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* Prevent buffer overrun in H5S_select_deserialize (#2956)mattjala2023-05-181-3/+17
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* Add buffer overrun checks to H5O__layout_decode and H5O__sdspace_decode ↵jhendersonHDF2023-04-151-34/+222
| | | | (#2679) (#2729)
* Update Copyright headers. (#2534)Larry Knox2023-03-131-1/+0
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* clang 13 format #1933 (#1939)Allen Byrne2022-07-271-11/+11
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* Commit codespell spelling corrections.Larry Knox2022-04-071-1/+1
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* Hdf5 merge issue 488 v112 (#534)Larry Knox2021-04-011-10/+19
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Full set of current H5F documentation. (#105) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST. * Doxygen - added (mostly) beginner functions (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206) * 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. * Fixes various warnings noticed on Windows (#425) * Fixes various warnings noticed on Windows - Adds a prototype for our implementation of vasprintf - Return type of H5_get_utf16_str() is now non-const - Fixes possible uninitialized return type in Wremove_utf8 - Better isolation of fork() code in accum.c:test_swmr_write_big() - Better isolation of non-zlib code in dsets.c:test_filter_delete() - Removed unused variable in trefer.c:test_reference_cmpnd_obj() * Fixes clang-format issues * Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429) * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Added C++11 override keyword where appropriate (#433) Added H5_OVERRIDE macro for compatibility with both C++11 and older. * Various clang tidy warning fixes (#448) * Fixed clang-tidy bugprone-reserved-identifier warnings * Fixed clang-tidy bugprone-assert-side-effect warnings * Fixed clang-tidy bugprone-copy-constructor-init warning * Fixed clang-tidy readability-redundant-preprocessor warning For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block. Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS. * Fixed clang-tidy readability-redundant-string-init warnings * Fixed some clang-tidy performance-type-promotion-in-math-fn warnings * Fixed clang-tidy performance-unnecessary-value-param warnings * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Removed checks/workarounds for pre-C++89 compatibility (#449) After 30+ years, just assume that the following exist: - extension-less includes - namespaces - std:: - static_cast - bool * Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451) * Fixed all clang-tidy bugprone-suspicious-string-compare warnings This change was generated entirely by clang-tidy itself. * Reformat code with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451. * Purge the buffer used in type conversion. (#263) Some of the uniniitialized bits in the buffer may get carried through all the way to disk, creating a risk for leaks. We observed an msan error during the floating point output conversion. Due to the encoding certain bits could remain untouched during the conversion. In this draft we zero initialize the dbuf used by every convertor. * Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) (#405) * Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) Description Checked against buffer size to prevent segfault, in case of data corruption. + HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode + HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode Platforms tested: Linux/64 (jelly) * Accidentally left in another occurrence of the previous patch from user after a more correct fix was applied, that is the check now accounted for the previous advance of the buffer pointer. Removed it. * Typo * Fixed format issues. * Added test. * Changed arguments to ADD_H5_TEST * Fixing arguments to ADD_H5_TEST again. * Fixing arguments again. * Took out the CMake changes until Allen can help. * Added files: tCVE_2018_11206_fill_old.h5 tCVE_2018_11206_fill_new.h5 * Revert "Took out the CMake changes until Allen can help." This reverts commit c21324d6e0044994c5cd24b0671e7d1dd41096cc. * Revert "Fixing arguments again." This reverts commit 5832a70674339e4b524749adde5a181f8c3a446a. * Revert "Fixing arguments to ADD_H5_TEST again." This reverts commit b45de823c22ce83a388d46466ef7c04b66ff05ed. * Revert "Changed arguments to ADD_H5_TEST" This reverts commit 16719824f57e52158451ddd261788c0dcaa3ec55. * Added first argument to ADD_H5_TEST for HDFFV-10480 fix. * Changed argument 0 to 1 * Revert "Changed argument 0 to 1" This reverts commit b343d6613ba681b43248dd5820e96389984ebcf7. * Revert "Added first argument to ADD_H5_TEST for HDFFV-10480 fix." This reverts commit b8a0f9a9e8ec8e6c6ff38d33195d63edff76a563. * Added first argument and corrected the second. * Updated fixes for HDFFV-10480 and HDFFV-11159/HDFFV-11049 * Improved error messages. * Added description of the current HDF5 branches; added a draft of contribution policy. (#445) * Added description of the current HDF5 branches. * Removed capitalization in from Develop, Release, Feature to reflect the real naming schema * Added a draft of contributions guidance document. * Fixed typos. * Fixed section title. * Fixed typo. * Fixed typos and formatting. * Fixed many typos and simplified the text (e.g., removed testing instructions and left pointers to where to find them, etc.) * Fixed a typo. Please enter the commit message for your changes. Lines starting * Added contributing.md file and rearranged doc entries in alphabetical order. * ddressed Gerd's review comments; found and fixed more typos. * Addressed comments from Larry and Scot. * Fix CMake error message location. (#478) Print error message if Perl is not found. * Committing clang-format changes Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Yu Feng <rainwoodman@gmail.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> Co-authored-by: epourmal <epourmal@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-201-1/+1
| | | | file - src and test directories.
