* commit 'abb2e30a0ec629c2e1ab86b19e027311299ff3f8':
Removed SZIP section of COPYING file.
Using SZIP/Libaec for clarity.
Add szip and zlib changes to makeInternalREADME.pl.
Update version to 1.10.7-2 Update packaging scripts => README file and RELEASE.txt.
* commit 'fdc8fd401eca8c1a382f1ddb2653c374b470f6ef':
Commit Makefile.ins for so number change.
Update the rest of the so numbers.
so numbers for libhdf5 were not up to date with numbers in 1.10.6 release.
* commit 'fea8f62bcf82514295d6ce6826493663d344ea90':
Restore empty sections.
Remove entries from previous release.
More tested platforms for RELEASE.txt.
Update tools lib SO numbers. More updates to additional platforms tested.
Update SO version numbers in lt_vers.am Update supported platforms and compilers in RELEASE.txt; add more release notes.
* commit '7a3f80a31e702c029ce7668bb985f37f485fdfc6':
Merge pull request #2841 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10
Revert "Merge pull request #2840 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_7 to hdf5_1_10_7"
* commit 'fc3129a92e29b50dac3bd3d3777df13d970a017a':
Revert H5_VERS_SUBRELEASE check
Add special case when H5_VERS_SUBRELEASE is 0
Condition if (H5_VERS_SUBRELEASE) is incorrectly false when H5_VERS_SUBRELEASE is 0, a valid value for H5_VERS_SUBRELEASE. Updated to if (${H5_VERS_SUBRELEASE} STREQUAL "") with corresponding reversal of action statements to avoid NOT.
Add hypen to subrelease regex
Add ifdef blocks to S3/HDFS test
* commit '09c6b077ec401f28c1dcc81d935afc9b1371e978':
Update configure with optino to disable memory sanity checks.
Add new Makefile.ins to MANIFEST. Delete H5config.h.in~ that shouldn't have been committed.
* commit 'aee3fb3d87359ec0e49f07c9d6d2f07f193875fc':
Commit changes for release branch: maintainer mode, default to production, set HDFF5_GENERATE_HEADERS to OFF, and add file generated by autogen.sh.
* commit 'f6ee6e59e1516bcc3c4c444e886835db89113e93':
Fixes typo and return types in version bounds test
Refactors the 1.10 reference/selection bounds tests
* commit 'c9f8ef3e185a7a2b16bc9d0200435c242969d0a2':
Fixed one last trailing whitespace character
Fixed trailing whitespace from revert.
Revert "Don't track file offset position when using pread / pwrite."
Description
Added initialization to local structs in the src function
H5MF_settle_raw_data_fsm() and the test function test_bt2_hdr_fd()
to prevent the following error in two different occurrences:
MemorySanitizer: use-of-uninitialized-value
Platforms tested:
Linux/64 (jelly)
* commit '3b9c648180fcdc7ac4e110f4455d00e67322b742':
Merge pull request #2753 in HDFFV/hdf5 from ~EPOURMAL/hdf5_ep:develop to develo
1. HDFFV-10830 part 2, move AC_CHECK_HEADERS([szlib.h] after AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress] to avoid compiling H5Z.c with szlib.h after its path is removed from AM_CPPFLAGS. 2. Remove unnecessary links to ${HDF5_TOOLS_LIB_TARGET} in utils/mirror_vfd/CMakeLists.txt that prevent building HDF5 with tools disabled.
AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress] to avoid compiling
H5Z.c with szlib.h after its path is removed from AM_CPPFLAGS.
2. Remove unnecessary links to ${HDF5_TOOLS_LIB_TARGET} in
utils/mirror_vfd/CMakeLists.txt that prevent building HDF5 with tools
disabled.
* commit 'c638d93f3e660ce669a36e50a02473aac126953d':
Fixes missing chunk_info entry in CMake files
Even more normalization with develop
More normalizations with develop
Misc normalizations with develop
Normalization of perform directory with develop
Brings monotonic timer changes from develop
Brings Mirror VFD to 1.10 from develop
Brings splitter VFD from develop
Brings file locking changes from develop
* commit 'e9305abf48426f265d7ec3ae54538e3ded8889ea':
Fixes missing chunk_info entry in CMake files
Even more normalization with develop
More normalizations with develop
Misc normalizations with develop
Normalization of perform directory with develop
Brings monotonic timer changes from develop
Brings Mirror VFD to 1.10 from develop
Brings splitter VFD from develop
Brings file locking changes from develop
Description:
Fixed to allow the creation of a dataset when the combination of type,
space, etc doesn't work for filter and the filter is optional. Currently,
it was supposed to be skipped as indicated in the documentation, but it
was not skipped and the creation failed.
The function H5Z_ignore_filters was added and used in H5D__create.
Platforms tested:
Linux/64 (jelly)
Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)
* commit 'a324025e00adf3dd0a9d475cfff5af2ec4c7576c':
Fixed typo
Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)
Description:
When a buffer overflow occurred because a name length was corrupted
and became very large, h5dump produced a segfault on one file and a
memcpy parameter overlap on another file. This commit added checks
that detect a read pass the end of the buffer to prevent these error
conditions.
Platforms tested:
Linux/64 (jelly)
* commit '24369a4ff14f873a63a1e77b7069078dac284098':
Remove mingw from windows copy
Additional warnings removed
More warnings reduction
Warnings reduction in tools
* commit '475120abfb493098e907fe40073260f48b35d15d':
Supply the appropriate file pointer to H5T_patch_vlen_file() without H5F_VOL_OBJ from develop branch.
Merge pull request #2693 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/HDFFV-11080-heap-use-after-free-by-the-call to develop
* commit 'bdc6edfc5ce07363faf79519389ef149a4094530':
Supply the appropriate file pointer to H5T_patch_vlen_file() without H5F_VOL_OBJ from develop branch.
Merge pull request #2693 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/HDFFV-11080-heap-use-after-free-by-the-call to develop
* commit '3023b34272cc6ada84aebfa7441a6a55afa3621c':
Update MANIFEST. Add new test to Cmake.
Fix for jira issue HDFFV-11080: (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads
Add build folder as Include for generated files
Add install option for copying Fortran mod files to include folder
Add PRI defines to win32defs file
Exclude mingw from extra flags
* commit '800f93f7c994f88dfa716746153ded4b1e690e3a':
Remove path to szip header file from AM_CPPFLAGS when configure check of libsz fails. Fix for HDFFV-10830.
* commit '443aa9a38f59bf4148925a86c07cfe14bac9e888':
Moved over the H5S_hyper_diminfo_t from develop.
Moved hyperslab code to use the new H5S_diminfo_valid_t enum.
H5S_hyper_adjust_s() optimization from develop.
Fixed Duff's device fall through warnings in hyperslab code.
H5F and H5FS normalization with develop.
Minor renaming in H5S hyperslab code.
* commit '30c756decb6101704a925443d623301656ba60e4':
Misc normalizations with develop.
Added missing types to bin/trace after develop normalization.
More normalization with H5S from develop.
Continued normalization of H5S with develop.
Normalization of H5MM and H5FL with develop. Adds the new stats calls.
Further normalization of H5S with develop
* commit 'c0702f601eb4e0b4116a7ed02999746c20420cad':
Change load path in libhdf5_java.dylib to unversioned libhdf5.dylib for junit tests on Macs.
Merge pull request #2667 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
Merge pull request #2670 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '32c483cb86031962a09ecdb49dcb331d28dddee9':
Copy lib files for junit.sh to temporary subdirectory of <build directory>/java/test instead of to the prefix/lib directory. Fix for HDFFV-11063.
* commit 'fc69de0e8ae30e80c1c3c542b156226a75444525':
Lib files needed are now copied to a subdirectory in the java/test directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. Fix for HDFFV-11063
Description:
h52gif produced a segfault when a buffer overflow occurred because
the data size was corrupted and became very large. This commit added
a check on the data size against the buffer size to prevent the segfault.
It also added error reporting to h52gif to display an error message
instead of silently exiting when the failure occurred.
Platforms tested:
Linux/64 (jelly)
* commit 'cafb6e572822c0a7bb985f237b600944f9fcdb3c':
Reduce overhead for H5open, which is involved in the public symbols like H5T_NATIVE_INT, etc.
H5PB and H5Faccum normalization with develop.
H5F normalizations with develop.
* commit '3c9eaf294fb1862af75837f0150990112c735530':
Reduce overhead for H5open, which is involved in the public symbols like H5T_NATIVE_INT, etc.
H5PB and H5Faccum normalization with develop.
H5F normalizations with develop.
* commit '538b1317646f52658c2a896bbde4dce4246a9761':
Squashed commit of the following:
Addition of clang-warnings flags
Update examples/teth5cc.sh.in for version 1.10.
* commit '34d57480f69123e947d5b2d7b5b4cc3d62bb00c2':
Merge pull request #2643 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/HDFFV-10961-h5clear-usage-statement-give to develop
* commit '01b632c69ca1c97c2b0e1aaeeab1dd2362b580a6':
Fix for HDFFV-10961: Couple changes to the tests' usage output files for h5clear.
Fix for HDFFV-10961: add description to usage for --increment option.
* commit 'fd404f711b8a587a5b5534f268a918115884bd56':
Added a RELEASE.txt note for the 0-size dataset fix.
Brought the dsets test in line with develop. Brings over the fix for 0-size dataset metadata allocation.
* commit 'af1cd63111adce03f81e2e497890080ef1f51113':
Update MANIFEST for removal of older warnings files. Fix max_index in make_vers - must equal current version.
-DH5_NO_DEPRECATED_SYMBOLS can no longer be tested with a previous version API: H5Version.h now has a check that disallows it.
* commit '22b61f470acc54afad5705dea23a7a8423e65cff':
Revise gnu-*flags and cmake/HDF*CompilerFlags.cmake files to add warning flags for GCC compilers version 4.8 and above. Removed files from gnu-warnings that only apply to versions < 4.8. Consolidated warnings from versions < 4.8 that apply to versions >= 4.8 into the 4.8 warnings files.
flags for GCC compilers version 4.8 and above.
Removed files from gnu-warnings that only apply to versions < 4.8.
Consolidated warnings from versions < 4.8 that apply to versions >= 4.8
into the 4.8 warnings files.
