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* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Fixes a bad memory read and unfreed memory in fsinfo code (#893)Dana Robinson2021-08-121-9/+12
| | | | | | | | | | | | | | * Fixes a bad memory read and unfreed memory in fsinfo code The segfaul from CVE-2020-10810 was fixed some time ago, but the illegal memory read and unfreed memory were not. This fix tracks some buffer sizes and errors out gracefully on errors, ensuring buffers are cleaned up and avoiding the H5FL infinite loop + abort on library close. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)Sean McBride2021-03-101-1/+1
| | | | | | | | | * 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>
* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * 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.
* develop revert source to clang-format version 11 (#293)Allen Byrne2021-01-291-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction
* Basic alignment with async branch (#115)Quincey Koziol2020-11-231-3/+3
| | | | | | | * Basic alignment with async branch - trivial changes to reduce clutter in overall diff. * Update minor error code to reflect change within library * Update the error output to match library
* Clang-format of source filesAllen Byrne2020-09-301-346/+322
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-7/+3
| | | | | | 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.
* Trim trailing whitespaceQuincey Koziol2020-04-201-29/+29
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* merge and fix conflictkmu2020-01-191-3/+3
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* | fix unused related warningskmu2020-01-131-3/+3
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* - Added H5MMprivate.h #includes where neededDana Robinson2019-03-161-0/+1
| | | | | - Added casts to quiet H5MM_memcpy warnings - Removed char * casts from HDmemcpy
* Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-3/+3
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* Merge pull request #1441 in HDFFV/hdf5 from ↵Binh-Minh Ribler2019-01-091-1/+2
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_bmr_fixbug:develop to develop * commit '90d13bef33f9e2e80b23996a0c39f16f7c34ecf8': Fixed typo Platforms tested: Darwin (osx1010test) Refixed HDFFV-10578 Description: Applied Neil's fix for this issue after removing previous attempt. The resources are now released in init_objs() when failure occurs there. Neil will fix HDFFV-10676 separately. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test) Removed previous change in H5O__chunk_deserialize(). Removed the previous change in H5O__chunk_deserialize() Removed previous change in table_list_add(). Removed the previous change in table_list_add() Updated per review Description: HDFFV-10676 - CVE-2018-13873 Changed the new assert to if statement, per Dana's comment. Platforms tested: Linux/64 (jelly) HDFFV-10578 and HDFFV-10676 Description: HDFFV-10578 - CVE-2018-17234 The file has some issue, however, there was a bug in h5dump that caused memory leaks after the problem in the file was encountered. The bug was that an if statement was missing in the function table_list_add() resulting in the memory not being freed at a later time. After the fix had been applied, there were no more leaks after h5dump detected the issue in the file and reported the error.
| * Removed previous change in H5O__chunk_deserialize().Binh-Minh Ribler2019-01-071-1/+0
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| * Removed the previous change in H5O__chunk_deserialize()Binh-Minh Ribler2019-01-071-2/+0
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| * Updated per reviewBinh-Minh Ribler2019-01-071-1/+2
| | | | | | | | | | | | | | | | Description: HDFFV-10676 - CVE-2018-13873 Changed the new assert to if statement, per Dana's comment. Platforms tested: Linux/64 (jelly)
| * HDFFV-10578 and HDFFV-10676Binh-Minh Ribler2019-01-061-1/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: HDFFV-10578 - CVE-2018-17234 The file has some issue, however, there was a bug in h5dump that caused memory leaks after the problem in the file was encountered. The bug was that an if statement was missing in the function table_list_add() resulting in the memory not being freed at a later time. After the fix had been applied, there were no more leaks after h5dump detected the issue in the file and reported the error. In H5O__chunk_deserialize, replaced an assert with an if statement and reporting error, per Neil's recommendation HDFFV-10676 - CVE-2018-13873 Also in H5O__chunk_deserialize, added an assertion to detect out of bound ids
* | Delay checking if decoded message's "shareable" flag is appropriate forNeil Fortner2019-01-071-5/+12
|/ | | | | | | | | | | the message type until we've verified we understand the message type. Reduce size of H5O_msg_class_g to *not* include space for H5O_BOGUS_INVALID. Make bogus messages shareable. Add new bogus message test with shareable messages to cover the formerly problematic code. Re-run gen_bogus.c to add this test case and also to fix the bogus_invalid messages that were no longer H5O_BOGUS_INVLAID due to a new message class being added in a previous commit. Added comment to remind developers to run gen_bogus.c when adding a new message class.
