Larry Knox
97b8fad8ed
Revert "Fix metadata cache bug when resizing a pinned/protected entry ( #1358 )" ( #1437 )
...
This reverts commit 01092658a3
2022-02-11 22:34:16 -06:00
Neil Fortner
0f847f30bc
Fix issue with H5_now_usec() with 32 bit systems ( #1416 )
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* Implement H5ESget_requests() to retrieve request pointers and
corresponding connector IDs from an event set. Add tests for this
function.
* Add "order" parameter to H5ESget_requests, to allow the user to specify
the order in which requests are returned.
* Fix bugs with H5ESinsert_request()
* Change H5ESget_requests() API to have separate input and output
parameters for the allocated array length(s) (in) and the number of events in
the event set (out).
* Fix issue with H5_now_usec() with 32 bit systems. Also improve event
set test.
* Committing clang-format changes
* Add comments to H5_now_usec() explaining rationale for uint64_t casts.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-02-10 17:23:26 -06:00
jhendersonHDF
01092658a3
Fix metadata cache bug when resizing a pinned/protected entry ( #1358 )
...
When resizing a pinned/protected cache entry, the metadata
cache code previously would wait until after resizing the
entry to attempt to log the newly-dirtied entry. This would
cause H5C_resize_entry to mark the entry as dirty and make
H5AC_resize_entry think that it doesn't need to add the
newly-dirtied entry to the dirty entries skiplist.
Thus, a subsequent H5AC__log_moved_entry would think it
needs to allocate a new entry for insertion into the dirty
entry skip list, since the entry doesn't exist on that list.
This causes an assertion failure, as the code to allocate a
new entry assumes that the entry is not dirty.
2022-02-07 22:04:41 -06:00
jhendersonHDF
36d9a165e4
Fix a few issues noted by LGTM ( #1421 )
2022-02-04 10:53:55 -06:00
jhendersonHDF
86ef00fd67
Unify handling of collective metadata reads status ( #1206 )
2022-01-29 14:22:30 -06:00
David Young
2b3bb3659c
Fix some spelling. ( #1402 )
2022-01-28 16:44:47 -06:00
Sean McBride
4ac6ccc021
Snprintf2 ( #1399 )
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* Replaced many uses of sprintf with safer snprintf
Many very straightforward, but in a few cases added a length parameter to some private functions, because buffer length was otherwise unknowable.
* Removed unnecessary use of static on small buffers
This improves thread safety.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-28 16:43:48 -06:00
Allen Byrne
ad71539d30
Remove const from the argv tools/tests main sig. ( #1390 )
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* Remove const from the argv tools/tests main sig.
* also remove const from H5_get_option and parse_command_line.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-28 16:30:33 -06:00
Sean McBride
b5eed1b563
Replaced several uses of sprintf with safer snprintf ( #1383 )
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* Replaced several uses of sprintf with safer snprintf
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-28 10:34:57 -06:00
Sean McBride
44de59b642
Used clang-tidy to change all floating point f suffixes to F ( #1359 )
2022-01-28 08:31:26 -06:00
Larry Knox
5fb634ca26
Revert 61464d7e ( #1396 )
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Commit 61464d7e61464d7e
2022-01-26 16:58:49 -06:00
jhendersonHDF
99d3962a83
Parallel rank0 deadlock fixes ( #1183 )
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* Fix several places where rank 0 can skip past collective MPI operations on failure
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-22 08:40:33 -06:00
Sean McBride
d45124d708
Open bsd fixes ( #1195 )
2022-01-20 08:38:56 -06:00
Neil Fortner
dd6ad33c75
Implement H5ESget requests function to retrieve requests from an event set ( #1355 )
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Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-20 07:34:43 -06:00
jhendersonHDF
6c184e28d8
Fix documentation for H5D_space_status_t enum values ( #1372 )
2022-01-19 14:29:37 -06:00
Allen Byrne
bd37363332
various cleanup java test, test files, comments ( #1363 )
2022-01-18 15:52:01 -06:00
Gerd Heber
e56b0a3d50
Documentation fixes right in time for the holidays ( #1321 )
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* Sketch of the H5S life cycle.
* Committing clang-format changes
* Fix H5S_UNLIMITED snafu.
* Updated RM template and RM page.
* Added H5S life cycle.
* Committing clang-format changes
* Added H5T life cycle.
* Committing clang-format changes
* Cleaner layout (?)
* Cleaned the H5F life cycle. Called out unfinished biz.
* Committing clang-format changes
* Remaining life cycle skeletons.
* Committing clang-format changes
* Committing clang-format changes
* Added H5Z life cycle.