* commit '6c1b7958de946720d920ff4d44417176ac43218e':
Updated code in H5Xtest.c files and associated tests. Reverted overlong-strings warning that gives jam issues.
Misc library test changes from develop.
* commit '67983bc4313fecf3763f5b337b612357a3ee033b':
Updated code in H5Xtest.c files and associated tests. Reverted overlong-strings warning that gives jam issues.
Misc library test changes from develop.
* commit 'eddcc2f800db71d4c4309f74f57ed58ae7854727':
Brought error tests in line with develop. Fixes warnings.
Brought H5E package in line with develop.
Reduce gratuitous casts---e.g., (size_t)1.
Use the right format string for a pointer.
In the H5C sanity checks, change a "size increase" variable from ssize_t
(too narrow) to int64_t (wide enough).
Parenthesize every appearance of `storage` in the macro
`H5D_CHUNK_STORAGE_INDEX_CHK(storage)` so that you can pass in an
expression like &sc and it works properly.
Disallow re-assignment of the `dset` parameter to H5D__chunk_init()
because it helped assure me that it's safe to replace the repeating
expression `&dset->shared->layout.storage.u.chunk` with `sc` throughout.
Replace lengthy expressions such as
`&dset->shared->layout.storage.u.chunk` with `sc` throughout several
functions in H5Dchunk.c ISTR that the compiler warned that `sc` was
declared but unused in a couple of functions, and then I found that `sc`
could be used in many places. Maybe the disused `sc` appeared because a
bunch of code was copied and pasted, I don't know. Anyway, it's a lot
tighter code now that I use `sc`.
In H5D__chunk_update_old_edge_chunks() and H5D__chunk_delete()
I actually expand `sc` and another temporary variable, `pline`,
because they're used only in !defined(NDEBUG) code. This squashes
unused-variable warnings in the defined(NDEBUG) configuration.
Don't drop the `volatile` qualification with a cast in
tools/src/h5import/h5import.c.
* commit '68adfb86d056af222ab80c349c56e0bd1d183f09':
Merge pull request #2537 in HDFFV/hdf5 from ~DYOUNG/werror:fix-werrors to develop
Move ADD_H5_FLAGS macro from *CompilerFlags.cmake files to config/cmake_ext_mod/HDFMacros.cmake for common use.
Restrict errors to gcc 4.8 and above.
Fix NoFilter build
TRILAB-244 separate CXX warnings and errors from C
Don't add general warnings flags for unsupported old versions of gcc and g++ (older than gcc/g++ 4.2). Correct gnu-cxxflags to determine warnings flags to be added based on C++ compiler version instead of C compiler version.
* commit 'd16eb45d536bd13ca3cf1b0bdc76c58d95d13f17':
For compatibility with non-C99 Visual Studio versions, use "%" PRIuMAX instead of "%ju".
Fix `test/swmr_sparse_reader.c:118:77: error: cast from pointer to integer of different size [-Werror=pointer-to-int-cast]` and `test/snapshots-hdf5/current/test/swmr_sparse_reader.c:129:100: error: cast from pointer to integer of different size [-Werror=pointer-to-int-cast]`.
Fix `src/H5FDdirect.c:1346:5: error: ISO C90 forbids mixed declarations and code [-Werror=declaration-after-statement]`.
g++ (older than gcc/g++ 4.2).
Correct gnu-cxxflags to determine warnings flags to be added based on
C++ compiler version instead of C compiler version.
* commit 'f4324635e142eacf7c4a72224038152ea73d1139':
A fix in the cleaning up code for datatype when datatype initialization via H5D__init_type() fails. The code to fix the problem is the same as what is done in H5D__open_oid().
* commit '665b71f94ec9ca81360c96867a1df5882b2ab19c':
A fix in the cleaning up code for datatype when datatype initialization via H5D__init_type() fails. The code to fix the problem is the same as what is done in H5D__open_oid().
* commit '311a9c9147cf03e8a4b33fb1500ad9a73d07e540':
Fix shadoweed type
TRILAB-192 - cleanup edits and match CMake CXX to autotools
Add missing " and update function calls incorrectly named load_gcc_arguments. Commit changes to gnu-cxxflags to remove unmatched " and to gnu-fflags to not add C warnings flags to H5_FCFLAGS.
TRILAB-192 update LTparse files
TRILAB-192 - merge changes from develop
Update release note for CMake warnings
Correct extra flags and merge TRILAB-24
Correct cb object name
TRILAB-192 merging warnings changes from develop
* commit '68a892f3f2eb6601b6254ff90c165c3b6412b97a':
Remove return statement from void function test_reference_sel_none().
Somehow missed in committing this file for the fix submitted previously.
Fix for HDFFV-11067:incorrect # of selected elements returned from region reference. The H5S_sel_none->deserialize callback should be called for H5S_SEL_NONE selection type.
* commit '2fe834f3d2ab501b4c7c99a7e2768bc5d559e1b8':
Somehow missed in committing this file for the fix submitted previously.
Fix for HDFFV-11067:incorrect # of selected elements returned from region reference. The H5S_sel_none->deserialize callback should be called for H5S_SEL_NONE selection type.
* commit 'f33bb733be2da42672b4b0264cd4c6318ba35e9a':
Fix issues when deserializing point/all/none selection with version beyond the library's supported version: (1) Verify the decoded version before proceeding further with deserialization (2) Close the dataspace if errors occurred after opening the dataspace
* commit '018f2364ed38ce6f7e210e440fc8954991a266a6':
Add void * --> char * back to HDmemcpy in HDF5 1.10 to fix dt_arith test failures. Fixes HDFFV-11056.
* commit '836eea4abafd270a532be0a2c521d81c8cd637cb':
Add \d to list of characters allowed after - in versions. Version with - and no alphabetic characters is required to allow building binaries on windows. Escape { and } in regex as required by newer version of perl in updated cori.nersc.gov. Cherry-picked c3c044cc00 from develop.
Escape { and } in regex as required by sh in updated cori.nersc.gov. Tested change on jam, jelly, emu, ostrich and osx1011test.
* commit 'e3dd392536da73b9e3940b8c19a1de835dc34d31':
Add \d to list of characters allowed after - in versions. Version with - and no alphabetic characters is required to allow building binaries on windows. Escape { and } in regex as required by newer version of perl in updated cori.nersc.gov. Cherry-picked c3c044cc00 from develop.
Escape { and } in regex as required by sh in updated cori.nersc.gov. Tested change on jam, jelly, emu, ostrich and osx1011test.
and no alphabetic characters is required to allow building binaries on windows.
Escape { and } in regex as required by newer version of perl in updated cori.nersc.gov. Cherry-picked c3c044cc00 from develop.
* commit '529a4a14b3aff2ae77a56cc784fe778d1bc461f8':
Fix comment
Remove deleted files
Changes to region reference in h5dump no longer have errstack
Check sizeof type to use correct ref_type
Update CMake compare command
Correct test script for errstack
Remove system command from valgrind reports
Fix h5ls attrreg
Fixed region refs
h5dump object reference fixed
Updated reference code
Fixed configure issue when building HDF5 with NAG Fortran 7.0.
Fixed issue building HDF5 with NAG Fortran 7.0.
revert type cast
Fix gif2h5 tool build on windows
Merge CMake and tools changes from develop
Merge pull request #2244 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings to develop
* commit '8249b1a97a3a30e553c20b44aea985a7aa149faf':
Fix comment
Remove deleted files
Changes to region reference in h5dump no longer have errstack
Check sizeof type to use correct ref_type
* commit '88082cce109b27efb885971fca87224e16b62879':
Remove system command from valgrind reports
Fix h5ls attrreg
Fixed region refs
h5dump object reference fixed
Updated reference code
Fix gif2h5 tool build on windows
Merge CMake and tools changes from develop
* commit '42106363903e7a7d4a0c2cd1b38aad9a54f2eeff':
Fixed configure issue when building HDF5 with NAG Fortran 7.0.
Fixed issue building HDF5 with NAG Fortran 7.0.
revert type cast
Merge pull request #2244 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings to develop
* commit 'a0881fa1cfbb735a013581c53f8003a13fb0383a':
revert type cast
Merge pull request #2244 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings to develop
* commit '276c4fdbcc1baf0748a617f10eb8aaaec2154151':
Fixed configure issue when building HDF5 with NAG Fortran 7.0.
Fixed issue building HDF5 with NAG Fortran 7.0.
* commit '04d4d9c93a824b7a860993fc217c9cc497ac5441':
HDFFV-11014, fix the h5repack issue that misses a few attributes during the repacking. The flag that checks the object reference attribute is not updated properly. The fix is trivial. Just need to move the flag update line into the inner loop. Tested at Jelly. Also update the release.txt.
* commit '872f5afa1b813afb7a991eb2d7959683d4438f27':
Add another warning variation
Add unknown pragma warning ignore
Correct CMake warnings to ignore
Only use sanitizers with clang
* commit 'e167cd9fe74feb31083994ade4b83f4f8dbcf782':
Merge of --Wc++-compat changes from develop
Changed -Wformat-truncation to level 2 in CMake w/ gcc.
Changed -Wformat-truncation's level from 2 to 1.
* commit '887aa3d05d0a64e1c8198138334c0fe761d0ab2f':
Merge of --Wc++-compat changes from develop
Changed -Wformat-truncation to level 2 in CMake w/ gcc.
Changed -Wformat-truncation's level from 2 to 1.
* commit 'e0fa36bfe008c03365ce8ea94d705f8fdebccdf0': (166 commits)
Update release date strings in README.txt and release_docs/RELEASE.txt
Add release note about using ompio instead of romio when collective writes fail with OpenMPI.
Fixed typos, grammatical errors, etc. Expanded entry for S3 and HDFS VFDs. Moved Mac 10.11 and 10.12 from Supported Platforms to More Platforms Tested.
Add qualification to RELEASE.txt regarding performance improvements
Standalone doesn't use h5test implementation.
Add missing note
Update COPYING file with new HDF5 license.
Update bin/config.guess and config.sub to current version available from git.savannah.gnu.org.
Fix include to correct memory calls - big-endian issue.
Revert BLDLIBDIR value in junit.sh.in.
