libtool.bak libtool to avoid non-portable -i option.
lrknox
requested review from
jhendersonHDF,
byrnHDF,
derobins,
brtnfld,
epourmal,
fortnern,
qkoziol,
vchoi-hdfgroup,
bmribler,
glennsong09 and
mattjala
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lrknox
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lrknox
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Priority - 0. Blocker ⛔
byrnHDF
approved these changes
May 20, 2024
byrnHDF
reviewed
May 21, 2024
CMakePresets.json
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The plugin tgzname needs changed from master to 1_14. (line 42)
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Also then the plugins repo needs the PR merged
| find_package (ZLIB) # Legacy find | ||
| endif () | ||
| if (ZLIB_FOUND) | ||
| if (H5_ZLIB_FOUND) |
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Looks like we'll either need to merge the zlib/szip fixes immediately after this PR or add them here.
src/H5public.h
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| /** | ||
| * Short version string | ||
| */ | ||
| #define H5_VERS_STR "1.15.0" |
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I think h5vers will maintain this in the future, but I'm guessing for this PR that this should be set to 1.14.5 or similar?
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I updated the version in line94 to 1.14.5-1. I'm not sure h5vers will maintain it as it is, because H5VERS_STR in line 94 is new, apparently duplicating line 98 but without the "HDF5 library version:" text. I think it's unlikely that h5vers was updated to maintain H5_VERS_STR in either develop or hdf5_1_14. It should be done, though.
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h5vers was updated in #4453 where H5_VERS_STR was introduced.
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ok, that's good. #4453 is in the sync, so it's adding H5_VERS_STR, but h5vers didn't run yet in the hdf5_1_14 branch to update the version. It should be fine.
lrknox
commented
May 22, 2024
* Set H5 specific vars immediately if legacy find * Correct find process vars (vs in-line build) * Correct SZIP find * Everything is libaec 1.0.6 or newer * Correct option help text
…nox/hdf5 into sync_develop_changes_to_1_14
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