* commit '6a52c26162f45e85b88aa6ddab5e5d861aaba7b8':
Revert "Fix for HDFFFV-10308. Initialize hid_ts in function check_objects and"
Remove extra spaces and 1 "currently under development" to match hdf5_1_10 version.
Fix for HDFFFV-10308. Initialize hid_ts in function check_objects and check for id > -1 before calling close functions.
* commit '23460c30f10e098a980c5466b6108269d2fd92f6':
Moved the SWMR + cache image check up before the root group is constructed to avoid the special case close.
Moved the 'cache image + SWMR' check from H5Fcreate/open to H5F_open. Prep for the VOL merge.
* commit 'd8a3782ce49d537d96020dfa250a253d90f4c14f':
Moved the SWMR + cache image check up before the root group is constructed to avoid the special case close.
Moved the 'cache image + SWMR' check from H5Fcreate/open to H5F_open. Prep for the VOL merge.
* commit '18ba8cb7d247cc2f535e53d66c2a47740724de6a':
Windows cannot share files easily
Avoid double free
Windows had issues - revert code changes for get_option
Remove extra command line
Correct name of file
Add Mask test to script
Add new output files to clear test
Correct name of err file
Fix name of output files
Fix format convert error mask test
Fix tools error handling and valgrind issues
Fix error handling issues
Correct test results
Cleanup valgrind issues
HDFFV-1097 Changed file columns
HDFFV-10297 add h5copy test and fix h5diff errors
Fix VS2012 declaration error
HDFFV-10297 Fix compiler compaliants
HDFFV-10296 Update tools lib to use the error handling macros.
Close ids in loop
* commit '8a391887be263e0ba7f1ba659dcf6559b5a5e01a':
in 'production' mode builds
Make fixes to avoid test failures in 'production' mode builds
Updated the code and RELEASE.txt note per comments from John Mainzer
Try to address most of the issues raised by Dana in the code review
Made edits suggested by John as part of the code review
Update the MANIFEST and release_docs/RELEASE files
Add a test for parallel reads of independent files using MPI subgroups
Edits to the file open optimization and associated test code to bring them closer to the HDF5 library's unwritten coding standards. Also bug fix to repair a hang in testphdf5.
The initial coding for the superblock read optization
* commit '3dde6d0e32461f46630f814a2fdfbd4c813703bf':
Updated the code and RELEASE.txt note per comments from John Mainzer
Try to address most of the issues raised by Dana in the code review
Made edits suggested by John as part of the code review
Update the MANIFEST and release_docs/RELEASE files
Add a test for parallel reads of independent files using MPI subgroups
Edits to the file open optimization and associated test code to bring them closer to the HDF5 library's unwritten coding standards. Also bug fix to repair a hang in testphdf5.
The initial coding for the superblock read optization
* commit '4a3998ac308c2bf24201e470c0b23f7f83f063e1':
Correct indentation in h5diff/Makefile.am.
Add "-rpath /nowhere" to *_la_LDFLAGS for plugin test libraries. This allows them to be successfully linked but not installed. The change was added for the HDF5 1.8.20 release, but is also needed for all other HDF5 branches.
allows them to be successfully linked but not installed. The change was
added for the HDF5 1.8.20 release, but is also needed for all other HDF5
branches.
code to bring them closer to the HDF5 library's unwritten
coding standards. Also bug fix to repair a hang in testphdf5.
Tested parallel/debug on Charis and Jelly, parallel/production on Jelly.
buildbot tests passing
* commit '68a9844991cfaaca2d0f97d7828f1f6f59af1349':
VS2012 and earlier cannot have execute stmnts before declare
Correct depends name
Fix list of names
new reference file
Fix repack plugin test - reorganize test macros
Adjust filter available variables
Fix STREQUAL if commands.
Update error handling to support ARGS and tools stack
* commit 'afc9ce25b68caff7744f8a8a41407a4bfdf34690':
Updated doxygen config file Description: Added C2Cppfunction_map.mht to HTML_EXTRA_FILES. Verified that the file is copied to cpplus_RM after running doxygen on cpp_doc_config.
* commit '9d6ba29a01079e0f81ffa530605d8cd830378f9c':
Better segregate clean & dirty LRU lists so that they are only defined when the H5C_MAINTAIN_CLEAN_AND_DIRTY_LRU_LISTS macro is defined.
* commit '744b6b282f087ce23310805dc24ce8f8b351fb61':
Better segregate clean & dirty LRU lists so that they are only defined when the H5C_MAINTAIN_CLEAN_AND_DIRTY_LRU_LISTS macro is defined.
* commit 'fded10f0815f593301ac88d08d05343c8077746a':
Add note to bin/release script with hint for situations where files generated by autogen.sh are missing, causing chkmanifest to fail.
This merge includes C2Cppfunction_map.mht, which Barbara will verify at a later time when documentation is re-generated.
* commit 'f1871c6ac48db02bd7e66f2c0df64bca50bccd90':
Updated for C2Cppfunction_map.mht
Added documentation file Description: Added a single page html file, C2Cppfunction_map.mht, that shows the current mapping of C APIs to C++ member functions. This page can be reached from the main page of the C++ reference manual.
Miscellaneous code cleanup Description: - Removed two inadvertently-added Group constructors in the header file. There was no implementation. - Removed deprecated H5Location and H5Object constructors that take an existing ID. - Miscellaneous improvements in comments, including updating URLs. Platforms tested: Linux/32 2.6 (jam) Linux/64 (jelly) Darwin (osx1010test)
* commit '75e6579cf232e6c2a8f8c0519a67801fd5dd1f7b':
Restore GEN_HDRS and remove cache sets for defaults
Test program generation should default off
Generate headers for 1.10 should default off
Description:
Added a single page html file, C2Cppfunction_map.mht, that shows
the current mapping of C APIs to C++ member functions. This page
can be reached from the main page of the C++ reference manual.
Description:
- Removed two inadvertently-added Group constructors in the header file.
There was no implementation.
- Removed deprecated H5Location and H5Object constructors that take an
existing ID.
- Miscellaneous improvements in comments, including updating URLs.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (jelly)
Darwin (osx1010test)
New overloaded functions and tests
* commit 'd708dca2831839714be6593b314acd59726b532f':
New overloaded functions and tests Description: - Added VarLenType::VarLenType(const DataType& base_type) - Marked VarLenType::VarLenType(const DataType* base_type) deprecated - Added a static wrapper for H5Tdetect_class for PredType static bool DataType::detectClass(const PredType& pred_type, ...) - Removed the deprecated function Exception::printError() from code - Miscellaneous improvements in comments - Added test functions test_detect_type_class() and test_vltype() Platforms tested: Linux/32 2.6 (jam) Linux/64 (jelly) Darwin (osx1010test)
* commit 'ff2c10c3f0f2174545e608dfbf668a05ad8d0f10':
Adding variable initialization Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Adding new C++ wrappers Description: Added wrappers for H5Tencode to class DataType and H5Tdecode to classes DataType and its subclasses.
Merge after making the changes Dana suggested.
* commit '47a2d5e48f5f3dcfed57c5be01178952030828c2':
Adding variable initialization Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Adding new C++ wrappers Description: Added wrappers for H5Tencode to class DataType and H5Tdecode to classes DataType and its subclasses.
* commit 'd3e98edab0282be98b9f5ce67e9083fb93b90cda':
HDFFV-9774 Apply standard mask to .err files
HDFFV-10276 Add filter mask for standard err
HDFFV-9774 Add enable-error-stack argument to h5diff
* commit 'bf570b1a7ca3b9cbd4a59f0933a19ce1bcc99103': (71 commits)
Amend tests to explicitly use H5Dcreate2 and H5Dopen2
Revert malloc's back to using hard-coded type for sizeof
Minor comment refactoring
Update documentation
Finish up Parallel Compression test scaling work
Partial update for scaling parallel filters tests
Modify t_dset.c in lieu of Parallel Compression changes
Updated H5C__flush_single_entry() in H5C.c to correct duplicate metadata write bug observed in 1.10.1.
Amend MANIFEST
Add test for write parallel; read serial case
Fix uninitialized array issue in test
Test updates
Fix bug where incorrect amount of data was being read from the file
Add data verification for first half of tests
Start adding data verification
Switch tests over to use testing macros
Updates to parallel filters tests
Move test files to testpar directory
Add test file to build process
Suggested changes from code review
...
* commit 'b95986e50d1d1043952b00cad6595e8ecbff414f': (71 commits)
Amend tests to explicitly use H5Dcreate2 and H5Dopen2
Revert malloc's back to using hard-coded type for sizeof
Minor comment refactoring
Update documentation
Finish up Parallel Compression test scaling work
Partial update for scaling parallel filters tests
Modify t_dset.c in lieu of Parallel Compression changes
Updated H5C__flush_single_entry() in H5C.c to correct duplicate metadata write bug observed in 1.10.1.
Amend MANIFEST
Add test for write parallel; read serial case
Fix uninitialized array issue in test
Test updates
Fix bug where incorrect amount of data was being read from the file
Add data verification for first half of tests
Start adding data verification
Switch tests over to use testing macros
Updates to parallel filters tests
Move test files to testpar directory
Add test file to build process
Suggested changes from code review
...
* commit 'abcf30f232914c1ec9b8c5f2a3bb3a621af7bfe4':
HDFFV-10284 Add VS2017 support
Add commentary around calling H5Screate_simple with a single element
Miscellaneous improvements (cont.) Description: Put back H5Location::getNumObjs and marked as deprecated in favor of Group::getNumObjs. Platforms tested: Linux/32 2.6 (jam) Darwin (osx1010test)
Miscellaneous improvements Description: Moved H5Location::getNumObjs to Group::getNumObjs (i.e., H5Gget_info) Switched reinterpret_cast to static_cast in H5Object::iterateAttrs Miscellaneous cleanup Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
HDFFV-10282 refactor out assert calls in tools
Fix the t_bigio test so that it runs on 32bit machines
* commit '289007567e6ab5e0893af787b1870f27f10644c7':
Add commentary around calling H5Screate_simple with a single element
Miscellaneous improvements (cont.) Description: Put back H5Location::getNumObjs and marked as deprecated in favor of Group::getNumObjs. Platforms tested: Linux/32 2.6 (jam) Darwin (osx1010test)
Miscellaneous improvements Description: Moved H5Location::getNumObjs to Group::getNumObjs (i.e., H5Gget_info) Switched reinterpret_cast to static_cast in H5Object::iterateAttrs Miscellaneous cleanup Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Fix for daily test failure Fix for the compilation error from the PGI compiler.
Modifications based on comments from pull request review (1) Remove unnecessary asserts (2) Add code to insert bad offset values to the test file in gen_bad_offset.c
Fix for HDFFV-10216 segfault in H5G_node_cmp3 with corrupt h5 file Fix H5HL_offset_into() to return error when offset exceeds heap data block size. Also fix other places that call this routine to detect error return.
Fix the t_bigio test so that it runs on 32bit machines
* commit '883a235d5ca81770228c5cb5f9d162afda0b411f':
Miscellaneous improvements (cont.) Description: Put back H5Location::getNumObjs and marked as deprecated in favor of Group::getNumObjs. Platforms tested: Linux/32 2.6 (jam) Darwin (osx1010test)
Miscellaneous improvements Description: Moved H5Location::getNumObjs to Group::getNumObjs (i.e., H5Gget_info) Switched reinterpret_cast to static_cast in H5Object::iterateAttrs Miscellaneous cleanup Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Added some commentary on the fact that 32 bit compilers appear to require actual array arguments to call H5Screate_simple rather than a pointer to a single size_t element.
* commit '22baab211d912f1012057b3a7ae217abd2a44a38':
Add commentary around calling H5Screate_simple with a single element
Fix the t_bigio test so that it runs on 32bit machines
Description:
Put back H5Location::getNumObjs and marked as deprecated in favor of
Group::getNumObjs.
Platforms tested:
Linux/32 2.6 (jam)
Darwin (osx1010test)
* commit '593e4038b3ab474a47e468bb3478d4ae3a6820e6':
Fix for daily test failure Fix for the compilation error from the PGI compiler.
Modifications based on comments from pull request review (1) Remove unnecessary asserts (2) Add code to insert bad offset values to the test file in gen_bad_offset.c
HDFFV-10188 force non-native type description
HDFFV-10188 emu insists on printing non-native description
Fix for HDFFV-10216 segfault in H5G_node_cmp3 with corrupt h5 file Fix H5HL_offset_into() to return error when offset exceeds heap data block size. Also fix other places that call this routine to detect error return.
HDFFV-10188 fix typo
HDFFV-10188 add missing copy commands
HDFFV-10188 Add tests and files
HDFFV-10188 enable null space test
HDFFV-10188 add release note
HDFFV-10188 - Check for empty string first
HDFFV-10188 error on NULL dataspace
Description:
Moved H5Location::getNumObjs to Group::getNumObjs (i.e., H5Gget_info)
Switched reinterpret_cast to static_cast in H5Object::iterateAttrs
Miscellaneous cleanup
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
* commit '1ef8577a4aaaa4120a819ff36747fdca99abdc26':
Modifications based on comments from pull request review (1) Remove unnecessary asserts (2) Add code to insert bad offset values to the test file in gen_bad_offset.c
Fix for HDFFV-10216 segfault in H5G_node_cmp3 with corrupt h5 file Fix H5HL_offset_into() to return error when offset exceeds heap data block size. Also fix other places that call this routine to detect error return.
* commit '678c3ae1535b9b3b9faa53bc48250f1635778dd7':
HDFFV-10188 force non-native type description
HDFFV-10188 emu insists on printing non-native description
duplicate metadata write bug observed in 1.10.1.
Tested parallel/production on jelly
parallel/debug & parallel/production on charis (in develop branch)
* commit 'a83b6a7c6e6aca1a329c274282c691ffb417abc4':
Moved H5PL diagnostic pragmas to comply with old gcc requirements that they be outside of functions.
* commit '81340c609ba5049b34845ff2f06b2025ec5d5b22':
Moved H5PL diagnostic pragmas to comply with old gcc requirements that they be outside of functions.
* commit '59e94f5009a1f738d9924be942448f8cf6355b00':
Add h5repack tests for paged aggregation Add tests to h5repack.sh.in to verify options added for paged aggregation work as expected.
* commit '00d97d556b3e57129d8c7bbecf8b15497b3f056b':
added test for NAG compiler and use the FC_BASENAME for NAG detection, (HDFFV-10037)
added test for NAG compiler and use the FC_BASENAME for NAG detection, (HDFFV-10037)
* commit 'f4e9bc21fa3d3d678ca80083dbd412b34c3ab91b':
HDFFV-10256 add release note
HDFFV-10256 Add test
HDFFV-10256 correct len of string copy to the len of esc string
* commit '9bcf8b2f2568083449ae3f9b6c2efbf6ed7f413a':
Minor tweaks in response to code review.
Fixed a failing Java plugin test.
Major rework of H5PL package code before bringing VOL changes over.
libtool does not pass the correct argument linking (-WL,-WL,,) for the
NAG Fortran compiler on Linux (other OSs have not been tested).
Therefore, detect if we are using the NAG Fortran compiler, and replace
the wl="-Wl," for Fortran to wl="-Wl,-WL,," in the libtool file. (HDFFV-10037)
* commit '92491aa4b6dc2d4fa3c394e0aa928300379e1ced':
added chmod 755 for h5fc
removed chmod 755 for h5fc
libtool does not pass the correct argument linking (-WL,-WL,,) for the NAG Fortran compiler on Linux (other OSs have not been tested). Therefore, detect if we are using the NAG Fortran compiler, and replace the wl="-Wl," for Fortran to wl="-Wl,-WL,," in the libtool file. (HDFFV-10037)
Removed FCFLAGS when building the examples since they should already be included the h5fc wrapper. NAG complains about doubly declared options.
NAG Fortran compiler on Linux (other OSs have not been tested).
Therefore, detect if we are using the NAG Fortran compiler, and replace
the wl="-Wl," for Fortran to wl="-Wl,-WL,," in the libtool file. (HDFFV-10037)
* commit '55d82c8f747b3a817a4a0b6b12e506b9c2dc0878':
Add test header for log
Verify default paths exist in table
Make sure zip_perf program does not run concurrently
* commit '08d63d17f9ba80f205d54bc6526cb709a81ff0cb':
Add the release note
Correct copy to file name
HDFFV-10246 Add check for string not null before use
Correct case of var
* commit '1fe3d5113aeedc4b67dae6b83984d1246c7a2701':
Skip test in test/fheap.c when: a) multi/split drivers and b) persisting free-space or using paged aggregation strategy because the library will fail file creation (temporary) for the above conditions.
Changes made based on RFC review comments Test the changes in a branch via daily testing.
* commit '1fe3d5113aeedc4b67dae6b83984d1246c7a2701':
Closed a wayward fapl ID in tools/test/misc/repart_test.c and tidied.
Stripped C standard library headers from tools test code.
* commit '558864b99d945191dbf679efcc1cbfdf4baa2810':
Skip test in test/fheap.c when: a) multi/split drivers and b) persisting free-space or using paged aggregation strategy because the library will fail file creation (temporary) for the above conditions.
Changes made based on RFC review comments Test the changes in a branch via daily testing.
* commit 'ec7450c4b4b44a61b282535b981576d888286fca':
Closed a wayward fapl ID in tools/test/misc/repart_test.c and tidied.
Stripped C standard library headers from tools test code.
* commit 'ee7816bbfb3f22d42d5db7d779efe54ae29528cb':
Stripped C standard library headers (and a couple of macros) from the tools code. This is all handled in H5private.h, which should be included in all tools source files.
a) multi/split drivers and
b) persisting free-space or using paged aggregation strategy
because the library will fail file creation (temporary) for the above conditions.
over.
Brings coding standards in line with the rest of the library,
enforces better software engineering principles, and makes
everything more maintainable.
* commit '6a5aa46e936340ed540359290374fa909f9213a6':
Added a brief outline for Large MPI-IO transfers into RELEASE.txt
Fix up the ExpressMode check for skipping slow running tests.
Include code fixes and additional modifications pointed out by code reviewers
Commited changes to the development branch here to allow a pull request to be published
Commit changes needed for pull request
* commit '8935c921f7e50607cd91c86b2237ac39a9b600af':
Fix for HDFFV-10217 infinite loop in H5VM_power2up(). The function H5VM_power2up() returns the next power of 2 for n. When n exceeds 2^63, it overflows and becomes 0 causing the infinite looping. The fix ensures that the function checks for n >= 2^63 and returns 0.
The function H5VM_power2up() returns the next power of 2 for n.
When n exceeds 2^63, it overflows and becomes 0 causing the infinite looping.
The fix ensures that the function checks for n >= 2^63 and returns 0.
* commit '191147ec90d72619632a24242c003ecb3bccfffd':
* Yanked the smoke check that was recently introduced to test the unused H5I_REFERENCE ID type in test_misc19(). This fails when running testhdf5 and skipping the reference test since the H5R package won't be initialized. H5I_REFERENCE will be going away soon and the ID type is unused so there's really no point to doing anything to test it. * Cleaned up test_misc13(), which is a basic test of userblock functionality, to not emit warnings due to the large global array.
the unused H5I_REFERENCE ID type in test_misc19(). This fails
when running testhdf5 and skipping the reference test since
the H5R package won't be initialized. H5I_REFERENCE will
be going away soon and the ID type is unused so there's really
no point to doing anything to test it.
* Cleaned up test_misc13(), which is a basic test of userblock
functionality, to not emit warnings due to the large global
array.
* commit '6428a637752753cc8a9007c0c3c38b9ea9cc97fd': (165 commits)
Skip HDFFV-10160 filenotclosed test for split/multi driver Temporary skip this test for split/multi driver. Further investigation to resolve the failure is needed. Please enter the commit message for your changes. Lines starting
More minor whitespace cleanup
Fixed a minor comment typo in H5R.c
* Reverted removal of H5I_REFERENCE to avoid breaking binary compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19() in tmisc.c.
Added missing free() call to test_misc19().
Purged the unused H5I_REFERENCE from the library.
Added a test for VFD IDs to testhdf5.
Revert "Partial removal of NDEBUG ifdefs from the library."
Partial removal of NDEBUG ifdefs from the library.
Removed compiler flag cleanup since Solaris chokes on it.
Fix for HDFFV-10160 Modifications to fix the assertion/abort failure when the application does not close the file.
Fixed a bug in autotools Fortran processing where a test for the presence of a C long double type always returned true.
Updated the --enable-debug/production handling in configure.ac so that it more reliably indicates that the configure option can no longer be used. Previously, using --enable-debug="", etc. would not trigger an error (even though such usage is unlikely).
Added awk processing to remove extraneous whitespace from H5_ flags in configure.
Fixed a comment in configure.ac
HDFFV-10219 another mode change
HDFFV-10219 change subset to use BINARY mode for h5dump
HDFFV-10219 default input binary to NATIVE
Set default of var to NATIVE
HDFFV-10219 - disable h5dump tests until h5import NATIVE is fixed
...
* commit '1e1403cf1d959d5a88b2ff595096ee52af26db58':
Skip HDFFV-10160 filenotclosed test for split/multi driver Temporary skip this test for split/multi driver. Further investigation to resolve the failure is needed. Please enter the commit message for your changes. Lines starting
Temporary skip this test for split/multi driver.
Further investigation to resolve the failure is needed.
Please enter the commit message for your changes. Lines starting
None of the constant functions use their parameters, so emitting
warnings for them generates a large amount of noise. Since these
are trivial wrappers, marking them up with H5_ATTR_UNUSED would
be a huge waste of time.
* commit '9a749a64f06187bc5ae17e848eab9aacdfc57f8a':
More minor whitespace cleanup
Fixed a minor comment typo in H5R.c
* Reverted removal of H5I_REFERENCE to avoid breaking binary compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19() in tmisc.c.
Added missing free() call to test_misc19().
Purged the unused H5I_REFERENCE from the library.
Added a test for VFD IDs to testhdf5.
* commit '804a88fafdca3d6a76312ab01ac4d6d5b103e9dc':
Fix for HDFFV-10160 Modifications to fix the assertion/abort failure when the application does not close the file.
* commit 'd2c7df4ac005e461df3a486791560821ab7b4585':
Revert "Partial removal of NDEBUG ifdefs from the library."
Partial removal of NDEBUG ifdefs from the library.
Removed compiler flag cleanup since Solaris chokes on it.
* commit '8c347d794a06b8b57c407499e1a441cc0f415380':
Fixed a bug in autotools Fortran processing where a test for the presence of a C long double type always returned true.
* commit 'cbca178410215a1fd60e3de85c4810487e327f8d':
Updated the --enable-debug/production handling in configure.ac so that it more reliably indicates that the configure option can no longer be used. Previously, using --enable-debug="", etc. would not trigger an error (even though such usage is unlikely).
Added awk processing to remove extraneous whitespace from H5_ flags in configure.
so that it more reliably indicates that the configure option
can no longer be used. Previously, using --enable-debug="", etc.
would not trigger an error (even though such usage is unlikely).
* commit 'c325dd2a6512ce02287771bfbbe9b81d65b3fd6f':
HDFFV-10219 another mode change
HDFFV-10219 change subset to use BINARY mode for h5dump
HDFFV-10219 default input binary to NATIVE
Set default of var to NATIVE
* commit '00f4456e70c7e53226085b4a96d3bab3fd0074f0':
HDFFV-10219 - disable h5dump tests until h5import NATIVE is fixed
Correct name of options variable
Synch with CMake original code
* commit '1ac4b918f182b6fc43e57788e9af0c4cce64efba':
HDFFV-10219 remove standard headers already included in h5private.h
HDFFFV-10219 fix file creation contention on windows
HDFFV-10219 - fix name templates
HDFFV-10219 add test headers
HDFFV-10219 - remove debug comments
HDFFV-10219 - Fix subset test
HDFFV-10219Fix binary test to use gen files
Add subset tests to script
Fix changes to reference files. Still need to add subset test.