Corrections to CMake functions
Update version for HDF5 1.10.6 release. Remove autom4te.cache directory that shouldn't have been added.
Remove duplicate instance
Fix merge issue
HDFFV-10979 - fix global name clash
Correct clang search and java include
Latest date first in RELEASE.txt
Update RELEASE.txt with performance improvements and Steven Varga's bugfix.
Update version numbers for shared lib files according to api compatibility report.
Created hdf5_1_10_6 branch for HDF5 1.10.6 release preparation. Set version to 1.10.6-pre1. Switched default maintainer mode to disabled and default build mode to production. Added files produced by autogen.sh to commit except for src/H5config.h.in~ and src/H5public.h~.
...
* commit '2b0a45a45c444706f703557af06c982ad4332f5d':
Fixed typos, grammatical errors, etc. Expanded entry for S3 and HDFS VFDs. Moved Mac 10.11 and 10.12 from Supported Platforms to More Platforms Tested.
* commit '53a516af074f6276a1e49298589a4404a63795ee':
Update version for HDF5 1.10.6 release. Remove autom4te.cache directory that shouldn't have been added.
* commit '10fdc1724e873c74dc5000d04e4e5f51b621f6e9':
Update version for HDF5 1.10.6 release. Remove autom4te.cache directory that shouldn't have been added.
* commit 'c58108ea4030e74a0b745cabbc8ccd366695de07':
Latest date first in RELEASE.txt
Update RELEASE.txt with performance improvements
Add fix of Jira 10934 to RELEASE.txt
* commit 'e66d5596f2d78ed48f82024d673a45f042fc789c':
Latest date first in RELEASE.txt
Update RELEASE.txt with performance improvements and Steven Varga's bugfix.
Set version to 1.10.6-pre1.
Switched default maintainer mode to disabled and default build mode to production.
Added files produced by autogen.sh to commit except for src/H5config.h.in~ and src/H5public.h~.
* commit 'b00a52c403e4b7b64be974080ddfef3aee1bf801':
Fix the segmentation fault when h5dump "vds_virt_0.h5", which is a test file produced by test/vds.c in the develop branch. The fix: verify the decoded version for hyperslab selection is within the correct range.
* commit '0662f060b2e5917b70360ed10aca3993b60f1434':
Fix the segmentation fault when h5dump "vds_virt_0.h5", which is a test file produced by test/vds.c in the develop branch. The fix: verify the decoded version for hyperslab selection is within the correct range.
* commit '91b2ae219cd631798f95f0a94e793f2a2366b618':
Set the dcpl for the context on dataset creation
Add DCPL to H5CX
Check for both default values
Use H5CX for LCPL property retrieval
* commit '54697cc596e7734c5890e58414833e97f5438861':
Set the dcpl for the context on dataset creation
Add DCPL to H5CX
Check for both default values
Use H5CX for LCPL property retrieval
* commit '36fc437467630d59894deca7aff15b282cb938fb':
Add clang toolchain
Fix missing option and incorrect close
small syntax addition
Whitespace fix and HD prefix
Whitespace updates
Remove obsolete code
Add missing class name
Small syntax changes
Remove unused command block
Change unused variable to generic form
HDFFV-10903 merge dev changes to 1.10
Correct HDF5 options to tristate values
HDFFV-10903 merge updated changes
Add new tools lib test folder
Merge S3 code from develop to 1.10
* commit 'fb05ff4c4a392d38a45e79fe461bc690dea6f325':
Added MPICH_SKIP_MPICXX and OMPI_SKIP_CXX to H5public.h to avoid inadvertant linking to the deprecated MPI C++ wrappers. Fixes HDFFV-10893.
* commit '71c80267ba0db1c1b439d39e4bd7c27b82510c92':
Added MPICH_SKIP_MPICXX and OMPI_SKIP_CXX to H5public.h to avoid inadvertant linking to the deprecated MPI C++ wrappers. Fixes HDFFV-10893.
* commit '406890277cbe92be1d68721a6fa115441ab1a726':
Fixed a bug where we incorrectly pass a lock struct to fcntl for file locking instead of a pointer. (HDFFV-10892)
* commit '247738c23af1a19ba2c4a7c098398b91b84b71cb':
Fixed a bug where we incorrectly pass a lock struct to fcntl for file locking instead of a pointer. (HDFFV-10892)
* commit 'b5c2b64307dc01128d2a90771cf51076bc1252db':
Correct threadsafe enable code
Mostly whitespace, HD prefix and remove obsolete #if blocks
fix get gethostname for windows
* commit '9c3e331ba31fdaea98354a05554beb8bdcd2e6fc':
Merge pull request #1892 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/HDFFV-10873-assertion-v-oh--nmesgs-failed to develop
* commit '13a3be1caa3bd32bbf556f4045708a880e54fc7f':
Merge pull request #1865 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/HDFFV-10813-swmr-test-fails-on-jelly-with to develop
* commit '538f743c145fbbfa7b1119693efd2ff61b34efae':
Changes based on PR feedback.
Fix for HDFFV-10813 H5Fset_metadata_read_retry_info() test fails on jelly with PGI/19.
* commit '8682040032371fd720eac5464eaa9b2638e166d9':
Changed a directory name left out from the previous commit.
Changed the name of the temporary directory from 'tmp' to a special name to avoid possible conflicts.
* commit 'afdd58b09a77b9e1b9e3e05a9a417284ab5220ea':
Added ifdef for intel compilers, __GNUC__ has to be defined for header files which use it to work with intel compilers. This gives a warning for intel compiler about fallthrough, so added a check not to include fallthrough if using intel compilers.
* commit 'a371dadd33d935636d2e0d0d873bf85845aef8ab':
HDFFV-10879 set default API version
Correct error test spelling and use
HDFFV-10879 fix option text
* commit '0329fe88c9d498b525820fb8f611816e97747d36':
HDFFV-10879 correct API version set command
Use a STRING option for API version
Fix API version option
* commit '32fd14afa4b4d77812dc510486aff6971a0d3b49':
Delete unused batch scripts for cori.
Add contents of HDF5 1.10.5 RELEASE.txt to HISTORY-1_10.txt file. Remove 1.10.5 entries from current RELEASE.txt and update version numbers.
* commit '9ca9deef1e5bf7a17481247a1646d3898cf8ae41':
Changed the external files to a directory (extern_env_dir) to avoid possible conflict in daily test on jelly.
* commit '58d941293aa7ab7d5a824ea5951d7eff32bc1ac5':
Mostly whitespace and consistent test format
Cleanup when merging to other branches
Correct syntax
Minor code fixes
Revert unintended whitespace
Minor comment fix
HDFFV-10845, 10529 and CMake changes from develop
Merge from develop, mostly HDFFV-10845
* commit '803ae1d1a87bb962a7d887a958bbd9ac8adf3da3':
Changes based on PR review.
Bring pull request #1772 from develop to 1.10. Fails file creation when non-default free-space info is set in fcpl and the library version high bound is less than v110 because free-space info message is introduced in library release v110.
* commit '452431960978a5693fb7c28096ee0f191a610b36':
Changes based on PR review.
Bring pull request #1772 from develop to 1.10. Fails file creation when non-default free-space info is set in fcpl and the library version high bound is less than v110 because free-space info message is introduced in library release v110.
* commit '3049d2c140b06d5b2b419562c3d4d1d1c66612e3':
A minor bug fix.
Updated the command for external_env and vds_env to the most recent changes.
1. Updated the commands for compiling two new tests (external_env.c and vds_env.c). 2. Changed the data file names for external.c and external_env.c to avoid potential name conflict.
HDFFV-10658: setting and getting properties in API context. Porting the changes to the develop branch into the 1.10 branch: mainly the external file prefix and VDS prefix.
* commit 'b20ffd84e3572cd506bf1f696431892258e9ab3b':
Updated the command for external_env and vds_env to the most recent changes.
1. Updated the commands for compiling two new tests (external_env.c and vds_env.c). 2. Changed the data file names for external.c and external_env.c to avoid potential name conflict.
HDFFV-10658: setting and getting properties in API context. Porting the changes to the develop branch into the 1.10 branch: mainly the external file prefix and VDS prefix.
* commit '64c17fd18b2649fe4f571b7c10a0b1cc82856af8':
Updated the command for external_env and vds_env to the most recent changes.
1. Updated the commands for compiling two new tests (external_env.c and vds_env.c). 2. Changed the data file names for external.c and external_env.c to avoid potential name conflict.
HDFFV-10658: setting and getting properties in API context. Porting the changes to the develop branch into the 1.10 branch: mainly the external file prefix and VDS prefix.
* commit '308393a020bd7a812c231eee8130c9365d192e18':
Change "bad" hid_t_value to H5I_INVALID_HID in test_libver_bounds_copy() test.
Bring pull request #1729 from develop to 1.10: Fix for HDFFV-10800 H5Ocopy failure: The value for the H5F_LIBVER_V18 index in H5O_fill_ver_bounds[], the format version bounds array for fill value message, should be version 3 not 2.
Fails file creation when non-default free-space info is set in fcpl and the library version
high bound is less than v110 because free-space info message is introduced in library release v110.
Merge pull request #1772 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/HDFFV-10808-h5pset_file_space_strategy-succeeds to develop
* commit '3768566139df18928aa29ece0eff3010b224633b':
Add release notes.
Correct hid_t error value to H5I_INVALID_HID in tests related to libver_bounds.
Fix for HDFFV-10808 H5Pset_file_space_strategy succeeds when using H5Pset_libver_bounds v18,v18. Fails file creation when non-default free-space info is set in fcpl and the library version high bound is less than v110 because free-space info message is introduced in library release v110.
Conflicts:
test/tfile.c
* commit '308393a020bd7a812c231eee8130c9365d192e18':
Change "bad" hid_t_value to H5I_INVALID_HID in test_libver_bounds_copy() test.
Bring pull request #1729 from develop to 1.10: Fix for HDFFV-10800 H5Ocopy failure: The value for the H5F_LIBVER_V18 index in H5O_fill_ver_bounds[], the format version bounds array for fill value message, should be version 3 not 2.
* commit '378ed8bebfe709156b24aacbf8013de1a776c04e':
Change "bad" hid_t_value to H5I_INVALID_HID in test_libver_bounds_copy() test.