* Committing clang-format changes
* Added H5G life cycle.
* Committing clang-format changes
* H5 and H5I life cycle updates.
* Committing clang-format changes
* Added H5PL life cycle.
* Committing clang-format changes
* Added H5L life cycle.
* Committing clang-format changes
* Fix for Chris' comment.
* Add a variable for Doxygen pre-processor definitions.
* Forgot to add the H5M API.
* Clarify the H5Z life cycle.
* Committing clang-format changes
* Add H5Zdevelop.h to Doxygen.in. Added H5I life cycle.
* Committing clang-format changes
* Clarified introduction and fixed missing label declaration.
* Added H5O life cycle.
* Committing clang-format changes
* H5O cleanup, part 1.
* Committing clang-format changes
* Cleaned up some of the endless repetition in H5O.
* Committing clang-format changes
* Cookbook & RFC draft layouts.
* Updated manifest.
* Updated the manifest, the example paths, and sketched the 1st recipe.
* Committing clang-format changes
* Outlined two more recipes.
* Committing clang-format changes
* More recipes and RFCs.
* Committing clang-format changes
* Draft of templatized RFC references.
* Another batch of RFC changes.
* Another batch of RFCs.
* Fixed reference.
* RFCs in reverse chronological order.
* First cut of RFCs.
* Fixed reference.
* Updated recipes.
* Updated recipes.
* More RFCs.
* Updated D*PL comments.
* Added H5P descriptions.
* Committing clang-format changes
* H5R life-cycle snapshot.
* Committing clang-format changes
* H5R life-cycle. Added line numbers to life-cycle examples.
* Committing clang-format changes
* Fixed formatting for H5Dchunk_iter().
* Added comment on collective mode requirement w/ compression.
* Simplified API compat. macro dox.
* More API vers. updates.
* Hide the async macro entrails.
* Latest VFD SWMR RFC.
* Create a tag file for permalinks.
* Added TODOs for metadoc.
* Removed duplication.
* Revised RM landing page.
* Trimmed more duplication.
* Committing clang-format changes
* Revised H5D.
* Committing clang-format changes
* Updated survey link.
* Added Doxygen RM entry template link.
* Added the "Multi-Thread HDF5" RFC.
* Added DOXYGEN_TAG_FILE.
* Added selection I/O RFC.
* Added the VFD Sub-filing RFC.
* Updated meta-documentation and added two old presentations.
* Added a few more RFCs (4).
* Fixed MANIFEST.
* Updated meta-documentation.
* Added Filters technical note.
* Fixed MANIFEST.
* Restore the path stripper.
* Experimental full-text search via Google.
* Better full-text search integration.
* Whoops. Forgot this one.
* Oh boy.
* Make CMake happy.
* Added "Debugging HDF5 Applications" technical note.
* Another batch of RFCs.
* Fixes for #1221 .
* Updated overview.
* Fixed image dependencies.
* CMake updates.
* Fixed SET.
* Better?
* Update doxygen/dox/Overview.dox
* Fixed documentation errors. Added missing version info.
* Callback documentation updates.
* Fixed indexing errors in the outline.
* Doxygen-ized the HDF5 glossary.
* Fix a few minor typos
.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2022-01-13 22:11:39 -06:00
jhendersonHDF
166ce5b027
Fix H5ACmpio dirty bytes creation debugging ( #1357 )
2022-01-12 16:58:45 -06:00
Allen Byrne
5fffd563de
cmake custom command fix ( #1356 )
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* From gitlab.kitware.com/third-party/hdf5 rework custom commands
commit/757aa42ebff8c9819c054f5e00559143c60f653d
* Correct stamp file generation
* Needs to support pregenerated H5Tinit.c file
* Adjust custom command for all build systems types
* Custom target only depends on OUTPUT of custom command
2022-01-12 14:27:56 -06:00
Scot Breitenfeld
4aabac62f8
Corrected H5Oget_info parameter description ( #1349 )
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* H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289
* H5Oget_info_by_name, name can be any object, not just a group
2022-01-11 12:17:05 -06:00
jhendersonHDF
a13bf24a39
Use appropriate printf format specifiers for haddr_t and hsize_t types directly ( #1340 )
2022-01-11 12:16:10 -06:00
Scot Breitenfeld
54237d777a
H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289 ( #1335 )
2022-01-10 18:47:57 -06:00
Baljak
8430e3d661
Fix compilation issues with Mingw ( #1342 )
2022-01-07 22:29:25 -06:00
H. Joe Lee
bf27121b5d
OESS-168: Remove clang warnings. ( #1308 )