Update release note
HDFFV-10219 - disable debug output
HDFFV-10219 Add new reference file file for new test
HDFFV-10219 - fix for native in bin file and possible non-native in h5
HDFFV-10219: add generated files to memcheck clear command
HDFFV-10219: Added keyword SUBSET to h5import list.
* commit '9808b44b6c7645ae760bfb497e598ae069827619':
Added -fno-omit-frame-pointer to gcc flags when symbols when building with debugging symbols.
Fix for HDFFV-7853 H5Ocopy doesn't work with open identifiers 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.
* commit '980d5b4266133490192ceb10ea13e320532c6f03':
Fix for HDFFV-7853 H5Ocopy doesn't work with open identifiers 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.
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.
Makes all non-global H5O_layout_t structs dynamic (quiets stack warnings).
* commit 'd391d8a690b4d595709e1274882fb5e5e0559f9e':
* Made STATIC free lists EXTERN for H5O_layout_t. * Made all non-global instances of H5O_layout_t in H5Pdcpl.c dynamic.
Updated H5O_layout_t dynamic work to use the H5FL interface.
Made some H5O_layout_t stack allocations dynamic (quiets warnings).
* commit '5cb9c40847d1706ce82a2b2cda4c6c5596b10994':
Fixed typo in vfd.c from 'updated VFD feature flag' checkin.
Rework of the POSIX file open permissions and macros to clean up HDopen() calls.
Changed the Windows POSIX open() file permissions to be correct according to MSDN. Partial fix for HDFFV-9630.
* commit '1e9354bcf551c16f3ad9d6a4ad42a2bce827c95e':
Rework of the POSIX file open permissions and macros to clean up HDopen() calls.
Changed the Windows POSIX open() file permissions to be correct according to MSDN. Partial fix for HDFFV-9630.
* commit '13d3d4bd0e0b799aa9c3a9b45e445d1f52294d47':
Added feature flag checks for a few other VFDs in test/vfd.c.
* Added new public H5FDdriver_query() API call. * Changed return type of H5FD_driver_query() to herr_t. * Updated swmr.c to use H5FDdriver_query() instead of the private call. * Added some flags tests to vfd.c.
* Made H5FD_driver_query() a private function instead of static. * Moved H5FD_driver_query() to H5FDint.c. * Minor typo fixes in H5I.c. * Updated swmr.c to check the VFD feature flags and skip the retries test when the VFD is not compatible with H5P_DEFAULT.
Initialized IDs to -1 and minor code tidy.
Fixed HDFFV-10214: * Updated comments in the library to accurately reflect the semantics of the H5FD_FEAT_POSIX_COMPAT_HANDLE flag. * Removed the check for the POSIX compatible handle feature flag when determining if a VFD supports SWMR. Partial work for HDFFV-10197: * Added a new H5FD_FEAT_DEFAULT_VFD_COMPATIBLE feature flag that is set when a VFD creates output that is compatible with the default VFD. Will be used in the testing but might also be generally useful to users.
* commit 'c059e6ecf7bafc6b5c1c9b8a39e8515e23f52303':
Spelling
Enhanced the release note using 'Writing Notes in a RELEASE.txt File'
Note HDFFV-8611 change
* commit '57f0a296c0b727e3d86cea312ba46efc98d76227':
Minor warning fix.
More minor warning fixes.
Minor warning fixes in the tools.
Minor type fixes to h5watch.
A few more warnings fixed.
Fixed additional minor warnings.
Fixed many minor warnings.
* commit '35aec6ab2ca6018a6f5babc943d29957d6595f67':
Updated the gnu-flags config file to remove gcc 3.x and 4.0 configurations as well as other minor rework and cleanup.
* Changed return type of H5FD_driver_query() to herr_t.
* Updated swmr.c to use H5FDdriver_query() instead of the private call.
* Added some flags tests to vfd.c.
* Moved H5FD_driver_query() to H5FDint.c.
* Minor typo fixes in H5I.c.
* Updated swmr.c to check the VFD feature flags and skip the
retries test when the VFD is not compatible with H5P_DEFAULT.
* commit '416ad00182e2d0fccc09d60a6da95aef8ad94d0e':
HDFFV-8611 add autotools test
Remove obsolete function
HDFFV-8611 change h5repack to save the root group creation order Added test and new arguments to control the the input file parsing.
* commit '9fc2b3ef8e7933da716e2d2f832e93d8fc8023c0':
add linking flag to cmake, does not fix the issue, still disabled shared with fortran
add documention comments for shared Fortran Fix on OSX
Fix for shared fortran libraries on mac (HDFFV-2772).
Fix for shared fortran libraries on mac (HDFFV-2772).
Fix for shared fortran libraries on mac (HDFFV-2772).
* commit '57ab1e7d6945c45107ebdd945bb89951ec90b8f1':
add linking flag to cmake, does not fix the issue, still disabled shared with fortran
add documention comments for shared Fortran Fix on OSX
Fix for shared fortran libraries on mac (HDFFV-2772).
Fix for shared fortran libraries on mac (HDFFV-2772).
Fix for shared fortran libraries on mac (HDFFV-2772).
* Updated comments in the library to accurately reflect the semantics
of the H5FD_FEAT_POSIX_COMPAT_HANDLE flag.
* Removed the check for the POSIX compatible handle feature flag
when determining if a VFD supports SWMR.
Partial work for HDFFV-10197:
* Added a new H5FD_FEAT_DEFAULT_VFD_COMPATIBLE feature flag that is
set when a VFD creates output that is compatible with the default
VFD. Will be used in the testing but might also be generally useful
to users.
* commit 'fcc56184f1699fc1d35b042acb1388cc76b8ea16':
Whitespace
Move execeutable command after declaration
HDFFV-9055 add test files
HDFFV-9055 Handle H5T_ARRAY types Create variables just for diff_array function Whitespace updates
* commit '54dff331778a660824961fdf6359e4eae998a13c':
Incorporate additional code changes for the H5DOread_chunk patch from GE Heathcare (HDFFV-9934) This is the similar set of changes that was checked in to 1.8 branch: Incorporate the code changes that were missing from the original patch: (1) Additional tests in hl/test/test_dset_opt.c (2) Fix in src/H5Dchunk.c for direct access when an entry is in chunk cache but not dirty Tested on platypus, ostrich, kituo, mayll, osx1010test, moohan, quail, emu.
This is the similar set of changes that was checked in to 1.8 branch:
Incorporate the code changes that were missing from the original patch:
(1) Additional tests in hl/test/test_dset_opt.c
(2) Fix in src/H5Dchunk.c for direct access when an entry is in chunk cache but not dirty
Tested on platypus, ostrich, kituo, mayll, osx1010test, moohan, quail, emu.
* commit 'ec0935a924a84b18b29473b4fcec7c3f4e1aca76':
HDFFV-10186 xml test also needs endianess aware files
HDFFV-10186 - h5tools_str_append is not printf
HDFFV-10186 braces formatting
Fix reference file contents
HDFFV-10186 Add endianess to bitfield and fix tests
* commit 'c8a5520d3aa3a526460c81507f2f985dc534b14f':
Call to H5Dopen has H5dopen2 arguments at line 12704 of test/dsets.c - changed to H5Dopen2 to fix failure with --with-default-api-version=v16 configure option.
* commit '8482314d7db83c47947af8ca50457cdb1ddae366':
Fix for HDFFV-10051 Fix missing declaration for H5D__layout_compact_dirty_test(). Tested on mayll and osx1010test.
* commit 'd436db6c6efdfe7e9dbe06a642715116ef0eb5e3':
Fix for the two issues reported in HDFFV-10051 Modifications made based on the review comments from pull request #494 Tested on moohan, mayll, kituo, platypus, ostrich, osx1010test, quail, emu.
Fix for the two issues reported in HDFFV-10051: (1) Repeated open/close of a compact dataset fails due to the increment of ndims in the dataset structure for every open. --This is done only for chunked dataset via H5D__chunk_set_sizes(). (2) layout "dirty" flag for a compact dataset is not reset properly after flushing the data at dataset close. --Reset the "dirty" flag before flushing the message to the object header via H5O_msg_write(). Tested on moohan, kituo, platypus, ostrich, osx1010test, quail, emu.
(1) Repeated open/close of a compact dataset fails due to the
increment of ndims in the dataset structure for every open.
--This is done only for chunked dataset via H5D__chunk_set_sizes().
(2) layout "dirty" flag for a compact dataset is not reset
properly after flushing the data at dataset close.
--Reset the "dirty" flag before flushing the message to the object header
via H5O_msg_write().
Tested on moohan, kituo, platypus, ostrich, osx1010test, quail, emu.
* commit '28f4873e7fc93de865c3e180f09d7221569f64ff':
Update one missed version string.
Update release_docs/HISTORY-1_10.txt and RELEASE.txt after HDF5 1.10.1 release.
* commit '006e56802196ee6a43261aec7027815ad24ad3db':
Remove duplicate defines
Add test file to list and fix test typo
Make test scripts fail if result files are created
* commit 'be49a9422654ac9eec07ffe3599b4a7f7561cdb6':
Comment out install-exec-hooks to remove libdynlib* files. Allen did the same for hdf5_1_10 and hdf5_1_10_1 because the hooks don't reliably work. In the develop branch they are causing make install failures because the autotools' install commands sometimes attempt to chmod these files when they no longer exist.
the same for hdf5_1_10 and hdf5_1_10_1 because the hooks don't reliably
work. In the develop branch they are causing make install failures
because the autotools' install commands sometimes attempt to chmod these
files when they no longer exist.
* commit '80d57c242a15edd983673e9bad4e966c72975289':
Set the HDF5_GENERATE_HEADERS CMake option to default to ON and removed the option from the CMake cache init files.
* commit 'bacb45b38ae8513024baf2dfe08c8918625489e2':
Modifications based on pull request review. Made couple changes based on the review comments.
Incorporate patch from GE Healthcare (HDFFV-9934) This is the same patch that had already been integrated to 1.8 branch (pull request #387). Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
This is the same patch that had already been integrated to 1.8 branch (pull request #387).
Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
* commit '89fbe00dec8187305b518d91c3ddb7d910665f79':
Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to hdf5_1_10
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
* 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.
* commit 'b1a5ba405393da68028cf1c8b159a3abb51d2187':
Updated bin/trace to emit errors and reordered autogen.sh processing so that script failures leave the library in a non-compilable state, making it harder to ignore errors.
* commit '0fb5ce7ad50664f800ffe7e107e0fb0f90f66e12':
Correct name of native function
Fix javadoc
Fix typo
Signature change requires a ptr
Change H5PLsize() signature
Revert HDFFV-9655
Changed signature of H5PLgetsize
Revert HDFFV-9655 by disabling test and not using new function.
Fix path to actual executable location
Windows ahs one more directory level
* commit '2deb953dbbde17712723529c4bca6a2bf3eedf6b':
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 'e9b289a3d1d031f594e8c5421144ac44f3d44bcb':
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 'ebb7bc7fadb86c48869439ea9137f1dfc1e1f158':
Comment out failing plugin test until fixed (unexpected .libs in plugin test directory path with '@').
* commit '7bd516f2ead21e8470cc25c0b664ad6b56c723a0':
Our best effort to build dynamic plugin tests and not install them with "make install". It seems the install-exec-hook doesn't remove the last to be installed.
Add targets for plugin test libraries to avoid linking to external libs.
* commit 'a995a63085d88e1a633770536efeff5b01569445':
HDFFV-9655 fix test and some warnings
HDFFV-9655 fix compile and test
HDFFV-9655 - Add functions for '@' - untested
* commit '9a7b106d3776a8454b5cb9443f11aae2873cc617':
Correct test options to match autotools script
Updates to CMake for the changes in the autotools script
* commit '5ed622b9ca432f1b440e8903680695ac83e28301':
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 '43e03c548ae2c405b92f95833251683d3eeb1440':
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.
* commit '8f34c3cfd46054f6478b34df6af324c353e44d62':
Update tool dyn lib
LDFLAGS module forces .so lib to be built on osx instead of .dylib
java jni lib also needs to avoid the version-info
HDFFV-10170 undo patch
Add plugin options for libs
* commit '62770c64326f844739c2753bfee49c297f2c7a39':
Update tool dyn lib
LDFLAGS module forces .so lib to be built on osx instead of .dylib
java jni lib also needs to avoid the version-info
HDFFV-10170 undo patch
Add plugin options for libs
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 '906c1819188755a04fde6cc0ad7346775a6e61b8':
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
Fix URL name
updated with README changes
DAILYTEST-250 change test props to reduce timeout
Combined the README_DEVEL and README, and removed out-dated README material
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.
Modified test/cache.c to skip the smoke checks with paged aggregation
for all express test levels other than 0
Change to src/H5PL.c seems to be the result of autogen.sh. As it
seems to be correct, I am checking it in.
Tested serial and parallel (debug only) on jelly.
* commit '3d1b227a67b557da247f6b683f58617b6d75bfdb':
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.
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.
* commit '265950a83a68ea55b5bc8dcbefa2d09b4f8110be':
updated with README changes
Combined the README_DEVEL and README, and removed out-dated README material
* commit '7eda1e3c6a57f79b59fc35518816db4e3a2b382d':
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.
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.
* commit '7883c0d01b4eadba84697c7bb3322a304d242ed6': (38 commits)
Add comments
In current implementation, list must be gathered to all
Correct error with usage of array_gather function
Make array_gather routine more general
Updated comments
Add comments to H5D_filtered_collective_io_info_t data structure
Remove debugging statements
Revert "Merge latest changes from develop"
Merge latest changes from develop
removed erroneous casts from non-rvalue H5MM_free() calls. Replaced assignment of void return values with explicit value of NULL
Fix issue with uninitialized chunk index during chunk re-insertion into index
Remove potential infinite loops caused by goto in error label region
Remove note about src_type_size vs dst_type_size
Trigger error if library tries to break to independent I/O with filters in the pipeline
Fix issue in H5D__mpio_array_gather when no one contributes anything
Iterator for initial chunk entry IO operation should use source datatype size
Fix bug where data doesn't write correctly when MEMSPACE isnt the same as FILESPACE
Check return value of H5S_GET_EXTENT_NPOINTS macro
Fix macro complaint in H5Dmpio.c
Test code for user passing one-chunk-per-process hint to library
...
* commit 'eb75dc1bb02e13902d73a36caafe763eea585d02':
Removed commeted out code from H5C_dump_coll_write_list()
Checkin of fix for CGNS bug (https://jira.hdfgroup.org/browse/HDFFV-10055).
* commit 'b3ff39585c3f8e6e9096fc84f02dd049f0d3ae36':
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.
(https://jira.hdfgroup.org/browse/HDFFV-10055).
Briefly, in H5C_collective_write() in H5Cmpio.c,
the metadata cache attempts to perform a collective
write of metadata cache entries.
This worked fine as long as all processes had at
least one entry to write.
However, when the process has no entries, the
function tries to participate in the collective write
by calling MPI_File_set_view(),
MPI_File_write_all() and then MPI_File_set_view()
again, to match the calls in H5FD_mpio_write().
After pull request 183, the CGNS test benchmark_hdf5
started failing. On investigation, I determined that
the failure occurred in the first call to MPI_File_set_view()
in the "no data to write" path through H5C_collective_write().
Note that pull request 183 did not create the problem,
it only exposed it. The bug can be observed after pull
request 182 if one executes the CGNS progam
src/ptests/benchmark_hdf5 with 90 processes.
The problem appears to have been that the calls to
MPI_File_set_view() in H5C_collective_write() and
H5FD_mpio_write() were using different values for the
info parameter. I patched the problem by adding a
MPI specific VFD call allowing me to get the MPI_Info
used in H5FD_mpio_write() for use in
MPI_File_set_view() calls in H5C_collective_write().
Tested serial & parallel, debug & production on
Jelly.
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.
* commit '1e0ecb4481e226239c1fd51bd214bd7e7490805d':
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
HDFFV-10143 fix use before set
HDFFV-10143 surround will fail with try block
HDFFV-10143 typo cleanup
HDFFV-10143 typo removed
Fix code error and use H5PL_MAX_PATH_NUM in test
HDFFV-10143 Cleanup due to comments
HDFFV-10143 remove debugging output
HDFFV-10143 change h5PLget to use buffer like H5Iget_name
HDFFV-10143 change put to replace and add const
Remove redundant code
HDFFV-10143 Use Windows A version of ExpandEnvironmentStrings
HDFFV-10143 Fix initial issues from review
Remove duplicated paths, add new paths
HDFFV-10143 add APIs to manipulate plugin path table
* commit 'b56fb149c9a3c9dca11b406b7a2488f0c93ee187':
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.
* commit '9876155d3fdb073dd3769f18665c86d04cda4806':
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.
* commit '60bb3fd1108e2006a79b008d031a0f68a1e6b393':
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.
* commit 'f060e05999849c1eb3ef653c08977e4b154749d8':
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.
* commit 'd522632b9e1f1d88db2117e89f3caba0dc4cf38b':
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.
* commit '1e4b2588b671a2172827bb422aee9ba96c0320b6':
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.
* commit '2412158ed8326a3f3d62fbd947e470667d0b5951':
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.
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)
Fix HDFFV-8089
* commit '52f8c2ed494ea1b89374981ecc6901abe8fd5fed':
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 'c1f95b28caae290a7c0136537daca9004db055b8':
Revert "Clear hdf5 1.10 entries from RELEASE.txt in the develop branch. Entries"
Add LBNL license file and modify COPYING file accordingly.
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.
1) Added code test/page_buffer.c to verify that page buffering is
disabled in parallel builds.
2) Added code to test/cache_image.c to verify correct interaction
between evict on close and cache image -- in particular management
of a file containing a cache image containing dirty metadata that
has been opened R/O. Also fix for the bug exposed.
3) Added code to testpar/t_cache_image.c to verify expected procedure
for reading cache images, and also supporting stats collection code
needed for the test.
4) Repair of an overactive sanity check in H5C__reconstruct_cache_contents().
5) Other minor tidies in passing.
Tested serial and parallel, debug and production on Jelly.
* commit 'be028580c8789301e4106d8d6e79a8fc8300e706':
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.
Extend h5vers to update version strings in java files and h5repack version test expected output file.
Add reference to CMake application framwork
Whitespace changes
Update notes
Run swmr tests in their own subdirectory of test to avoid signal file deletion by other tests.
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 '436bfedcbd1152e9aa47d50f9d8ad78817488ce1':
Update RELEASE.txt based on review comments from pull request.
Update RELEASE.txt to reflect changes for new features and bug fixes since 1.10.0-patch1.
* commit '46c9ab600de491657520897322b75659c3bdfb5f':
Minor style cleanups
Revert "Switch h5clear for cache images to use existing H5Pget_cache_image_config()"
* commit '82183c7cdc50f9dc41ef8238c6a2bef6f1c7fcde':
Run all scripts using signal files between processes in their own directories to avoid accidental deletion of the signal files.
* commit 'fa5ca5272d7aa6f25656541b72a24697b36dd52b':
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
* commit '778a16daafe5d8edc4df9ddb35eb3e692d3adfbe':
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)
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)
* commit 'dbff1180b763ae41c4ac6aba6a1ca8c782713f4a':
Extend h5vers to update version strings in java files and h5repack version test expected output file.
Run swmr tests in their own subdirectory of test to avoid signal file deletion by other tests.
* commit '214100d05bd2b479a20f97e5c46d1dab2eeca759':
Use global variable for test command - update reference
Minor code changes to address comments in pull request
Checkin of additions to cache image parallel test code and associated bug fixes.
* commit 'b7c58f7dfca66d4caa26d7f8b318ad3514b8c46f':
Minor code changes to address comments in pull request
Checkin of additions to cache image parallel test code and associated bug fixes.
* commit 'b359e8f1a2349d177e70d34560d0a089ce37c4c8':
Description: Removed "#ifndef H5_NO_DEPRECATED_SYMBOLS" in file space tests, because the wrappers only use the latest functions now. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Purpose: Add new C++ wrappers Description: Because H5Pset_file_space and H5Pget_file_space are deprecated, changed to make wrappers for the new functions instead: H5Ps/get_file_space_strategy H5Ps/get_file_space_page_size
Description: Fixed typos. Platforms tested: Linux/64 (jelly)
Description: Deprecating versions of PropList::setProperty that have arguments that miss "const" Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
Description: Miscellaneous clean-up: format and comments Platforms tested: Linux/64 (jelly) Darwin (osx1010test)
Add toolset option to cmake configure
Update cmake pubconf to match autotools and add strtoll checks
Switch from HDatoll to HDstrtoll, for Windows compatibility.
output_filter.sh: Comment added to address HDFFV-8270. The sample ontput in the file's comments are not up-to-date with the scripts in the file that remove output unique to certain systems when running test scripts. This output doesn't match expected output files for the tests, causing them to fail. Ther output_filter.sh file removes such output. Currently we don't have access to these systems to update the comments.
Correct double sourcedir name on copied datafiles.
HDFFV-10138 Merge app framework to examples
Final merge of page buffering branch to develop
Purpose: Add new C++ wrappers Description: Added wrappers for H5Iis_valid, H5Ps/get_nlinks, H5Tget_create_plist, H5Oopen, H5Oclose and H5Pset_virtual
Bring changes to I/O parameters from page_buffering branch.
Merge in reentrency changes to "make space in cache" from page_buffering branch.
Minor cleanups and bring over "prefetched dirty" fixes for entries loaded from a cache image.
Remove some usage of "prefetched_dirty" flag (which hasn't been merged from the page_buffering branch yet. Also, bring over improvements to flush candidate entries for parallel code.
Align with incoming page buffering changes: minor cleanups, centralize removing entries from collective metadata read list
* commit 'b359e8f1a2349d177e70d34560d0a089ce37c4c8': (22 commits)
Description: Removed "#ifndef H5_NO_DEPRECATED_SYMBOLS" in file space tests, because the wrappers only use the latest functions now. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Purpose: Add new C++ wrappers Description: Because H5Pset_file_space and H5Pget_file_space are deprecated, changed to make wrappers for the new functions instead: H5Ps/get_file_space_strategy H5Ps/get_file_space_page_size
Description: Fixed typos. Platforms tested: Linux/64 (jelly)
Description: Deprecating versions of PropList::setProperty that have arguments that miss "const" Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
Description: Miscellaneous clean-up: format and comments Platforms tested: Linux/64 (jelly) Darwin (osx1010test)
Add toolset option to cmake configure
Update cmake pubconf to match autotools and add strtoll checks
Switch from HDatoll to HDstrtoll, for Windows compatibility.
output_filter.sh: Comment added to address HDFFV-8270. The sample ontput in the file's comments are not up-to-date with the scripts in the file that remove output unique to certain systems when running test scripts. This output doesn't match expected output files for the tests, causing them to fail. Ther output_filter.sh file removes such output. Currently we don't have access to these systems to update the comments.
Correct double sourcedir name on copied datafiles.
HDFFV-10138 Merge app framework to examples
Final merge of page buffering branch to develop
Purpose: Add new C++ wrappers Description: Added wrappers for H5Iis_valid, H5Ps/get_nlinks, H5Tget_create_plist, H5Oopen, H5Oclose and H5Pset_virtual
Bring changes to I/O parameters from page_buffering branch.
Merge in reentrency changes to "make space in cache" from page_buffering branch.
Minor cleanups and bring over "prefetched dirty" fixes for entries loaded from a cache image.