Bring pull request #1729 from develop to 1.10: Fix for HDFFV-10800 H5Ocopy failure: The value for the H5F_LIBVER_V18 index in H5O_fill_ver_bounds[], the format version bounds array for fill value message, should be version 3 not 2.
Fix for HDFFV-10800 H5Ocopy failure:
The value for the H5F_LIBVER_V18 index in H5O_fill_ver_bounds[], the format
version bounds array for fill value message, should be version 3 not 2.
* commit '346fe1a0bcb2da5e3b1de04f24195ce9781e846a':
Fix CMake module include and note text
HDFFV-10581 Correct PDB files and debug naming.
Fixed name for 'Build HDF Tests' in CMake's libhdf5 settings
Merge parallel static fix from develop
Fixed options for CMake to correct names
Added Tests/Tools to libhdf5.settings in cmake equivalent
Minor fix in libhdf5.settings.in
Squash commit of options to build tools and tests
* commit 'c56b9846c5277271dd07900b884da1abf1c9c21f':
Fixed name for 'Build HDF Tests' in CMake's libhdf5 settings
Fixed options for CMake to correct names
Added Tests/Tools to libhdf5.settings in cmake equivalent
Minor fix in libhdf5.settings.in
Squash commit of options to build tools and tests
* commit '8ab0727d54cd147930aea5fdb025f3aeeb4f82c1':
Correct sentence structure.
Add H5_DLL prefix to fix link
HDFFV-10805 Merge SHARED ONLY option from develop
* commit '519685d05cdb53e6e641587863c45773cca571db':
Address daily test failure for hdf5_1_10: Fix the testhdf5 failing test in the selection code which segfaults.
* commit '1d87374f68a28a215878a47e1203711dc95ac716':
Make corresponding changes for H5Sencode based on PR #1645 to develop branch. The core changes are to revert previous modifications now that we use API context for fapl.
* commit '4dfcc225ba98a5ad1bc4283b8eacde0bb6f7484c':
Fix Java JUnit-TestH5P failure on 32-bit arch
Added new C++ wrappers - HDFFV-10622
Make the corresponding fix for HDFFV-10579 H5Arename fails when creation order of attributes is tracked.
Description:
Added wrappers for H5Pset/get_create_intermediate_group:
// Specifies in property list whether to create missing
// intermediate groups
void setCreateIntermediateGroup(bool crt_intmd_group) const;
// Determines whether property is set to enable creating missing
// intermediate groups
bool getCreateIntermediateGroup() const;
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
* commit '36149c8a669146eb73750f03b8dd85a1f1c02c2e':
Make the corresponding fix for HDFFV-10579 H5Arename fails when creation order of attributes is tracked.
* commit '3e30d019214eaee6f345f45eae478e7f464df8ad':
Make corresponding changes for hyperslab encoding incorrect length (HDFFV-10271). This is based on PR #1644 merged to develop branch. The fix for the incorrect length was already checked in to 1.10 on Dec 2017.
* commit '670c6c1389c1c66598a365a9bfe2b19237d9e93a':
Make corresponding changes for moving dataspace selection-specific coding to the callbacks. This is based on the PR #1642 merged to the develop branch.
* commit '76b4748e78b2de806114100f7b82133b6983c60c':
Make corresponding changes for setting API context for fapl and libver_bounds to be used later in dataspace selection. This is based on PR #1640 merged to develop branch.
* commit '4feb2100591c802ea450dc26dae4e0546479fa96':
Make corresponding changes for version bounds in V110. This is based on PR#1639 merged to develop branch.
* commit 'a8443acaa76b79ebe74624af363008f0163a44f8':
Fix issue with direct chunk write not updating the "last chunk" index cache. Fix issues involving datasets being "no allocated" when they contain cached raw data.
* commit '2f3c34c649b8ec04d399296fa6203f68615e55a0':
Revised the entry of bug fix for HDFFV-10705.
Minor change: revised the note from the previous commit about HDFFV-10705.
HDFFV-10705: added a release note.
HDFFV-10705: Fixed memory leak in scale offset filter.
* commit '6819c11508b0610f222fe3bfe8a19f637bf4319c': (154 commits)
CMake needs a tar.gz examples file for windows, too.
Correct file permissions on README.txt.
Address merge anomalies and incorrect file permissions.
Update release date in README.txt and RELEASE.txt.
Revisions to Platforms tested.
Updated LT_VERS_AGE in config/lt_vers.am due to reinstatement of previously removed symbols, then ran autogen.sh to propagate so number changes and H5E_LOGFAIL_g addition to files checked in on release branch.
Updated H5err.txt to replace a global variable that was removed during the metadata cache logging changes (to maintain binary compatibility).
HDFFV-10552,10686 restore H5O_*1 functions
Minor fix in h5str_sprintf for NULL region references
Add new files to MANIFEST.
Update so version numbers. fix 2 typos.
Update RELEASE.txt for TRILABS-34 and remove unused sections.
Add script for building HDF5 with CMake on HPC machines that use sbatch. Add README file for inclusion in CMake-hdf5-<version>.tar.gz file. Add updated README_HPC file with cross compile instructions.
set version to 1.10.5-pre1. Change default build mode to production.
Merge pull request #1560 in HDFFV/hdf5 from hdf5-1-10-documentation-only to hdf5_1_10_5
Update HISTORY-1_10.txt and RELEASE.txt files.
Modify RELEASE.txt in response to PR comments
Check in files generated by autogen.sh for hdf5_1_10_5 release branch.
Check in files generated by autogen.sh for hdf5_1_10_5 release branch. 2019/02/16.
Code improvement
...
* commit '2418415fb9f67e8a15f62f1972a9394e48a9c97d':
Updated LT_VERS_AGE in config/lt_vers.am due to reinstatement of previously removed symbols, then ran autogen.sh to propagate so number changes and H5E_LOGFAIL_g addition to files checked in on release branch.
* commit 'd628025b500a9480ce08ced10d566a700d82f8e3':
Updated H5err.txt to replace a global variable that was removed during the metadata cache logging changes (to maintain binary compatibility).
* commit 'c50008c7663c96c4452c4f0d4cf7de9d0118dec9':
Updated H5err.txt to replace a global variable that was removed during the metadata cache logging changes (to maintain binary compatibility).
* commit '6f2831ceccfe2edd166252eaf91caa1779ac7628':
Add new files to MANIFEST.
Update so version numbers. fix 2 typos.
Update RELEASE.txt for TRILABS-34 and remove unused sections.
Add script for building HDF5 with CMake on HPC machines that use sbatch. Add README file for inclusion in CMake-hdf5-<version>.tar.gz file. Add updated README_HPC file with cross compile instructions.
* commit '49766a8ffb43e640c1a28ea853d2bfc40f7236ba':
Merge pull request #1560 in HDFFV/hdf5 from hdf5-1-10-documentation-only to hdf5_1_10_5
Update HISTORY-1_10.txt and RELEASE.txt files.
* commit '247cb2989f4cc0e730be27bc57baae23e8814178':
Merge pull request #1560 in HDFFV/hdf5 from hdf5-1-10-documentation-only to hdf5_1_10_5
Update HISTORY-1_10.txt and RELEASE.txt files.
* commit 'ce85a157bf8f212d7a2158de2d5bd60ef9ac5d49':
Check in files generated by autogen.sh for hdf5_1_10_5 release branch.
Check in files generated by autogen.sh for hdf5_1_10_5 release branch. 2019/02/16.
Added C++ wrapper for H5Ovisit2
* commit '2a4e26146dfc2f51edb7b9bb8317d3816172f86d':
Code improvement
Adding a C++ wrapper
Fixing typo in documentation
Description:
- Added a wrapper for H5Ovisit2 to class H5Object
// Recursively visit elements reachable from this object.
void visit(H5_index_t idx_type, H5_iter_order_t order, visit_operator_t user_op, void *op_data, unsigned int fields);
- Fixed various typos in documentation
- Removed a pair of [] in a delete statement for a non-array pointer.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
* commit '4e31361dad4add06792b652dbe5b97e501f9031d':
I'm bringing the fixes for the following Jira issues from the develop branch 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.
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.
* commit '7f5741825db0737db5ac46c43009681508a73002':
Add release notes information.
Modification based on feedback from pull request.
Modification based on feedback from pull request.
There is performance issue when closing an object. The slow down is due to the search of the "tag_list" to find out the "corked" status of an object. The fix: (1) Add a counter "num_objs_corked" in the cache structure to track the number of "corked" objects. (2) Skip the search of "tag_list" if the counter is zero i.e. no "corked" objects.
Conflicts:
release_docs/RELEASE.txt
Description:
Renamed data file with long name to a shorter name.
Revised an entry in RELEASE.txt
Platforms tested:
Linux/64 (jelly)
Darwin (osx1010test)
Description:
HDFFV-10586 CVE-2018-17434 Divide by zero in h5repack_filters
Added a check for zero value
HDFFV-10588 CVE-2018-17437 Memory leak in H5O_dtype_decode_helper
This is actually an Invalid read issue. It was found that the
attribute name length in an attribute message was corrupted,
which caused the buffer pointer to be advanced too far and later
caused an invalid read.
Added a check to detect attribute name and its length mismatch. The
fix does not cover all cases, but it'll reduce the chance of this issue
when a name length is corrupted or the attribute name is corrupted.
HDFFV-10684 H5Ewalk does not stop until all errors in the stack are visited
The test for HDFFV-10588 has revealed a bug in H5Ewalk.
H5Ewalk did not stop midway even when the call back function returns
H5_ITER_STOP. This is because a condition is missing from the for
loops in H5E__walk causing the callback functions unable to stop until
all the errors in the stack are iterated. Quincey advised on the final
fix. In this fix, "status" is switched to "ret_value" and HGOTO_ERROR
to HERROR, and the for loops won't continue when "ret_value" is not 0.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
* commit 'e90d59a69f2750ac55ef5da20df5e8cba7693134':
Add RELEASE.txt note for parallel filters test fix
Updates to t_filters_parallel for missing filters
* commit 'd26963b180a052ac063907f95596a7ecad08ef8e':
Add clear objects to ignore tests
Add new clear tests to ignore list
Cleanup variable names
HDFFV-10685 Always set version flags on OSX
* commit '7367fc0c1b916cffe50d1b8d729ccccfd6a9ec77':
Add clear objects to ignore tests
Add new clear tests to ignore list
Cleanup variable names
HDFFV-10685 Always set version flags on OSX
* commit '7880089c0be7eb6625cc9982775b522aee523b65':
Merge pull request #1450 in HDFFV/hdf5 from ~SONGYULU/hdf5_ray:TRILAB-98-dt_arith-and-cpp_testhdf5-tests to develop
* commit 'b02de315b93ac29d2483a91d526b110a25073505':
NNSA Tri-LabsTRILAB-98: Another two test cases out.