* Merge changes from developAllen Byrne2020-10-081-11/+10
| | | | | Comments and whitespace Skip file-locking and cache changes
* Source formattedAllen Byrne2020-10-011-298/+317
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-221-2/+2
| | | | | | header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* Whitespace cleanupAllen Byrne2020-05-131-1/+1
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* Merge pull request #2071 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings ↵Kimmy Mu2020-01-081-1/+1
| | | | | | | | | | | | | | | | | | | | | | to develop * commit '0a2bb11b248df6841daabca3970df5d8504adfc7': address problems from comments fix and address comments change according to previous comments add missing piece remove unnecessary check macro fix intel compile warnings Revert "fix warnings from Intel compiler" Revert "fix warnings and some text alignment" Revert "let hdf5 pick up the right compiler in Intel environment" Revert "fix issues from previous PR comments" Revert "using a different MACRO" using a different MACRO fix issues from previous PR comments let hdf5 pick up the right compiler in Intel environment fix warnings and some text alignment fix warnings from Intel compiler
* Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-6/+6
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* Fix issue with direct chunk write not updating the "last chunk" indexNeil Fortner2019-03-061-2/+4
| | | | | cache. Fix issues involving datasets being "no allocated" when they contain cached raw data.
* HDFFV-10571: Minor format changes.Songyu Lu2018-11-151-1/+1
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* HDFFV-10571: Minor change - reformatting the error check.Songyu Lu2018-11-151-1/+2
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* HDFFV-10571: Minor change - adding the error check right after decoding of ↵Songyu Lu2018-11-151-1/+6
| | | | chunk dimension for safeguard.
* Fix for HDFFV-10333:Vailin Choi2018-07-111-2/+2
| | | | | | | | | 1) Check for valid object header version for a refcount messge 2) Check for invalid fill value size 3) Check for invalid dimension size in a layout message 4) Add --enable-error-stack option to h5stat 5) Add error checks to h5stat.c 6) Add tests to h5stat and h5dump
* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-3/+42
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Fix for HDFFV-10355 (CVE-2017-17506).Dana Robinson2018-02-271-2/+3
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| * Changes made based on code reviews.Vailin Choi2018-01-121-2/+3
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| * (1) Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-11-251-1/+38
| | | | | | | | | | | | (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.
* | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-126/+20
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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.
* [svn-r29770] Description:Quincey Koziol2016-04-231-0/+12
| | | | | | | | Bring 'none' chunk index from revise_chunks branch to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (w/check-vfd) (h5committest forthcoming)
* [svn-r29738] Description:Quincey Koziol2016-04-191-0/+23
| | | | | | | | Bring "single" chunk index from revise_chunks branch to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (w/check-vfd) (h5committest forthcoming)
* [svn-r29659] Added fixed array chunk indexing from revise_chunks.Dana Robinson2016-04-071-0/+21
| | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 Autotools serial w/ Java, Fortran, & C++
* [svn-r29635] Description:Quincey Koziol2016-04-051-7/+90
| | | | | | | | | Bring support for earray and v2 B-trees from revise_chunks branch to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29607] Description:Quincey Koziol2016-04-021-31/+97
| | | | | | | | | Bring "don't filter partial edge chunks" capability from revise_chunks to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/debug, production & parallel (h5committest forthcoming)
* [svn-r29548] Minor normalization w/ trunk in preparation for big merge.Dana Robinson2016-03-241-36/+36
| | | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial autotools parallel (MPICH 3.1.4)
* [svn-r29081] - merge in the phdf5_metadata_opt/ branch with the collective ↵Mohamad Chaarawi2016-02-101-1/+1
| | | | | | | | metadata optimizations. - rename H5AC_dxpl_id to H5AC_ind_read_dxpl_id and update all usage in the library tested on bb-8 with parallel and serial.
* [svn-r28950] - remove META_FLUSH_COLLECTIVELY property for delayed sanity ↵Mohamad Chaarawi2016-01-211-1/+1
| | | | | | | | | | checks from metadata dxpls - remove H5AC_ind_dxpl_id and use only H5AC_dxpl_id everywhere instead. - remove flush_me_collectively flag from cache entries - add a collective sanity check (MPI_Barrier) for every HDF5 API routine that could possibly touch the file. This is trigerred when the environment variable H5_COLL_API_SANITY_CHECK is set to a non 0 digit. tested on BB-8 with serial and parallel.