2022-01-07 16:30:18 -06:00
H. Joe Lee
58e2157c7e
OESS-168: Remove clang warnings. ( #1305 )
2022-01-07 16:29:56 -06:00
H. Joe Lee
a564ec39af
OESS-168: Remove clang warnings. ( #1304 )
2022-01-07 16:29:30 -06:00
jhendersonHDF
9e6de287e7
Fix usage of several HDfprintf format specifiers after HDfprintf removal ( #1324 )
2022-01-04 11:00:55 -06:00
H. Joe Lee
86b8062699
Fix typo. ( #1303 )
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chksum -> checksum
2022-01-04 11:00:14 -06:00
H. Joe Lee
227d7d927b
Fix typo. ( #1301 )
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If the are -> If they are
2022-01-04 10:59:54 -06:00
H. Joe Lee
6fc53b39a2
OESS-168: Remove clang warnings. ( #1300 )
2022-01-04 10:58:58 -06:00
H. Joe Lee
69251f58aa
OESS-168: Remove clang warnings. ( #1297 )
2021-12-15 16:21:15 -06:00
jhendersonHDF
300a4e2478
Call FUNC_ENTER immediately in H5_init_library ( #1287 )
2021-12-13 17:31:02 -06:00
jhendersonHDF
ca28e3e631
Fix free list tracking and cleanup cast alignment warnings ( #1288 )
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* Fix free list tracking and cleanup cast alignment warnings
* Add free list tracking code to H5FL 'arr' routines
2021-12-13 17:30:22 -06:00
jhendersonHDF
dd3c61c384
Fixes for async operations ( #1272 )
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Setup VOL wrapping context for each "request" callback
Set H5ES_event_t "next" pointer to NULL when appending to event list
2021-12-10 22:48:50 -06:00
jhendersonHDF
c0a13fd9d8
Remove duplicate memcpy in chunk_file_cb ( #1285 )
2021-12-10 20:22:49 -06:00
jhendersonHDF
364d8cc3e7
Initialize filter mask and chunk nbytes for 'Single' chunk index ( #1261 )
2021-12-09 15:28:52 -06:00
Larry Knox
40a23b67ea
Correct spelling correction of preceed incorrectly to proceed. Should ( #1268 )
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* Correct spelling correction of 'preceed' incorrectly to 'proceed'. It should be 'precede'.
2021-12-07 15:07:15 -06:00
Scot Breitenfeld
f859cb732b
Fixed Spelling Errors ( #1166 )
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* fixed missed closing of a dataset
* fixed missed closing of a dataset
* fixed typo in error return
* Committing clang-format changes
* minor edits
* code format
* Committing clang-format changes
* code format
* minor edit
* switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging
* Committing clang-format changes
* changed size_i in printf to reflect the I/O.
* Committing clang-format changes
* Fixed seg fault with xlf on BE with -qintsize=8
* fixed error function string
* spelling corrections via codespell, added new spell check github actions
* Committing clang-format changes
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* Committing clang-format changes
* misc
* misc
* misc
* misc
* misc
* misc
* Committing clang-format changes
* misc
* work around for https://github.com/codespell-project/codespell/issues/2137
* misc
* added missing file
* misc
* misc.
* misc
* switch to using Codespell with GitHub Actions
* misc.
* misc.
* fixed more sp errors
* Fix new typos found by codespell.
* fixed proceed with precede
* fixed variable in fortran test
* fixed minnum
* updated spelling list
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2021-12-07 08:27:29 -06:00
Larry Knox
89ad105b1c
Update version to 1.13.1-1 after creation of branch for 1.13.0 release. ( #1236 )
2021-11-30 12:53:45 -06:00
jhendersonHDF
ed92286131
Only check HDF5_DRIVER in MPI I/O VFD if VFD isn't initialized ( #1213 )
2021-11-24 21:14:45 -06:00
jhendersonHDF
b3262c75d5
Fix a few H5CX warnings from recent init changes ( #1224 )
2021-11-24 16:22:09 -06:00
jhendersonHDF
7cf5c29615
Fix a few warnings after recent H5S const-related changes ( #1225 )
2021-11-24 16:20:30 -06:00
Dana Robinson
ca6f9e3716
Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs ( #1222 )
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* Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs
Filter IDs < 0 or > H5Z_FILTER_MAX could trip an assert in the
library due to missing ID range checks in H5Pget_filter_by_id1/2.
The library now returns a normal error code when filter IDs are
out of range. Fixes HDFFV-11286.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-24 16:20:13 -06:00
Gerd Heber
5c06121976
Closes #1221 ( #1223 )
...