NNSA Tri-Labs TRILAB-98: Taking out a few more test cases.
NNSA Tri-Labs TRILAB-98 dt_arith and cpp_testhdf5 tests fail on sierra.llnl.gov: According to the group decision, simply provide a macro to disable some failing test cases on sierra (IBM power9 cpu). All failing cases involve long double data type.
Description:
- HDFFV-10578 - CVE-2018-17234 Memory leak in H5O__chunk_deserialize()
Actually, the leak was in h5tools_util. Applied Neil's fix.
- Changed an assert to if/HGOTO_ERROR to fail gracefully.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1010test)
* commit '3476c7d13d4124f7e0752f251a667bef6b4fbf68':
Merge pull request #1429 in HDFFV/hdf5 from HDFFV-10596-fortran-library-names-differ to develop
Work around compiler fussiness on platypus.
Fix for debug assert in H5FDmpio.c
* commit 'f4c9ec5d41aa53829617274d3286f1e9a45ae57e':
Add RELEASE.txt entry for HDFFV-10596.
Uninstall should remove the libhdf5_hl_fortran links.
Add symlinks named libhdf5_hl_fortran* to libhdf5hl_fortran in Makefile.am to match cmake install and the name pattern for other hl lib files.
* commit 'a043211d9edf2df3ea8049bda4be6bdcbf0970e9':
Delay checking if decoded message's "shareable" flag is appropriate for 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.
Remove H5O_BOGUS_INVALID_ID from H5O_msg_class_g initialization, since space for it was removed.
Fortran wrappers for dataset obj header minimization API calls.
* commit '55806ff1be0d559a204e84e595403b309239085f':
Delay checking if decoded message's "shareable" flag is appropriate for 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.
Remove H5O_BOGUS_INVALID_ID from H5O_msg_class_g initialization, since space for it was removed.
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.
Remove H5O_BOGUS_INVALID_ID from H5O_msg_class_g initialization, since
space for it was removed.
* commit '1a50622733c14d89b3fd8c6bab684af9205a3b96':
Fix for daily test failure: too many arguments to function 'H5Gopen1'.
Fix the git merge leftover in RELEASE.txt.
Fix the git merge leftovers in RELEASE.txt.
Fix for HDFFV-10659: The library aborts with "infinite loop closing library" after deleting attributes in densed storage. The fix: When deleting attribute nodes from the name index v2 B-tree, if an attribute is found in the intermediate B-tree nodes, which may be merged/redistributed in the process, we need to free the dynamically allocated spaces for the intermediate decoded attribute.
after deleting attributes in densed storage.
The fix: When deleting attribute nodes from the name index v2 B-tree,
if an attribute is found in the intermediate B-tree nodes, which may be
merged/redistributed in the process, we need to free the dynamically
allocated spaces for the intermediate decoded attribute.
* commit '82dd54c26b11245c36f65a044e9b717dc2c337e0':
Revised text
Fixed CVE division-by-zero issues Description: Fixed HDFFV-10577 and similar issues found in H5Dchunk.c. All the occurrences are in: H5D__create_chunk_map_single H5D__create_chunk_file_map_hyper H5D__chunk_allocate H5D__chunk_update_old_edge_chunks H5D__chunk_prune_by_extent H5D__chunk_copy_cb H5D__chunk_collective_fill Also updated RELEASE.txt for the chunk query functions and removed some blank lines in chunk_info.c. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
Description:
Fixed HDFFV-10577 and similar issues found in H5Dchunk.c. All
the occurrences are in:
H5D__create_chunk_map_single
H5D__create_chunk_file_map_hyper
H5D__chunk_allocate
H5D__chunk_update_old_edge_chunks
H5D__chunk_prune_by_extent
H5D__chunk_copy_cb
H5D__chunk_collective_fill
Also updated RELEASE.txt for the chunk query functions and removed
some blank lines in chunk_info.c.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1010test)
Minimized dataset object headers
* commit 'e1d865a11d7864f4c0733aa22a8c96f0f015ef75':
Remove "bad" statements from end of TEST_ERROR. Formerly arguments to FAIL_PUTS_ERROR.
Add semicolon at end of TEST_ERROR() invocation for consistency.
Change FAIL_PUTS_ERROR to TEST_ERROR. Remove VOL-related merge cruft.
Change H5Dcreate() to H5Dcreate2(). Fix return value (int -> void).
Change H5Acreate to H5Acreate2
Remove unnecessary s
Incoporate minimized dataset headers code and tests.
This is merged now so it can be tested.
* commit '74a3710a996fca5ed7fcb4dd8919a7a8521de1de':
Revised per review. Description: Changed H5EA_iterate and H5FA_iterate as suggested. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
Addressed HDFFV-10661 Description: - Fixed a bug triggered by tests in chunk_info.c. The returned value from a callback function was not checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). This oversight caused a callback function to continue iterating even though it's supposed to stop. Vailin confirmed. - Addressed review comments and made various improvements on the tests. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
* commit '029491e877a3c5c4f5947df3cc74785ce01be2ba':
Merge of logging framework updates.
Updated the H5I debug function so it's more robust and always available.
Removed 'VOL' from some H5PL comments.
Removed 'VOL' versions of FUNC_ENTER macros as well as empty functions orginally intended to support the full SWMR feature (from develop).
Replaced all MPI-1 calls with MPI-2 equivalents (from develop).
* commit 'e2349130608e013e610a750b28fb00fc92866e0c':
Add H5I_INVALID_HID
Manifest fix
Tools cleanup
HDFFV-10660,-10594 merge from develop
HDFFV-10632 separate stderr and stdout in tests
Description:
- Fixed a bug triggered by tests in chunk_info.c. The returned value
from a callback function was not checked in H5EA_iterate(), H5FA_iterate(),
and H5D__none_idx_iterate(). This oversight caused a callback function
to continue iterating even though it's supposed to stop. Vailin confirmed.
- Addressed review comments and made various improvements on the tests.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1010test)
* commit '51076d40617aa6f0236809c2c919cc6921b3bbc1':
Fixed exit() to HDexit() in use_append_chunk.c and use_append_mchunks.c
Fixed fprintf to HDfprintf in the following routines: 1) read_uc_file() in use_common.c 2) main() of use_append_chunk.c and use_append_mchunks.c
Fix for HDFFV-10554 use_append_chunks in swmr use case test failure Fix the timing issue of the test by moving the open/close of the test file for the writer to use_append_chunk.c and use_append_mchunks.c.
Description:
Moved the test function test_get_chunk_info from dsets.c to chunk_info.c
because chunk_info.c was created for the purpose of testing chunk information.
Platforms tested:
Linux/64 (jelly)
* commit '91771bdf4d6c2ddcdbc127ee2f9d29525d490757':
Updated new API functions Description: - Addressed additional review comments - Moved the test function test_get_chunk_info from dsets.c to chunk_info.c because chunk_info.c was created for the purpose of testing chunk information. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
Updated new API functions Description: - Per Vailin's review, revised H5Dget_chunk_info_by_coord to handle non-existing chunk and H5Dget_num_chunks and H5Dget_chunk_info to handle dataset with no data. - Addressed other review comments - Note that additional tests will be added as we need to send users these functions asap for feedback. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
New API functions Description: Added functions to query chunk information:
Merged now to create tar ball today for user asap.
* commit 'a1a79203b8027631061cb626a5efdd37268752c2':
Updated new API functions Description: - Addressed additional review comments - Moved the test function test_get_chunk_info from dsets.c to chunk_info.c because chunk_info.c was created for the purpose of testing chunk information. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
Updated new API functions Description: - Per Vailin's review, revised H5Dget_chunk_info_by_coord to handle non-existing chunk and H5Dget_num_chunks and H5Dget_chunk_info to handle dataset with no data. - Addressed other review comments - Note that additional tests will be added as we need to send users these functions asap for feedback. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
New API functions Description: Added functions to query chunk information:
Description:
- Addressed additional review comments
- Moved the test function test_get_chunk_info from dsets.c to chunk_info.c
because chunk_info.c was created for the purpose of testing chunk information.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
Description:
- Per Vailin's review, revised H5Dget_chunk_info_by_coord to handle
non-existing chunk and H5Dget_num_chunks and H5Dget_chunk_info to
handle dataset with no data.
- Addressed other review comments
- Note that additional tests will be added as we need to send users
these functions asap for feedback.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
* commit '81b2943b6fc01b52de2048d9503d524b2780112b':
Fix typo in whitespace area
Merge CMake changes from develop Improved cross-compiling and toolchains
* commit 'b81adf00bcf45f4bce1c6f1ef8ee6c703e40b945':
Trial commit Description: Just committing some typo fix to see whether my changes can be merged successfully to this branch Platforms tested: Linux/64 (jelly)
Description:
Added functions to query chunk information:
H5Dget_num_chunks(dset_id, fspace_id, *nchunks)
Gets the number of written chunks that intersect with the given
dataspace. However, in this version, the intersection is not
yet completed. Thus, the number of all written chunks will be
returned.
H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size)
Given a chunk's coordinates, returns the chunk's filter, address,
and size.
H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size)
Given a chunk's index, returns the chunk's coordinates, filter,
address, and size. The chunk belongs to a set of chunks that have
nonempty intersection with the specified dataspace. However, in
this version, the intersection is not yet completed, and the index
is of all the written chunks.
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1011test)
* commit '202d7403282230e2071412237ac7ba86ccb7f3db':
Trial commit Description: Just committing some typo fix to see whether my changes can be merged successfully to this branch Platforms tested: Linux/64 (jelly)
* commit 'f3f29dc7df5f3cc41a5e9462d8c415e540cda3d6': (42 commits)
Commit version string changes for HDF5 1.10.4 release.
