Commit Graph

22145 Commits

Author SHA1 Message Date
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
Allen Byrne
96cf19499b
Add -showconfig to h5cc scripts to dump libhdf5.settings file (#1391)
* Add -showconfig to h5cc scripts to dump libhdf5.settings file

* Added note
2022-02-11 07:46:09 -06:00
David Young
4ce6373a0b
Make a buffer bigger: GCC 8.3.0 warned that a snprintf may be (#1403)
truncated because the recipient buffer was too small, and the warning is
one that we promote to an error.  Now there is a warning that the buffer
is too big (-Wlarger-than=), but we don't promote those to errors, yet.
2022-02-11 07:39:52 -06:00
Scot Breitenfeld
7bfa873983
Fixed H5Dget_storage_size_f for zero sized datasets (#1430)
* 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

* fixed handling size 0 datasets

* fixed handling size 0 datasets

* format
2022-02-11 06:56:33 -06:00
Neil Fortner
0f847f30bc
Fix issue with H5_now_usec() with 32 bit systems (#1416)
* 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
Allen Byrne
c9347450c1
Implemented suggestion in #1381 for dtransform test (#1415)
* Implemented suggestion in #1380

* fix typo

* Use differently named files in tests

* format fix

* Revise comments

* fic typos

* Change test display and file name
2022-02-04 16:50:45 -06:00
jhendersonHDF
36d9a165e4
Fix a few issues noted by LGTM (#1421) 2022-02-04 10:53:55 -06:00
David Young
856de93673
Don't use a nonliteral format string in test/fheap.c:begin_test(). (#1401)
* Avoid using a non-literal formatting string with sprintf in begin_test.
Use snprintf.  Don't duplicate a string on the heap unnecessarily.

* Do not deactivate -Wformat-nonliteral: we don't use a nonliteral format
string any more.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-02-03 10:41:41 -06:00
Allen Byrne
1d598182d6
Update doc with HDF5_ROOT usage. (#1414) 2022-02-02 13:45:59 -06:00
jhendersonHDF
86ef00fd67
Unify handling of collective metadata reads status (#1206) 2022-01-29 14:22:30 -06:00
Sean McBride
bcf9565535
Added another missing override keyword on a dtor (#1384) 2022-01-29 14:21:30 -06:00
David Young
2b3bb3659c
Fix some spelling. (#1402) 2022-01-28 16:44:47 -06:00
Sean McBride
4ac6ccc021
Snprintf2 (#1399)
* 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)
* 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)
* 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)
Commit 61464d7e was a fix for a compiler error on OpenBSD where
int_fast8_t is in fact larger than 1 byte. However, the changes broke
H5detect.c generation of H5Tinit.c on Power8 big-endian, and probably on
all big-endian machines.  Switching DETECT_BYTE to DETECT_I for 8 byte types doesn't work on our big-endian Power8 machine because switching the last parameter of DETECT_I_BYTE_CORE from "int" to the 8 byte type incorrectly sets dt->shared->u.atomic.order = H5T_ORDER_LE on a big-endian machine.  A different fix to accomodate both big-endian and OpenBSD is needed.  See commit 61464d7e for OpenBSD info.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-26 16:58:49 -06:00
Allen Byrne
5222abdd19
Update code owners file with more names (#1386) 2022-01-26 09:05:25 -06:00
Allen Byrne
4d45d05078
Fix cmake dynamic analysis on windows (#1373)
* Fix sanitizer flag form on windows

* Add search paths to windows code-coverage
2022-01-24 07:46:17 -06:00
jhendersonHDF
99d3962a83
Parallel rank0 deadlock fixes (#1183)
* 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)
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
Matt McCormick
1a9662e04c
Do not set CMAKE_INSTALL_PREFIX when built externally (#1380) 2022-01-18 22:28:27 -06:00
Allen Byrne
bd37363332
various cleanup java test, test files, comments (#1363) 2022-01-18 15:52:01 -06:00
Allen Byrne
8dc72928b8
Develop java newrefs fixes for obj ref datasets (#1354)
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
2022-01-18 14:02:53 -06:00
Allen Byrne
2f34c433dc
Update the java slf4j logging jars to latest 1.7.33 (#1369) 2022-01-18 07:44:11 -06:00
Scot Breitenfeld
8b3c09f780
Updated README.txt to README.md (#1375)
* 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

* Converted README.txt to README.md and updated files referring to README.txt to README.md.

* removed references to README.txt

* updated MANIFEST
2022-01-14 17:28:04 -06:00
Gerd Heber
e56b0a3d50
Documentation fixes right in time for the holidays (#1321)
* 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)
* 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)
* 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
80017cba4f
fixed off-by-one error in h5fget_name_f, HDFFV-11290 (#1345)
* fixed off-by-one error in h5fget_name_f, HDFFV-11290

* fixed typo
2022-01-10 19:01:14 -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
Allen Byrne
f8f1fefe53
sort out/ref files for line compare (#1337) 2022-01-08 11:10:59 -06:00
Allen Byrne
03217eca81
Add tests for H5Ocopy of new object refs (#1338)
* Add tests for H5Ocopy of new object refs

* Correct class name

* Skip test because of issue with debug assertions

* Update reference file

* Fix object examples for new refs
2022-01-08 08:19:52 -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)
chksum -> checksum
2022-01-04 11:00:14 -06:00
H. Joe Lee
227d7d927b
Fix typo. (#1301)
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
Scot Breitenfeld
cf1aab28fb
Changed to correct return datatype for H5Lexists (#1330)
* changed to correct return datatype for H5Lexists

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-01-04 09:12:11 -06:00
H. Joe Lee
db61a888e6
OESS-168: Remove clang warnings. (#1295) 2021-12-15 16:22:04 -06:00
H. Joe Lee
c60bc0a07c
OESS-168: Remove clang warnings. (#1294) 2021-12-15 16:21:42 -06:00
H. Joe Lee
69251f58aa
OESS-168: Remove clang warnings. (#1297) 2021-12-15 16:21:15 -06:00