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* More includes cleanupAllen Byrne2018-02-141-812/+811
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* Additional testsBinh-Minh Ribler2018-02-131-0/+199
| | | | | | | | | | Description: - Revised and add more variety to version bound tests per review - Revised gen_bounds.c per review Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
* Fix for HDFFV-7853 H5Ocopy doesn't work with open identifiersVailin Choi2017-06-111-117/+475
| | | | Changes made so that raw data for dataset objects are copied from cached info when possible instead of flushing objects to file and read them back in again.
* 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.
* Misc. small cleanups to sync against incoming page buffering changes.Quincey Koziol2017-03-021-1/+1
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* Merge pull request #100 in HDFFV/hdf5 from ↵Frank Willmore2016-11-031-1/+1
|\ | | | | | | | | | | | | ~FRANK.WILLMORE/hdf5:HDFFV-8882-replace-numeric-exit-code-with to develop * commit '526bcc242d03a6fc4fd28d3a0f68cc31f4f2a850': Changes to be committed: modified: bittests.c modified: cmpd_dset.c modified: dsets.c modified: dt_arith.c modified: dtypes.c modified: extend.c modified: fillval.c modified: filter_fail.c modified: flush1.c modified: gen_cross.c modified: hyperslab.c modified: istore.c modified: links.c modified: links_env.c modified: objcopy.c modified: plugin.c modified: tcheck_version.c modified: unlink.c modified: unregister.c
| * Changes to be committed:Frank.Willmore2016-10-251-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | modified: bittests.c modified: cmpd_dset.c modified: dsets.c modified: dt_arith.c modified: dtypes.c modified: extend.c modified: fillval.c modified: filter_fail.c modified: flush1.c modified: gen_cross.c modified: hyperslab.c modified: istore.c modified: links.c modified: links_env.c modified: objcopy.c modified: plugin.c modified: tcheck_version.c modified: unlink.c modified: unregister.c Minor fixes to replace numeric exit codes with MACRO declarations. Not all codes found were boolean, and those cases were not changed.
* | Uncomment line in test/objcopy.c, clean up whitespace and POSIX call wrappingQuincey Koziol2016-11-031-1/+1
|/ | | | in tools code.
* [svn-r30308] Fix for HDFFV-7991--error when copying dataset with attribute ↵Vailin Choi2016-08-191-2/+317
| | | | | | | which is a compound datatype consisting of a variable length string. Tested on mayll, platypus, osx1010test, emu, kituo, kite, quail, moohan, ostrich.
* [svn-r30238] Follow-on to HDFFV-9928: remove unconditional call of time.h ↵Allen Byrne2016-08-011-1/+0
| | | | type headers. Also remove duplicated includes when h5private.h is used.
* [svn-r29770] Description:Quincey Koziol2016-04-231-6/+6
| | | | | | | | 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 Koziol2016-04-191-11/+11
| | | | | | | | 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-r29718] Description:Quincey Koziol2016-04-161-3/+938
| | | | | | | | Bring changes from revise_chunks branch to trunk Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel, and production (h5committest forthcoming)
* [svn-r29612] Description:Quincey Koziol2016-04-031-38/+1
| | | | | | | | | Bring updated layout and EFL property comparisons and new "latest format" flags from revise_chunks branch. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29607] Description:Quincey Koziol2016-04-021-0/+141
| | | | | | | | | 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-r28972] Removed option to clear file buffers from autotools, CMake, and ↵Dana Robinson2016-01-261-2/+0
| | | | | | | | | | | | library. Buffers that will be written to disk will now always be cleared since not doing this has huge security implications. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0, x86_64) gcc 5.2.1 serial autotools parallel autotools (MPICH 3.1.4) serial CMake
* [svn-r28761] Description:Quincey Koziol2016-01-011-18/+132
| | | | | | | | | | | | Clean up many mismatches between malloc/free and H5MM_malloc/H5MM_xfree in the library and tests (and use of H5free_memory and H5Dvlen_reclaim). Also make H5Ocopy use a private version of H5Lexists, which doesn't internally throw (and suppress) errors when an object (or the path to it) isn't found in the destination. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28696] Minor normalization with revise_chunks.Dana Robinson2015-12-171-25/+29
| | | | | Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only
* [svn-r28138] Add first support for _Bool and make hbool_t a "real" _Bool if ↵Jerome Soumagne2015-10-201-1/+1
| | | | | | | | | | | | | | available Fix tests accordingly and fix misuse of hbool_t in various places Fix initialization of H5Pgcpl/ocpl structs in property decoding routines Tested on: Linux/32 (jam) Linux/64 (platypus) Linux/PPC64 (ostrich) MacOSX/64 10.11
* [svn-r27811] Description:Quincey Koziol2015-09-161-4/+0
| | | | | | | | | | | 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 Koziol2015-09-141-2/+2
| | | | | | | | | | | | | | | | | | | | | | 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-r27572] Removed VMS-specific code from the library.Dana Robinson2015-08-241-2/+0
| | | | | | | | | The only remaining code consists of a few floating-point tests that rely on pre-generated and checked-in VMS files. These have been left alone, even though they will not be possible to recreate, since testing VMS float behavior is still important. Tested on: h5committest
* [svn-r27548] Revert r27545Jerome Soumagne2015-08-211-1/+1
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* [svn-r27545] Add first support for _Bool and make hbool_t a "real" _Bool if ↵Jerome Soumagne2015-08-211-1/+1
| | | | | | available Fix tests accordingly
* [svn-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-1/+1
| | | | | | | | * 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-r26333] Eliminates gcc warnings due to -Wunsuffixed-float-constants.Dana Robinson2015-03-011-10/+10
| | | | | | | | | | | | - Adds 'F' suffixes for most float constants. - A few constants MUST be of type double. These now receive the long double L suffix and are then cast to double. I do this via a new H5_DOUBLE() macro which was added to H5private.h. Fixes: HDFFV-9148 Tested on: h5committest
* [svn-r25496] Description:Quincey Koziol2014-07-301-8/+8
| | | | | | | | | Merge 64-bit ID changes from branch to trunk. (Plus a few minor cleanups that aren't on the branch) Tested on: Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN (h5committested on branch already for a week)
* [svn-r24020] Description:Quincey Koziol2013-08-171-18/+0
| | | | | | | | Clean up compiler warnings Tested on: Mac OSX/64 10.8.4 (amazon) w/C++ & FORTRAN (too minor to require h5committest)
* [svn-r22646] Description:Quincey Koziol2012-08-081-1/+1
| | | | | | | | | Changes resulting from Klocwork static analysis tool, from Mark Miller @ LLNL (miller86@llnl.gov). Tested on: Mac OS X/64 10.7.4 (amazon) w/debug, C++ & FORTRAN, using gcc 4.7.x (too minor to require h5committest)
* [svn-r22601] Purpose: Fix HDFFV-5853Neil Fortner2012-07-251-0/+99
| | | | | | | | | | | | | | Description: When jumping out from between H5_BEGIN_TAG and H5_END_TAG macros using HGOTO_ERROR or HGOTO_DONE, the previous metadata tag is not reset on the dxpl. This could cause problems when, for example, calling H5Ocopy within an H5Literate callback. Added new HGOTO_ERROR_TAG and HGOTO_DONE_TAG macros which must be used in place of the above between H5_BEGIN_TAG and H5_END_TAG. Tested: jam, koala, ostrich (h5committest), durandal
* [svn-r22173] Purpose: Fix HDFFV-7762Neil Fortner2012-03-281-1/+169
| | | | | | | | | | | | | | | | Description: When copying an object with attribute creation order tracked, the attribute creation order was not copied correctly to the destination file, causing an error if the creation order was also indexed (due to attempting to insert duplicate keys) or incorrect creation orders otherwise. Fixed to copy the creation order correctly. Also fixed the attribute character set not being copied, and fixed an issue where an attribute opened with H5Aopen (or similar, but not by_idx), from an object using the latest format but without creation order being tracked, would always report the creation order as 0 (and marked as valid). Tested: jam, koala, ostrich (h5committest), durandal
* [svn-r22171] Description:Quincey Koziol2012-03-281-1/+3220
| | | | | | | | | Bring "merge committed datatypes during H5Ocopy" feature from branch to trunk. (Also has some minor bugfixes with it) Tested on: Mac OSX/64 10.7.3 (amazon) w/debug (h5committest coming up)
* [svn-r22164] Fixed a bug in H5Ocopy(): When copying an opened object, call ↵Vailin Choi2012-03-281-0/+314
| | | | | | | the object's flush class action to ensure that cached data is flushed so that H5Ocopy will get the correct data. (HDFFV-7853)
