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* Next batch of Doxygen updates. (#1180)Gerd Heber2021-11-2320-49/+2479
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the (#1171)David Young2021-11-231-4/+10
| | | | | | | | | | | | | | | | * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the raw H5R_ref_t bytes to a heap buffer that's known to have the right alignment. * Committing clang-format changes * Use an automatic H5R_ref_t instead of malloc'ing one. Go ahead and initialize the H5R_ref_t to all-0s so that arbitrary stack content doesn't foul things up. Bail out with an error if `size` exceeds `sizeof(H5R_ref_t)`. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Make sure plugin interface is initialized before property list interface ↵jhendersonHDF2021-11-233-8/+60
| | | | phase 2 (#1216)
* Stop lying about H5S_t const-ness (#1209)Dana Robinson2021-11-2018-239/+289
| | | | | | 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.
* Quiets a 'set but not used' warning in h5diff_array.c (#1210)Dana Robinson2021-11-181-0/+3
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* Fixes const warnings in H5ES package (#1211)Dana Robinson2021-11-181-5/+5
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* Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201)jhendersonHDF2021-11-181-4/+2
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* Github #969 Use stdout instead of file for configure check (#1089)Allen Byrne2021-11-184-158/+93
| | | | | | | | | | | | | * Use stdout instead of file for configure check * Make change requested by #1157 * Change fortran to use stderr for configure * Correct typo * remove obsolete file check * Fortran statement fix
* Add javadoc to packages - HDFFV-11285 (#1197)Allen Byrne2021-11-177-9/+282
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* Move -Werror=int-conversion from error-general to error-5 in (#1194)Larry Knox2021-11-142-1/+1
| | | gnu-warnings (unrecognized command line option for gcc 4.85/4.93.
* Quiets most const warnings in the fractal heap code (#1188)Dana Robinson2021-11-133-9/+32
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* Make it an error if the library implicitly converts from integer to (#1165)David Young2021-11-131-0/+2
| | | | | pointer or from pointer to integer (-Werror=int-conversion). Also, make it an error if the library explicitly converts to pointer from an integer of a different size (-Werror=int-to-pointer-cast).
* Fixes unused parameter warnings in the null VFD (#1179)Dana Robinson2021-11-131-0/+31
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* Fix MPI Comm and Info leak in H5FD__mpio_delete (#1189)jhendersonHDF2021-11-121-0/+6
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* Cleans up pointer and ID reset code in H5Pint.c (#1182)Dana Robinson2021-11-101-74/+112
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* Quiets const warning in H5RS code (#1181)Dana Robinson2021-11-101-2/+10
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* Fix H5DS warnings related to new H5DSwith_new_ref and H5VLobject_is_native ↵jhendersonHDF2021-11-104-30/+34
| | | | APIs (#1184)
* Fixes FUNC_ENTER warnings in VFDs due to recent init changes (#1178)Dana Robinson2021-11-106-15/+9
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* Fixes const issues in the version 2 B-trees (#1172)Dana Robinson2021-11-092-24/+21
| | | | The operations that were changed are fundamentally not const since the shadow operation can modify the node structure when SWMR is in use.
* Re-enable collective metadata reads after disabling for chunk lookup (#1173)jhendersonHDF2021-11-092-7/+28
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* Simplify function enter macros for performance benefits (#1024)David Young2021-11-0882-1989/+1115
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Take a stab at using constructors to initialize instead of function-entry macros. This is a work in progress. It's good enough to run `many_dsets`. * Committing clang-format changes * Add the `many_dsets` benchmark and some scripts I used on jelly for setting up the build/test environment and for recording/flame-graphing profiles. * Committing clang-format changes * Change my Makefile and environment script to work both on jelly and on mayll (and probably on Summit). * Disable clang-format "fix." * Replace the `if (!H5_TERM_GLOBAL)` test in each FUNC_ENTER_ macro with `if (true)`. * Fix bad grammar in a comment. * Instead of labeling the H5*__init_package routines constructors, fold each into an initialization routine, H5*_init(), and call each of the H5*_init() routines. Call most of the H5*_init() routines from H5_init_library() in an explicit order that I found out earlier by instrumenting each __init_package routine and running the library tests. Roll H5FD*__init_package routines into H5FD*_init() routines. This change ends just-in-time initialization of package dependencies by package initializers. Don't track in per-package variables (H5_PKG_INIT_VAR) whether each package has been initialized. Instead, track in a single library variable whether the whole library is initialized or not. Drive the initialization of packages by H5_init_library() with a table of initializer routines. Also drive the termination of packages by H5_term_library() with a