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* Fixes for various warnings/alignment with develop branch (#1755)jhendersonHDF2022-05-081-1/+1
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* [1.10 Merge] Hdf5 1 10 warnings merge (#1754)jhendersonHDF2022-05-081-7/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Warnings fixes (#1680) * Clean stack size warnings in sio_engine (#1687) * Fixes stack size warnings in tcoords.c (#1688) * Address some warnings from casting away of const (#1684) * Fixes stack size warnings in dtransform (#1696) * Fixes stack size warnings in set_extent test (#1698) * Be a bit safer with signed arithmetic, thus quieting some signed-overflow warnings from GCC (#1706) * Avoid a signed overflow: check the range of `entry_ptr->age` before increasing it instead of increasing it and then checking the range. This quiets a GCC warning. * Avoid the potential for signed overflow by rewriting expressions `MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`. This change quiets some GCC warnings. * Change some local variables that cannot take sensible negative values from signed to unsigned. This quiets GCC warnings about potential signed overflow. * In a handful of instances, check the range of a signed integer before increasing/decreasing it, just in case the increase/decrease overflows. This quiets a handful of GCC signed-overflow warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix object size warnings in cache.c test (#1701) * Fix some const cast and stack/static object size warnings (#1700) * Fix various warnings * Move HDfree_const to H5private.h for wider use * Print output from all ranks in parallel tests on allocation failure * Move const pointer freeing macro to h5test.h for now * Fixes a bug where t_cache fails due to a string size being too small (#1720) * Fixes a bug where t_cache fails due to a string size being too small Recent warning reductions led to an incorrect string size being passed to h5_fileaccess, causing the test to silently fail. In addition to fixing the bug, the test will now fail noisily on setup failures. * Updates the t_cache test to fail noisily on setup errors * Fix a few Clang sanitizer warnings (#1727) * 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. * Fix a few warnings after recent H5S const-related changes (#1225) * Adjustments for HDF5 1.10 * Hdf5 1 12 Miscellaneous warnings fixes (#1718) * Fixes const issues in the version 2 B-trees (#1172) The operations that were changed are fundamentally not const since the shadow operation can modify the node structure when SWMR is in use. * Quiets const warning in H5RS code (#1181) * Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the (#1171) * 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> * Miscellaneous warnings fixes Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix several warnings (#747) Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 1 10 parallel comp (#1644)jhendersonHDF2022-04-141-34/+21
| | | | | * Hdf5 1 10 parallel compression merge
* Hdf5 1 10 Update license url (#403)Larry Knox2021-03-011-1/+1
| | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Update license url (#332) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* Source formattedAllen Byrne2020-10-011-861/+860
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* Merge of clang-format changes from developAllen Byrne2020-09-301-0/+3
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* Fixed HDFFV-10933Binh-Minh Ribler2020-08-141-13/+21
| | | | | | | | | | | Description: Fixed to allow the creation of a dataset when the combination of type, space, etc doesn't work for filter and the filter is optional. Currently, it was supposed to be skipped as indicated in the documentation, but it was not skipped and the creation failed. The function H5Z_ignore_filters was added and used in H5D__create. Platforms tested: Linux/64 (jelly)
* Further normalization of H5S with developDana Robinson2020-07-081-1/+1
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* Normalization with develop in H5D and H5CX.Dana Robinson2020-06-021-63/+72
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* Brought the dsets test in line with develop. Brings over the fixDana Robinson2020-05-201-1/+1
| | | | for 0-size dataset metadata allocation.
* Moved H5MM_memcpy and H5MM_xfree_const from developDana Robinson2020-05-151-7/+7
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* Manual merge of H5T_copy constification (avoids VOL changes andDana Robinson2020-05-141-2/+2
| | | | messy diff).
* A fix in the cleaning up code for datatype when datatype initialization via ↵vchoi2020-04-081-3/+11
| | | | | | H5D__init_type() fails. The code to fix the problem is the same as what is done in H5D__open_oid().
* Add changes from PR #2049 to 1.10Chris Hogan2019-12-021-15/+62
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* Add DCPL to H5CXChris Hogan2019-11-271-5/+6
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* HDFFV-10658: setting and getting properties in API context. Porting the ↵Songyu Lu2019-07-261-26/+39
| | | | changes to the develop branch into the 1.10 branch: mainly the external file prefix and VDS prefix.
* Fix issue with direct chunk write not updating the "last chunk" indexNeil Fortner2019-03-191-1/+2
| | | | | cache. Fix issues involving datasets being "no allocated" when they contain cached raw data.
* Merge branch 'hdf5_1_10' of ↵Jacob Smith2018-12-311-131/+22
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into dset_ohdr_minimize_105
| * Removed 'VOL' versions of FUNC_ENTER macros as well as empty functionsDana Robinson2018-12-311-131/+22
| | | | | | | | orginally intended to support the full SWMR feature (from develop).