* [svn-r22111] Removed incorrect 'executable' svn properties.Dana Robinson2012-03-211-0/+0
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* [svn-r21675] Description:Quincey Koziol2011-10-261-1/+2
| | | | | | | | | Don't check dataset storage size for compressed datasets with region reference datatypes. (The address of the region reference type in the file varies and affects the compressed size) Tested on: Mac OS X/32 10.7.2 (amazon) w/debug & production + check-vfd
* [svn-r21629] Purpose: Update fix committed in r21556Neil Fortner2011-10-201-1/+2
| | | | | | | | Description: An old patch was mistakenly committed in r21556. Replaced this fix with the latest. Tested: jam, koala, heiwa (h5committest)
* [svn-r21617] Description:Quincey Koziol2011-10-201-413/+434
| | | | | | | | | | Recalculate the size of destination attribute message when the source and destination versions are different during an object copy operation. (Jira: HDFF-7718) Tested on: Mac OS X/32 10.7.2 (amazon) w/debug (h5committest upcoming)
* [svn-r21556] Purpose: Fix bug in H5OcopyNeil Fortner2011-10-131-3/+147
| | | | | | | | | | | | | Description: H5Ocopy could get confused when copying a named datatype containing an attribute which used that named datatype as its datatype. This happened because H5Ocopy would recurse into the attribute's datatype before the object the attribute was in was fully copied (i.e. before the "post-copy" pass). Modified H5Ocopy to avoid recursing before the post-copy step in this case. Required many changes, including to how non-committed shared messages are copied. Tested: jam, koala, heiwa (h5committest); durandal
* [svn-r21121] Description:Quincey Koziol2011-07-181-4/+4
| | | | | | | | | Switch from H5P_DATASET_ACCESS_DEFAULT to H5P_DEFAULT for calls to H5Rdereference2(). Tested on: Mac OS X/32 10.6.8 (amazon) w/debug (too minor to require h5committest)
* [svn-r21117] Issue 2763 - I added a new parameter of object access property ↵Raymond Lu2011-07-181-4/+4
| | | | | | list to the function H5Rdereference. It's called H5Rdereference2 now. H5Rdereference function has been deprecated to H5Rdereference1. I also added some test cases in trefer.c. Tested on jam, heiwa, and koala.
* [svn-r20529] Purpose: Add testing for bug 1864Neil Fortner2011-04-151-0/+3
| | | | | | | | | Description: Added internal tesitng routines to traverse a file and verify that symbol table information is *always* cached, whenever possible. Added this check to the end of many tests to check all the test files, right before the call to h5_cleanup. Tested: jam, amani, heiwa (h5committest)
* [svn-r19272] Description:Quincey Koziol2010-08-201-13/+20
| | | | | | | | | | | | Close out various resource leaks and usages of uninitialized memory that were flagged by valgrind. [There's still some more valgrind warnings, but it's better now... :-/ ] Also clean up warnings and code formatting. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & valgrind (h5committest forthcoming)
* [svn-r18535] Purpose: Fix bug 1815Neil Fortner2010-04-081-1/+164
| | | | | | | | | | | Description: Attempting to copy an object with NULL references (all bytes zero) with the H5O_COPY_EXPAND_REFERENCE_FLAG flag set would cause a failure or an assertion (depending on whether it was in debug mode). Changed copy routine to detect NULL references (object and region) and avoid attempting to expand the reference in this case. Tested: jam, linew, amani (h5committest)
* [svn-r18419] Description:Quincey Koziol2010-03-181-0/+1
| | | | | | | | | Clean up srcdir querying code more, extracting it into single header file, to avoid compiler warnings. Tested on: Mac OS X/32 10.6.2 (amazon) w/debug & prod Linux/32 2.6 (jam)
* [svn-r18413] Description:Quincey Koziol2010-03-171-9/+1
| | | | | | | | | | | | | | Unify srcdir handling for test executables and allow them to use the srcdir setting from configure time without requiring the 'srcdir' environment variable be set (although you still can, to override the built in setting). Attempted to get this right for Windows builds also. Also add dependency between src/H5Tinit.c and src/libhdf5.settings, so that the test/testcheck_version.sh script works correctly. Tested on: Linux/32 2.6 (jam) Mac OS X/32 10.6.2 (amazon)
* [svn-r18376] Purpose: Fix bug 1733Neil Fortner2010-03-051-38/+212
| | | | | | | | | Description: Support for expanding external links was not implemented in H5Ocopy, even though a flag existed for H5Pset_copy_object to enable this. This patch implements this feature. Tested: jam, amani, linew (h5committest); Fedora