Remove some usage of "prefetched_dirty" flag (which hasn't been merged from the page_buffering branch yet. Also, bring over improvements to flush candidate entries for parallel code.
updated AM_SILENT_RULES syntax
Added a check for AM_SILENT_RULES before enabling it.
Fix alignment
...
* commit 'b6cb20d608aa6f5d9a7d825c1f38cfcea6ff5234':
Description: Removed "#ifndef H5_NO_DEPRECATED_SYMBOLS" in file space tests, because the wrappers only use the latest functions now. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Purpose: Add new C++ wrappers Description: Because H5Pset_file_space and H5Pget_file_space are deprecated, changed to make wrappers for the new functions instead: H5Ps/get_file_space_strategy H5Ps/get_file_space_page_size
Removed "#ifndef H5_NO_DEPRECATED_SYMBOLS" in file space tests,
because the wrappers only use the latest functions now.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
Because H5Pset_file_space and H5Pget_file_space are deprecated, changed
to make wrappers for the new functions instead:
H5Ps/get_file_space_strategy
H5Ps/get_file_space_page_size
New wrappers in FileCreatPropList:
// Sets the strategy and the threshold value that the library will
// will employ in managing file space.
void setFileSpaceStrategy(H5F_fspace_strategy_t strategy, hbool_t persist, hsize_t threshold) const;
// Returns the strategy that the library uses in managing file space.
void getFileSpaceStrategy(H5F_fspace_strategy_t& strategy, hbool_t& persist, hsize_t& threshold) const;
// Sets the file space page size for paged aggregation.
void setFileSpacePagesize(hsize_t fsp_psize) const;
// Returns the threshold value that the library uses in tracking free
// space sections.
hsize_t getFileSpacePagesize() const;
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
* commit '5acc8b9e169e6416e353433791321bc9c4e7b725':
Description: Fixed typos. Platforms tested: Linux/64 (jelly)
Description: Deprecating versions of PropList::setProperty that have arguments that miss "const" Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1010test)
Deprecating versions of PropList::setProperty that have arguments that
miss "const"
Platforms tested:
Linux/64 (jelly)
Linux/64 (platypus)
Darwin (osx1010test)
* commit '50ac3cd6ecc37bb2196bcebe8a202711e315759d':
Description: Miscellaneous clean-up: format and comments Platforms tested: Linux/64 (jelly) Darwin (osx1010test)
* commit '4c6f538770f92a09c6be46e44de056ad7ec68426':
Add toolset option to cmake configure
Update cmake pubconf to match autotools and add strtoll checks
* commit '98090fe3b08a0ff85ae9bc93218a14017a6f37fe':
Purpose: Add new C++ wrappers Description: Added wrappers for H5Iis_valid, H5Ps/get_nlinks, H5Tget_create_plist, H5Oopen, H5Oclose and H5Pset_virtual
associated bug fixes.
Also, modifications to H5PB_dest() to flush the page buffer before
destroying the page buffer. This is necessary, as when persistant
free space managers are enabled, the page buffer will typically contain
dirty FSM data at page buffer destroy time.
Tested serial/debug, serial/production, serial/check-vfd/debug,
parallel/debug, parallel/production on Jelly.
* commit 'cee9624b0febcb60a7b2699262104e9eaf20313d':
output_filter.sh: Comment added to address HDFFV-8270. The sample ontput in the file's comments are not up-to-date with the scripts in the file that remove output unique to certain systems when running test scripts. This output doesn't match expected output files for the tests, causing them to fail. Ther output_filter.sh file removes such output. Currently we don't have access to these systems to update the comments.
Correct double sourcedir name on copied datafiles.
* commit '98567db19290dc07cc86efae720b0dc457ae9f65':
output_filter.sh: Comment added to address HDFFV-8270. The sample ontput in the file's comments are not up-to-date with the scripts in the file that remove output unique to certain systems when running test scripts. This output doesn't match expected output files for the tests, causing them to fail. Ther output_filter.sh file removes such output. Currently we don't have access to these systems to update the comments.
Comment added to address HDFFV-8270. The sample ontput in the
file's comments are not up-to-date with the scripts in the file
that remove output unique to certain systems when running test
scripts. This output doesn't match expected output files for
the tests, causing them to fail. Ther output_filter.sh file
removes such output. Currently we don't have access to these
systems to update the comments.
testflushrefresh.sh.in:
flushrefresh and other SWMR tests have been failing
occasionally but regularly since bringing them to the develop
branch. The logs and debugging point to unexpected deletion of
signal files as the point of failure, and John Mainzer suggests
that two such tests running simultaneously in the same directory
may lead to the operating system deleting the other test's
signal file. Running the flushrefresh test in its own directory
seems to solve the problem.
Description:
Added wrappers for H5Iis_valid, H5Ps/get_nlinks, H5Tget_create_plist,
H5Oopen, H5Oclose and H5Pset_virtual
// Checks if the given ID is valid.
static bool isValid(hid_t an_id);
// Sets the number of soft or user-defined links that can be
// traversed before a failure occurs.
void setNumLinks(size_t nlinks) const;
// Gets the number of soft or user-defined link traversals allowed
size_t getNumLinks() const;
// Returns a copy of the creation property list of a datatype.
PropList getCreatePlist() const;
// Opens an object within a group or a file, i.e., root group.
hid_t getObjId(const char* name,...);
hid_t getObjId(const H5std_string& name,...);
// Closes an object opened by getObjId().
void closeObjId(hid_t obj_id) const;
// Maps elements of a virtual dataset to elements of the source dataset.
void setVirtual(const DataSpace& vspace, const char *src_fname,...);
void setVirtual(const DataSpace& vspace, const H5std_string src_fname,...);
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
* commit '4fad103187db9095afc8eab90b5f5544feb1d19b':
Bring changes to I/O parameters from page_buffering branch.
Merge in reentrency changes to "make space in cache" from page_buffering branch.
Minor cleanups and bring over "prefetched dirty" fixes for entries loaded from a cache image.
Remove some usage of "prefetched_dirty" flag (which hasn't been merged from the page_buffering branch yet. Also, bring over improvements to flush candidate entries for parallel code.
Align with incoming page buffering changes: minor cleanups, centralize removing entries from collective metadata read list
* commit '56e5b4ed05fb3bad51c226ec5b567871a45e0bce': (112 commits)
updated AM_SILENT_RULES syntax
Added a check for AM_SILENT_RULES before enabling it.
Fix alignment
Fix vds tests
Correct result code for strings test
Add extension to filename
HDFFV-10128 fix string compare and add tests
Description: Only format changes: mostly tabs vs. spaces Platforms tested: Linux/64 (jelly) - very minor
Lowercase math and set CMake commands
Added "flush" and "refresh" to testflushrefresh.sh error output so it's easier to see where errors in the script occur.
Misc. small cleanups to sync against incoming page buffering changes.
Update CMake formatting
Update CMake files and formatting
Normalize against incoming page buffering changes.
HDFFV-10120 verify nozlib checking with tools tests
cmake non-code typo
Correct issues from pull request reviews.
Corrected version of 4b5e05c084: Fix some more signed -> unsigned value issues with cache data structures, also misc. style cleanups. All to align w/incoming page_buffering changes.
Revert "Fix some more signed -> unsigned value issues with cache data structures, also"
Added virtual to list
...
* commit '7942414b24288d497d4878754319dffa24bbec11':
Description: Only format changes: mostly tabs vs. spaces Platforms tested: Linux/64 (jelly) - very minor
Replaces tabs with spaces.
* commit '8f5a1f43d0cf527488be2b2805bac2b6c86b8c66':
Description: Only format changes: mostly tabs vs. spaces Platforms tested: Linux/64 (jelly) - very minor
* commit 'cceddc6b4f002fe98470f9f6af5dbf9f6461c95a':
Correct result code for strings test
Add extension to filename
HDFFV-10128 fix string compare and add tests
Lowercase math and set CMake commands
* commit 'acdd8463bf97f84f9d50e10b16bfd3e3945207c1':
Added "flush" and "refresh" to testflushrefresh.sh error output so it's easier to see where errors in the script occur.
* commit 'cf932610999de00867c0a0bb3a08ee3bbf39a158':
Correct issues from pull request reviews.
Corrected version of 4b5e05c084: Fix some more signed -> unsigned value issues with cache data structures, also misc. style cleanups. All to align w/incoming page_buffering changes.
Revert "Fix some more signed -> unsigned value issues with cache data structures, also"
Added H5File::getFileInfo; IdComponent::getNumMembers and typeExists
* commit '4fc97f28531bd89640c10389dd36270335e5a971':
Purpose: Add new C++ wrappers Description: Added wrappers for H5Fget_info2, H5Inmembers, and H5Itype_exists
Description:
Added wrappers for H5Fget_info2, H5Inmembers, and H5Itype_exists
// Gets general information about this file.
void getFileInfo(H5F_info2_t& file_info) const;
// Returns the number of members in a type.
static hsize_t getNumMembers(H5I_type_t type);
// Determines if an element type exists.
static bool typeExists(H5I_type_t type);
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (jelly)
Darwin (osx1010test)
* commit 'c3321cba03450d8d70934505f40676c3a530a2cb':
Fix some more signed -> unsigned value issues with cache data structures, also misc. style cleanups. All to align w/incoming page_buffering changes.
* commit 'be6e9282f6ed824c367d364b4edd79d00b23f9f1':
Make release script fail and return failing exit code when any of the steps for creating the docs.tar file fails.
h5vers: Added code to update version strings in config/cmake/scripts/HDF5config.cmake.
* commit 'fb7cbe8acb05c9a74378efb66cd60ed3a9c6061f':
removed erroneous casts from non-rvalue H5MM_free() calls. Replaced assignment of void return values with explicit value of NULL
Added code to update version strings in
config/cmake/scripts/HDF5config.cmake.
release:
Added options to create CMake tar.gz and zip files containing the
HDF5 source and scripts to build and test HDF5 with cmake and ctest
by running a single command. These were previously assembled
manually.
Added a call to h5vers to set the version being released where it
occurs in files. In particular, the sub-release version string
"currently under development" was not being removed from
cpp_doc_config or HDF5config.cmake.
* commit '101fa7af8ebe26ad015b64d3b881df8a9124ccc2':
Cleanups and normalizations against incoming page_buffering changes.
Switch major error code from H5E_FSPACE [back] to H5E_RESOURCE
Misc. style cleanups from the page_buffering branch.
New C++ wrappers for H5P[s/g]et_file_space.
* commit '5f759d6d9f804d99572f605f9d9933c897ef3671':
Description: Fixed and added function comments. Platform tested: Jam (very minor)
Description: Fixed small typos Platform tested: Jam (very minor)
Purpose: Add new C++ wrappers Description: Added wrappers for H5Pset_file_space and H5Pget_file_space
* commit '92f4153a86a6a77f8d10507f3f922677da19a4b9':
Resolve missed conflicts.
Remove references to SVN.
Check in changes to snapshot script from hdfdts repository to copy in HDF5 develop branch. Most of the changes are for the switch from subversion to it repositories. This copy is not used for THG daily tests, but is available for testing on remote machines.
* commit '08b5edca0b6df7c50696ecf777ae5f108b19a953':
Fix parallel h5diff test comapare
Set depends test dependency for parallel h5diff
Convert string APPEND to set commands
Revert whitespace
Close file before trying to remove it
Description:
Added wrappers for H5Pset_file_space and H5Pget_file_space
// Sets the strategy and the threshold value that the library will
// will employ in managing file space.
void setFileSpace(H5F_file_space_type_t strategy, hsize_t threshold) const;
// Returns the strategy that the library uses in managing file space.
H5F_file_space_type_t getFileSpaceStrategy() const;
// Returns the threshold value that the library uses in tracking free
// space sections.
hsize_t getFileSpaceThreshold() const;
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (jelly)
Darwin (osx1010test)
HDF5 develop branch. Most of the changes are for the switch from
subversion to it repositories. This copy is not used for THG daily
tests, but is available for testing on remote machines.
* commit '46ede7f0399d4adf2696193ea083bffdfcc69f7e':
Deleted an extraneous remove() call from a test function that might be causing the flushrefresh test to fail.
* commit '04540598cde3f166eea35c19f5b94e33c2deeb92':
Updated platform and compiler versions in "More Tested Platforms" for current versions of EC2 cloud machines tested.
Remove obsolete platforms.
Update "Supported Platforms" and "Tested Configuration Features Summary" sections. Remove changes made before HDF5 1.10.0-patch1 from "New Features" and "Bug Fixes" sections.
current versions of EC2 cloud machines tested.
Linux 2.6.18-431.11.2.el6 MPICH mpich 3.1.4 compiled with
#1 SMP x86_64 GNU/Linux gcc 4.9.3 and gfortran 4.9.3
(platypus)
Fix bug where a process with no selection during Multi-chunk IO could
cause other processes to copy back incorrect chunk information after
chunk re-allocation
* commit '3c169f947382da170c8589f6c00896a9c4ea8e6c':
HDFFV-10123 Use generator expression
HDFFV-10123 fix shared name
HDFFV-10123 Add SHARED tools
HDFFV-10046 add shared versions of tools for plugin filters
HDFFV-10046 build a shared version of h5repack tool for plugins
* commit 'a9808853d52b368f9ab7336a261c0555f22526f1':
Add missing files
Cache image feature and testing
Bring change to use array of metadata cache entry classes for H5C_create instead of array of class names from cache image branch.
Switch list lengths to unsigned integers (to align better w/cache image merge)
* commit '081955fdd17f546e005238fd2ceae0526399e805':
Additional minor changes from revise_chunks->develop.
Moved remaining SWMR-related test files to develop.
* commit '7e73366e912920eb374a404653cd7ad026c63970':
HDFFV-10118 fix data
HDFFV-10118 change h5ls to not display extra info
HDFFV-10118 fixed plugin tests for tools
Modify single chunk entry function to handle both read and write cases
Store array of MPI derived types in Multi-chunk IO so that all freeing
can be done at end instead of during processing
Add read support for Multi-chunk IO only currently
Separate update phase for chunk entry into its own function, since code
for multi-chunk IO and link-chunk IO is exactly the same
Remove last IO mode code from multi-chunk IO, since filtered collective
writes cannot break to independent IO mode
Fix collective overlapping IO for multi-chunk IO by iterating equal to
the max number of chunks on any process
Make hard separation between collective read and write since trying to
mix the two into one loop becomes messy
Add preliminary code for asynchronous sending of chunk modification data
to new owning process when redistributing chunks
* commit 'e4b314c47c1c50b326c5f72254a662c284a26b97':
Fix indentation
Fix script varnames
Chnage test dir to avoid parallel test collisions
Add autotools version of plugin tests for UD filters
HDFFV-9994 add h5ls reference file to copy
HDFFV-9994 - correct reference file
HDFFV-9994 add UD tests for tools
Add goto error for dataset read failure. Fixed comments
* commit '110073450f84fb373a6f28579cdc5751c3eca3b0':
Add unused -parameters to developer group.
Add addition hint info about option
Correct variable name
Missing file remove added to test
Update developer flags to account for gcc version
Move Windows level 4 warnings to developer option
Fix test output file name
Changed severity of message state
Remove duplicate command
CMake command cleanup
HDFFV-10094: upgrade cmake command conventions Also converted tests to use macros
Update cmake min version and cmake command convention
* commit 'bd85e57904f1f943774bb99ea5e8b0d074db0edb':
tools/test/h5diff/testh5diff.sh.in: Add code to delete copies of test .h5 files copied from tools/testfiles/vds to tools/test/h5diff/testfiles when running "make check" for an in-source build.
* commit '8452976de5d770adcf3892b25c8480042170fccd':
tools/test/h5diff/testh5diff.sh.in: Add code to delete copies of test .h5 files copied from tools/testfiles/vds to tools/test/h5diff/testfiles when running "make check" for an in-source build.
Add code to delete copies of test .h5 files copied from
tools/testfiles/vds to tools/test/h5diff/testfiles when running
"make check" for an in-source build.
tools/test/misc/testh5repart.sh.in:
Change the name of the temporary test directory from "testfiles"
which is also used for 2 h5mkgrp test files under source control to
"testrepart" to avoid deleting source controlled files when running
"make check" in the source directory.
Fix test scripts that remove source-controlled files during "make check" when run in-source.
Fix test scripts that don't remove test files because they add files to test directories but don't remove them if the build directories are the same as the source directory.
Fix any test source file or Makefile.am files for tests that leave data files are removed by neither "make check" nor "make distclean".
* commit '089afc48561ba8838d6a515c6b00fc6f7032ca13':
Updated the developer flags so that they respect gcc versions.
Description: Added data files from the packet table vlen tests to the CHECK_CLEANFILES list. Platforms tested: Linux/64 (jelly)
Delete data files in cleaning.
* commit 'afd5bf4b913951169406764a70880529bf7f6620':
Description: Added data files from the packet table vlen tests to the CHECK_CLEANFILES list. Platforms tested: Linux/64 (jelly)
* commit '8b4c9f848d63351c85cab3a5b2034f8e7e1a29db':
h5format_convert was not built (missing from subdirs in tools/src and tools/test Makefile.ams) but created dependencies that were not cleaned up by make clean and make distclean.
Create h5repack convenience library for common code used by h5repack tool and h5repacktst. Fixes broken distclean.
Added an --enable-developer-warnings option to configure so users can ignore -Wsuggest-attribute warnings and other noise that doesn't indicate poor code quality.
* commit 'e6a12a3feaa3a111510d899102af77f61950b8bf':
Added an --enable-developer-warnings option to configure so users can ignore -Wsuggest-attribute warnings and other noise that doesn't indicate poor code quality.
* commit '630d668954f56f5138f2bffe3994e2c1da2e3f5c':
h5format_convert was not built (missing from subdirs in tools/src and tools/test Makefile.ams) but created dependencies that were not cleaned up by make clean and make distclean.
Create h5repack convenience library for common code used by h5repack tool and h5repacktst. Fixes broken distclean.
* commit '066e01f967da27df000f6bdbbf88514c1f7bfb91':
Skip h5watch tests Tests for h5watch are skipped temporarily. Debugging for test failures will be done.
* commit '8d4c84eae2954a77c725f42298b20d694a6150c8':
Bring changes to metadata cache "get entry status" call and new "child serialized / unserialized" messages and support from the cache image branch.
Add "image up to date" flag / parameter to metadata cache entry status calls.
Merged file shutdown changes from cache_image.
* commit '49fa0e8dbabe5019b1491845a963d8cfe41b59c1':
Bring file shutdown code from cache image branch
Merge code from cache image branch to split FSM ring into two types: raw data and metadata. Also, some more ring reset safeties and minor code cleanups.
Align w/incoming cache image changes, and improve recovery on errors.
Revert accidental changes to freespace open and close routines.
Remove 'const' from cache client pre_serialize callback, to reduce warnings, and correspondingly remove 'const' from some internal routines. Also rename some H5MF* routines to reflect their static/package usage.
Align with incoming cache_image branch changes: use the index list (instead of the hash buckets) for scanning the entries during a flush, and also add in counters for tracking operations during cache flushes.
Added subclass LinkAccPropList, exception ObjHeaderIException, and members H5Location::exists() and H5Object::objVersion(). This concluded HDFFV-10004.
* commit '7aff4266f85f850ee8d4ce25e8ceaa354ee3baee':
Description: Added H5LaccProp.[h,cpp].
Removed commented section left in by mistake.
Purpose: Add more tests Description: Added more tests for the new constructors that replaced openXxxType() Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Purpose: Add new wrappers Description: Added wrappers H5Location::exists() for H5Lexists. Added wrapper H5Object::objVersion() to return the header version of an HDF5 object. Added new class LinkAccPropList to be used by H5Location::exists() Added new exception: ObjHeaderIException for H5Object::objVersion() Rearranged source files in Makefile.am Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Description:
Added more tests for the new constructors that replaced openXxxType()
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Fix production mode cache macro.
* commit '54629912ebf3aa7feb454502fce659b61f038671':
Fixed a macro in H5Cpkg.h that was only updated in the version that is used in develop/debug mode.
flush1/2 fix w/ non-SWMR VFDs + code overhaul
* commit 'fcb7e204b568efb785f47153172147b83da5418a':
Updated the flush1/2 test to not be a mess and to handle non-SWMR-enabled VFDs.
* commit 'c2492712037dcf7353601410cb4a83776de92441':
AM_MAINTAINER_MODE should be set to "disable" for releases. Check to see if it's enabled, and if it is, call switch_maint_mode -disable before creating release files, then set it back to enable afterward.
Added a missing "vfd check" test file for use in scripts (should have been brought from revise_chunks).
* commit 'e41a15b7f07dc39b7d68f4635965d0b8b440d299':
Added a missing test file needed for the flushrefresh script.
Merged incoming changes from cache_image.
* commit '0610c41c75920b145a144e62df142977b605fc97':
Bring support for doubly-linked list of all entries in cache from incoming cache image branch.
Align with name change of "user" ring in incoming cache image changes.
Refactor several cache clients to have only one copy of their deserialization code.
Merged naming check improvement in function enter macros.
* commit '441c8ea43ab6a6559d1f167bdfbbaf3720621804':
Added text to the function check macros so that a more helpful error message is emitted when there is a problem.
Buildbot tests passed
* commit '69f975f56792acb9c7a4a8109c43081045b0eafe':
hdf5 lib needed for extend_dset link.
Add test lib to extend_dset test link line
Add hl test dir and test dlib
Fix h5test.h include issue
Description:
Added wrappers H5Location::exists() for H5Lexists.
Added wrapper H5Object::objVersion() to return the header version
of an HDF5 object.
Added new class LinkAccPropList to be used by H5Location::exists()
Added new exception: ObjHeaderIException for H5Object::objVersion()
Rearranged source files in Makefile.am
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
- Replacing openXxxType with individual type constructors
- Put back CommonFG
- Removed overloaded constructors that take an Attribute where there is one that takes an H5Location
* commit 'e05da1b533d5eb9527a5b67ba2683379f8e1e7ac':
Description: Removed commented out code and fixed miscellaneous typos. Platforms tested: Linux/32 2.6 (jam) (very minor)
Purpose: Improvement for HDFFV-10004 Description: When adding wrappers for H5Lexists, a new class, LinkAccPropList, was added to the C++ API, triggered complicated circular dependencies. Thus, some improvement was made to resolve the problems. - Replaced existing functions openXxxType with individual type constructors + Added individual XxxType constructors to replace the existing functions openXxxType because it's rather awkward to use these functions. + Moved openXxxType from H5Location back to CommonFG + Put back CommonFG as a baseclass of Group for openXxxType functions. + This replacement should improve usability and prevent the problem of circular dependencies. - Removed overloaded constructor that takes an Attribute when there is already one that takes H5Location because Attribute inherits from H5Location now. Platforms tested: Linux/32 2.6 (jam) Darwin (osx1010test) Linux/64 (platypus)
* commit 'a5e31139832075774a96d3f6dc23f31250f76c8b':
HDFFV-10053: add check for zlib support before running test
Revert "Load plugins into vitual process space"
Load plugins into vitual process space
* commit 'ab3963b28e59419f8e857ec224dd4efa3ea6dd8e': (214 commits)
Merge SWMR-related testing to existing tests.
Bring over tweak for missing environment variable.
Update CMake configuration files with SWMR accumulator changes.
Add missing accumulator test.
Merge SWMR-oriented accumulator tests from revise_chunks to develop.
Bring Java SWMR changes from revise_chunks to develop branch
Snapshot version 1.9 release 235
Change dlopen from RTLD_NOW to RTLD_LAZY
Fix bad implementation of Windows nanosleep equivalent.
Removed NDEBUG guards from H5AC test functions.
