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* 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.
* | [svn-r27104] Add support for printf-style source dataset name resolution.Neil Fortner2015-05-221-17/+24
| | | | | | | | | | | | | | | | Passes use case test, no regression tests yet. Add functions H5Pset/get_virtual_printf_gap (not tested yet). Other minor fixes/cleanup. Tested: ummon
* | [svn-r27049] Rename H5Pset/get_virtual_dataspace_bounds to ↵Neil Fortner2015-05-111-2/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | H5Pset/get_virtual_view and rename enum argument. Add support for AND and NOTA/NOTB operations with unlimited selections. Add some tests for unlimited selections. Other minor fixes/cleanup. Note: "clipped" status of unlimited selections is not properly updated with H5Sselect_copy. This is a deliberate omission since fixing it would take work and we are planning to eliminate the clipped status anyways. Tested: ummon
* | [svn-r27022] Add new functions H5Pset_virtual_dataspace_bounds andNeil Fortner2015-05-051-1/+1
| | | | | | | | | | | | | | | | | | H5Pget_virtual_dataspace_bounds. Minor refactor of dataset initialization code to make this cleaner. Update h5_vds-percival-unlim-maxmin.c Other minor fixes/cleanup. Tested: ummon
* | [svn-r26967] Refactor VDS unlimited dimension code to correctly handle case ↵Neil Fortner2015-04-291-0/+1
| | | | | | | | | | | | | | | | | | where selections have discrete blocks and the extent is set by the minimum (untested, and there is still no way to set that preference). Tested: ummon
* | [svn-r26962] Add support for unlimited selections to VDS code.Neil Fortner2015-04-291-1/+14
| | | | | | | | | | | | | | | | Not tested (except for percival-unlim example) Fix percival-unlim example Other bug fixes/cleanup Tested: Fedora 64
* | [svn-r26878] Fix errors in unlimited selection serialize/deserializeNeil Fortner2015-04-211-2/+2
| | | | | | | | | | | | Other minor fixes Tested: jam
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