table. Perform initialization as needed from FUNC_ENTER_API_INIT(err). This basically restores the old behavior of that macro. Delete a bunch of #definitions in H5private.h that have fallen out of use with these changes. * Committing clang-format changes * Undo the bad auto-formatting that appears to have occurred in spite of my disabling it. Bracket some code in /* clang-format off */ /* clang-format on */ to prevent a recurrence. * Remove a diagnostic abort(). * Fix a logic error: print a comma between every package terminator run, and don't print an initial comma. * Complete the changes I started in H5_term_library() that undo the bad auto-formatting. Stop tracking whether package "tops" were initialized in per-package variables H5*_top_package_initialize_s. H5_term_library() takes care of that for them. Remove H5R_top_term_package() and H5R_term_package(), they don't do anything. * Committing clang-format changes * NFCI. Simplify macro text: replace `if (true) {` with `{`. * Fix formatting and suppress clang-format on a longer range. * Quiet some unused label, unused variable complaints that cropped up after I simplified the FUNC_ENTER_ macros for the sake of performance. * Committing clang-format changes * Delete some programs and scripts that don't belong in the pull request. * Use the right function-entry macro. * Use a sensible format and disable auto-formatting. * Stop calling do-nothing initializer H5FS_init(). Delete it. * Document what changes to make if the default VFD changes. * While I am here, change an `await_prior` flag on the terminator table to `true` to match the previous, non-table-driven code that was here. Found the oversight making the following changes: NFCI: insert an empty line and copy over slightly-edited comments from the previous version, where those comments still correctly explained how library termination operated. * NFCI: lower a staircase. * Replace every occurrence of FUNC_ENTER_NOAPI_INIT(...) with H5_PUSH_FUNC since that is all that that macro does any more. Quiet a bunch of new warnings by changing FUNC_ENTER_NOAPI(...) to FUNC_ENTER_NOAPI_NOERR and removing disused `done:` labels. * NFCI: add curly braces around a multiline statement. * Quiet a signed/unsigned comparison warning. * Add some documentation about library initialization and shutdown. * Make sure that the library is initialized, or else that initialization is already underway, before performing any VFD's initialization. * Committing clang-format changes * Committing clang-format changes * Reduce differences from `develop` branch. * Always initialize `tot_init`. * Committing clang-format changes * Fix typo: H5SL_init initializes skip lists, not VOL. * Remove H5_TERM_GLOBAL test in H5T_init. H5T_init was unusual in that it tested H5_TERM_GLOBAL and exited early if it was set. No other module initializers did that, and I cannot find any reason that should be necessary. Tests still pass when I remove it, so away it goes. * Use HD prefix. * Add function header comments. * Drop the intermediate variable, it's only used once. * Extract subroutine `H5FDperform_init(hid_t (*init)(void))` that initializes the library, if necessary, before calling its VFD-initializer argument. Use H5FDperform_init in the definition of the symbols H5FD_<vfd> (e.g., H5FD_SEC2), which may be evaluated before the library is initialized, like so: ``` ``` I implement H5FDperform_init in its own source file, H5FDperform.c, and exclude that file from trace processing because the `bin/trace` cannot deal with the function-pointer type. * Straggler from last: add new source file src/H5FDperform.c. * Committing clang-format changes * Add a missing file to the MANIFEST. * Switch to FUNC_ENTER_API_NOINIT in H5FDperform_init() and hbool_t in H5_term_library(). Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix the function cast error in H5Dchunk.c and activate (#1170)David Young2021-11-082-5/+15
| | | `-Werror=cast-function-type`. Again.
* Add option for h5repack timing (#1142)Allen Byrne2021-11-086-51/+168
| | | | | | | | | | | | | | | | | * Add timing option to h5repack * Adjust help text * fix format * fix typos * Correct spacing * Change timing to use H5Timer * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Assume C99 fixed sized ints exist, use them (#470)Sean McBride2021-11-0827-506/+199
| | | | | | | | | | | | | * Committing clang-format changes * Assume C99 fixed sized ints exist, use them * Assume H5_SIZEOF_LONG_DOUBLE != 0, `long double` has existed since C89 Note, this is only assuming that `long double` exists, no assumptions about its size have been touched. Didn't remove any code that does things like test if `long double` and `double` have different sizes. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1124)H. Joe Lee2021-11-052-12/+22
| | | | | | | | | | | * OESS-168: Remove clang warnings. * OESS-168: Remove clang warnings. * Committing clang-format changes * OESS-168: Address @derobins review for FALLTHROUGH. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1136)H. Joe Lee2021-11-051-2/+2
| | | | | * OESS-168: Remove clang warnings. * OESS-168: Address @byrnHDF and @derobinson review.
* OESS-168: Remove clang warnings. (#1137)H. Joe Lee2021-11-051-68/+69
| | | | | * OESS-168: Remove clang warnings. * OESS-168: Address @derobins review.