Bring SWMR-related tools changes from revise_chunks to develop.
Bring over changes from revise_chunks that cleanup recent SWMR changes from code review feedback.
Updated the H5FS cache code to grab the correct tag and modified the freespace test to use dxpls that have been tagged with the H5AC__FREESPACE_TAG global tag instead of H5AC_ind_read_dxpl_id. The library code now expects the owner of the free space manager to tag it so the owner-less free space managers in the freespace tag had to be tagged with *something* to avoid cache errors.
Updated the comment for the valgrind fix.
Fixed a valgrind problem in file shutdown exposed by the swmr.c test.
Reduce timeout as normal run time on windows is less then 10 min
Updated the icc flags (C flags only).
Another Java oversight (sorry, don't have Java configured on my Mac)
Correct oversight in Java test and remove direct VFD from SWMR supported drivers.
Bring SWMR support in to the main development branch. (Finally!) More tests and the tool and API wrappers will be coming in over the weekend.
...
Description:
When adding wrappers for H5Lexists, a new class, LinkAccPropList, was
added to the C++ API, triggered complicated circular dependencies. Thus,
some improvement was made to resolve the problems.
- Replaced existing functions openXxxType with individual type constructors
+ Added individual XxxType constructors to replace the existing functions
openXxxType because it's rather awkward to use these functions.
+ Moved openXxxType from H5Location back to CommonFG
+ Put back CommonFG as a baseclass of Group for openXxxType functions.
+ This replacement should improve usability and prevent the problem of
circular dependencies.
- Removed overloaded constructor that takes an Attribute when there is
already one that takes H5Location because Attribute inherits from
H5Location now.
Platforms tested:
Linux/32 2.6 (jam)
Darwin (osx1010test)
Linux/64 (platypus)
Fixed bad implementation of Windows nanosleep equivalent.
* commit '651c2f30304ed9b8e9470039e46279635356a3cc':
Fix bad implementation of Windows nanosleep equivalent.
Final fix for evict-on-close issues with new-style groups.
* commit '02879bc4b2ba161dc259bf28a71e7a99b44be0e3':
Updated the H5FS cache code to grab the correct tag and modified the freespace test to use dxpls that have been tagged with the H5AC__FREESPACE_TAG global tag instead of H5AC_ind_read_dxpl_id. The library code now expects the owner of the free space manager to tag it so the owner-less free space managers in the freespace tag had to be tagged with *something* to avoid cache errors.
Changed the name of H5MF_alloc_close() to H5MF__alloc_close() to make the FUNC_ENTER macro happy.
Reverted the freespace test. The TAG macros in H5MF_get_freespace() make the changes unnecessary.
Added missing TAG macros to H5MF_get_freespace().
Updated the freespace test so functions take a common, tagged dxpl so the test will work with the new H5FS tag changes.
Updated the cache_tagging test so it correctly analyzes the new fractal heap free space manager behavior.
Added TAG macros to the H5MF package code so H5AC__FREESPACE_TAG gets set on the dxpl correctly. Also restored the TAG macro to H5FS__cache_hdr_pre_serialize() since otherwise the tag won't be initialized.
First cut at fixing the tagging issue with the free space managers. * Converted the tag macros to regular ones so the parent's tag is used via the dxpl.
the freespace test to use dxpls that have been tagged with
the H5AC__FREESPACE_TAG global tag instead of H5AC_ind_read_dxpl_id.
The library code now expects the owner of the free space manager
to tag it so the owner-less free space managers in the freespace
tag had to be tagged with *something* to avoid cache errors.
Fixed valgrind issues in H5F_open() exposed by swmr.c.
* commit '0f2f51bb7bdac91ba670bd810bab687594a60251':
Updated the comment for the valgrind fix.
Fixed a valgrind problem in file shutdown exposed by the swmr.c test.
* commit '53d3a619f8a076cb1d0ba9cbc207fc07a6fcc5d8':
Change examples to match junit test
Add missing character
Change where test copies libs because of osx1011 SIP
Merged minor fixes from revise_chunks.
* commit 'e1026bd354443ae9c4e0cf197feb7191920c9f13':
Correct oversight in Java test and remove direct VFD from SWMR supported drivers.
Merged the final library SWMR changes from revise_chunks.
* commit '15e04901a0cea65b2b0fa3ca869341a2b656bfdf':
Bring SWMR support in to the main development branch. (Finally!) More tests and the tool and API wrappers will be coming in over the weekend.
Add some Java methods that were missed earlier.
Minor normalization cleanups.
Merged fix for missing VS2012 round commands.
* commit '488f19a9cbd2e89e83847a628e59f57f4293fed0':
Fixed a comment.
Added Windows-only versions of the round() functions, which do not exist in VS2012 and earlier.
the new fractal heap free space manager behavior.
Also converted the debug output of the cache_tagging
test to use the revised H5AC_dump_cache() function.
* Converted the tag macros to regular ones so the parent's tag
is used via the dxpl.
* Updated the tag sanity check logic so for free space managers.
* Turned new-style group checks back on in test/evict_on_close.c
Fix for some evict-on-close issues revealed by Valgrind.
* commit 'd3dbe9d90ee71b231b3264e1d62d3efbae3242ef':
Tentative fix for valgrind issues related to EoC.
Updated the evict-on-close test to better exercise groups.
* commit '30bd7247d80f08aee4fc7038df86c43258344de8':
Updated the evict-on-close test to create a large number of subgroups in a containing group. This will ensure that many cache entries will be used, making a better test of EoC functionality.
* commit 'b092dbcdfdfc7477596ae49f816f18e0dadf0fb1':
Bring over another batch (hopefully the last) of non-SWMR "normalization" changes from the revise_chunks branch.
Updated H5AC_dump_cache() to emit more information.
* commit '7a8c7c6063e328fdac28aa3f77ead4bdc91860e5':
Updated the cache dump to use the stored type name instead of the (redundant) array of names I previously created.
Updated the format of H5AC/C_dump_cache() to include more information and be easier to read.
* commit '2cb2d5a533c2de7503014da3250c3088e1ba089d':
Remove "collective write list" parameter from H5C__flush_single_entry() as it is only used in a couple of places. The collective write list has been moved to be internal to the cache data structure instead.
Eliminate unnecessary data structure for parallel collective metadata cache I/O
Fix for tfile.c valgrind issues.
* commit '191cc19ae0a2feb72d2171a0808fdc71a3b862dd':
Added vlen reclaim functions to a test in tfile.c that leaks memory.
Updated .gitignore to be more manageable and future-proof.
* commit '1aa2373b2e1a651bec507dcb14a89b51815a972c':
Simplified .gitignore by using patterns.
Added src/H5config.h.in~ to .gitignore.
Adds /*out*/ parameters to H5O_close() and H5F_try_close() so
that H5D/G_close() will know when H5O_close() has triggered a
file close and thus the file struct is not reliable.
Also removes the H5F_CLOSING() macro and related which were
formerly used to check if the file was closing.
* commit 'ea4d18c3d9c3b6c77030abdf2f0509bc68224559':
Remove unnecessary assert.
Add a flag for H5C__flush_single_entry() to allow the parallel code to request that images for entries be generated, even when not writing the entry from an MPI rank.
Fixed a few memory issues in the tests.
* commit 'e2863ca880a6983558d3ba3e5219164a57287f04':
Fixed a few memory problems in test/cache_logging.c and test/h5test.c (which show up in test/vfd.c).
Applied the evict-on-close "check for file closing" change that was successful for groups to datasets.
* commit '88b6f2e24cafcfaffe7d99ab6c5afc2290ce93b4':
Added the H5F_CLOSING() check that makes valgrind happy in the evict-on-close code in H5G_close() to H5D_close().
Two minor evict-on-close changes:
* Fix for a valgrind-reported issue where invoking EoC behavior when the file is closing leads to garbage file data being passed to downstream calls. The solution is to ignore EoC when the file is closing anyway.
* Added brackets so an infinite loop that arises when evicting tagged entries (due to pinned entries preventing progress) raises an error instead.
* commit '4e7b19f8260a7adb0e3b3df30e2d8289fccdcca6':
Two minor cache changes:
* commit '3b0c2b24da5689990c4bc0fcd3afecdf063086c8':
Bring over support for retrying metadata cache entry loads, along with all the supporting metadata cache callback changes, etc.
* Evict-on-close behavior is now skipped when the file is closing.
This fixes a potential issue discovered by Valgind on Windows
where potentially garbage data would be availble for manipulation.
* Added brackets to some code in the tagged entry evict iterators
so that the flag that determines if progress was made only gets
set if things are actually evicted. This prevents an infinite
loop (and emits an error) when pinned entries prevent eviction
and thus progress.
* commit 'eba0ff43c968ef9a0b09edf19c1e337cfcae0816':
Remove 'clear' callback from metadata cache client interface, using the new 'entry cleaned' notify action innstead.
* commit 'be27e1ad79dfa0507f589b29d938b7e1020a5b2d':
Remove explicit support within the metadata cache for tracked compressed entries, they are now completely handled in the clients.
Removed the obsolete macros H5_NO_NAMESPACE and H5_NO_STD from the examples.
* commit '51ea7245dfdbda8311961ea4755c8d9c8ce99d76':
Description: Removed H5_NO_NAMESPACE from the examples. They were missed from the previous cleanup. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus)
* commit 'd4591ff54d9319346f49a3bc67431f0fa26a8d65':
Bring over new 'notify' metadata cache client callback actions for when an entry is cleaned / dirtied or its [flush dependency] child entry is cleaned / dirtied.
Moved Win32 variables in log VFD to top of function like in revise_chunks.
* commit 'be0dfa3e22bcd1454215e2a348756bf21e749044':
Moved Win32 variables to top of function in H5FDlog.c.
Added autogen "undo" script to bin/
* commit '57a8bb60811b6d788d586836674ab8ea779131d3':
Adds a script to undo the action of autogen.sh. Useful when git complains about Makefile.in clobbers, etc.
* commit 'e40faaa8fbc8490af626dd9da3ff741284327e65':
Update installdir format for windows
Correct name of list
Factor out path
On windows there could be a conflict when two processes try to read the same file
* commit 'ea55d4192e14411e3c67facac57bb547b6fc3402':
Added subdir-objects to AM_INIT_AUTOMAKE. Quiets automake warnings about forward-compatibility after tools split.
Adds subdir-objects to AM_INIT_AUTOMAKE to quiet forward-compatibility warnings from automake after the tools directory rework.
* commit 'a203f2369af79f4b2b838ab457d81749456c2a4b':
Added subdir-objects to AM_INIT_AUTOMAKE. Quiets automake warnings about forward-compatibility after tools split.
Changed the return type of H5Pget_driver_info() from void * to const void *
* commit '8eaa0af30585adbbab29686541cd33e058abd6e8':
Changed the return type of H5Pget_driver_info() from void * to const void *. Fixes HDFFV-10017.
* commit '9504d3f337c94c1a2d00bc5b05561e6ed1cee798':
Switch to new, more scalable, metadata cache entry tagging.
Remove routines not yet used in develop
* commit 'b2878dec04c120e4e3cdf00e943283e359862c84':
Move cache debugging routines into separate module.
Change file memory type for extending to default, and correct error in backward compatibility for multi VFD.
Warning and whitespace cleanup.
Improvements to the log VFD, for helping with SWMR debugging.
Minor code cleanups.
Uncomment line in test/objcopy.c, clean up whitespace and POSIX call wrapping in tools code.
Merged EoC for groups. Will expand the tests as discussed in the code review at a later date.
* commit '30f5f7d9f97e7e4e331894c3574cc1b6c4df6d9e':
Removed commented-out lines that clean up test files.
Added a test for old- and new-style groups under evict-on-close.
Evict-on-close now works with groups.
* commit 'de57917e58b53d19ef9ac9379f24a1de69d3dd15':
minor cleanup to utils defines
Add util programs for tests
Correct test command line
refactor repart test to use test dir
* commit '0f94a43c46186eba3a536ab3b60433f469b5672c':
Update with changes from buildbot process
Remove duplicate block
Update with latest changes used in buildbot process
Re-merge HDFFV-9942 to new folder structure
Correct dir reference
Split tools code - remove old change
Add new file to ignore
Split tools into src and test - update locations
Split tools into src and test - update with new files or locations
Split tools into src and test - add folders
Split tools into src and test - remove folders
Split the code into src and test
Add error log for dlopen
* commit 'b96f0bc9ed9212ad0f9248a701ebce59ee8e14fa':
Add new file to ignore
Split tools into src and test - update locations
Split tools into src and test - update with new files or locations
Split tools into src and test - add folders
Split tools into src and test - remove folders
Split the code into src and test
Add error log for dlopen
Work-around for Emu's alignment problem.
* commit '889d7fd73341a377dff98673d08031e422c18ab0':
Description: - In the test for HDFFV-9758, a pragma pack(1) caused failure on Emu because Sparc cannot access misaligned data. Changed it to pack() to do the default alignment. - Added DOXYGEN_SHOULD_SKIP_THIS blocks to private elements to prevent warnings from doxygen. Platforms tested: SunOS 5.11 (emu) Linux/32 2.6 (jam)
- In the test for HDFFV-9758, a pragma pack(1) caused failure on Emu
because Sparc cannot access misaligned data. Changed it to pack() to
do the default alignment.
- Added DOXYGEN_SHOULD_SKIP_THIS blocks to private elements to prevent
warnings from doxygen.
Platforms tested:
SunOS 5.11 (emu)
Linux/32 2.6 (jam)
* commit 'a903cbafa863f22d360e7ef59f787b4fe0c0d2c3':
Description: Removed obsolet macros from C++ API: H5_NO_NAMESPACE, H5_NO_STD, __cplusplus Leave OLD_HEADER_FILENAME because iostream.h might still be in use, until further checking is done. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test) Jelly
Fixed typo
* commit '4c91c858beb4933669d5855ba0648bc044d0d09e':
Description: User's sample code used "not" instead of "!" and Windows does not like that. Fixed. Platforms tested: Linux/32 2.6 (jam) Darwin (osx1010test)
Fix HDFFV-9758
May also fix HDFFV-9927 and HDFFV-9042
* commit 'b3b7ae087edbc20891a088db2f4e4f83e186c8b0':
Purpose: Fix Packet Table issues cont. Description: Misc cleanups and comments in tests. Platforms tested: Linux/32 2.6 (jam) Darwin (osx1010test) Linux/64 (jelly)
Miscellaneous code cleanup. Platforms tested: Linux/32 2.6 (jam) Darwin (osx1010test)
Description: - Removed calls to H5Tget_native_type in the PT code. The application would need to do that if desired. - Added Abhi's program to tests to verify the fix. - This fix might have fixed HDFFV-9927, HDFFV-9042, and the issue reported by Barbara Jones from Ametek as well. Platforms tested: Linux/32 2.6 (jam) Linux/64 (jelly) Darwin (osx1010test)
Accidentally in the wrong branch so merging over to "develop" now.
* commit 'be613da6b804e56a51f43a053bf35d898dccb420':
Miscellaneous code cleanup. Platforms tested: Linux/32 2.6 (jam) Darwin (osx1010test)
Description: - Removed calls to H5Tget_native_type in the PT code. The application would need to do that if desired. - Added Abhi's program to tests to verify the fix. - This fix might have fixed HDFFV-9927, HDFFV-9042, and the issue reported by Barbara Jones from Ametek as well. Platforms tested: Linux/32 2.6 (jam) Linux/64 (jelly) Darwin (osx1010test)
* commit '0a27add8d71a9e623a99e7fc6eeff988e54a8566':
Change return statement format.
remove unneeded defines
Add new testlib to copy
Correct multiple lib setting
HDFFV-9996: Test file to verify that that multiple params are parsed
- Removed calls to H5Tget_native_type in the PT code. The application would
need to do that if desired.
- Added Abhi's program to tests to verify the fix.
- This fix might have fixed HDFFV-9927, HDFFV-9042, and the issue reported
by Barbara Jones from Ametek as well.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (jelly)
Darwin (osx1010test)
Removed obsolet macros from C++ API:
H5_NO_NAMESPACE, H5_NO_STD, __cplusplus
Leave OLD_HEADER_FILENAME because iostream.h might still be in use,
until further checking is done.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Jelly
* commit '43affeb0f388466b5be555879d91d14037be0e99':
Correct text - missing GIT option
Correct text - missing GIT option
Correct typo of variable format
* commit '321db89a65909c02d7279fed7e8b7a3585cde8da':
Remove test only tools from exports
Fix typo
Correct typo in variable format
Description: Fixed typo that caused daily test failed when --enable-deprecated-symbols is used. Also, removed a commented-out function. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) with --enable-deprecated-symbols
Description: Added test file titerate.cpp. Platform tested: Verified with bin/chkmanifest
Description: Removed commented out lines. Platform tested Jam (only comments)
Purpose: Fix bug HDFFR-9920 cont. Description: Added new test file titerate.cpp.
Fix:HDFFV-9987 With HDF5-1.10 you cannot specify default dataspace for Fortran (H5S_ALL_F)
Removed unused H5T_NATIVE_INTEGER_# variables due to NAG fixes.
Purpose: Updated documentation Description: Revised class brief description and other comments for up-to-date info. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Purpose: Fix bug HDFFR-9920 cont. Description: Adding user's test revealed a flaw in the fix. Moved CommonFG's functions in Group to H5Location, so that they could be called by objects that can be used to specify a location Also, rearranged many "#include" header files to resolve conflicts.
Add support for namespace and add tools to binaries config
Merged (minor) fix for Windows dsets test failure.
* commit '53099719497a5a5561cabdac96a710f91d0fa21b':
Fixed Windows dsets.c test failure.
Revert "Added C++ wrappers (get/setCoreWriteTracking()) for new"
Revert "Fixed Windows test failures."
Fixed Windows test failures.
Added C++ wrappers (get/setCoreWriteTracking()) for new H5Pset/get_core_write_tracking() API calls.
A 'static' keyword was removed from an array that needs it on Windows
during a warning removal overhaul. Replacing it fixes the error.
Tested on: 64-bit Windows 7 w/ VS 2015
* commit '321db89a65909c02d7279fed7e8b7a3585cde8da':
Remove test only tools from exports
Fix typo
Correct typo in variable format
Description: Fixed typo that caused daily test failed when --enable-deprecated-symbols is used. Also, removed a commented-out function. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) with --enable-deprecated-symbols
Description: Added test file titerate.cpp. Platform tested: Verified with bin/chkmanifest
Description: Removed commented out lines. Platform tested Jam (only comments)
Purpose: Fix bug HDFFR-9920 cont. Description: Added new test file titerate.cpp.
Fix:HDFFV-9987 With HDF5-1.10 you cannot specify default dataspace for Fortran (H5S_ALL_F)
Removed unused H5T_NATIVE_INTEGER_# variables due to NAG fixes.
Purpose: Updated documentation Description: Revised class brief description and other comments for up-to-date info. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Purpose: Fix bug HDFFR-9920 cont. Description: Adding user's test revealed a flaw in the fix. Moved CommonFG's functions in Group to H5Location, so that they could be called by objects that can be used to specify a location Also, rearranged many "#include" header files to resolve conflicts.
Add support for namespace and add tools to binaries config
Fixed typo that caused daily test failed when --enable-deprecated-symbols
is used. Also, removed a commented-out function.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus) with --enable-deprecated-symbols
Description:
Revised class brief description and other comments for up-to-date info.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
Adding user's test revealed a flaw in the fix.
Moved CommonFG's functions in Group to H5Location, so that they
could be called by objects that can be used to specify a location
Also, rearranged many "#include" header files to resolve conflicts.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
* commit '052ca6a74199005efe7f324f2a3ac508b18cdc27':
Correct name and usage of cmake variable
Add STGZ to mac cpack list
Merge from master cmake_conf project
Merged in
- added titerate.cpp to MANIFEST
- moved H5Location::throwException to outside of an H5_NO_DEPRECATED_SYMBOLS block to fix daily test failure.
* commit '78e597427c6ffc32ed7cf515234c4cf18d05004f':
Description: Fixed typo that caused daily test failed when --enable-deprecated-symbols is used. Also, removed a commented-out function. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) with --enable-deprecated-symbols
Description: Added test file titerate.cpp. Platform tested: Verified with bin/chkmanifest
Fixed typo that caused daily test failed when --enable-deprecated-symbols
is used. Also, removed a commented-out function.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus) with --enable-deprecated-symbols
This should be the final change for HDFFV-9920.
* commit 'c38f4af65bf9f8e3811eeb1fcf2ff2f44457bf3d':
Description: Removed commented out lines. Platform tested Jam (only comments)
Purpose: Fix bug HDFFR-9920 cont. Description: Added new test file titerate.cpp.
Purpose: Updated documentation Description: Revised class brief description and other comments for up-to-date info. Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
Purpose: Fix bug HDFFR-9920 cont. Description: Adding user's test revealed a flaw in the fix. Moved CommonFG's functions in Group to H5Location, so that they could be called by objects that can be used to specify a location Also, rearranged many "#include" header files to resolve conflicts.
* commit 'd817b63020310b6f275a569529075551dd2b756e':
Fix copyright to point to cmake
Fix cyclic depends due to typo
Correct how include is used when located inside project
HDFFV-9961: Add GIT option to ext lib macros
Update copyright to latest from kitware
* commit 'f9364c0080405bb36d704eb3f9505029d3da41f4':
removed the use of C_SIZEOF for non BIND(C) derived type
Fixed test to use storage_size instead of c_sizeof when available.
fixed missing closing bracket
Removed unused variables.
Fixed: Fortran_DOUBLE was being set to C_LONG_DOUBLE when C_LONG_DOUBLE is not available.
Removed duplicate FCFLAG
Removed duplicate FCFLAG.
Added number of integer KINDs found to the header files.
Added path to source include files when building buidiface.
Added rule to build buildiface program, without a rule, build would add repeated compile options when using the NAG compiler.
Misc. cleaning up of the program.
Added SEQUENCE to derived types for NAG:
misc. format code-cleanup
Removed the use of hard-coded integer KINDs.
Code clean-up.
HDFFV-9973 Fortran library fails to compile and fails tests with NAG compiler
Fixes the v16 API failures in the evict-on-close test.
* commit 'dd47e42313fd4d76da95b7e48013bcd0d8879434':
Changed H5Dcreate to H5Dcreate2 in test/evict_on_close.c
Merged evict-on-close feature from branch (via develop in cloned repo).
* commit 'cbc260e636e258cc55d9fb8fdafd3bff0877ac23': (21 commits)
- Removed BRANCH.txt and MANIFEST entry - Fixed a missing line in H5Dint.c
- Removed non-implemented code from H5Gint.c - Removed commented-out debug code from H5Dint.c - Added blank lines to eliminate delta in a fortran file.
Added full implementation of EoC cache test.
Added code to create the test file for all chunk index and layout types.
Fleshed out evict on close test that inspects cache.
Added the beginnings of a file generator to the test.
Fixed typo
Added "Purpose:" information to the API call comments for the new functions.
Cleaned up feature for dissemination to LLNL: - Removed support for datatypes. - Commented out support for groups - General change clean-up - Added a list of improvements to BRANCH.txt
Removed blank line in Fortran file (leftover from last commit)
Reverted H5T code since datatypes will not be supported at this time.
Fixed format_convert and fortran files (bad merge?).
Updated manifest. Was missing BRANCH.txt.
Added missing evict on close test file line to test/CMakeLists.txt.
[svn-r30110] Added missing evict_on_close.c file to test/.
[svn-r30108] Moved group flush and evict code to H5G_close from H5Gclose.
[svn-r30107] Moved dataset flush and evict code to H5D_close from H5Dclose.
