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* Hdf5 1 10 merge of printf specifiers and VS2015 min changes (#612)Allen Byrne2021-04-301-7/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 merge issue 488 v110 (#535)Larry Knox2021-04-021-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. * Cleans up a couple of MSVC warnings in testhdf5 (#475) * Fixes a few testhdf5 warnings raised in Visual Studio Visual Studio is grumpier about treating pointers like integers than gcc. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix typos and grammar errors. (#476) * Suppresses the tcheck_version test's abort dialog on Windows (#477) * Suppresses the tcheck_version test's abort dialog on Windows Windows raises a modal abort/retry/ignore dialog box when CRT calls abort(). This change installs a report hook that suppresses the dialog so that the CMake tests don't time out waiting for a nonexistent user to click a dialog box. * Committing clang-format changes * Removes __cdecl from callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * 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 * Update MANIFEST. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@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>
* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) (#417)bmribler2021-03-041-5/+14
| | | | | | | | | | | | | | | * 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 and A user's patch was applied to this previously, but it is redone for a more correct fix, that is the check now accounted for the previous advance of the buffer pointer. Platforms tested: Linux/64 (jelly) * Fixed format issues with clang formatter.
* 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 Byrne2020-10-011-296/+313
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* Normalizations with developDana Robinson2020-08-161-10/+4
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* Removed trailing whitespace from source files.Dana Robinson2020-05-261-1/+1
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* Moved H5MM_memcpy and H5MM_xfree_const from developDana Robinson2020-05-151-6/+6
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* merge intel warning fixKimmy Mu2020-01-091-1/+1
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* Fix issue with direct chunk write not updating the "last chunk" indexNeil Fortner2019-03-191-2/+4
| | | | | cache. Fix issues involving datasets being "no allocated" when they contain cached raw data.
* I'm bringing the fixes for the following Jira issues from the develop branch ↵Songyu Lu2019-02-121-1/+7
| | | | | | | | | to 1.10 branch: HDFFV-10571: Divided by Zero vulnerability. HDFFV-10601: Issues with chunk cache hash value calcuation. HDFFV-10607: Patches for warnings in the core libraries. HDFFV-10635: HDF5 library segmentation fault with H5Sselect_element.
* Fix for HDFFV-10333:Vailin Choi2018-07-261-2/+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
* removed extraneous lib. ver. bound, PR commentM. Scot Breitenfeld2018-05-101-6/+0
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* temporary fix for HDFFV-10469M. Scot Breitenfeld2018-05-091-101/+1
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* Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-05-081-25/+20
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| * 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
| * | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-126/+20
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* | | Merge branch 'develop' into hdf5_1_10_mergeM. Scot Breitenfeld2018-03-091-2/+40
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| * | 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.
| * 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.
* | Resolve compilation errors.Vailin Choi2018-03-091-8/+14
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* | Fix for HDFFV-9947 H5SencodeVailin Choi2017-11-281-4/+10
| | | | | | | | Modifications to fix H5Sencode bug when num points selected is > 2^32.
* | Change copyright headers to replace url referring to file to be removedlrknox2017-04-141-6/+4
|/ | | | | | | | and replace it with new url for COPYING file. Fix 2 lines in java error test expected output file where messages include line numbers changed by reducing the copyright header by 2 lines.
* [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)
generated by cgit v0.12 at 2024-09-12 18:31:36 (GMT)