* [svn-r28606] Description:Quincey Koziol2015-12-131-84/+82
| | | | | | | | | | Revisions to normalize revise chunks vs. trunk, plus push dataset metadata changes into the cache immediately (instead of holding them within the dataset data structures). Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r27835] Description:Quincey Koziol2015-09-211-7/+11
|\ | | | | | | | | | | | | | | Sync w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
| * [svn-r27811] Description:Quincey Koziol2015-09-161-0/+3
| | | | | | | | | | | | | | | | | | | | | | Refactor property list code to "deep copy" properties in the correct way, retraining the rest of the library to copy & release things correctly. This cleans up another batch of memory leaks, etc. within the library. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial & parallel (h5committest forthcoming)
| * [svn-r27768] Description:Quincey Koziol2015-09-141-7/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* | [svn-r27646] Add version number to VDS global heap object encoding.Neil Fortner2015-09-011-4/+21
| | | | | | | | | | | | | | | | | | Fix handling of layout version number. Other minor fixes/cleanup. NOTE: This commit changes the file format for VDS, all files must be re-generated. Tested: ummon
* | [svn-r27632] Description:Quincey Koziol2015-08-311-6/+6
| | | | | | | | | | | | | | | | | | | | Revert changes to pass file pointer to selection serialize/deserialize routines. Also patch back in some changes that were merged out in the previous merge w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial (h5committest not required on this branch)
* | [svn-r27630] Description:Quincey Koziol2015-08-311-16/+32
|\ \ | |/ | | | | | | | | | | | | Bring in changes from the trunk, through r27628. Tested on: MacOSX/64 10.10.5 (amazon) w/serial (h5committest not required on this branch)
| * [svn-r27614] Description:Quincey Koziol2015-08-291-12/+28
| | | | | | | | | | | | | | | | | | Align w/vds branch: Change code in H5O_layout_copy() to use switch for different types of dataset layouts. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest forthcoming)
| * [svn-r27612] Description:Quincey Koziol2015-08-291-3/+3
| | | | | | | | | | | | | | | | | | Align w/vds branch: Whitespace cleanup, move common code for opening a dataset into a new routine, misc. style cleanups. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest upcoming)
* | [svn-r27527] Add tests to hit code coverage assertions in H5Olayout.c.Neil Fortner2015-08-191-3/+0
| | | | | | | | | | | | Fix issue in VDS delete routine. Tested: ummon
* | [svn-r27501] Add mapping validity checking to VDS open.Neil Fortner2015-08-121-2/+10
| | | | | | | | | | | | Other minor fixes/cleanup. Tested: ummon
* | [svn-r27424] Implement support for h5debug for VDS.Neil Fortner2015-07-221-6/+21
| | | | | | | | | | | | | | | | | | | | Implement support for H5Pencode/decode with VDS properties. Testing for H5Pencode/decode with VDS. Relax assertion check for number of elements written to buffer as we do not check for overlaps in mappings. Other minor fixes/cleanup. Tested: ummon
* | [svn-r27323] Implement support for H5Dflush for VDS.Neil Fortner2015-07-021-1/+4
| | | | | | | | | | | | | | | | | | | | Implement support for H5Ocopy on VDS. Testing for H5Ocopy on VDS. Fix check-vfd failure. Other minor fixes/cleanup. Note there is a preexisting failure in h5repack testing. Tested: ummon
* | [svn-r27284] Modify VDS implementation to always use FAPL and DAPL from VDS ↵Neil Fortner2015-06-251-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | file and dataset to open source files and datasets, instead of using the default property lists. Modify VDS to reject attempts at parallel I/O, fix parallel compile error. Modify VDS to not write fill value to memory buffer if the fill value is undefined. Other minor fixes/cleanup. Tested: ummon
* | [svn-r27215] Fix issue where % characters could not be used in non-printf ↵Neil Fortner2015-06-161-12/+25
| | | | | | | | | | | | | | | | mappings. Other minor fixes/cleanup. Tested: ummon
* | [svn-r27192] Improve support for printf selections (support partial blocks withNeil Fortner2015-06-121-0/+6
| | | | | | | | | | | | | | | | | | | | H5_VDS_FIRST_MISSING) Add test for this Rework VDS code to not depend on unlimited selections having a "clipped" state in preparation for removing the clipped state from unlimited selections. Other bug fixes/cleanup Tested: Kubuntu 64 (home computer)
* | [svn-r27191] Merged r26781 to r27185 from trunkDana Robinson2015-06-111-6/+6
|\ \ | |/ | | | | | | Tested on: 64-bit Ubuntu Linux VM w/ gcc 4.8.2 (C++ and Fortran 2003 also tested)
| * [svn-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-6/+6
| | | | | | | | | | | | | | | | * H5_ATTR_FORMAT(X,Y,Z) __attribute__((format(X, Y, Z))) - Rename UNUSED attribute characterstic to H5_ATTR_UNUSED. - Rename NORETURN attribute characterstic to H5_ATTR_NORETURN tested with h5committest.
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