[svn-r30106] Moved datatype close code to new internal function. H5Oclose() now supports evict-on-close for datatypes.
[svn-r30105] Datatypes and Groups now support evict-on-close.
[svn-r30084] First pass at the evict-on-close feature.
...
* commit '5a7880183025f56421cf6f2274d9f1ac36f59641':
Clean up hardcoded constants and check return values better. (Comments from group code review)
Description: Cleanups from Dana's review.
Description: Further warning cleanups: from 667 warnings to 503.
Description:
Revised class brief description and other comments for up-to-date info.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
* commit 'a7fb4ede8601e135433ef2d23bf4bbb466d9f58d':
Fix bug in "nooptype" decode in fix for TALOS-0177.
Change check for number of dimensions for old-style arrays in datatype decoding routine from an assertion to an if/HGOTO_ERROR check, since it is inappropriate to assert the contents of a file will be what we expect.
Fix issues in H5Znbit.c where the decompression algorithm would not check the compressed data for validity, potentially causing a buffer overflow.
Replace assertion in H5O_dtype_decode_helper for number of array dimensions with a check and error. The assertion was inappropriate because it is operating on data read from the file, which the library does not always have direct control of.
Section 81 of the compiler manual, e.g. at
http://www.nag.co.uk/nagware/np/r61_doc/np61_manual.pdf
covers details about the compiler's internal representations, including
"
Fortran derived types are translated into C structs.
If BIND(C) or SEQUENCE is used, the order of the items within
the struct is the same as the order within the derived type definition.
Otherwise, the order of items is permuted to
put larger types at the front of the struct so as to improve alignment
and reduce storage; the C output code can be
inspected to determine the ordering used.
"
Removed INTENT(IN) to fix segfaults in C APIs for TYPE(C_PTR).
Tested: NAG (gnu)
* commit '748d6f318c5ebe4fa7ee5d8e4ca2681d69792b70':
Change check for number of dimensions for old-style arrays in datatype decoding routine from an assertion to an if/HGOTO_ERROR check, since it is inappropriate to assert the contents of a file will be what we expect.
* commit '866d17f57f47414b6e778d63fcdcc2a82b208683':
Fix bug in "nooptype" decode in fix for TALOS-0177.
Fix issues in H5Znbit.c where the decompression algorithm would not check the compressed data for validity, potentially causing a buffer overflow.
* commit '62d7562fbd6c6f9f2892cc9a3894f5a68a2b6fdc':
Replace assertion in H5O_dtype_decode_helper for number of array dimensions with a check and error. The assertion was inappropriate because it is operating on data read from the file, which the library does not always have direct control of.
Description:
Adding user's test revealed a flaw in the fix.
Moved CommonFG's functions in Group to H5Location, so that they
could be called by objects that can be used to specify a location
Also, rearranged many "#include" header files to resolve conflicts.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Sync with develop and cleaned up feature. Feature works with datasets but testing is minimal.
* commit '2646f917adb5b2e17404260e433dc3ed7c39a602': (102 commits)
Cleaned up feature for dissemination to LLNL: - Removed support for datatypes. - Commented out support for groups - General change clean-up - Added a list of improvements to BRANCH.txt
Removed blank line in Fortran file (leftover from last commit)
Reverted H5T code since datatypes will not be supported at this time.
Fixed format_convert and fortran files (bad merge?).
Updated manifest. Was missing BRANCH.txt.
Add missing command to set shared generated file
Add default site names
Separate fortran generation into static and shared folders.
Revert to using old set command
Change string to list - older usage
Add option to submit to Cdash
Change UPDATE_TYPE to git
Update CMake java functions
Added missing evict on close test file line to test/CMakeLists.txt.
Restrict git commit hash in tar file names to first 7 characters with --short option.
Add longer timeout to cache tests - test has consistently exceeded default timing.
Removed -p option from invocation of autogen.sh by h5vers script to allow running h5vers on machines without /usr/hdf/bin/AUTOTOOLS.
Add bin/pkgscrpts files to MANIFEST.
dd bin/pkgscrpts directory with scripts to package deployed unix binaries into tarfiles.
Purpose: Code cleanup Description: - Used FP_EPSILON in comparing float values to verify read data - Casted C macro to fix mismatched types in verify_val calls Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
...
Purpose: Code cleanup
Description:
- Used FP_EPSILON in comparing float values to verify read data
- Casted C macro to fix mismatched types in verify_val calls
Platforms tested:
Linux/32 2.6 (jam), Linux/64 (platypus), Darwin (osx1010test)
* commit '478f771243b4e7b7c416dde22b5dcde13e1f3541':
Purpose: Code cleanup Description: - Used FP_EPSILON in comparing float values to verify read data - Casted C macro to fix mismatched types in verify_val calls Platforms tested: Linux/32 2.6 (jam) Linux/64 (platypus) Darwin (osx1010test)
* commit '49ea5bd2a9f23d53f94377457376c91f51e1d287':
Removed -p option from invocation of autogen.sh by h5vers script to allow running h5vers on machines without /usr/hdf/bin/AUTOTOOLS.
* commit '1bad18cc24e0108dea2a9e48402bba9d32e3b96c':
Add bin/pkgscrpts files to MANIFEST.
dd bin/pkgscrpts directory with scripts to package deployed unix binaries into tarfiles.
* commit 'a4c60918a741e029c9ace1a8737f414cc0f49903':
Added .gitignore and .gitattributes files with contents from the last git mirror or the hdf5 repository prior to the manual migration of the hdf5 svn repository to the git repository in bitbucket. Added entries to MANIFEST for the 2 new files.
Description:
- Used FP_EPSILON in comparing float values to verify read data
- Casted C macro to fix mismatched types in verify_val calls
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
git mirror or the hdf5 repository prior to the manual migration of the
hdf5 svn repository to the git repository in bitbucket.
Added entries to MANIFEST for the 2 new files.
* commit '5aee5213190f145b5a734f5dc76a67c82f7d6b82':
emoved .gitattributes and .gitignore, as the manual migration did not create them. Corrected bbrelease script to create new release version with revision hash.
Translate svn commands to git commands for chkmanifest and bbrelease scripts with source in git repository. Removed the -p option from the command to run autogen.sh. It interfered with running chkmanifest on a machine with the correct autotools versions but without access to /usr/hdf/bin/AUTOTOOLS. The autogen.sh script says the option is for HDF group use only and is likely to be removed. The same effect can be achieved by adding /usr/hdf/bin/AUTOTOOLS to the beginning of PATH.
Removed the -p option from the command to run autogen.sh. It interfered with running chkmanifest on a machine with the correct autotools versions but without access to /usr/hdf/bin/AUTOTOOLS. The autogen.sh script says the option is for HDF group use only and is likely to be removed. The same effect can be achieved by adding /usr/hdf/bin/AUTOTOOLS to the beginning of PATH.
* commit 'b368f0de8d53ca536e95f71d88504cd1ee3ea33c':
Removed the -p option from the command to run autogen.sh. It interfered with running chkmanifest on a machine with the correct autotools versions but without access to /usr/hdf/bin/AUTOTOOLS. The autogen.sh script says the option is for HDF group use only and is likely to be removed. The same effect can be achieved by adding /usr/hdf/bin/AUTOTOOLS to the beginning of PATH.
with running chkmanifest on a machine with the correct autotools
versions but without access to /usr/hdf/bin/AUTOTOOLS. The autogen.sh
script says the option is for HDF group use only and is likely to be
removed. The same effect can be achieved by adding
/usr/hdf/bin/AUTOTOOLS to the beginning of PATH.
* commit 'ba5652ffc27be96fa7275b039ce2c8e249751657':
Translate svn commands to git commands for chkmanifest and bbrelease scripts with source in git repository.
Added windows name suffix for debug to CMake cmd_arg for examples and test.
Fix issues discovered under debug testing;
Create a version of H5Iget_name that correctly returns the name.
Rework PIN_JAVA_STRING macro and usage to eliminate possible memory leaks by using if-else instead of mid-routine return.
Update example to use new H5Iget_name API.
Tested: windows under debug
trunk:
Description:
Continued rearranging the classes to model the relationship of HDF5
objects more accurately. The changes included:
- in the baseclass list of Attribute, changed "public IdComponent" to
"public H5Location", because location sometime can be specified with
attribute
- moved H5A wrappers in H5Location to H5Object because H5A functions
can't be called on attribute id
- removed the stubs Attribute::iterateAttrs and Attribute::renameAttr
- removed Attribute::getFileName and Attribute::flush, because
H5Location has them
- result of the modified partial class diagram, regarding Attribute
IdComponent
|
H5Location AbstractDs
/ \ /
H5Object Attribute
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
Rearranged the classes to model the relationship of HDF5 objects more
accurately. The changes included:
- moved CommonFG's methods to Group
- removed CommonFG from Group's base class list
- removed CommonFG from H5File's base class list and changed
"public H5Location" to "public Group" in the base class list
- CommonFG became unused
- result of the modified partial class diagram:
IdComponent
|
H5Location
/
H5Object
|
/ / \
DadaType Group DataSet
|
H5File
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Prevents the test from segfaulting in other sub-tests
when a previous test fails.
Tested on: 64-bit Ubuntu Linux 16.04 LTS w/ gcc 5.4.0
Autotools serial + direct VFD (vfd test only)
Also tested with a forced error to ensure
that the test no longer segfaults and
confirmed that all test files are cleaned up.
More warning cleanups, bringing the build down to 25 unique types of
warnings, with 550 warnings in 122 files (down from 28, 770, and 134).
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Description:
Removed deprecated functions in previous releases due to missing const.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
- Added "const" to arguments that should be const
- Added "const" to const functions, i.e., function that don't change
the objects they operate on.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
with an alignment threshold set to be larger than the chunk size but smaller
than the size of the small data aggregator.
Tested: koala, ostrich (h5committest); jelly, ummon
Checked the return value of a read() call to clean up a warning.
Tested on: 64-bit Ubuntu Linux 16.04 LTS w/ gcc 5.4.0
Autotools serial, file_image test only
More warning cleaups: down to 770 warnings (from ~940) in 134 files (from
148), with 28 unique kinds of warnings (from 31).
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Switch test framework to dynamically allocate the testing array, and
expand the length of the description field.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Clean up more warnings: drop the warning count from ~1310 down to ~940,
with only 31 types of warnings in 148 files (down from 38 types in 167 files).
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Since it only tests the core VFD, there's no need to get a
VFD-dependent fapl.
Tested on:
64-bit Ubuntu Linux w/ gcc 5.3.1
vfd test w/ all VFDs tested by make check-vfd
More warning cleanups. This brings us down to ~1300 warnings in 167 files
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Use internal rounding routine, if the StdC ones aren't available (like on
Windows).
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Clean up warnings (from 2774 -> 1560, with my standard debug build)
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Move updated flush dependency code in metadata cache from revise_chunks
branch to trunk. Also many of the cleanups from r30111 in the revise_chunks
branch.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Bring over fixes for CMake testing from the revise_chunks branch
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
The features is controlled via H5Pset/get_evict_on_close()
and is currently enabled by default (it will be disabled
by default in the final implementation).
There is a bug in the code where the eviction of tagged
metadata fails due to some of the metadata being dirty,
resulting in error return values and test failures.
Bring object/dataset/group/named datatype features from revise_chunks
branch to trunk. Also CMake support for h5format_convert and a bunch of
misc. cleanups.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Create iterator routine for tagged entries and refactor current routines
to use it.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Bring a few code cleanups in from thr revise_chunks branch.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Bring r29992 from revise_chunks branch to trunk:
Turn off error reporting for h5debug and hdf2gif.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & produciton
(h5committest forthcoming)
Extract query routines into separate source module.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial & parallel
(h5committest not required on this branch)
Bring r29914 from revise_chunks branch to trunk:
Banished -Wformat= warnings from the library, tools, and tests.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Bring over remaining piece of r29675 from revise_chunks branch:
Refactor coding in H5D__farray_idx_delete() to be similar to H5D__earray_idx_delete()
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Bring r29909 from revise_chunks to trunk:
Cleaned up "conflicts with C++ keyword" warnings.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Bring r29934 from revise_chunks branch to trunk:
(1) Fix for HDFFV-9434: throw an error instead of assertion when v1 btree level hits the 1 byte limit.
(2) Modifications to better handle error recovery when conversion by h5format_convert fails.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
- Cleaned up mixed tabs and spaces that mis-aligned brackets.
- Test functions now return hbool_t to match the global pass variable.
- Main now returns EXIT_SUCCESS/EXIT_FAILURE.
- The invalid_configs array is now allocated dynamically instead
of statically. This reduces the frame size, removing some
warnings and making it easier for platforms/compilers that
have frame size issues (e.g.: zOS).
Tested on: 64-bit Ubuntu Linux w/ gcc 5.3.1
Autotools serial
configure fails to detect valid KINDs on FreeBSD
Added the exponential option to SELECTED_REAL_KIND to distinguish KINDs of same precision.
Tested: FredBSD, jam, platypus.
Bring h5format_convert tool from revise_chunks branch to trunk.
Tested on:
MacoSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Bring H5LD* routines from revise_chunks branch to trunk.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Bring H5DOappend(), H5P[s|g]et_object_flush_cb, and H5P[s|g]et_append_flush
from revise_chunks branch to trunk. Brings along updated metadata cache
entry tagging, and the internal object flush routine.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Minor rearrangements, to align with revise_chunks branch
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Description:
The constructor FL_PacketTable added in 1.10.0 did not have good
prototype; it didn't allow the property list to be default. Marked
it deprecated and added this one:
FL_PacketTable(hid_t fileID, const char* name, hid_t dtypeID,
hsize_t chunkSize = 0, hid_t plistID = H5P_DEFAULT)
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
The "warning: deprecated conversion from string constant to âchar*â
[-Wwrite-strings]" was already removed by adding const to char*
parameter in the FL_PacketTable. This change is to remove the use
of literal strings in code for maintainability.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
This flag generates a large number of warnings and is considered obsolete
since its primary purpose seems to have been to support ancient compilers
that could not return an aggregate.
Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1
Autotools serial w/ C++
Description:
- Removed ArrayType::rank and ArrayType::dimensions and modified the methods
ArrayType::getArrayNDims and ArrayType::getArrayDims to always call the
C functions to get the rank and dimensions.
- Overloaded ArrayType::getArrayNDims and ArrayType::getArrayDims to provide
const version and marked the non-const version deprecated.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Bring over some of the tool testing for the new chunk indices.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Bring "file pointer patching" code & test from revise_chunks to trunk.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
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)
config/linux-gnulibc1 reapply filx for HDFFV-9439 which was partially removed, probably by merge from revise_chunks branch.
Tested with h5committest.new on kituo, ostrich, osx1010dev and platypus.
Close another FAPL in the test_missing_chunk() routine.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (w/check-vfd)
(h5committest forthcoming)
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)
Close FAPL that was leaked in zero_dims test.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production, including check-vfd
(h5committest forthcoming)
Bring over more dataset tests from the revise_chunks branch.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Correct chunk index computation for earrays and farrays, particularly when
copying datasets with H5Ocopy() and other operations (like H5Dget_storage_size)
that require iterating over all chunks.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial & parallel
(h5committest forthcoming)
Clean up coding to increment/decrement underlying FAPL for multi/split
VFDs, to avoid copying property lists as much.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial & parallel
(h5committest forthcoming)
Switch to use internal DXPL ID, to align with recent changes within the
library.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial & parallel
(Too minor to require h5committest)
Description:
- Replaced "goto out" and "out:" with "goto error" and "error:" to indicate
the failure situations.
- Replaced old-style casts with static_cast to remove warnings.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Finish correcting initializer for chunked layouts.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(to minor to require h5committest)
Bring support for earray and v2 B-trees from revise_chunks branch to
trunk.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Minor style cleanups, from revise_chunks branch
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel and production
(too minor to require h5committest)
Bring updated code for setting chunk size information from revise_chunks
branch.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
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)
Corrects a problem where H5Dget_access_plist() returns a dapl that
does not contain all dapl fields.
Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1
autotools serial
Description:
Performed similar improvement as the C Packet Table library.
- Removed the VLPT_REMOVED ifdef around class VL_PacketTable
- Moved VL_PacketTable::IsVariableLength to PacketTable
- Moved VL_PacketTable::FreeReadBuff to PacketTable::FreeBuff
- Added overloaded constructor to FL_PacketTable that takes a
property list ID and call the new C API H5PTcreate.
- Added accessor wrappers to class PacketTable, per HDFFV-8623/patch 003.
/* Returns the ID of the dataset associated with the packet table */
hid_t GetDataset();
/* Returns the ID of the datatype the packet table uses */
hid_t GetDatatype();
- Replaced appropriate calls in tests
- Various cleanup
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
Replaced static_cast with reinterpret_cast for "void *".
Removed some commented-out old code.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
Added several tests for packet table that were missing from the
previous update.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Svn revisions reverted: 29341, 29326
Branch features/h5check_version was created for further development.
Files changed
test/tcheck_version.c
test/testcheck_version.sh.in
src/H5public.h
src/H5.c
config/lt_vers.am
bin/h5vers
Tested with h5committest.new
Description:
- Removed many warnings:
warning: use of old-style cast
warning: enumeration value ‘H5D_VIRTUAL’ not handled in switch
warning: comparison between signed and unsigned
There are others of the same warnings and they will be taken care of
in the next release.
- Made some code reuse between overloads
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
This flag generates a large number of spurious warnings in our code
so we've disabled it for now.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
autotools serial w/ C++
bin/h5vers:
Changed to copy the shared lib version from lt_vers.am to H5public.h
(Thanks to Larry who made the changes.)
config/lt_vers.am:
cosmetic change, nothing material.
src/H5public.h:
Changed by bin/h5vers.
src/H5.c:
Changed H5check_version() to use shared library version for compatibility
checking.
test/tcheck_version.c:
test/testcheck_version.sh.in:
Changed to use shared library version numbers instead of the HDF5 library
version numbers for testing.
Tested: tested in Jam (C only), platypus and osx1010dev (enable fortran and C++).
Description:
Removed obsolete functions from the documentation. They are still
in the code, however, until the next two releases, just in case.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
Added member function ArrayType::operator= because ArrayType has
pointer data members.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Other main changes that were done to trunk should be documented before the 1.10.0 code freeze.
This file will be added as HISTORY-1_9_0-1_10_0.txt to the 1_10 branch when the branch is created and will be part
of the HDF5 1.10.* source distribution.
Description:
The Packet Table API used to have fixed-length and variable-length functions
(i.e., H5PTcreate_fl and H5PTcreate_vl), but in 2006, the vlen functions
were ifdef'ed out with VLPT_REMOVED, see HDFFV-442. The majority of this
revision includes removing unused vlen stuff, adding various vlen tests,
initial code cleanup, and first pass of commenting.
Details:
- Removed the VLPT_REMOVED ifdef, but keep H5PTis_varlen and the free
function because they are useful or even needed, but the free
function's name is changed to be more appropriate for both
read/write buffers, i.e., H5PTfree_vlen_buff.
- The new test file, test_packet_vlen.c, contains tests showing packet
tables, containing various types of vlen data, can be created with
the fixed-length function
- Two accessor functions were added per HDFFV-8623/patch 003.
/* Returns the ID of the dataset associated with the packet table */
hid_t H5PTget_dataset(hid_t table_id);
/* Returns the ID of the datatype the packet table uses */
hid_t H5PTget_type(hid_t table_id);
- Various cleanup: replacing 0/-1 with SUCCEED/FAIL and H5I_BADID with
H5I_INVALID_HID, and removing many warnings.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
external dataset storage path behavior.
This check-in fixes a bug in the original check-in where the
external path stored in the file struct was not copied on reopen
causing subsequent dataset operations to fail.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
autotools serial w/ fortran and C++
autotools parallel (MPICH 3.1.4) w/ fortran
replace functions like h5_clean_files() that also do things like
reset the error handler and close fapls.
Existing tests have not yet been updated to use these new
functions.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
autotools serial
--disable-symbols is specified and to ensure that production
mode (where symbol stripping is usually a part of the FLAGS)
doesn't conflict with --enable-symbols. This will allow better
(though still limited) debugging of production/optimized code.
The PGI, XLC, Intel, and Solaris files were not modified and
do not generate the symbol removal flag at this time. They'll
be updated in future check-ins. In the meantime, production
mode on those platforms still usually strips symbols.
This check-in also updates the Cygwin-specific files to use
the new autotools FLAGS and option scheme when uncommon
(non-gnu, etc.) Fortran compilers are used.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
autotools serial (prod/debug w/ and w/o symbols)
symbol presence/absence checked with objdump
platform-specific build information so the debug and production
flags are not clobbered.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
autotools serial (production & debug)
can be configured to generate extra debugging output in both
the autotools and CMake.
This can still be set by defining H5B_DEBUG manually or by
using a custom string in configure.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
autotools serial
CMake serial
r29069 and 72 (gheap cleanup)
r29041 and 43 (HDFFV-8740 external storage)
These cause problems in the daily tests. They will be
re-introduced when their respective problems have been
addressed.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
autotools serial (check-vfd) w/ Fortran and C++
autotools parallel w/ Fortran
CMake serial
Normalize against the trunk, in preparation for final merge.
Tested on:
MacOSX/64 10.11.3 (amazon) w/serial & parallel
(h5committest not required on this branch)
Normalize against the phdf5_metadata_opt branch, in preparation for
merging it to trunk.
Tested on:
MacOSX/64 10.11.3 (amazon) w/serial, parallel, and production builds
h5committest forthcoming
- Fixed typo in Wsetenv().
- Changed HDoff_t back to off_t in test/external.c. The function signature is off_t so the types must match or you can get conversion errors.
Tested on 64-bit Windows 10 w/ VS 2015
for external dataset files set via H5Pset_external().
Resolves HDFFV-8740
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
autotools serial
This test is duplicated more comprehensively in the links.c file so
there is no need to copy it over.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial autotools
* We assume that fseeko and ftello exist.
* The *64 IO functions and types are no longer explicitly used.
We now rely on a mapping provided by _FILE_OFFSET_BITS (or its
equivalent).
* _LARGEFILE(64)_SOURCE is no longer exposed via AM_CPPFLAGS.
The CMake files have not yet been updated but CMake is still
functional. The CMake configure files will just run a few
unecessary tests and create unneeded #defines until they are
updated in a few days.
Tested on: Linux, OS X, Solaris, z/OS
symbols, asserts, profiling, and optimization.
Also much refactoring, improved help, and --enable-<foo> options will
now emit errors on nonsense (e.g.: --enable-foo="asdfasdf").
The libhdf5.settings.in file was also reformatted.
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial and parallel autotools w/ various options
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
- remove H5AC_ind_dxpl_id and use only H5AC_dxpl_id everywhere instead.
- remove flush_me_collectively flag from cache entries
- add a collective sanity check (MPI_Barrier) for every HDF5 API routine that could possibly touch the file. This is trigerred when the environment variable H5_COLL_API_SANITY_CHECK is set to a non 0 digit.
tested on BB-8 with serial and parallel.
I missed changes to a couple of expected error output files with the last
checkin.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
I missed changes to a couple of expected error output files with the last
checkin.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
Normalize against incoming changes from the phdf5_metadata_opt branch.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
Description:
User Adam Rosenberger reported a failure when using the member function
AbstractDs::getArrayType(). This problem was caused by missing
initialization of the ArrayType's members in some cases.
Solution:
- Added ArrayType::setArrayInfo() to retrieve rank and dimensions of
an array and store them in memory for easy access.
- Re-factored a few functions to use the new function.
- We'll give him 1.8.16 patch
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
The current implementation for Mac OSX platform is a kludge that sometimes left behind mounted volumes.