* [svn-r18197] Description:Quincey Koziol2010-01-301-1/+1
| | | | | | | | | Trim trailing whitespace from source code files with this command: find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//' Tested on: None - eyeballed only
* [svn-r17953] Description:Quincey Koziol2009-12-031-6/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes into the trunk: r17877: Error 266: Uninitialized memspace set to -1. Changed malloc and free to HDmalloc and HDfree. Removed unused dtype var. r17878: Error 265: Uninitialized mem_space set to -1. Changed malloc and free to HDmalloc and HDfree. Error 267: Uninitialized smspace set to -1. Changed malloc and free to HDmalloc and HDfree. r17879: Error 242: Uninitialized aid set to -1. Error 243: Uninitialized sid set to -1. Uninitialized tid set to -1 for consistency r17880: Error 242: reinitialized aid to -1 after close to be ready for reuse. Error 243: reinitialized sid to -1 after close to be ready for reuse. reinitialized tid to -1 for consistency after close to be ready for reuse. r17881: use valgrind to check there is a memory leak. The fix is to free ptrstr in line 5838 at xml_dump_group() of h5dump.c after it is used. run the valgrind after the fix, no memory leak for that part of the code. r17882: Fix Coverity items 256 and 269. r17883: Error 222-230: initialized hid_t vars to -1 after close to be ready for reuse. Also added H5Tclose for tid in gent_bigdims r17884: Bug fix (Coverity run2, view 23, dead code) (this is pair-program done by Albert, Elena and Larry). Confirmed and fixed the deadcode in hyperslab read branch of function diff_datasetid. (Discovered other bad code that diff_datasetid() should be recoded. Bug 1693 is entered for this.) r17906: Fix Coverity item 260. r17907: 262: Initialized hid_t's dtype, dtype_tmp and file to -1. Initialized H5T_t * dt to NULL. r17908: Fix Coverity item 261. r17909: Fix Coverity item 248. r17910: Revise fix for Coverity item 248. r17911: Resolved coverity issues #s 263, 162, 163, 164. All issues in dsets.c. Initialized fid and did hid_t's. filter_corrupt function was returning in the middle of an if statement, bypassing free calls. Updated error handling to free buffers and hid_t's appropriately. r17912: (done by Larry and Albert) Cleanup Coverity view warnings (#231-241) about using uninitialized variables. Initialized all of them. r17913: Resolved issue 251 and 264. Initialized tid2 to -1 and initialized buffers that were freed in case of an error. r17914: Resolved coverity issues 66, 220, and 221: 66: Negative Return assignment ignored 220,221: Initialized hid_t's. r17915: Fix Coverity item 247. r17916: Fix Coverity item 246. r17917: Fix Coverity item 245. r17918: Fix Coverity item 244. r17919: Coverity Issue #84: Moved asserts in H5T_cmp to the top of the function, and converted them to HDassert. Coverity complaining about using potentially NULL pointer without checking it. Want to see if Coverity will accept Assertions as acceptable checking before using the value. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17585] Purpose: Fix bug 1597Neil Fortner2009-10-021-3/+518
| | | | | | | | | | | Description: When copying a dataset using a vlen inside a compound, the various dataset copying callbacks would allocate a background buffer but would not use it when converting from disk to memory, only memory to disk. This caused an assertion failure as compounds always need a background buffer. These callbacks have been modified to use the background buffer for both conversions. Tested: jam, linew, smirom (h5committest)
* [svn-r16710] Purpose: Fix bug 1423Neil Fortner2009-04-081-10/+15
| | | | | | | | | | | | | | Description: Versions of the library between 1.3.0 and 1.6.3 have a bug which prevents them from opening any file that does not have the root group's symbol table information cached in the root group's entry in the superblock. Prior to 1.8 this was not an issue as this information was always cached. However, 1.8.0 stopped writing this information (which is not required by the file format specification), and these older versions can therefore not read files created or last written by versions 1.8.0 to 1.8.2. This fix modifies the library to once again add this information to the superblock (when using the old file format). Tested: jam, linew, smirom (h5committest)
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