Merge hdf5_1_10 changes to hdf5_1_10_4.
Merge in changes from hdf5_1_10.
Commit release date change.
Update RELEASE.txt for HDF5 1.10.4 release.
Add notes about unsupported options
Add contents of HDF5 1.10.3 RELEASE.txt to HISTORY-1_10.txt and update RELEASE.txt for continuing development.
Switch maintainer mode to disable, build mode to production, version to 1.10.4, and commit files generated by autogen.sh for release branch hdf5_1_10_4.
HDFFV-10568 fix hdf5_java library dependency
Fix Java library location for testing
Java groups example fix
Update system commands with HD prefix and whitespace
Merge pull request #1224 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop
Disable failing tests because of execution issue
Add testfiles to data copy
Same changes needed for examples as test
Correct name of test jar
Only remove test jars
Remove obsolete var
Change prefix in example scripts to relative path to bin. This was done for 1.8, and works wherever installed without the need to replace the original prefix.
...
* commit '1f73a6d16b540bc8b7dfcec1df3eb7bdca5810d8':
Update RELEASE.txt for HDF5 1.10.4 release.
Add notes about unsupported options
Add contents of HDF5 1.10.3 RELEASE.txt to HISTORY-1_10.txt and update RELEASE.txt for continuing development.
Switch maintainer mode to disable, build mode to production, version to 1.10.4, and commit files generated by autogen.sh for release branch hdf5_1_10_4.
* commit '3110fd53c0b072e6be250235061a6349921765e9':
Add contents of HDF5 1.10.3 RELEASE.txt to HISTORY-1_10.txt and update RELEASE.txt for continuing development.
* commit '763b95c6b0f027025a5a5bfb203b77317ffa2368':
Update RELEASE.txt with suggested changes
Update MANIFEST file for new t_coll_md_read.c file
Remove now-unused local variable
Add fix for HDFFV-10501
* commit '9e466086f49e6e36b2dc71c0e6e94c01368d7d00':
Disable failing tests because of execution issue
Add testfiles to data copy
Same changes needed for examples as test
Correct name of test jar
Only remove test jars
Remove obsolete var
Correct osx installer extension
revert build install change for DT
Merge CMake and Java OSX changes from develop
* commit '21eef8a98ee6949c69d79c6c4d87fc8e4e38dc29': (354 commits)
Commit version with new release date.
Add example packaging option and fix html5 issues
Commit version with new release date.
Commit files changed by autogen.sh.
Merge pull request #1208 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to hdf5_1_10
Merge pull request #1207 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10
Merge pull request #1203 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10
Commit version with new release date. Commit new generated H5version.h including #defines for H5_USE_110_API.
Correct nested c-style comment.
Merge pull request #1197 in HDFFV/hdf5 from ~BYRN/hdf5_merge_adb:hdf5_1_10 to hdf5_1_10
Merge pull request #1194 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:hdf5_1_10 to hdf5_1_10
Updated the H5Dread/write_chunk() release note.
Added a release note for the H5Dread/write_chunk() API calls.
Update Intel Fortran version for Windows 10.
RELEASE.txt updates. Version change for 1.10.3 release.
Revised entry on CVE issues
Added notes about CVE issues
Update version for HDF5 1.10.3 release.
Add placeholder for performance improvement in RELEASE.txt
updated fortran fixes
...
* commit '4393a79e966a946cd7682e4177cbfeacf68e4a92':
Change prefix in example scripts to relative path to bin. This was done for 1.8, and works wherever installed without the need to replace the original prefix.
* commit 'ddba83b27b461fd3282e89beb3fb0975dce9b575':
Commit files changed by autogen.sh.
Merge pull request #1208 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to hdf5_1_10
Merge pull request #1207 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10
Merge pull request #1203 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10
* commit '1029540525688e9dd7f487fd0c8e5cd0f8e6c098':
Update Inel Fortran version for Windows 10.
Merge pull request #1189 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:hdf5_1_10_3 to hdf5_1_10_3
Merge pull request #1190 in HDFFV/hdf5 from ~BMRIBLER/hdf5_1_10_3-bmr:hdf5_1_10_3 to hdf5_1_10_3
Merge pull request #1195 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:hdf5_1_10_3 to hdf5_1_10_3
* commit '476072a8b469206e2a2de6eb5ad9fcae36c7bdd6':
Updated the H5Dread/write_chunk() release note.
Added a release note for the H5Dread/write_chunk() API calls.
* commit 'a246d73aca19f9934bb2b2883742a66ac355be59':
Merge pull request #1197 in HDFFV/hdf5 from ~BYRN/hdf5_merge_adb:hdf5_1_10 to hdf5_1_10
Merge pull request #1194 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:hdf5_1_10 to hdf5_1_10
* commit '476072a8b469206e2a2de6eb5ad9fcae36c7bdd6':
Updated the H5Dread/write_chunk() release note.
Added a release note for the H5Dread/write_chunk() API calls.
* commit 'd761a22f4bbfb27848584e6466d100057bf495f6':
Update Intel Fortran version for Windows 10.
RELEASE.txt updates. Version change for 1.10.3 release.
Update version for HDF5 1.10.3 release.
Add placeholder for performance improvement in RELEASE.txt
* commit 'db1c015f1c5a7b3cfdd0be59d9a052f190587cc7':
Switch default build mode to production. Propagate configure.ac changes to configure and Makefile.ins with autogen.sh.
Update RELEASE.txt.
* commit 'f378513a67dcda5cf4750a2422f5f646abdcbbe9': (86 commits)
HDFFV-10544 writeVL subfunction is unimplemented
Merge pull request #1178 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
HDFFV-10544 Improve JNI exception handling
Change exception text
Move unimplemented exception throw to just one function
Typo fix
Set CMAKE_REQUIRED_INCLUDES instead of using path in call
Add Autotools and CMake checks for big I/O MPI-3 functions
Add hdf5settings section for parallel compression status in CMake builds
Switch to CheckSymbolExists in CMake
Add configure check for MPI_Mprobe and MPI_Imrecv functions
Revert "Merge pull request #1149 in HDFFV/hdf5 from hdf5_1_10.sync to hdf5_1_10"
Update HDF5 examples to correct version.
Correct a few typos.
Correct typo in comment in config/gnu-flags.
Update bine/release to create batch scripts and build-unix-sh, and to put files in a subdirectory.
misc. fixed version paths
misc. versioning fixes
Fixed versioning
Add missing '\' in the middle of the public headers list in Makefile.am.
...
* commit 'a52beb6566c29c4f2d9f4722c3a9a40a48cbafba':
Update version to 1.10.3-pre2.
Merge pull request #1178 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '73ffe6b6df8df935e1cc6e31cf2bdaed6c6448e9':
Update version to 1.10.3-pre2.
Merge pull request #1178 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit 'a3385675b3cdc2102457a9f91877cc27778ab29a':
Reorder bugfix release notes from latest to earliest, and miscellaneous format cleanup.
Add RELEASE.txt entry for HDFFV-10475
* commit 'a3385675b3cdc2102457a9f91877cc27778ab29a':
Reorder bugfix release notes from latest to earliest, and miscellaneous format cleanup.
Add RELEASE.txt entry for HDFFV-10475
* commit 'afa166154f1d4175a9d8cbc2f6bc1584dca859f8': (81 commits)
Typo fix
Set CMAKE_REQUIRED_INCLUDES instead of using path in call
Add Autotools and CMake checks for big I/O MPI-3 functions
Add hdf5settings section for parallel compression status in CMake builds
Switch to CheckSymbolExists in CMake
Add configure check for MPI_Mprobe and MPI_Imrecv functions
Revert "Merge pull request #1149 in HDFFV/hdf5 from hdf5_1_10.sync to hdf5_1_10"
Update HDF5 examples to correct version.
Correct a few typos.
Correct typo in comment in config/gnu-flags.
Update bine/release to create batch scripts and build-unix-sh, and to put files in a subdirectory.
misc. fixed version paths
misc. versioning fixes
Fixed versioning
Add missing '\' in the middle of the public headers list in Makefile.am.
Fixed typos
Entered entries for HDFFV-10150, HDFFV-10458, HDFFV-1047
Updated for C2Cppfunction_map.htm
Added class DSetAccPropList Description: - Added class DSetAccPropList for the dataset access property list. - Added wrapper for H5Dget_access_plist to class DataSet // Gets the access property list of this dataset. DSetAccPropList getAccessPlist() const;
Code improvement Description: Moved the new H5Object::getInfo member functions to H5Location and made them overloaded with the existing H5Location::getObjinfo. This way is cleaner than the previous approach. Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
...
Add line to libhdf5settings file for status of Parallel writes to
filtered datasets status
Surround Parallel Compression code in MPI_VERSION >= 3 checks
Add disabled message for Parallel Compression built w/ MPI-2
Modify Parallel Compression tests to only run the parallel filtered read
tests when parallel filtered writes are disabled
Update big I/O code to handle being built with MPI-2
Add checks to CMakeLists.txt for MPI_Mprobe and MPI_Imrecv
* commit '3e7979902ade13ba8f37e020e5ae95f03a82b0f9':
Merge pull request #1158 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp4:develop to develop
Merge from develop
* commit '0636e97e42c78f39c5b4dd5d5120394566bfb35f':
Merge pull request #1158 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp4:develop to develop
Merge pull request #1158 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp4:develop to develop
Merge from develop
HDFFV-10534 add note
HDFFV-10534 change to runtime exception
* commit '3e7979902ade13ba8f37e020e5ae95f03a82b0f9':
Merge pull request #1158 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp4:develop to develop
Merge from develop
HDFFV-10534 add note
HDFFV-10534 change to runtime exception
* commit '23b96a8dc8ccb7d60150a30133183df3a7ac270d': (53 commits)
HDFFV-10534 add note
HDFFV-10534 change to runtime exception
Revise H5D__mpio_array_gatherv() to not allocate memory needlessly
Add test to continually grow and shrink chunks
Changes to test with checksum filter as well as deflate filter
Eliminate warning about signed to unsigned conversion
Remove unused local variable
Fix bug in parallel reads of compressed data
Add data verification to parallel filtered compound write tests
Add seven of fourteen parallel filtered data partial read tests
Add missing file and remove deleted
Correct git synch error
Add swmr tests, fix java script
Update macros and cygwin flags
Revert Sencode h5dump test
RELEASE.txt updates for HDFFV-10467 and HDFFV-10509
Update HDF5 examples to correct version.