Temporary screen out the checking of installtion_check step (so that daily test may pass).
Tested: by hand running cmakehdf5 in platypus and osx1010test.
Switch filter plugin to use H5allocate_memory and H5free_memory instead of
malloc and free.
Tested on:
Linux/32 2.6.x (jam) w/serial
Linux/64 2.6.x (jam) w/serial
MacOSX/64 10.11.2 (amazon) w/serial & parallel
Switch v2 B-tree min & max records to be void*'s to be cleaner and generate
less warnings.
Tested on:
Linux/32 2.6.x (jam) w/serial
MacOSX/64 10.11.2 (amazon) w/serial & parallel
Add --enable-memory-alloc-sanity-check option to configure, to track and
sanity check memory allocations within the library. This is orthogonal to the
--enable-using-memchecker option and can be used with/without it.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
Clear memory for shared message info when "deferring" and using memory
checker, so valgrind doesn't whine.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
Bump the nunmber of v2 B-tree records for the random 4-level B-tree update
test by another 25,000 records.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(Too minor to require h5committest)
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)
Minor code neatening and cleanups (same as r28755) on revise_chunks branch.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(Too minor for h5committest)
Bump number of records for level 4 B-tree test, so that it's more likely to
always get to level 4.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
Add 'update' operation to v2 B-trees, which will insert a new record, or
modify an existing one, depending on if the record exists or not.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
Bring over rest of performance improvements for extending chunked datasets
and normalize against revise_chunks branch.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel)
(h5committest forthcoming)
Bring r28708 from revise_chunks branch:
Fix earray, farray and btree2 use of incorrect file pointer when two files
are opened and used to access the data structure. Misc. minor code cleanups
as well.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
h5committest forthcoming
h5tools_dump.c
Removed 3 lines commented out with //.
h5_vds-percival-unlim.c
Changed C++-style comment to C-style comment.
Tested with h5committest.new.
Also purged obsolete /*ARGSUSED*/ from the library.
Tested on:
Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial only
(these changes have been in revise_chunks for a long time)
Normalization for future single chunk indexing.
Tested on:
Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial only
(these changes have been in revise_chunks for a long time)
NOTE: Flush dependency code was not moved.
Tested on:
Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 w/ CMake 3.3.2
serial only (Autotools and CMake since new files were added)
(these changes have been in revise_chunks for a long time)
Mostly minor fixes like warnings, etc.
Tested on:
Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial only
(these changes have been in revise_chunks for a long time)
Mostly minor fixes like warnings, etc.
Tested on:
Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial only
(these changes have been in revise_chunks for a long time)
Revisions to normalize revise chunks vs. trunk, plus push dataset metadata
changes into the cache immediately (instead of holding them within the dataset
data structures).
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Fixes OS X compilation problems and brings some Linux symbols in
line with the Autotools when building with CMake.
Tested on: 64-bit OS X 10.11.1 El Capitan (Darwin 15.0.0)
Xcode 7.1 Apple LLVM 7.0.0 (clang-700.1.76)
Revert most of r27549, since revise_chunks code requires debugging contexts
for v2 B-trees. Also, misc. warning cleanups and alignments w/changes on
revise_chunks branch.
Tested on:
MacOSX/64 10.11.1 (amazon) w/serial & parallel
(h5committest forthcoming)
Refactor time conversion code to put all the system-specific changes into
one routine, H5_make_time, in H5system.c.
Tested on:
MacOSX/64 10.11.1 (amazon) w/serial & parallel
(h5committest forthcoming)
bin/release uses the content of MANIFEST file to build the release tarball. But all the files generated by autogen had been removed. Therefore the release would not contain those needed generated files for a proper release.
Solution: Added all those generated files to the tail of MANIFEST and titled it accordingly. (Somehow bin/chkmanifest does not complain against these entries though they are not svn managed. This needs further investigation.)
Test: bin/release generated the release tarball in jam, then use it in Platypus to do a full build (--enable-fortran --enable-cxx). All passed.
installation.
Tried to find out what went wrong but all output files were deleted already.
Added a verbose option to display all cmake process output in order to see what
might have gone wrong. Default is on.
Using --disable-verbose will turn it off.
Tested: osx1010dev, osx1010test, playtypus.
This was giving a lot of users headaches and the parser code rarely
changes. There is now a new script (bin/genparser) which can be
run as needed.
Tested on: Ubuntu 15.10 (x86_64 Linux 4.2.0)
gcc 5.2.1, flex 2.5.39, bison 3.0.2
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
Description:
- Implemented the friend function
void f_PropList_setId(PropList* plist, hid_t new_id)
to work around the same problem described in trunk r26655, for the
API DataSet::getCreatePlist()
- Cleaned up some comments and obsolete functions
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Description:
- Removed H5Library::instance because it is unnecessary. All H5Library's
methods are static. This, in turn, removed the memory leaks by
H5Library::instance not being deleted.
- Added ObjCreatPropList::deleteConstants to atexist() list
- Cleaned up comments and format inconsistencies with 1.8
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Clear buffer for driver info block before writing it to the file. (Avoids
'uninitialized memory read' warning from valgrind)
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & valgrind
(too minor for h5committest)
Clean up memory leak when generating group creation property list for user.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & valgrind
Linux/64 4.1.8 (Jerome's laptop) w/serial & valgrind
Description:
Merged from hdf5_CppAPI_Constants
r27942:
------
Description:
- Added H5dont_atexit() to getPredType and all the getConstant's to prevent
the C library from terminating before the C++ library cleanup.
- More cleanup and added more comments
r27923:
------
- Updated more comments and moved some things around for consistency
- Removed check for "new" failure, exceptions would be thrown
r27922:
------
Description:
Added function headers and more comments for clarity.
r27917:
------
Description:
The C++ library has several types of global constants from different
classes, such as PropList, PredType, DataSpace, etc... Previously,
these global constants were declared statically and the C++ library used
a constant, called PredType::AtExit, to detect when all the global
contants are destroyed then close the C library (H5close). This method
relied on the order of the constants being created and destroyed and
that PredType constants be the last to be destroyed. In September 2015,
it was recognized that the order in which the global constants were
created and destroyed was actually undefined, thus can be different
between different compilers. This resulted in failure when compilers
destroy PredType constants before others because when PredType::AtExit
was destroyed, the C library was closed, so when the constants of other
classes such as PropList or DataSpace were being deleted, the C library
would not be available.
Solution:
The static approach is changed to dynamic. In order to avoid an impact
on existing applications, the static global constants are changed to
constant references to the dynamically allocated objects.
A detailed explanation of the new method and a description of the
changes are in a Design Notes at the end of the file H5PredType.cpp.
New functions added to support the new methods are listed below.
class H5Library:
// Returns a singleton H5Library to initialize the global
// constants, invoked in IdComponent default constructor
static H5Library* getInstance(); // public
// Registers cleanup and terminating functions with atexit(),
// called in IdComponent default constructor
static void initH5cpp(void); // public
// Calls H5close to terminate the library, registered with
// atexit(), as the last thing to be done.
static void termH5cpp(void); // public
class PredType:
// Creates the constants
static void makePredTypes(); // private
// Calls makePredTypes to create the constants and returns
// the dummy constant PREDTYPE_CONST;
static PredType* getPredTypes(); // private
class DataSpace:
// Creates the constant
static DataSpace* getConstant(); // private
class PropList:
// Creates the constant
static PropList* getConstant(); // private
class DSetCreatPropList:
// Creates the constant
static DSetCreatPropList* getConstant(); // private
class DSetMemXferPropList:
// Creates the constant
static DSetMemXferPropList* getConstant(); // private
class FileCreatPropList:
// Creates the constant
static FileCreatPropList* getConstant(); // private
class FileAccPropList:
// Creates the constant
static FileAccPropList* getConstant(); // private
This function is added to PredType, DataSpace, PropList, and the four
subclasses of PropList:
// Deletes the constant
static void deleteConstants(); // public
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 (platypus)
Darwin (osx1010test)
Avoid duplicating source FAPL & DAPL if they are already available.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest not required on this branch)
Description:
In the friend functions that setId, changed the direct assignment of
id to using p_setId() so that the previous id can be closed first to
avoid memory leaks.
This change was tested and confirmed by user Jorj on Forum when his
application stopped running out of memory. Currently, the C++ library
doesn't have a way to test this. A function such as H5Inmembers for
library ids would be helpful.
Platforms tested:
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Darwin (osx1010test)
r27860-27883
r27892-27916
Tested on: - h5committest
- jam (parallel) fails with an existing, unrelated MPI config error
- platypus fails with due to an existing, unrelated cmakehdf5 error
where it does not recognize --enable-fortran2003.
H5S recursive functions where an aliased pointer was
incorrectly set too early.
Tested on: Ubuntu 15.04 (Linux 3.19 x86_64) w/ gcc 4.9.2
serial and parallel (w/ MPICH 3.1.4)
changes will be merged more carefully so we can more easily
identify any errors that arise.
Tested on: Ubuntu 15.04 (Linux 3.19 x86_64) w/ gcc 4.9.2
serial and parallel (w/ MPICH 3.1.4)
Revert changes to 'all' and 'none' selections: the serialized header info
is handled in the general H5S_select_deserialize() routine.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Remove 'unused' attribute from decoding pointer flag that I missed in the
last checkin.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Advance the decoding pointer for 'all' and 'none' selections properly.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Check if the layout has been retrieved before setting it again.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest not required on this branch)
- Removed the long options, which are not supported under
the getopts builtin.
- Correctly labeled the autogen.sh script as requiring bash
(via the #!). We may need to remove the bash constructs
before the 1.10 release and revert to sh.
- The help output is now correct.
Tested on: local linux
Make virtual layout return to the property list occur in all cases, even
on failure.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest not needed on this branch)
Normalization changes that wouldn't otherwise be necessary if the VDS branch
wasn't coming in shortly.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Clean up warnings and some normalization against trunk.
Tested:
McaOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest not required on this branch)
Close FAPL for external link test, to fix infinite loop closing the library.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial
(too minor to require h5committest)
This removes all of the TRY_* macros and replaces them with *_IFELSE
macros, which are better for cross-compiling.
Tested on: h5committest (cmake fails due to --enable-fortran2003)
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)
compatible between 32 and 64 bit systems.
Expand cross platform property list encode/decode testing.
Fix warning in H5P__fill_value_enc.
Tested: jam, koala, ostrich (h5committest), ummon
NOTES:
- Developers will have to run autogen.sh before building with the autotools.
- autogen.sh takes the -p option to mimic the old bin/reconfigure behavior.
- The generated error, overflow and version headers have been left in place.
- The generated H5LT parser code has also been left in place.
- There are no changes for CMake users at this time.
Tested on: h5committest
Removes .pl extension from Perl scripts. This may be returned in the future,
but it's best to keep the script names unchanged while we merge with the
trunk.
Tested on: h5committest
Merge in part of Neil's property list fixes: Fix a minor memory leak,
add some sanity checks, clean up the code a little, and verify that encoding/
decoding default versions of the property lists works correctly.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial
(Too minor to require h5committest)
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
macro checks from src/H5api_adapt.h to H5private.h, which is where
they belong anyway.
Tested on: h5committest (manually inspected for attribute warnings)
Added -qflag=w:w to config/ibm-flags. This will suppress informational
messages on AIX, suppressing thousands of "__attribute__ is non-portable"
messages in the AIX nightly test output.
Tested on: Nothing. I have no access to an AIX machine.
Bring the "metadata rings" code from its branch (mdc_rings_v2) to the trunk.
(This change will support the page buffering feature)
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Misc. minor cleanups in preparation for merging "metadata rings" branch to
trunk.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial
(Too minor to require h5committest)
when building the thread-safe library.
Configure will quit with an error when --disable-hl or
--enable-unsupported is not used with --enable-threadsafe.
Fixes HDFFV-8719
Tested on: h5committest
configure w/ various combinations of --enable-threadsafe,
--disable-hl, and --enable-unsupported
Removed _BSD_SOURCE and _DEFAULT_SOURCE from the autotools
C flags. They are no longer needed by the library. Fixes HDFFV-9079.
Tested on: h5committest
Removed library checks for nsl and socket from the autotools configure on
Solaris.
The nsl and socket libraries are no longer used by the library. Fixes
HDFFV-9118.
Tested on: jam w/ autotools and CMake
emu w/ autotools
Solaris.
The nsl and socket libraries are no longer used by the library. Fixes
HDFFV-9118.
Tested on: h5committest (CMake fortran fails due to an unrelated error)
jam w/ CMake
# Source files are used for both the library and fortranlib_test.
# Automake will complain about this without the following workaround.
fortranlib_test_FCFLAGS=$(AM_FCFLAGS)
fortranlib_test_CFLAGS=$(AM_CFLAGS)
because they caused Fortran build rules (.f90.o, .F90.o) to be ignored, causing the CPP flags to be passed to the Fortran compiler, causing the xlf compiler to fail.
Tested: ostrich (xlf), h5committest
Updates to older special config files in configure.ac:
- solaris2.x renamed to solaris. There are recent changes to this file
but the "2.x" is misleading since the changes are applied to all
versions.
- Removed support for OSF 4.x/5.x (Digital and Tru64 Unix). We no
longer have the config files for these.
Tested on: h5committest
Fix handling of layout version number.
Other minor fixes/cleanup.
NOTE: This commit changes the file format for VDS, all files must be
re-generated.
Tested: ummon
- solaris2.x renamed to solaris. There are recent changes to this file
but the "2.x" is misleading since the changes are applied to all
versions.
- Removed support for OSF 4.x/5.x (Digital and Tru64 Unix). We no
longer have the config files for these.
Tested on: jam (autogen.sh only)
emu (Solaris 11)
gen_* files in test/. These files will remain distributable since
they are needed if a user specifies --enable-build-all.
Fixes HDFFV-8236
Tested on: jam (bin/chkmanifest only)
Replaced AC_CONFIG_HEADER (obsolete macro) with AC_CONFIG_HEADERS
followed by bin/reconfigure (which changed nothing at this time).
Fixes HDFFV-9284
Tested on: jam
Revert changes to pass file pointer to selection serialize/deserialize
routines. Also patch back in some changes that were merged out in the
previous merge w/trunk.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial
(h5committest not required on this branch)
gcc 4.9.2 was used to create the warning list
- implicit casts
- shadowed variables
- various enum issues
- other minor fixes (comments, unused macros, etc.)
Tested on: h5committest
Align w/vds branch: Remove extraneous sieve buffer flush in chunk
flush callback, and move error check out of the middle of retrieving properties
for dataset.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Protect dataset that's closing from being flushed again, if it's the last
one holding a file open.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Align w/vds branch: Change code in H5O_layout_copy() to use switch for
different types of dataset layouts.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Align w/vds branch: Whitespace cleanup, move common code for opening a
dataset into a new routine, misc. style cleanups.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
(h5committest upcoming)
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
Update the file format debugging routines to match the recent changes to
the metadata cache, along with a few other cleanups and miscellaneous
enhancements.
Tested on:
MacOSX/64 10.10.5 (amazon)
(h5committest forthcoming)
Tested w/ h5committest
NOTES: - The manifest may still be messed up.
- Cmake fails since the dual binary work needs to be merged with
this repo's CMake externals.
Description:
Added footer to include copyright and helpdesk info.
Platform tested:
Re-run Doxygen on cpp_doc_config and verified the html files on a
Windows 7 machine.
numbers of elements selected, incorrect "slice" through limited dimensions,
incorrect number of printf substitutions.
Patch source selection space extent with bounds of selection if extent is
unknown before returning via H5Pget_virtual_srcspace.
Write updated VDS dataspace to file when it changes due to unlimited selections.
Other minor fixes/cleanup.
Tested: ummon
Put "" around PROJECT_NUMBER string, otherwise, Doxygen would remove
all the spaces when displaying.
Platform tested:
Re-run Doxygen on cpp_doc_config and verified the html files on a
Windows 7 machine.
Renamed a few "h5tri_t extended" variables to "h5tri_t was_extended".
Apparently, "extended" is a typedef name someplace in the headers used
on Solaris, which causes potentially confusing warnings to be emitted.
Tested on: h5committest
Solaris w/ Solaris Studio (emu)
Description:
XL compilers in ostrich (PowerPC64 linux) fail in test/dt_arith
because of the removal of the LLONG_TO_LDOUBLE_CORRECT (removed in
r26625) and LDOUBLE_TO_LLONG_ACCURATE (removed in r26623).
Solution:
Reverse revisions
r26623: bring back LDOUBLE_TO_LLONG_ACCURATE configure macro
r26625: bring back LLONG_TO_LDOUBLE_CORRECT configure macro
r26627: bring back WANT_DATA_ACCURACY configure macro which is
used together with the above two macros. This also brings
back the enable-dconv-accuracy configure option.
Tested:
h5committested.
Also tested in ostrich using the XL compilers.
Implement support for H5Pencode/decode with VDS properties.
Testing for H5Pencode/decode with VDS.
Relax assertion check for number of elements written to buffer as we do not
check for overlaps in mappings.
Other minor fixes/cleanup.
Tested: ummon
a different ID in the same type. Added a new skiplist routine,
H5SL_try_free_safe, which iterates over items, freeing some of them, and which
intercepts and defers attempts to remove from the list outside of the main
iteration. Changed H5I_clear_type to use this function.
Tested: jam, koala, ostrich (h5committest); ummon
- Updated the preprocessor logic that defines the H5_ATTR_* macros. The Solaris
Studio compiler understands __attribute__ but not the specific attributes
that we use. The H5_ATTR_* macros are now defined as blank with that
compiler which significantly cleans up the warnings, making debugging
easier.
- Replaced a few lingering __attribute__ macros with H5_ATTR_* markup.
Tested on: h5committest
Solaris w/ Solaris Studio (emu)
Implement support for H5Ocopy on VDS.
Testing for H5Ocopy on VDS.
Fix check-vfd failure.
Other minor fixes/cleanup.
Note there is a preexisting failure in h5repack testing.
Tested: ummon
Separate H5AC layer from using package-scoped pieces of the H5C layer,
moving from including H5Cpkg.h to H5Cprivate.h.
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial, parallel & production
Linux/32 2.6.x (jam) w/serial & parallel
Correct error with braces around macro (in production builds), also clean
up a few warnings.
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial, parallel & production
Linux/32 2.6 (jam) w/serial & parallel
Clean up parameters to H5C__flush_single_entry: accept cache entry instead
of address, and make new flag for deleting entry from skiplist on destroy
instead of a separate parameter to the routine.
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
Linux/32 2.6.x (jam) w/serial & parallel
Split parallel metadata cache code into separate source code modules.
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
(too minor for h5committest)
Bring 'fail if unknown always' object header message flag from the
avoid_truncate branch, strengthen error checking for unknown messages, and try
to catch object header code configurations at compile time (instead of runtime).
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
(h5committest forthcoming)
to open source files and datasets, instead of using the default property lists.
Modify VDS to reject attempts at parallel I/O, fix parallel compile error.
Modify VDS to not write fill value to memory buffer if the fill value is
undefined.
Other minor fixes/cleanup.
Tested: ummon
Changes that allow the autotools to correctly deal with inline
functions.
- Inline markup schemes are now checked with AC_COMPILE_IFELSE
tests instead of AC_C_INLINE.
- The inline designator is now H5_INLINE instead of H5_inline.
This is now set in H5private.h instead of H5pubconf.h.
Tested on: h5committest
functions.
- Inline markup schemes are now checked with AC_COMPILE_IFELSE
tests instead of AC_C_INLINE.
- The inline designator is now H5_INLINE instead of H5_inline.
This is now set in H5private.h instead of H5pubconf.h.
Tested on 64-bit linux VM
extent.
Improve algorithm for calculation of VDS extent by removing the need for a
temporary copy of a dataspace.
Other minor fixes/cleanup.
Tested: ummon
missing source datasets. Decided not to attempt to open the source dataset in
this case, as doing so could create issues related to the sizing of the VDS.
Users should call H5Dget_space to open these datasets. No regression test yet.
Tested: ummon
- Moving truncate to H5F_flush() where it was done a long time ago.
- Add a second H5AC_flush() call after the truncate is done to make sure we write the correct EOA.
tested with h5committest
Large code cleanups and optimizations, in preparation for the upcoming
v3 metadata cache merge.
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
Linux/32 2.6.x (jam) w/serial & parallel
library no longer iterates over all source datasets in the printf mapping, it
now only looks at the ones that could be involved in I/O (the ones whose bounds
overlap with the selection in the unlimited dimension).
Tested: ummon
H5_VDS_FIRST_MISSING)
Add test for this
Rework VDS code to not depend on unlimited selections having a "clipped" state
in preparation for removing the clipped state from unlimited selections.
Other bug fixes/cleanup
Tested: Kubuntu 64 (home computer)
- Check for mpi is_initialized and is_finalized before making MPI calls in init/terminate of HDF5.
- Add a test to make sure we can make serial HDF5 calls from rank 0 after MPI_Finalize is called.
tested with h5committest
test/Makefile.in was updated due to changes in the Makefile.am
file that missed a reconfigure. The changes just added a few
VDS test files to the deletion list.
Note that there are trace issues with a new VDS struct that
show up when running bin/reconfigure. I reverted these for
fixing at a future date.
Tested on: jam
Normalize trunk against the metadata_cache_merge branch, in preparation
for merging the branch into the trunk.
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
Linux/64 2.6.x (koala) w/serial
Linux/32 2.6.x (jam) w/serial & parallel
Clean up obsolete and unsupported versions of GCC, and update for GCC 5.1
release.
Tested on:
Mac OSX/64 10.10.3 (amazon) w/C++, FORTRAN, serial, production & parallel
(gcc 5.1 not available on other systems)
Convert internal chunk structures to use 'scaled' coordinates instead of
absolute coordinates.
Tested on:
Mac OSX/64 10.10.3 (amazon) w/parallel & serial
Linux 2.6.x/32 (jam) w/parallel & serial
Linux 2.6.x/64 (koala) w/serial
enum argument.
Add support for AND and NOTA/NOTB operations with unlimited selections.
Add some tests for unlimited selections.
Other minor fixes/cleanup.
Note: "clipped" status of unlimited selections is not properly updated with
H5Sselect_copy. This is a deliberate omission since fixing it would take work
and we are planning to eliminate the clipped status anyways.
Tested: ummon
Use H5_GCC_DIAG_ON/OFF to suppress larger-than and float-equal warnings
Variables used with sigsetjmp/siglongjmp must be declared as volatile
Remove unnecessary use of volatile after r24171 fix and fix prototypes
Tested in release mode on:
- jam (CentOS 5.11 i386 GCC 4.1.2)
- ostrich (RHEL 6.6 ppc64 GCC 4.4.7)
- local linux (OpenSuSE 13.2 x86_64 GCC 4.8.3)
- local linux (Fedora 21 x86_64 GCC 4.9.2)
- local linux (Fedora 21 x86_64 ICC 15.0.2)
- local windows (Windows 8.1 x86_64 MSVC 2013 update 4)
- lemur (MacOSX 10.10.3 x86_64 clang-602.0.49 Xcode 6.3.1)
- ibm p95a07 (Ubuntu 14.10 ppc64le GCC 4.9.1)
- ibm p95a07 (Ubuntu 14.10 ppc64le IBM XL C V13.1.1)
- bluewaters (Cray PE 2.2.1 x86_64 GCC 4.8.2)
- bluewaters (Cray PE 2.2.1 x86_64 Cray C 8.3.3)
- bluewaters (Cray PE 2.2.1 x86_64 PGCC 14.2)
H5Pget_virtual_dataspace_bounds.
Minor refactor of dataset initialization code to make this cleaner.