* New references for Dimension Scale APIs (#1139)jhendersonHDF2021-11-0519-425/+826
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Enable usage of new-style references with dimension scale APIs * Add API to check if an object ID represents a native connector object * Modified code to use new function H5DSwith_new_ref to determine if new references should be used with Dimension Scales. The new function return TRUE if non-native connector is used or if H5_DIMENSION_SCALES_WITH_NEW_REF varible is define at configure time (--enable-dimension-scales-with-new-ref). Tested on jelly. ToDo: generate testing file on BE system and enable the test; add flag to CMake; test netCDF-4 with the new references. * Adding new test files generated on BE system (hedgehog) created by 32 and 64-bit library. test_ds chokes on test_ds_le_new_ref.h5 on BE system; test passes for test_ds_be_new_ref-32bit.h5 for the 32-bit library and fails for the 64-bit library, and vice versa. I am checking the files for further investigation; but current implementation of the new references is not portable between LE and BE systems, and 32 and 64-bit systems. * Minor fixes for testing issues * Update test_ds.c Enabled broken test; tests pass now. * Update RELEASE.txt Documented new option to use new references with the HDF5 dimension scales APIs (H5DS*). * Update MANIFEST for new 32-bit new-style references test file for H5DS APIs * Update 'dimension scales w/ new-style refs' feature based on review Co-authored-by: Elena <epourmal@hdfgroup.org>
* OESS-168: Remove clang warnings. (#1105)H. Joe Lee2021-11-041-33/+33
| | | | | | | | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes * OESS-168: Address @soumagne review. * Committing clang-format changes * OESS-168: Address @soumagne review. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix Java VOL tests (#1158)Allen Byrne2021-11-034-316/+15
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* OESS-168: Remove clang warnings. (#1146)H. Joe Lee2021-11-021-3/+3
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* OESS-168: Remove clang warnings. (#1135)H. Joe Lee2021-11-021-1/+1
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* OESS-168: Remove clang warnings. (#1127)H. Joe Lee2021-11-021-6/+6
| | | | | * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox clang-format review.
* Set the plugin path to the library default (#1144)Allen Byrne2021-10-291-0/+2
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* correct error checking string (#1143)Scot Breitenfeld2021-10-291-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Split dir create into separate macro (#1141)Allen Byrne2021-10-288-21/+31
| | | | | * Split dir create into separate macro * Correct VFD settings
* Github #1019 - add Fortran developer flags (#1090)Allen Byrne2021-10-275-10/+11
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* H5repack tests should fail if a corrupted file causes h5repack to (#1138)Larry Knox2021-10-263-6/+28
| | | | | | * H5repack tests should fail if a corrupted file causes h5repack to segfault/core dump. * Add release note for HDFV-10590, CVE-2018-17432.
* Consolidate VFD create list macro (#1132)Allen Byrne2021-10-267-10/+5
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* Removes the "try free" behavior from the skip lists (#1126)Dana Robinson2021-10-223-678/+200
| | | | | | | | | | | | | | * Removes the "try free" behavior from the skip lists This was only used in the ID code when iterating and a callback could delete IDs. It is not used anywhere else in the library and is now pointless overhead. Also quiets the const warnings when returning stored elements. They only need to be const with respect to the skip list code, which should never modify them. The library can do whatever it wants with the elements it stored. * Formatted source
* OESS-168: Remove clang warnings. (#1117)H. Joe Lee2021-10-211-1/+1
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* Fix map open to use correct VOL argument structure (#1116)jhendersonHDF2021-10-211-1/+3
| | | Fix map iterate by setting key memory type ID field
* Add release note for HDFFV-11150 fix. (#1106)Larry Knox2021-10-211-1/+23
| | | | | * Add release note for HDFFV-11150 fix. * Add note about gif tool CVEs.
* Correct java exception declarations (#1121)Allen Byrne2021-10-201-16/+19
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* Fixed HL_test_packet, incorrect length assignment (#1100)Allen Byrne2021-10-202-3/+7
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* Move test utilities to utils/test folder (#1109)Allen Byrne2021-10-2032-333/+340
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Move test utilities to utils/test folder * Fix makefile assignment * Add new dir * add new folder * Correct copied makefile * Fix dir typo * Add missing include dir * Remove unnecessary lib link * Correct dependent dirs * Fix conditional checks * Disable test if not built * fix path to executable * Use fixture for swmr_vfd check * Add release note * Correct shell tests and c++ flag warning * Update autotools c++ warning * Fix typo
* OESS-168: Remove clang warnings. (#1075)H. Joe Lee2021-10-201-12/+12
| | | | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes * OESS-168: Fix CI failure. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1072)H. Joe Lee2021-10-151-13/+13
| | | | | | | | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes * Address review by @jehndersonHDF. * Address review by @jehndersonHDF. * OESS-168: Fix CI failure. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1077)H. Joe Lee2021-10-081-1/+1
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* OESS-168: Remove clang warnings. (#1076)H. Joe Lee2021-10-082-10/+10
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