* HDFFV-10607 Fixing two compiler warnings in the library.Songyu Lu2018-11-271-1/+1
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* Remainder of vol_normalization changes (dataset, attribute, files, objects).Dana Robinson2018-09-241-10/+10
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* Fixed HDFFV-10476, HDFFV-10478, HDFFV-10480Binh-Minh Ribler2018-07-171-0/+2
| | | | | | | | | Description: Fixed potential out of bound read and NULL pointer dereferences. Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
* Fix for HDFFV-10333:Vailin Choi2018-07-111-11/+17
| | | | | | | | | 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 Koziol2018-03-181-9/+34
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Fix for HDFFV-10209 VDS SWMR test failureVailin Choi2018-03-091-7/+32
| | | | | | | | Free the object header when there are chksum retries.
| * Fix for HDFFV-10355 (CVE-2017-17506).Dana Robinson2018-02-271-2/+2
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* | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-40/+28
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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.
* Bring changes to metadata cache "get entry status" call and newQuincey Koziol2017-01-061-0/+4
| | | | | "child serialized / unserialized" messages and support from the cache image branch.
* Refactor several cache clients to have only one copy of their deserializationQuincey Koziol2016-12-301-138/+186
| | | | code.
* Merge SWMR-related testing to existing tests.Quincey Koziol2016-12-181-6/+0
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* Bring SWMR support in to the main development branch. (Finally!) More testsQuincey Koziol2016-12-021-3/+96
| | | | and the tool and API wrappers will be coming in over the weekend.
* Bring over support for retrying metadata cache entry loads, along with all theQuincey Koziol2016-11-201-201/+273
| | | | supporting metadata cache callback changes, etc.
* Remove 'clear' callback from metadata cache client interface, using theQuincey Koziol2016-11-181-147/+132
| | | | new 'entry cleaned' notify action innstead.
* Remove explicit support within the metadata cache for tracked compressedQuincey Koziol2016-11-171-20/+7
| | | | entries, they are now completely handled in the clients.
* Refactor H5O code to clean up message allocation, align cache deserialize codeQuincey Koziol2016-11-121-145/+144
| | | | with revise_chunks changes, and remove unused "message locking" code.
* Code style and warning cleanups, from revise_chunks branch.Quincey Koziol2016-11-061-2/+2
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* [svn-r30189] Description:Quincey Koziol2016-07-181-2/+2
| | | | | | | | | Clean up more warnings: drop the warning count from ~1310 down to ~940, with only 31 types of warnings in 148 files (down from 38 types in 167 files). Tested on: MacOSX/64 10.11.5 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r30131] Fix bug reported by Cisco Talos TALOS-CAN-0178. Added check for ↵Neil Fortner2016-07-011-0/+4
| | | | | | | | | a message that should not be sharable being marked as sharable on disk, returns failure in this case. Needs testing. Tested: ummon
* [svn-r29548] Minor normalization w/ trunk in preparation for big merge.Dana Robinson2016-03-241-1/+0
| | | | | | Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial autotools parallel (MPICH 3.1.4)
* [svn-r29202] Fix for unknown message HDFFV-9697.Vailin Choi2016-02-241-6/+7
| | | | Tested on jam, ostrich, platypus, kite, quail, osx1010test, emu, mayll, moohan.
* [svn-r27768] Description:Quincey Koziol2015-09-141-3/+3
| | | | | | | | | | | | | | | | | | | | | | 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-r27623] Added some parallel #ifdefs to H5Ocache.c to quiet compilerDana Robinson2015-08-311-1/+21
| | | | | | warnings. tested on: h5committest
* [svn-r27292] Description:Quincey Koziol2015-06-271-4/+5
| | | | | | | | | | Bring 'fail if unknown always' object header message flag from the avoid_truncate branch, strengthen error checking for unknown messages, and try to catch object header code configurations at compile time (instead of runtime). Tested on: MacOSX/64 10.10.3 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r27237] Description:Quincey Koziol2015-06-181-505/+524
| | | | | | | | | Merge v3 metadata cache changes to trunk. Yay! :-) Tested on: MacOSX/64 10.10.3 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial & parallel (daily tested on branch)
* [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.
* [svn-r27082] Description:Quincey Koziol2015-05-151-48/+40
| | | | | | | | Clean up H5O interface, to align w/v3 metadata cache changes Tested on: MacOSX/64 10.10.3 (amazon) w/serial & parallel Linux/32 2.6.* (jam) w/serial & parallel
* [svn-r27045] Renamed H5_ASSIGN_OVERFLOW() to H5_CHECKED_ASSIGN() and re-orderedDana Robinson2015-05-101-1/+1
| | | | | | the arguments to be in a more logical order. Tested on: h5committest
* [svn-r25984] change the message flag H5O_MSG_FLAG_FAIL_IF_UNKNOWN toMohamad Chaarawi2015-01-201-2/+3
| | | | | | | | H5O_MSG_FLAG_FAIL_IF_UNKNOWN_AND_OPEN_FOR_WRITE. Will add a new H5O_MSG_FLAG_FAIL_IF_UNKNOWN_ALWAYS with the new avoid_truncate patch coming later. tested h5committest
* [svn-r24463] Issue 8484 - Segfault during H5Fopen of corrupt file. I put a ↵Raymond Lu2013-11-221-1/+1
| | | | | | condition check to make sure a pointer isn't NULL. Tested on jam - very simple change.
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