Update h5_vds-percival-unlim-maxmin.c
Other minor fixes/cleanup.
Tested: ummon
Eliminate unneccessary 'rdcc' field from common chunk info struct.
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
(Too minor to require h5commitest)
Clean up chunk 'prune by extent' and flush code, and make the rehashing
routine 'update cache' hold onto more chunks, instead of evicting them as
aggressively.
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
(h5committest forthcoming)
Align w/incoming chunk performance changes, including some small performance
improvements here, as well as a few minor general code cleanups.
Tested on:
Mac OSX/64 10.10.3 (amazon) w/serial & parallel
(Too minor to require h5committest)
The H5F_ACC_DEBUG symbol remains but has been defined to zero and
has been listed as deprecated.
Fixes: HDFFV-1074
Tested on:
h5committest
32-bit Linux w/ C++ and Fortran and multi VFD
32-bit Linux w/ C++ and Fortran and multi VFD (no deprec symbols)
The error is that $EXAMPLETOPDIR is used without setting a value first.
Solution is to set them with the proper values.
Tested: jam only to confirm the error no longer exists.
Clean up H5I code, to eliminate duplicated sections of code.
Tested on:
Mac OSX/64 10.10.3 (amazon) w/serial & parallel
(Too minor to require h5committest)
The configure summary (libhdf5.settings) was missing from the configure output.
Solution:
Append the configure summary to the configure logfile if configure succeeds.
Tested:
hand ran cmakehdf5 in jam and inspected the logfile.
Cache the dataset's rank & dimension sizes, instead of querying them
frequently, to speed up various checks & algorithms. Also, a few minor
cleanups.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
Linux/32 2.6.18 (jam) w/serial & parallel
Minor formatting cleanups and remove unused field from callback struct.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial & parallel
(Too minor to require h5committest)
configure.ac
hl/src/H5LTparse.c
hl/src/H5LTparse.h
Address HDFFV-9010: configure issue with gcc 4.9.2 "-l ".
Change default to disable_shared on CYGWIN.
release_docs/INSTALL_Cygwin.txt
release_docs/RELEASE.txt
Update for changed default and no CYGWIN szip binary.
c++/src/cpp_doc_config
bin/h5vers
AddressHDFFV-9010: Add cpp_doc_config to h5vers
Tested with h5committest, on CYGWIN.
Separate allocating chunk on disk from inserting the chunk record into the
index. This allows a "SWMR-safe" insert/update of chunks (the chunk is always
allocated -> written -> inserted/updated in the index).
Tested on:
Mac OSX/64 10.10.2 (amazon) w/parallel & serial
Linux/32 2.6.18 (jam) w/serial & parallel
Description:
- In DataType::DataType(const PredType& pred_type), using DataType::copy
will invoke DataType::close() unnecessarily, which will produce undefined
behavior. Changed to call H5Tcopy directly, code reuse is not useful in
this case.
- Also, fixed CommonFG::childObjVersion to return expected value outside of
an if/else block.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/64 (platypus)
Linux/32 2.6 (jam)
That broke the testings as some testfiles have zlib compressed datasets.
Added options control to enable the linking of zlib external libarary by
default and turn off the szip library linking as szip library may not be
avaiable. This matches the established settings.
Tested: run cmakehdf5 by hand in jam and platypus.
Also tested in wren but it failed in the testing stage.
Also tried "cmakehdf5 --script" in jam. It failed.
Description:
The test added failed in some machines because the data file contains infinity values that different machines print them differently as "inf", "INF", "Inf", ...
Solution:
Added a "ignorecase" option to TOOLTEST() to do caseless matching between generated output vs expected output. This solved most machines problem for now.
Tested: h5committest, emu by hand for both development and production modes.
But cmake built h5dump failed to read the data file. Using the same source to build h5dump by autotools produced a h5dump that can read the test data file. Don't know why cmake could not produce a correct binary.
Description:
- Put back the UNUSED parameters in dsets test because the change to remove
the warning last time caused failure in setting filter, in turn, caused
failure in the test with such obscure/unrelated errors!
- Added incRefCount() to other constructors that missed from last time.
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
When the selection is set to all, H5Sextent_copy did not update the number of
elements in the selection in the destination space. Fixed H5Sextent_copy to do
this. Added tests for this functionality.
Tested: jam, koala, ostrich (h5committest)
The tool claimed it could handle 24bit images but there was no code to handle it.
(or might be there were but was removed by previous revisions.)
Also discovered that it does not accept multiple images nor -p for palette
as its user document and online help message indicated.
Solution:
Added code to verify dimension sizes are within 8 bit raster images limit and
added tests to verify the tools correctness.
Need to update user document tool.
Tested: h5committested.
Fix off by 1 error in H5S__hyper_project_intersection algorithm.
Add many tests for fixed size hyperslab I/O.
Note make check still fails in h5dump test (unrelated to this checkin).
Tested: ummon
Description:
Per user Jason Newton request, the following constructor is added:
H5File(hid_t existing_id);
Also, fixed H5File::openFile to close current file first before re-using
the object.
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6 (jam gnu and Intel 15.0)
SunOS 5.11 (emu)
Description:
When copy constructor or constructor that takes an existing id is invoked,
the C ref counter stays the same but there is an extra C++ object which
later is destroyed and may cause the HDF5 id to be closed prematurely. The
C++ library needs to increment the ref counter in these situations, so that
the C library will not close the id when it is still being referenced.
However, the incrementing of ref count left some objects opened at the end
of the program, perhaps, due to compiler's optimization on cons/destructors. The constructor, that takes an existing id, needs to increment the counter
but it seems that the matching destructor wasn't invoked. The workaround
is to have a function for each class that has "id" that only sets the id
and not increment the ref count for the library to use in these situations.
These functions are "friend" and not public.
The friend functions are:
void f_Attribute_setId(Attribute *, hid_t)
void f_DataSet_setId(DataSet *, hid_t)
void f_DataSpace_setId(DataSpace *, hid_t)
void f_DataType_setId(DataType *, hid_t)
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6 (jam gnu and Intel 15.0)
SunOS 5.11 (emu)
Bring r26639 from autotools_rework branch to trunk:
Switch AC_TRY_RUN macros to AC_RUN_IFELSE macros.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Description: h52gif crashed when it was asked to convert a 24bitimage.
Upon viewing the code, it did not prepare to handle images other than 2 dimensions.
It has no concept of multiple planes images. Further examinations showed past attempts
to fix it ended up removed some abilities (-p or multiple planes, animation, ...) have
been removed but documentation was not updated. Even its online help message still
shows -p is an option.
Solution: added protection code to flag errors if input request is not an
8bit image within size limits. (I don't have enough knowledge of the GIF
format to fix this tool. All I did was plugging known bug from crashing the
program.)
Tested: h5committest.
Description:
Added wrappers for C functions H5P[s/g]et_libver_bounds and wrappers
for getting object header version
// Sets bounds on versions of library format to be used when creating
// or writing objects.
void setLibverBounds(H5F_libver_t libver_low, H5F_libver_t libver_high) const;
// Gets the current settings for the library version format bounds.
void getLibverBounds(H5F_libver_t& libver_low, H5F_libver_t& libver_high) const;
// Returns the object header version of an object in a file or group,
// given the object's name.
unsigned childObjVersion(const char* objname) const;
unsigned childObjVersion(const H5std_string& objname) const;
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6
SunOS 5.11
Remove VPATH and related search path syntax checking.
Remove check for H5_LONE_COLON and checking for lone colon compiler confusion.
tools/h5dump/testh5dumpxml.sh.in
tools/h5dump/CMakeTestsXML.cmake
Remove test skipping for compilers that were formerly confused by lone colon.
Tested with h5committest.
Description:
- Changed DataType::operator= to simply copy the id of rhs instead of
calling H5Tcopy because, when the operator= is invoked, a different
datatype id is created and it won't have the same characteristics as
rhs', specifically, if the rhs represents a named datatype, "this"
would still be a transient datatype.
- Added a DataType constructor that takes a PredType object, and this
constructor will cause H5Tcopy to generate another datatype id, from a
predefined datatype.
- Fixed various mistakes in tests.
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6 (jam/gnu and jam/icc 15)
SunOS 5.11 (emu development/production)
Bring r26651 from autotools_rework branch to trunk:
Remove the VSNPRINTF_WORKS macro, it's working around bugs in old SGI
& HP compilers.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26550 from autotools_rework branch to trunk:
Remove orphaned macro definitions (not attached to anything in the library)
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
in recent versions of glibc, and -D_DEFAULT_SOURCE is the replacement. Keep
-D_BSD_SOURCE for now to support older systems. gcc will not issue a warning
about -D_BSD_SOURCE being deprecated when -D_DEFAULT_SOURCE is supplied as well.
Tested: jam, koala, ostrich (h5committest)
Bring r26549 from autotools_rework branch to trunk:
Remove the BAD_LOG2_CODE_GENERATED macro/define, it's working around bugs
in old SGI compilers.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26545 from autotools_rework branch to trunk:
Remove the WANT_DATA_ACCURACY macro/define/configure option, since it's no
longer attached to any library behavior.
Tested on:
Linux/32 2.6.8 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26543 from autotools_rework branch to trunk:
Remove the LLONG_TO_LDOUBLE_CORRECT macro/define, it's working around
bugs in very old SGI/FreeBSD/Windows compilers.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26513 from autotools_rework branch to trunk:
Remove the LDOUBLE_TO_LLONG_ACCURATE macro/define, it's working around
bugs in older SGI, HP/UX, MacOSX and Windows .NET 2003 compilers.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26546 from autotools_rework branch to trunk:
Convert AC_TRY_RUN to AC_RUN_IFELSE, for the LDOUBLE_TO_LONG_SPECIAL and
LONG_TO_LDOUBLE_SPECIAL checks.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26511 from autotools_rework branch to trunk:
Remove the FP_TO_INTEGER_OVERFLOW_WORKS macro/define, which is for working
around bugs in the Cray X1 compiler and is no longer supported.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26508 from autotools_rework branch to trunk:
Remove HW_FP_TO_LLONG_NOT_WORKS macro/define, it was only addressing
Windows .NET 2003 compiler issues.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26503 & r26528 from autotools_rework branch back to the trunk:
Remove old platform configure files: craynv, dec-flags, hpux11.23,
ia64-linux-gnu, nec-superux14.1, sv1-cray, x86_64-redstorm-linux-gnu
Also remove CONVERT_DENORMAL_FLOAT, since this was only set in the
configure files being removed.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26502 from autotools_rework branch to trunk:
Remove the H5_SW_ULONG_TO_FP_BOTTOM_BIT_WORKS and
H5_FP_TO_ULLONG_BOTTOM_BIT_WORKS macros/defines, as they are no longer used by
supported platforms.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26501 from the autotools_rework branch to the trunk:
Remove ULLONG_TO_LDOUBLE_PRECISION macro/define, as it's targeting bugs
in the FreeBSD and Cygwin compilers.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26500 from autotools_rework branch to trunk:
Remove the LLONG_TO_FP_CAST_WORKS macro/define, as it targets problems with
the Visual Studio 6 compilers.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26499 from autotools_rework branch to trunk:
Remove ULLONG_TO_FP_CAST_WORKS macro/define, as it only applies to older
platforms we aren't supporting any longer.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Bring r26494 from autotools_rework branch back to trunk:
Remove the LDOUBLE_TO_UINT_ACCURATE macro/define, it was addressing
problems with older Intel compilers on Linux that are no longer supported.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for several days)
Bring r26492 from autotools_rework branch back to trunk:
Remove the FP_TO_ULLONG_ACCURATE and FP_TO_ULLONG_RIGHT_MAXIMUM
macros/defines, which were added to address problems with older PGI
compilers and HP-UX systems and are no longer supported.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(daily tested on branch for >1 week)
Bring r26489 from autotools_rework branch to trunk:
Remove the ULONG_TO_FP_BOTTOM_BIT_ACCURATE macro/define, as it was added
for SGI systems and old Solaris systems, which are no longer supported.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested for >1 week)
Bring r26485 from the autotools_rework branch to the trunk:
Remove the ULONG_TO_FLOAT_ACCURATE macro/define, we no longer support the
Sandia system where it was necessary.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(daily tested for >1 week)
Note there are still some code coverage assertions in the selection matching
algorithm - if you hit these try taking them out.
Note make check still fails in h5dump test (unrelated to this checkin).
Tested: ummon
Bring r26483 from autotools_rework branch back to trunk:
Remove INTEGER_TO_LDOUBLE_ACCURATE macro/define - we no longer support
SGI systems.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(daily tested on branch for >1 week)
elements selected with "all" slections nor reset sharing state.
Fix error in H5S__hyper_project_intersection algorithm.
Note there are still some code coverage assertions in the selection matching
algorithm - if you hit these try taking them out.
Note make check still fails in h5dump test (unrelated to this checkin).
Tested: ummon
Remove the VSNPRINTF_WORKS macro, it's working around bugs in old SGI
& HP compilers.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove orphaned macro definitions (not attached to anything in the library)
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove the BAD_LOG2_CODE_GENERATED macro/define, it's working around bugs
in old SGI compilers.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Convert AC_TRY_RUN to AC_RUN_IFELSE, for the LDOUBLE_TO_LONG_SPECIAL and
LONG_TO_LDOUBLE_SPECIAL checks.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove the WANT_DATA_ACCURACY macro/define/configure option, since it's no
longer attached to any library behavior.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove the LLONG_TO_LDOUBLE_CORRECT macro/define, it's working around
bugs in very old SGI/FreeBSD/Windows compilers.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not needed on this branch)
H5Pset_istore_k() will validate the "ik" value to not exceed the max v1 btree entries (2 bytes)
The same check for H5Pset_sym_k() "ik" value.
h5committested.
Remove the LDOUBLE_TO_LLONG_ACCURATE macro/define, it's working around
bugs in older SGI, HP/UX, MacOSX and Windows .NET 2003 compilers.
Tested on:
MacOSX/64 (amazon) 10.10.2 w/serial & parallel
(h5committest not required on this branch)
Remove the FP_TO_INTEGER_OVERFLOW_WORKS macro/define, which is for working
around bugs in the Cray X1 compiler and is no longer supported.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove HW_FP_TO_LLONG_NOT_WORKS macro/define, it was only addressing
Windows .NET 2003 compiler issues.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove old platform configure files: craynv, dec-flags, hpux11.23,
ia64-linux-gnu, nec-superux14.1, sv1-cray, x86_64-redstorm-linux-gnu
Also remove CONVERT_DENORMAL_FLOAT, since this was only set in the
configure files being removed.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove the H5_SW_ULONG_TO_FP_BOTTOM_BIT_WORKS and
H5_FP_TO_ULLONG_BOTTOM_BIT_WORKS macros/defines, as they are no longer used by
supported platforms.
Tested on:
MacOSX/64 10.10.x (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove ULLONG_TO_LDOUBLE_PRECISION macro/define, as it's targeting bugs
in the FreeBSD and Cygwin compilers.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove the LLONG_TO_FP_CAST_WORKS macro/define, as it targets problems with
the Visual Studio 6 compilers.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove ULLONG_TO_FP_CAST_WORKS macro/define, as it only applies to older
platforms we aren't supporting any longer.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Bring r26258 from the autotools_rework branch to the trunk - remove
the LDOUBLE_TO_INTEGER_WORKS macro/define, which was addressing issues with
SGI systems that are no longer supported.
Tested on:
Linux 2.6.x (jam) w/serial & parallel
Daily tested on branch for >2 weeks
Remove the LDOUBLE_TO_UINT_ACCURATE macro/define, it was addressing
problems with older Intel compilers on Linux that are no longer supported.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove the FP_TO_ULLONG_ACCURATE and FP_TO_ULLONG_RIGHT_MAXIMUM
macros/defines, which were added to address problems with older PGI
compilers and HP-UX systems and are no longer supported.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Bring r26257 from autotools_rework branch back to the trunk - removes
the LDOUBLE_TO_INTEGER_ACCURATE macro/define, which was addressing problems
with SGI systems and is no longer supported.
Tested on:
Linux 2.6.x/32 (jam) w/serial & parallel
Daily tested on branch for >2 weeks.
Remove the ULONG_TO_FP_BOTTOM_BIT_ACCURATE macro/define, as it was added
for SGI systems and old Solaris systems, which are no longer supported.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required)
Remove the ULONG_TO_FLOAT_ACCURATE macro/define, we no longer support the
Sandia system where it was necessary.
Tested on:
Mac OSX 10.10.2 (amazon) w/serial & parallel
(h5committest not necessary on this branch)
Remove INTEGER_TO_LDOUBLE_ACCURATE macro/define - we no longer support
SGI systems.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Added tests for I/O on virtual dataset with source datasets in unopened files.
Note there are still some code coverage assertions in the selection matching
algorithm - if you hit these try taking them out.
Note make check still fails in h5dump test (unrelated to this checkin).
Tested: ummon
h5pget_class_f should return hid_t for classtype
Also removed all left over C comment artifacts /* and */ in the Fortran comments.
Tested: h5committest
Also removed disabling shared when building Fortran on the Mac.
These fixes should fix all the building shared with Fortran problems. HDF5-247
Also fixes array bounds starting from zero in H5Pff.f90 routines.
Tested: h5committest
selections.
Add source dataspace extent patching (should allow closing the source file).
Note fill values and various other features are not yet supported.
Note there are still some code coverage assertions in the selection matching
algorithm - if you hit these try taking them out.
Note make check still fails in h5dump test (unrelated to this checkin).
Tested: ummon
Description:
The following two constructors of classes: AbstractDs, IdComponent,
H5Location, and H5Object are no longer appropriate after the data member
"id" had been moved from IdComponent to the sub-classes.
The copy constructors are noop and will be generated by the compilers if
needed so they can be removed in 1.8.15 without effecting applications. The
other constructors will be removed from 1.10 release, and then from 1.8 if
their removal does not raise any problems in at least two 1.10 releases.
<Classname>(const hid_t h5_id);
<Classname>(const <Classname>& original);
Deprecation warnings are added to each of these classes.
The other classes are changed to call the default constructor instead of
one of the constructors above.
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Description:
Fixed base classes that were in wrong order on the prototype lines and
some misc. warnings.
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Description:
Parameter had the same name as the class' member's. Replaced parameter
with a different name.
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Description:
Missing initializing one of the base classes in multiple inheritance.
Added CommonFG() to constructors' prototype.
Platforms tested:
Linux/64 (platypus)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
A detailed error message is emitted if this combination is attempted.
Builders can use --enable-unsupported to build the combo.
Note that default builds will now need to use --disable-hl with
--enable-threadsafe since the high-level library is built by default.
Part of: HDFFV-8719
Tested on: Local Linux w/ various combinations of configure options.
CXX_SHARED_CONDITIONAL does not appear in AM_CONDITIONAL
This was due to a removed AM_CONDITIONAL macro in configure.ac.
The CXX_SHARED_CONDITIONAL code was removed from the Makefile.am
files. Additionally, the C++ shared library build settings field in
libhdf5.settings file was updated.
Tested on: local linux VM w/ C++
--enable-shared --enable-static
--enable-shared --disable-static
--disable-shared --enable-static
Various tweaks for autotools thread-safety and Pthreads support.
- Moved the check for pthread_attr_setscope() into the thread-safe
checks section. Documented its necessity and added a cross-compiling
option and helpful comment.
- Moved the high-level library checks up to the same place where
Fortran and C++ are checked. This will make it easier to handle
threadsafe/high-level combinations later.
- Also changed the default of --enable-pthread to 'check', which is
the same as the old 'yes' behavior where we just check the standard
locations. 'yes' and 'no' are still accepted, though 'no' will
currently produce an error since the autotools only support Pthreads.
Fixes: HDFFV-9087
Tested on: h5committest
jam (w/ threadsafe)
Solaris and OS X.
Added public API functions that expose the C library's memory allocator
for use in filter functions that need to allocate or resize buffers.
Intended for use with filter plugins, particularly on Windows, where C
runtime (CRT) issues can cause problems.
Fixes: HDFFV-9100
Tested on: h5committest + OS X (quail) + Solaris (emu)
Purpose:
Fix HDFFV-9124 - Remove old libtool post-processing
Description:
This revision removes some post-processing of the generated libtool
script, which was added back in 2003 (see svn revisions 6285 and 6293)
to address a deficiency in which the script failed to set the '$wl'
variable for icc and pgcc compilers. Libtool has since fixed the issue,
and the post-processing we've been running has essentially been a no-op
for years, so it's safe for us to remove the post-processing snippet.
Tested:
Jam using pgcc and icc compilers.
H5Rdereference should check for default (HADDR_UNDEF) value and not continue processing and return so that ret value can be checked and handled properly
Tested: jam (gnu)
Since off_t is exposed by the C API, the large file definitions MUST
be exposed so that client code matches the library.
These definitions have been switched back to AM_CPPFLAGS, which is
exported to h5cc, etc. The POSIX and GNU definitions changes from
r26347 have been left as using H5_CPPFLAGS, which is not sent to
h5cc as we don't want to inflict our needs on external users.
Fixes: HDFFV-9152
Tested on: h5committest
columns that are output by svn stat.
Previously, the script assumed that they would all be blank for newly-
added files. This is not always true when merging.
Part of: HDFFV-8895
Tested on: jam (bin/chkmanifest only)
which is where the rest of the #defines reside.
The key difference is that AM_CPPFLAGS is exported to h5cc. These #defines
are not necessary to consume the HDF5 API and it's bad form to inflict
our build configuration on users. In particular, the GNU/POSIX defines
could easily conflict with a user's.
Fixes: HDFFV-9152
Tested on: h5committest
- 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
branch.
Removed the configure option that allows selective disabling of individual
internal filters (fletcher32, shuffle, etc.).
This feature mucked up the code with a lot of #ifdefs, saved very little space,
and was not scalable to a general scheme for library size reduction. We've
decided to remove the feature while we investigate a more general scheme for
decreasing the library size.
Part of: HDFFV-9086
Tested on: h5committest
for use in filter functions that need to allocate or resize buffers.
Intended for use with filter plugins, particularly on Windows, where
C runtime (CRT) issues can cause problems.
Fixes: HDFFV-9100
tested on: jam (minor, localized change)
calls that use a FUNC_ENTER macro that does not include parentheses.
This does not affect any source code at this time.
Part of: HDFFV-9141
Tested on: jam (bin/trace behavior only)
Updates the bin/chkmanifest script so that it parses the output
of svn commands instead of hacking at the .svn/entries file. This
will make the script more future-proof and allows it to work with
current Subversion repositories.
Tested on: jam (bin/chkmanifest only)
It should no longer be necessary to use --enable-using-memchecker
make check fails due to an issue with h5ls apparently unrelated to the merge
Tested: ummon
Revise dataspace encode/decode routines to make them work better with
future virtual dataset feature.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial
(h5committest forthcoming)
Add H5Sis_regular_hyperslab() and H5Sget_regular_hyperslab() API routines,
along with tests.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial
(h5committest forthcoming)
Fix HDFFV-9124 - Remove old libtool post-processing
Description:
This revision removes some post-processing of the generated libtool
script, which was added back in 2003 (see svn revisions 6285 and 6293)
to address a deficiency in which the script failed to set the '$wl'
variable for icc and pgcc compilers. Libtool has since fixed the issue,
and the post-processing we've been running has essentially been a no-op
for years, so it's safe for us to remove the post-processing snippet.
Tested:
Jam using pgcc and icc compilers.
Cleans up time functions in the autotools input files. Removed deprecated
gettimeofday() time zone code and configure processing. Also removed
some unused time function configure checks and defines.