Correct a few typos.
Correct typo in comment in config/gnu-flags.
Update bine/release to create batch scripts and build-unix-sh, and to put files in a subdirectory.
...
* commit 'ed1bfe373316567b57ddf2199853db815fff6b4b': (51 commits)
Revise H5D__mpio_array_gatherv() to not allocate memory needlessly
Add test to continually grow and shrink chunks
Changes to test with checksum filter as well as deflate filter
Eliminate warning about signed to unsigned conversion
Remove unused local variable
Fix bug in parallel reads of compressed data
Add data verification to parallel filtered compound write tests
Add seven of fourteen parallel filtered data partial read tests
Add missing file and remove deleted
Correct git synch error
Add swmr tests, fix java script
Update macros and cygwin flags
Revert Sencode h5dump test
RELEASE.txt updates for HDFFV-10467 and HDFFV-10509
Update HDF5 examples to correct version.
Correct a few typos.
Correct typo in comment in config/gnu-flags.
Update bine/release to create batch scripts and build-unix-sh, and to put files in a subdirectory.
Add missing '\' in the middle of the public headers list in Makefile.am.
Fixed typos
...
Description:
- Added class DSetAccPropList for the dataset access property list.
- Added wrapper for H5Dget_access_plist to class DataSet
// Gets the access property list of this dataset.
DSetAccPropList getAccessPlist() const;
- Added wrappers for H5Pset_chunk_cache and H5Pget_chunk_cache to class
DSetAccPropList
// Sets the raw data chunk cache parameters.
void setChunkCache(size_t rdcc_nslots, size_t rdcc_nbytes, double rdcc_w0)
// Retrieves the raw data chunk cache parameters.
void getChunkCache(size_t &rdcc_nslots, size_t &rdcc_nbytes, double &rdcc_w0)
- Added two more arguments to H5Location::createDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
const LinkCreatPropList& lcpl = LinkCreatPropList::DEFAULT
- Added one more argument to H5Location::openDataSet:
const DSetAccPropList& dapl = DSetAccPropList::DEFAULT
Platforms tested:
Linux/64 (jelly)
Linux/32 (jam)
Darwin (osx1010test)
Description:
Moved the new H5Object::getInfo member functions to H5Location and
made them overloaded with the existing H5Location::getObjinfo. This
way is cleaner than the previous approach.
Platforms tested:
Linux/64 (jelly)
Linux/32 (jam)
Darwin (osx1010test)
Description:
- Fixed doc issue
Added an html version for the C++ function mapping table and removed
the single web page version.
Updated cpp_doc_config to use the html file.
- Added a couple more minor tests
Description:
Fixed HDFFV-10481 and HDFFV-10477, division by 0.
Fixed another occurrence beside what were reported.
Also, changed a local variable to avoid an unnecessary cast.
Platforms tested:
Linux/64 (jelly)
Linux/32 (jam)
Darwin (osx1010test)
Description:
Applied the typo fixes from user's report.
The previous pull request couldn't be merged because it was too old,
and it was too complicated for me to resolve conflicts.
Platform tested:
Linux/64 (jelly) - very minor
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
* commit 'fe8d5bcb7aebbade60c8f128758c2c37c6799040': (74 commits)
Update HDF5 examples to correct version.
Correct a few typos.
Correct typo in comment in config/gnu-flags.
Update bine/release to create batch scripts and build-unix-sh, and to put files in a subdirectory.
misc. fixed version paths
misc. versioning fixes
Fixed versioning
Add missing '\' in the middle of the public headers list in Makefile.am.
Fixed typos
Entered entries for HDFFV-10150, HDFFV-10458, HDFFV-1047
Updated for C2Cppfunction_map.htm
Added class DSetAccPropList Description: - Added class DSetAccPropList for the dataset access property list. - Added wrapper for H5Dget_access_plist to class DataSet // Gets the access property list of this dataset. DSetAccPropList getAccessPlist() const;
Code improvement Description: Moved the new H5Object::getInfo member functions to H5Location and made them overloaded with the existing H5Location::getObjinfo. This way is cleaner than the previous approach. Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
Fix for HDFFV-9277: update the ainfo message after removing an attribute.
Add cmakehdf5 command line option to turn on shell script testing. Option is on by default but can be disabled with --disable-shell-testing.
Apply Cygwin pathches from Marco Atzeri. Commit Joe Lee's typo corrections for src/H5MF.c.
Adjust error handling
TRILABS-137 Convert tcheck_version script to cmake tests
Fixed EED-319 Description: - Fixed doc issue Added an html version for the C++ function mapping table and removed the single web page version. Updated cpp_doc_config to use the html file. - Added a couple more minor tests
ifdef around std flag for cygwin
...
* commit 'cc2eea14f6a6532a201dde13af13353d4d73fd92': (1014 commits)
Commit release date changes.
Fix typo in INSTALL_Cygwin.txt
Update references and merge from 1_10
Corrected email address
Commit Barbara's INSTALL* file updates.
Commit Elena's RELEASE.txt edits and Les'/Lori's README.txt revision.
ommit Elena's RELEASE.txt edits and Les'/Lori's README.txt revision.
Remove stray '/'.
Add subdirectory for CMake-HDF5-1.10.2.zip.
Correct name of hl compile script
Add directory in release CMake...tar.gz file.
Minor edits in RELEASE.txt. Set version for HDF5 1.10.2 release.
release branch should not generate headers
Switch default build mode to production. Set version to 1.10.2-pre2..
HDFF5-1.10.2-pre1 releaseed. Add links for security bug fixes to RELEASE.txt.
Fix VS2017 binary readme
Couple fixes to the test routine for HDFFV-10425.
Add test and release info for the fix to HDFFV-10425 test failure with H5DOwrite_chunk.
Updated RELEASE.txt
Remove known probelem that was fixed.
...
* commit '0f210c2c33a22c2fb78d95b63942af5b4cc9a168':
Add directory in release CMake...tar.gz file.
Minor edits in RELEASE.txt. Set version for HDF5 1.10.2 release.
* commit '2cecea8f06b46f5d694db618e693fc28ed67094c':
Switch default build mode to production. Set version to 1.10.2-pre2..
HDFF5-1.10.2-pre1 releaseed. Add links for security bug fixes to RELEASE.txt.
* commit 'e79f9a73feb1b18c52a1608336aff612d2732d5b':
Couple fixes to the test routine for HDFFV-10425.
Add test and release info for the fix to HDFFV-10425 test failure with H5DOwrite_chunk.
* commit 'f30b6593e252f7593e476e6d4c2f6cd8428b8fae':
Remove known probelem that was fixed.
Update bin/release. Remove some unused sections in RELEASE.txt.
* commit '0a7ae62dca4b33cbda87df41ff60bfe359f52444':
Fix date.
Correct the date in RELEASE.txt for H5DOread_chunk.
Add release info for H5DOread_chunk.
* commit 'ac6d811800eff708f821e2dbd1019a78a201c9ac':
Update Introduction. Add OpenMPI known problem
Remove empty sections and clean up entries in RELEASE.txt.
* commit '2f0566208ed0e5b654e619df6f9d7ebee16a0bd4':
Updated RELEASE.txt Description: Wrappers for H5Tencode and H5Tdecode No code change.
Fixed HDFFV-10151 Description: Added a document to the HDF5 C++ API Reference Manual to show the mapping from a C API to C++ wrappers.
Fix memory leak simply by capturing allocation in var
Change max value
Chnage values so test will fail when new latest is added
Exception changed
Exception type changed
Correct constant var names
Java constants for new lib verbounds values
* commit 'f205b5787043e3c96805738d763ed9695939aecf':
bin/release: Add hdf5-examples.tar.gz for CMake tar and zipt files. release_docs/RELEASE.txt: Update platforms supported and tested.
* commit '76dc40e3128b96b74fb67eee2e7aa5e732315990':
Switch maintainer_mode off (disabled). Commit files generated by autogen.sh script for the release branch.
* commit '02a9433fa0aac34ae81ab5f0d5b97a7934881215':
Add 2 parallel test files to CHECK-CLEANFILES so that if their tests fail before removing them, make check-clean will remove them.
Fixed memory leak Description: Added LinkCreatPropList to initH5cpp to cleaning up resource at exit. Platforms tested: Linux/64 (jelly) Linux/ppc64 (ostrich)
HDFFV-10412 add note for new H5error_on Java API
* commit 'ae26f655387bea73e8333765f83c0bc970696065':
Increment library version information for so numbers in lt_vers.am according to code and interface changes from interface compatibility report and manual checking.
* commit '184fc09bf7f429790fb2457999c469c80e47f5b9':
Commit release version changes. Add CMake-$version directory in CMake source files produced by bin/release.
* commit '9f6640afd48a9d03ff2fd44c050c64d45dc0816e':
More edits to Supported Platforms section of RELEASE.txt.
Final edits to RELEASE.txt and to correctly remove a test directory and test file.
* commit 'ed01c3ec1cea922aa9f2d2b0ede2ca317e04fcd7':
Documentation clean-up Description: - Rearranged public/non-public functions relative to the DOXYGEN_SHOULD_SKIP_THIS blocks to display them correctly in the RM - Moved internal comments outside of the \brief blocks so they will not be displayed in the RM - Updated RELEASE.txt about the changes in PR#466 Platforms tested: Verified document on Windows 10. Linux/64 (platypus) Darwin (osx1010test)
Description:
- Rearranged public/non-public functions relative to the
DOXYGEN_SHOULD_SKIP_THIS blocks to display them correctly in the RM
- Moved internal comments outside of the \brief blocks so they will
not be displayed in the RM
- Updated RELEASE.txt about the changes in PR#466
Platforms tested:
Verified document on Windows 10.
Linux/64 (platypus)
Darwin (osx1010test)
* commit '4a425eabc70cf5236afc41c2e56d4a57cc7c536e':
Commit version change to 1.10.1 and changes to Makfile.ins and other files generated by running autogen.sh.