* | Incoporate minimized dataset headers code and tests.Jacob Smith2018-12-311-6/+227
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* Combined macro lines as Dana commentedBinh-Minh Ribler2018-07-261-2/+1
| | | | | Platforms tested: Linux/64 (jelly) (very minor)
* Fixed division-by-zero issuesBinh-Minh Ribler2018-07-261-16/+21
| | | | | | | | | | | Description: Fixed HDFFV-10481 and HDFFV-10477, division by 0. Fixed another occurrence beside what were reported. Also, changed a local variable to avoid an unnecessary cast. Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
* Fixed HDFFV-10404Binh-Minh Ribler2018-07-261-2/+2
| | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-05-081-359/+361
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| * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-04-291-963/+822
| |\ | | | | | | | | | merge_hyperslab_updates
| | * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-70/+92
| | |\ | | | | | | | | | | | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| | | * Modifications made based on comments from pull request.Vailin Choi2018-02-071-0/+1
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| | | * Merge branch develop into bugfix/version_boundsVailin Choi2018-01-121-24/+54
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| | | * | Changes made based on code reviews.Vailin Choi2018-01-121-10/+15
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| | | * | (1) Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-11-251-497/+325
| | | |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (2) Add two new options to h5repack for low and high bounds as in H5Pset_libver_bounds. (3) Modify message pre_copy callbacks so that H5Ocopy can handle version bounds check. (4) Add version bounds check for cache image feature.
| | | * | | Initial checkin for library version boundsVailin Choi2017-10-031-46/+31
| | | | | | | | | | | | | | | | | | | | | | | | Code changes to provide versioning support when adding to the enumerated defines for H5F_libver_t.
| | * | | | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-363/+364
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| * | | | Checkpoint normalization against incoming hyperslab / selection / dataspaceQuincey Koziol2017-03-281-5/+5
| | | | | | | | | | | | | | | | | | | | improvements.
* | | | | Needs to sync with lib version and Sencode.M. Scot Breitenfeld2018-03-071-47/+38
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* | | | | synced with developM. Scot Breitenfeld2018-01-051-24/+54
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| * | | | HDFFV-9724 Corrected files and verified testsAllen Byrne2017-12-281-24/+54
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| * | | | Revert "Merge pull request #826 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to ↵lrknox2017-12-221-54/+24
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop" This reverts commit b1223dd653e65e076af92b2dfe236f3704da81c8, reversing changes made to b25f123f5f5e25c1447a6a02861cb7c7265c12f2.
| * | | | HDFFV-9724 combine efc and vds into one functionAllen Byrne2017-12-131-101/+30
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| * | | | HDFFV-9724 Initial changes and testAllen Byrne2017-12-111-0/+101
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* | | | Fix for daily test failures.Vailin Choi2017-12-071-1/+1
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* | | Remove tabsAllen Byrne2017-11-081-516/+344
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* | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Jordan Henderson2017-08-111-3/+11
|\ \ | | | | | | | | | develop
| * | Fix for HDFFV-10217 infinite loop in H5VM_power2up().Vailin Choi2017-07-101-3/+11
| | | | | | | | | | | | | | | | | | The function H5VM_power2up() returns the next power of 2 for n. When n exceeds 2^63, it overflows and becomes 0 causing the infinite looping. The fix ensures that the function checks for n >= 2^63 and returns 0.
* | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Jordan Henderson2017-07-051-103/+107
|\ \ \ | |/ / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '6428a637752753cc8a9007c0c3c38b9ea9cc97fd': (165 commits) Skip HDFFV-10160 filenotclosed test for split/multi driver Temporary skip this test for split/multi driver. Further investigation to resolve the failure is needed. Please enter the commit message for your changes. Lines starting More minor whitespace cleanup Fixed a minor comment typo in H5R.c * Reverted removal of H5I_REFERENCE to avoid breaking binary compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19() in tmisc.c. Added missing free() call to test_misc19(). Purged the unused H5I_REFERENCE from the library. Added a test for VFD IDs to testhdf5. Revert "Partial removal of NDEBUG ifdefs from the library." Partial removal of NDEBUG ifdefs from the library. Removed compiler flag cleanup since Solaris chokes on it. Fix for HDFFV-10160 Modifications to fix the assertion/abort failure when the application does not close the file. Fixed a bug in autotools Fortran processing where a test for the presence of a C long double type always returned true. Updated the --enable-debug/production handling in configure.ac so that it more reliably indicates that the configure option can no longer be used. Previously, using --enable-debug="", etc. would not trigger an error (even though such usage is unlikely). Added awk processing to remove extraneous whitespace from H5_ flags in configure. Fixed a comment in configure.ac HDFFV-10219 another mode change HDFFV-10219 change subset to use BINARY mode for h5dump HDFFV-10219 default input binary to NATIVE Set default of var to NATIVE HDFFV-10219 - disable h5dump tests until h5import NATIVE is fixed ...
| * | Revert "Merge pull request #567 in HDFFV/hdf5 from ↵Dana Robinson2017-06-091-24/+16
| | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:develop to develop" This reverts commit 4242753848c44ab3b5d226e66225eac2f64db314, reversing changes made to b0e79fe6dd20ec7aa1b3e5f0f8b370639a4ef5bd.
| * | * Made STATIC free lists EXTERN for H5O_layout_t.Dana Robinson2017-06-071-1/+1
| | | | | | | | | | | | * Made all non-global instances of H5O_layout_t in H5Pdcpl.c dynamic.
| * | Updated H5O_layout_t dynamic work to use the H5FL interface.Dana Robinson2017-06-071-2/+5
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| * | Made some H5O_layout_t stack allocations dynamic (quiets warnings).Dana Robinson2017-06-061-16/+21
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| * | Fixed many minor warnings.Dana Robinson2017-05-251-97/+103
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| * | Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| |/ | | | | | | | | | | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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