* Sketch of the H5S life cycle.
* Committing clang-format changes
* Fix H5S_UNLIMITED snafu.
* Updated RM template and RM page.
* Added H5S life cycle.
* Committing clang-format changes
* Added H5T life cycle.
* Committing clang-format changes
* Cleaner layout (?)
* Cleaned the H5F life cycle. Called out unfinished biz.
* Committing clang-format changes
* Remaining life cycle skeletons.
* Committing clang-format changes
* Committing clang-format changes
* Added H5Z life cycle.
* Committing clang-format changes
* Added H5G life cycle.
* Committing clang-format changes
* H5 and H5I life cycle updates.
* Committing clang-format changes
* Added H5PL life cycle.
* Committing clang-format changes
* Added H5L life cycle.
* Committing clang-format changes
* Fix for Chris' comment.
* Add a variable for Doxygen pre-processor definitions.
* Forgot to add the H5M API.
* Clarify the H5Z life cycle.
* Committing clang-format changes
* Add H5Zdevelop.h to Doxygen.in. Added H5I life cycle.
* Committing clang-format changes
* Clarified introduction and fixed missing label declaration.
* Added H5O life cycle.
* Committing clang-format changes
* H5O cleanup, part 1.
* Committing clang-format changes
* Cleaned up some of the endless repetition in H5O.
* Committing clang-format changes
* Cookbook & RFC draft layouts.
* Updated manifest.
* Updated the manifest, the example paths, and sketched the 1st recipe.
* Committing clang-format changes
* Outlined two more recipes.
* Committing clang-format changes
* More recipes and RFCs.
* Committing clang-format changes
* Draft of templatized RFC references.
* Another batch of RFC changes.
* Another batch of RFCs.
* Fixed reference.
* RFCs in reverse chronological order.
* First cut of RFCs.
* Fixed reference.
* Updated recipes.
* Updated recipes.
* More RFCs.
* Updated D*PL comments.
* Added H5P descriptions.
* Committing clang-format changes
* H5R life-cycle snapshot.
* Committing clang-format changes
* H5R life-cycle. Added line numbers to life-cycle examples.
* Committing clang-format changes
* Fixed formatting for H5Dchunk_iter().
* Added comment on collective mode requirement w/ compression.
* Simplified API compat. macro dox.
* More API vers. updates.
* Hide the async macro entrails.
* Latest VFD SWMR RFC.
* Create a tag file for permalinks.
* Added TODOs for metadoc.
* Removed duplication.
* Revised RM landing page.
* Trimmed more duplication.
* Committing clang-format changes
* Revised H5D.
* Committing clang-format changes
* Updated survey link.
* Added Doxygen RM entry template link.
* Added the "Multi-Thread HDF5" RFC.
* Added DOXYGEN_TAG_FILE.
* Added selection I/O RFC.
* Added the VFD Sub-filing RFC.
* Updated meta-documentation and added two old presentations.
* Added a few more RFCs (4).
* Fixed MANIFEST.
* Updated meta-documentation.
* Added Filters technical note.
* Fixed MANIFEST.
* Restore the path stripper.
* Experimental full-text search via Google.
* Better full-text search integration.
* Whoops. Forgot this one.
* Oh boy.
* Make CMake happy.
* Added "Debugging HDF5 Applications" technical note.
* Another batch of RFCs.
* Fixes for #1221 .
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-24 08:32:53 -06:00
jhendersonHDF
3f2271364e
Make sure plugin interface is initialized before property list interface phase 2 ( #1216 )
2021-11-23 08:04:11 -06:00
Dana Robinson
3a2b3bb035
Stop lying about H5S_t const-ness ( #1209 )
...
Hyperslabs can be reworked inside several H5S callbacks, making H5S_t
non-const in some places where it is marked const. This change switches
these incorrectly const H5S_t pointer parameters and variables to
non-const where appropriate.
2021-11-20 08:34:50 -06:00
Dana Robinson
56ba9da70b
Fixes const warnings in H5ES package ( #1211 )
2021-11-18 16:56:32 -06:00
jhendersonHDF
cae59a0f11
Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs ( #1201 )
2021-11-18 10:07:29 -06:00
Dana Robinson
d224f98dbc
Quiets most const warnings in the fractal heap code ( #1188 )
2021-11-12 22:36:32 -06:00
jhendersonHDF
b9da39d19f
Fix MPI Comm and Info leak in H5FD__mpio_delete ( #1189 )
2021-11-12 11:28:47 -06:00