* commit '4bc55bbf94d7fce7521b2efd766f677ca45c9ecc':
Code clean-up. Description: - Removed function prototypes left in by mistake - Moved H5Location::getNumObjs() to class Group because the C function in this wrapper only takes a group or file id. - Moved H5Object::getNumAttrs to H5Location because the C function in this wrapper can also take an attribute id. - Misc improvements in comments Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Description:
- Removed function prototypes left in by mistake
- Moved H5Location::getNumObjs() to class Group because the C
function in this wrapper only takes a group or file id.
- Moved H5Object::getNumAttrs to H5Location because the C function
in this wrapper can also take an attribute id.
- Misc improvements in comments
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
* commit '89483c19461623b77319a83ec0c6609e0e5f37a8':
Fix for HDFFV-10166 h5watch tests fail randomly to match expected output files (1) Re-structure tests to do one "extend" action at a time (2) Re-try test till max limit before final failure
* commit '0f9c0a31645ddc58ec7fc92c344bae9c04f13ebf':
Modifications based on review comments from pull request. Made changes according to review comments and discussion with Allen.
Fix for DAILYTEST-259 h5clear test failure Deposit the test files in test/misc/testfiles for testh5clear.sh to use instead of depending on h5clear_gentest. Tested on kituo, osx1010test, quail, platypus and ostrich.
Deposit the test files in test/misc/testfiles for testh5clear.sh to use instead of depending on h5clear_gentest.
Tested on kituo, osx1010test, quail, platypus and ostrich.
* commit '435214cb555725d3690826caeb7c255057b9f09a':
Fixed problems that prevent bin/trace from marking up some functions.
The cache_image test shows a skipped message about EoC in parallel.
Added code to disable the evict-on-close feature in the parallel library.
* commit 'd39deb8b323c95e2fba1a453c78ea31759eb4ce9':
Updated Copyright header in H5PLpkg.h.
Update version to 1.10.1-pre3.
Commit version changes in README.txt and RELEASE.txt for 1.10.1-pre2 release.
* commit '32e706e2cc1cb73cc6cacf78e9174b7afa5e5430':
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Skip tests for page buffering in test/fheap.c for parallel build Skip the two tests for page buffering in test/fheap.c because this feature is disabled in parallel. Activate full testing when this feature is re-enabled in the future for parallel build.
Due to HDFVIEW-19 add read VL as string function
* commit 'f574d627d8122c6ac7dcc16c9fd0d04cf97b6b67':
updated with README changes
Combined the README_DEVEL and README, and removed out-dated README material
* commit 'f83622042a8a6271dd502194867c00e8a89ec9fc': (34 commits)
Add 1.8 complete HISTORY file.
Add history files from 1.10.0 release.
Fix URL name
DAILYTEST-250 change test props to reduce timeout
Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771) 1) Calculate chunk index for extensive array index based on swizzled max chunks when unlim_dim > 0 2) Minor fixes to test/fheap.c that somehow were missed from last check in. See pull request #396 review comments.
Removed commeted out code from H5C_dump_coll_write_list()
Checkin of fix for CGNS bug (https://jira.hdfgroup.org/browse/HDFFV-10055).
HDFFV-10143 add missing javadoc param
Add missing test status
Fix CMake regex commands
Modify test/fheap.c to run with various file space strategies and/or page buffering Modify test/fheap.c to run with different combinations of file space strategies and page buffering only when ExpressMode is 0 (HDF5TestExpress is 0). Tested on ostrich, platypus, mayll, emu, osx1010test, quail, kite, kituo.
Updated the H5L.c error message after additional thought. Fix for HDFFV-10141.
Updated an error message in H5L.c to be more helpful. Fixes HDFFV-10141.
Re-enabled fixed array index testing in the test_random_rank4_vl() test in test/set_extent. This was fixed some time ago, but the test was never re-enabled for that index type.
Fix typo deletion
HDFFV-10143 Update new feature section.
HDFFV-10143 clean up format and function return
HDFFV-10143 Add plugin APIs to Java interface
Update with checks for index bounds
Update tools issues
...
* commit '9c661e3589c1e5f20601e6388bdfc996ed2ebbd7':
Update text in COPYING files in subdirectories to match changes to copyright notices in source files. Update Copyright notices in acsite.m4 and bin/yodconfigure that were overlooked by chkcopyright. Remove broken and unnecessary urls from comments in hl/fortran/src/H5IMcc.c and hl/src/H5IM.c.
copyright notices in source files.
Update Copyright notices in acsite.m4 and bin/yodconfigure that were
overlooked by chkcopyright.
Remove broken and unnecessary urls from comments in
hl/fortran/src/H5IMcc.c and hl/src/H5IM.c.
* commit '0d05cb607e5951f3a28a101be56ca194022a7fa1':
Reverted addition of The HDF Group copyright headers to 3rd party CMake files for Java.
Add Copyright headers to 90 files (mostly .cmake files) without Copyright headers.
Add "Copyright by The HDF Group."" to copyright header.
* commit '106102eb606bcda0caa62dd894001be9d045f730':
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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.
* commit '8c06d9564ed7662899e6a3e3a8cd96127b70833c':
Update RELEASE.txt with note for fixing failed SWMR tests.
Switch to using flag in signal handler, to trigger dropping out of main loop and shutdown cleanly, instead of calling leave() from the signal handler.
Fix HDFFV-8089 Description: Some code within an "ifdef H5D_CHUNK_DEBUG" block was using outdated data structure but not caught because the case of H5D_CHUNK_DEBUG being defined was never tested. It was commented out. I defined H5D_CHUNK_DEBUG, tested, and commented out again. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
* commit 'fa9214c5dedd8b6b61de34ca42fd0576b779395d':
Correct incosistent spacing.
Replaced text for HDFFV-9938 entry. Re-ordered bugs fixed entries in descending date order and made order consistent for all (developer, date, bug ids) entries.
Add entries to Bugs Fixed section of RELEASE.txt.
* commit '47dcd9af7997008c14def94651599c79085be7d9': (22 commits)
Add new file COPYING_LBNL_HDF5.
Revert "Clear hdf5 1.10 entries from RELEASE.txt in the develop branch. Entries"
Add LBNL license file and modify COPYING file accordingly.
Omnibus checkin for several relatively minor modifications:
Clear hdf5 1.10 entries from RELEASE.txt in the develop branch. Entries in this branch version of RELEASE.txt should be intended for the future 1.12.0 release.
Update with extra checks for reference
Update cdash max test output and VS version matching
Stop skipping h5watch tests.
Add H5_DLL to H5AC_get_mdc_image_info() prototype
Update RELEASE.txt based on review comments from pull request.
Description: Removed notes about the C++ API in develop. Only keep in 1.10 branch.
Add prototype for H5AC_get_mdc_image_info
Minor style cleanups
Revert "Switch h5clear for cache images to use existing H5Pget_cache_image_config()"
Update RELEASE.txt to reflect changes for new features and bug fixes since 1.10.0-patch1.
Run all scripts using signal files between processes in their own directories to avoid accidental deletion of the signal files.
Remove extra space added by h5vers to version string in H5.java, which then failed to match the pattern after the first run.
Remove incorrect " marks added to java files by bin/h5vers. Pull version from configure for version test in h5repack_plugin.sh.in
Description: Fixed typos and missing items in function headers, that were revealed by Doxygen, and revised various comments. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Description: Updated the C++ API sections.
...
* commit 'dd965e4b1498003a2a15d03afdc7e8049d61a5c0':
Changing default build mode in configure.ac requires running autogen.sh to propagate the change to configure.
* commit 'faffe4725005734038bc54346ccfb808e3c2274e':
Switch header generation off for release branch (CMake).
Update version to 1.10.1-pre2. Switch default build mode from debug to production.
* commit '20efd11df7a8cd604b1b62ed2fa2b69d16922956':
Update RELEASE.txt Remove "currently under development" from h5vers for HDF5Config.cmake that causes cmake not to find HDF5.
Merge bin/h5vers changes from develop. Pull version from configure for version test in h5repack_plugin.sh.in Update version to 1.10.2-snap0 for hdf5_1_10 branch.
* commit 'b32bd7bc3e5f8e74dc21f9f6df20a0c75495c34b':
Update RELEASE.txt and version in HDF5config.cmake
Update RELEASE.txt Remove "currently under development" from h5vers for HDF5Config.cmake that causes cmake not to find HDF5.
Fix bin/release: batch files were in a subdirectory one mkdir line was missing Check in bin/release changes to README.txt and RELEASE.txt.
Git deleted autom4te.cache files.
Switch maintainer mode off. Update version to 1.10.1-pre1. Check in files generated by autogen.sh, and comment those out in .gitignore.
Update version to HDF5 1.10.1-pre1.
message(FATAL_ERROR"Set to use libhdfs library, but could not find or use libhdfs. Please verify that the path to HADOOP_HOME is valid, and/or reconfigure without HDF5_ENABLE_HDFS")
* Write the data to the dataset using default memory space, file
* space, and transfer properties.
*/
dataset.write(data,PredType::NATIVE_INT);
}// end of try block
/*
* Write the data to the dataset using default memory space, file
* space, and transfer properties.
*/
dataset.write(data,PredType::NATIVE_INT);
}// end of try block
// catch failure caused by the H5File operations
catch(FileIExceptionerror)
{
error.printErrorStack();
return-1;
}
// catch failure caused by the H5File operations
catch(FileIExceptionerror){
error.printErrorStack();
return-1;
}
// catch failure caused by the DataSet operations
catch(DataSetIExceptionerror)
{
error.printErrorStack();
return-1;
}
// catch failure caused by the DataSet operations
catch(DataSetIExceptionerror){
error.printErrorStack();
return-1;
}
// catch failure caused by the DataSpace operations
catch(DataSpaceIExceptionerror)
{
error.printErrorStack();
return-1;
}
// catch failure caused by the DataSpace operations
catch(DataSpaceIExceptionerror){
error.printErrorStack();
return-1;
}
// catch failure caused by the DataSpace operations
catch(DataTypeIExceptionerror)
{
error.printErrorStack();
return-1;
}
// catch failure caused by the DataSpace operations
catch(DataTypeIExceptionerror){
error.printErrorStack();
return-1;
}
return0;// successfully terminated
return0;// successfully terminated
}
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