Fixes: HDFFV-9083 and HDFFV-9085
Tested on: 32-bit linux, serial and parallel (jam)
OS X (kite)
Solaris (emu)
- Updated configure.ac so that the direct VFD can now be built
without specifying _GNU_SOURCE, etc. on the command line.
- The direct VFD is now disabled by default. It was previously
enabled, but the configuration script couldn't configure it
properly, making it a moot point.
Fixes: HDFFV-9057, HDFFV-7567, HDFFV-9088, HDFFV-7566
Tested on: h5committest
jam w/ direct VFD (*very* slow!)
NOTE: platypus cmake fails, but this is not a new error.
Removes the --with-default-vfd option from configure. This was basically
useless and only allowed selecting the stdio VFD. Since this is a demo
VFD and not really a production VFD, we decided to retire this option.
Fixes: HDFFV-9081
Tested on: h5committest
NOTE: platypus cmake fails, but this is not a new error.
by default (unlike the trunk and 1.8 branches, where it's disabled
by default).
Users can build with --disable-maintainer-mode to remove autotools
build dependencies.
Part of: HDFFV-9122
Tested on: 64-bit linux VM (configure and autogen only)
Remove LDOUBLE_TO_INTEGER_WORKS macro/define from configure/library/tests,
since it was added to support non-standard behavior on SGI IRIX & HP-UX, which
we don't support any longer.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
Remove the LDOUBLE_TO_INTEGER_ACCURATE macro, since it was added to work
around non-standard behavior on SGI IRIX, which we are no longer supporting.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial
(h5committest not required on this branch)
unsupported Code Warrior compiler. Also removes the H5_NO_SHARED_WRITING
symbol from the pubconf file.
Fixes: HDFFV-9080
Tested on: jam only, after bin/reconfigure
(all platforms should see no source changes)
Adds a comment to configure.ac indicating that Cygwin still has
problems with srcdir and time.
Fixes: HDFFV-9082
Tested on: jam (comment only change) w/ bin/reconfigure
Switch from enum H5D_CHUNK_BTREE to H5D_CHUNK_IDX_BTREE, along with a couple
of minor whitespace touchups.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial & parallel
Linux/32 2.6.x (jam) w/serial
Fix locking error when splitting root node of v1 B-tree, and simplify
the iteration over entries in a v1 B-tree (avoiding using the sibling pointer
also).
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial & parallel
Linux/32 2.6.x (jam) w/serial
Track the min & max keys for a v2 B-tree, so it can more efficiently
determine if a key is present in the B-tree.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/parallel & serial
Linux/32 2.6.x (jam) w/serial
- Remove Infering parallel compilers (C and Fortran) from configure.ac
- Remove restriction to build shared with parallel
- Cleanup parallel sections in configure.ac
- remove large file support checks
- MPE fixes.
tested with h5committest.
Long time ago, the tr command in some platform does not work properly and this test was added
to detect broken tr and abort the configure process.
We are not aware of such broken tr command in current systems and decided to retire this test.
The setup of ${TR} is still needed as it is used to process DEBUG_PKG.
Tested: h5committested plus using "./configure --enable-debug=all" in jam.
Long time ago, the tr command in some platform does not work properly and this test was added
to detect broken tr and abort the configure process.
We are not aware of such broken tr command in current systems and decided to retire this test.
The setup of ${TR} is still needed as it is used to process DEBUG_PKG.
Tested: in jam using "./configure" and "./configure --enable-debug=all".
when available. Also added the --copy option to to libtoolize
so files are copied and not symlinked.
Part of HDFFV-9114
Tested on jam.
- autogen.sh -p
- configure (out-of-source)
- Modified configure.ac
- Re-run autogen.sh -p
- Re-run configure
- make
Without the fix, make fails when it notes out-of-date autotools
files and re-runs the tools, picking up jam's elderly versions.
With the fix, make succeeds.
H5D__link_chunk_collective_io. This would occur when performing collective I/O
on a dataset with only 1 chunk, and a participating process had nothing to read
or write.
Tested: jam, koala, ostrich (h5committest)
been permanently deleted. I've not removed all the generated
files from the MANIFEST, though, since I'm waiting on a decision
as to whether we leave those in or not.
Tested on: bin/chkmanifest after running autogen.sh
installing the autotools via a package manager like Homebrew since
they are not installed with XCode.
Part of: HDFFV-9114
Tested on: OS-X 10.10.2 (Yosemite) with XCode 6.1.1
bin/genltanalyze script, which has been deleted. Also removed the
generated hl/src/H5LTparse.c/h and H5LTanalyze.c files.
Part of: HDFFV-9120
Tested on: Local Ubuntu VM
the -s option from autogen.sh. Removed several generated H5E
files from version control as well as H5version.h since these
will always be regenerated.
Part of: HDFFV-9120
Tested on: Local Ubuntu VM
- Modified autogen.sh to run libtoolize.
NOTE: OS-X often uses glibtoolize. This will be fixed soon.
- Addational helpful output added to autogen.sh.
Part of HDFFV-9120
Tested on: 64-bit Linux VM
Removed restiction of disabling shared libraries on the MAC, H5_FORTRAN_SHARED was replaced with HAVE_SHARED_CONDITIONAL since H5_FORTRAN_SHARED was removed.
tested: jam
Developers will now have to run bin/reconfigure (deprecated, will be removed
soon) or autogen.sh after checking out code.
Part of: HDFFV-9120
Tested on: jam with Fortran and C++
Developers will now have to run bin/reconfigure (deprecated, will be removed
soon) or autogen.sh after checking out code.
Part of: HDFFV-9120
Tested on: jam with Fortran and C++
- Results of O_DIRECT and posix_memalign() checks are now
output so users can more easily diagnose problems.
- Configure now fails if --enable-direct-vfd was requested
but either O_DIRECT or posix_memalign() are not
present.
Part of HDFFV-7566
Tested on: jam (configure only)
to build and run a program using it, which is problematic (depends on
file system, issues with cross-compiling).
Part of HDFFV-9057
Tested on: jam (configure only)
Fortran and C++ are checked. This will make it easier to
handle threadsafe/high-level combinations later.
Also changed the default of --enable-pthread to 'check' and
removed yes/no behavior. If you ask for thread-safety, you
can't disable Pthreads...
Part of HDFFV-8719
Tested on: jam (configure only)
section. Documented its necessity and added a cross-compiling option
and helpful comment.
Also removed a check for BSDgettimeofday from configure.ac, which
was for Irix 5.3 support.
Part of HDFFV-9087
Tested on: jam with threadsafe
405-408::fortran vars should be scoped
Scoped:
HAVE_SIZEOF
HAVE_C_SIZEOF
HAVE_STORAGE_SIZE
FORTRAN_DEFAULT_REALisDBLE
to where the tests are (in m4/aclocal_fc.m4)
Tested: jam (gnu)
4159:: Check if Fortran's default real is double precision. If it is and HL is being built then configure should fail due to bug HDFFV-889.
Fix:
This check should be located where HL is check for, and it is. Updated the comment to elimenate confusion.
Change AC_TRY_RUN TO AC_TRY_COMPILE
Changed all the instances of AC_TRY_RUN for the Fortran and C++ tests to use
AC_COMPILE_IFELSE and moved all the tests to new files in m4 directory:
aclocal_cxx.m4 (for C++ tests)
aclocal_fc.m4 (for Fortran tests)
tested: jam
are defined. The former is for posix_memalign() and the latter for
the O_DIRECT flag for open(). Both are for direct VFD support.
Fixes HDFFV-9088
Tested on: jam
CodeWarrior as a work-around to broken open() functionality (it's not clear
which version). The only effect of this #define was to cause test_file_close()
in test/tfile.c to be skipped.
Fixes HDFFV-9080
Tested on: jam
We don't have CodeWarrior, so I just ensured the deletion didn't adversely
affect a typical build.
HDFFV-9049
Intel 15.0 15.0.1 Fails with --enable-fortran2003
Added BIND to the Fortran 2003 functions.
Tested: windows (tested concept)
linux (--enable-fortran and --enable-fortran2003)
-----------------------
Remove the numbers in the comments associated with:
H5G_UNKNOWN_F (-1)
H5G_LINK_F 0
H5G_GROUP_F 1
H5G_DATASET_F 2
H5G_TYPE_F 3
These should not be defined as a number since they can changed. They should be considered named parameters, not actual values.
HDFFV-9040
h5rget_object_type_f returns different types than indicated by API
H5O_MSG_FLAG_FAIL_IF_UNKNOWN_AND_OPEN_FOR_WRITE. Will add a new
H5O_MSG_FLAG_FAIL_IF_UNKNOWN_ALWAYS with the new avoid_truncate patch
coming later.
tested h5committest
Last changes had caused problems with Windows platform:
1. H5private.h in io_timer.h is not accessible in the distributed shared library of tools.
Need to move it to io_timer.c.
2. debug_start_stop_time() would not be available outside of h5perf. Some favor of compiler
does not like it. Screened it out for now.
3. mere "extern" is not good enough for Windows shared library. Must mark them as DLL. Need to mark them as
"H5TOOLS_DLL".
4. STANDALONE mode is broken. Screened out the code for now.
Tested; h5committest.
Move timing measurement routines used by h5perf and h5perf_serial to tools/lib
so that they can be used by other tools too.
tools/lib/io_timer.c
tools/lib/io_timer.h
tools/perform/io_timer.c
tools/perform/io_timer.h
renamed perform/io_timer.[ch] to lib/io_timer.[ch]
tools/lib/Makefile.am
tools/lib/Makefile.in
tools/lib/CMakeLists.txt
tools/perform/Makefile.in
tools/perform/Makefile.am
tools/perform/CMakeLists.txt
MANIFEST
updated due to the move.
Tested; h5committest and jam (serial)
tools/perform/sio_timer.h:
tools/perform/pio_timer.c:
tools/perform/io_timer.h:
tools/perform/io_timer.c:
Renamed pio_timer.[ch] as io_timer.[ch];
merged content of sio_timer.[ch] into io_timer.[ch] so that both h5perf and h5perf_serial
call the combined io_timer.[ch].
Moved the debug printing code segment in set_time() in [sp]io_timer.c to as debug_start_stop_time() in [sp]io_perf.c where it belongs.
Screened out set_timer_type() and get_timer_type() which were not used by any code.
tools/perform/Makefile.am:
tools/perform/Makefile.in:
tools/perform/CMakeLists.txt
Adjusted to use io_timer.c for both h5perf and h5perf_serial.
tools/perform/pio_perf.c:
tools/perform/sio_perf.c:
tools/perform/pio_perf.h:
tools/perform/sio_perf.h:
Renamed [sp]io_time_destory() to same io_time_destroy();
Moved the debug printing code segment in set_time() in [sp]io_timer.c to as debug_start_stop_time() in [sp]io_perf.c where it belongs.
tools/perform/pio_engine.c:
tools/perform/sio_engine.c:
Removed #include io_timer.h since it was already #include by [sp]io_perf.h.
MANIFEST:
Updated the merge of [sp]io_timer.[ch] into io_timer.[ch].
Tested: h5committest and jam in extra.
Clean up EOF code within library and add 'mem_type' parameter to 'get_eof'
VFD callback, to avoid various ambiguous situations, particularly with the
multi VFD. (Supports changes for 'avoid_truncate' feature also)
Tested on:
MacOSX/64 10.10.1 (amazon) w/serial & parallel
h5committest forthcoming
Minor code cleanups found while reviewing 'avoid_truncate' changes.
Tested on:
MacOSX/64 10.10.1 (amazon) w/serial & parallel
(too minor to require h5committest)
Benchpar.c is retired/deleted. If it is ever needed, it can be retrieved from the SVN repository
or even previous version of HDF5 source code.
Tested: jam parallel make passed.
Minor code cleanups found while reviewing 'avoid truncate' branch.
Tested on:
MacOSX/64 10.10.1 (amazon) w/serial & parallel
(too minor to require h5committest)
Minor code/comment cleanups, found while reviewing 'avoid truncate' code.
Tested on:
MacOSX/64 10.10.1 (amazon) w/serial & parallel
(Too minor to require h5committest)
Fix cmakehdf5 so that it can figure out where the source directory is.
It expects cmakehdf5 itself resides at $srcdir/bin/cmamkehdf5.
Tested: Jam by invoking cmakehdf4 with different paths.
different language API's and testings. See "cmakehdf5 --help" for details.
Tested: jam using different combinations of option and verified correctness
by inspeacting libhdf5.settings output.
Previously, ph5diff may hang in a test in Linux 32 platform(HDFFV-587).
No solution was available and a patch to bypass the test is implemented.
Since the company is changing domain name soon, the patch would not be valid any more.
Tests were done (repeat 100 mpiexec -np 6 ./ph5diff -v h5diff_hyper1.h5 h5diff_hyper2.h5)
and the previous hanging problem did not occur. It is likely the newer versions of
mpich no longer have this problem. Therefore, it is decide to remove this patch
to make the test script cleaner, if nothing else.
Tested: ran build and test in Jam (linux 32) and the repeat 100 command mentioned above.
All passed.
Revert r25273, 25283 & 25439 (the hyperslab improvement changes). They
are buggy and it's taking me a long time to correct the problem. I'll check
in a revised form of the changes when I've got them straightened out.
Tested on:
Mac OSX 10.10.0 (amazon) w/gcc 4.9.x, C++, FORTRAN
Linux 2.6.x (jam) w/parallel
script. The warnings that this generates cannot easily be resolved in
platform-independent C code since gnu expects the non-standard (gnu)
'D' suffix for double constants.
It's still technically useful for catching float and long double
constants, but should probably be enabled by developers on an
as-needed basis for that purpose so the spurious warnings are
avoided.
Tested on a local linux VM with gcc 4.8.2. This is a very minor change.
Discovered when I temporarily #defined HDfree() to a more complicated
function while investigating something.
Tested on a local linux VM. This is a very minor change.
but the test was not changed (still doing H5A_create(...) < 0).
Fixed the error by changing to compare against NULL.
Tested: ADA AIX machine where the old code was flagged as an error by the AIX compiler.
Did not provide default values for clang++ options.
Also, applied wrong values for the *_CPPFLAGS.
Solution:
Added default values for *_CXXFLAGS.
Fixed the *_CPPFLAGS values.
Tested: wren with and without --enable-production.
Description:
Added notes regarding UTF-8 and extended ASCII, provided in HDFFV-8899,
to C++ API.
Platforms tested:
Linux/32 2.6 (jam) - only in comments
Description:
Mac has changed to use the clang/clang++ compilers but compiler settings for production, debug and profile
were not setup.
Solution:
Setup default values for PROD_CFLAGS, PROD_CPPFLAGS, DEBUG_CFLAGS, DEBUG_CPPFLAGS.
PROFILE_CFLAGS and PROFILE_CPPFLAGS were set too but clang does not -pg or such for
profiling. Need to fix it later.
Tested: duck, swallow, and quail using --enable-production.
Removed the try/block with new/bad_alloc that were unintentionally
committed previously.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Description:
Followed hints on the JIRA issue to remove several potential memory
leaks.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Description:
- Used H5I_INVALID_HID instead of 0 to initialized member "id" in classes
that represent HDF5 objects. For PropList, H5P_DEFAULT has to be used
instead of H5I_INVALID_HID.
- Added try/catch block to some dynamically allocating memory code and
re-throw the bad_alloc exception with a message informing the location of
the failure.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Description:
H5F_ACC_CREAT was included in the C++ API while the C library doesn't
allow it yet. Possibly, in the future, but not now. In addition, the
two flags H5F_ACC_RDONLY and H5F_ACC_RDWR were missing from the
documentation, causing confusion that appending is not supported.
Solution:
- Removed H5F_ACC_CREAT from the function until the C library support it
- Added H5F_ACC_RDONLY and H5F_ACC_RDWR to the comments to update the
documentation
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
as NULL. The library is supposed in that case to equally divide the
address space among all members, but there was a bug causing an
overflow in the assignment.
tested with h5commitest
H5Pset_core_write_tracking(). This ensures that the behavior
matches the description in the reference manual.
Tested on a local linux VM. This is a very minor change.
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)
testfrome.c has incorrectly exit code (using -1). Fixed by replacing them
with C defined EXIT_FAILURE. Verified by temporary decreaing MAXNUMTESTS
to introduce failure in testhdf to see the changed code did work.
Also replaced all other correctly coded exit codes with the C defined
EXIT_SUCCESS and EXIT_FAILURE. This would help portability for non-Unix
systems.
Tested: h5committest.
Minor tweaks to updated hyperslab code, before larger revision coming.
Tested on:
Mac OSX/64 10.9.3 (amazon) w/gcc 4.9 & parallel
(h5committest forthcoming)
uninitialized variable bug in passing.
Added the H5C_get_entry_ptr_from_addr() and H5C_verify_entry_type()
in H5C.c, along with their pass through functions in H5AC.c. Note
that H5C_get_entry_ptr_from_addr() is quite slimey, and should be
avoided if possible.
Updated fractal heap to use flush ordering to force children
in the hdr / iblock / dblock tree to be flushed prior to parents.
This is part of a port of the fractal heap to the V3 cache, although
I gather that it will also be useful for SWMR.
Added sanity checking code to the fractal heap to verify that direct
blocks are flushed before their parent indirect blocks, child indirect
block are flushed prior to their parent indirect blocks, and that the
root iblock or dblock is flushed prior to the header
Tested on:
Jam: Serial and parallel
Phoenix (Debian): serial, debug and production
amazon (MacOS): serial
HDFFV-8653
replace non-standard sizeof in the fortran tests with c_sizeof
(1) Removed the overloaded h5_sizeof functions for characters and integer arrays since Sun compilers don't allow them to be passed into a function that uses sizeof.
(2) Requested min. precision for reals to avoid duplicate interfaces when the flag -r8 (or equiv.) is set.
tested:
*jam: intel, -i8 -r8 --enable-fortran2003
*jam: pgi, --enable-fortran2003
*emu: sun, --enable-fortran2003
Correct error in new hyperslab selection test to use the right # of
dimensions for start/stride/count/block arrays. Also, switch H5Sselect_select
to H5Smodify_select.
Tested on:
MacOSX/64 10.9.3 (amazon) w/gcc 4.9.1, OpenMPI, C++, FORTRAN & threadsafe
(Too minor to require h5committest)
Bring in Chao/Neil/my changes to optimize hyperslab selection operations
further, along with 3 new public API routines: H5Scombine_hyperslab(),
H5Sselect_select() and H5Scombine_select(), along with many minor cleanups to
the code and fixing a few compiler warnings.
Tested on:
Mac OSX/64 10.9.3 w/gcc 4.9.x and parallel w/OpenMPI
(h5commttest forthcoming)
Bring changes from Coverity branch back to trunk:
r20914:
Use HDstrncpy and HDstrncat! --gh
20915:
Use HDstrncpy and HDstrncat! --gh
Tested on:
Mac OSX/64 10.9.3 (amazon) w/gcc 4.9.0, C++, FORTRAN & parallel
(too minor to require h5committest)
Merge changes from Coverity branch to trunk:
r20907:
Original issue was #338.
Refactored code to clean up allocations consistantly, completely, check all returns, assign initialization values and handle errors.
Tested on:
MacOSX/64 10.9.3 (amazon) w/gcc 4.9, FORTRAN, C++, parallel & multi-threaded
(too minor to require h5committest)
Set OUTPUT_DIRECTORY to cpplus_RM and HTML_OUTPUT to '.' because
they were reset by accident causing "bin/release doc" to fail.
Ran bin/release to verify the failure was gone.
Bring changes from hdf5_1_8_coverity branch back to trunk:
r20878:
Issue 76: Check if H5Tget_nmembers(type) fails and simply return(FALSE). Also move printf to after check.
r20880:
Issue 192: Create ret_val var set to -1. Add out label for failures to jump to, return ret_val at bottom.
r20882:
Fixes for coverity:
1) bug #1679: remove dead code in test/mf.c
2) bug #1680: remove dead code in tools/lib/h5diff_dset.c
r20883:
Fix coverity issue 585
Description:
Changed variable "c" in processStrData in h5import.c to an int, to match fgetc
return value, and removed call to feof, instead checking if c == EOF.
Tested on:
MacOSX/64 10.9.3 (amazon) w/C++, FORTRAN & parallel
(too minor to require h5committest)
The temporary directory used by zip is the same as the rest but it has to be different.
Changed tar2zip to use a different (ztmpdir) name.
Tested: by hand running "bin/release ... gzip zip md5".
Made printError() virtual as the original; missed it from the previous fix.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
ib files. The fix also removed dependencies on libhdf5, etc. when the --disable-sharedlib-rpath co
nfigure option was invoked.
Added instead configure variable hardcode_into_lib=no. This removes rpath from lib files on Linux
and solaris machines.
Tested with h5committest on jam, koala, ostrich and platypus (cmake), and with configure option --disable-sharedlib-rpath on emu, platypus and quail.
- Put back Exception::printError for backward compatibility
- Added static member function Exception::printErrorStack to print
error stack without an instance of Exception.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Make progress toward moving from DXPL IDs to property list structures
within the library. Also move the signature location code from the H5F
package to the H5FD package, where it's a better fit. Also, clean up some
more compiler warnings along the way.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(h5committest forthcoming)
Need to unify Windows release process (zip file) and Unix release process (bin/release-> tarfile)
Solution:
Added a new option (zip) to generate Windows zip file from the release tarball.
Tested: by hand running "bin/release ... gzip zip" to verify zip file looks right.
Allen and Dana then confirmed the zip file can be used to build and test HDF5
library without error.
More migration to using H5F_io_info_t pointers and away from using
property list IDs internally. Also, clean up some compiler warnings in the
cache code.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(h5committest forthcoming)
Introduce "file I/O info" struct, to hold file & dxpl pointers, and start
propagating up through library.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(h5committest coming)
Begin process of migrating from using property list IDs internally to the
library to using the internal generic property list data structure.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(h5committest forthcoming)
h5diff issues "unable to read attribute" error message when comparing two files
Description:
h5diff did not handle attributes of variable length strings correctly. It created the wrong memory type if one but not both compared attributes are of the variable strings type. It ended in H5Aread() failure.
Solution:
We decided to treat the case when one type is variable length string and the other is not as incomparable. That bypassed the above error. We still need to figure out the proper way, if possible, to compare variable string with non-variable string types.
Tested: h5committested plus tested in Swallow (OS X 10.8).
Put back overloaded functions for backward compatibility:
- were replaced by better prototyped versions, such as Attribute::getName.
- were modified to add const to constant arguments.
Added notes for future removal in documentation.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Reviewed and revised version information for unix daily tested machines in supported a
d tested platforms sections.
Added description of LD_LIBRARY_PATH change to configure and using scripts to compile
nd run installed example files to Bug Fixes/Configuration section.
Text change only.
core VFD paging changes were brought over.
Tested on:
32-bit LE linux (jam)
64-bit LE linux (koala)
64-bit BE linux (ostrich)
All were tested with HDF5_DRIVER set to "core_paged".
- Fixed a few comments that Doxygen gave warnings on.
- Removed stylesheet from configuration so Doxygen will use the default
stylesheet and removed the CLANG-related lines to eliminate another
error since we're not using that feature, so the lines should not
present. (from cpp_doc_config)
Platforms tested:
Linux/32 2.6 (jam) - only changing comments
Updated configuration file to use Doxygen 1.8.5 properly.
Verified with Doxygen 1.8.5 on Jam, using bin/release.
After committing, this will be checked out and verified
again to make sure.
h5diff segfaults with user's files
Solution:
Added a variable to indicate if real data are in the buffer and will call H5Dvlen_reclaim()
only when real data are in the buffer.
Tested: with the user provided data files and no more segmentaion fault.
Also h5committ tested.
For make installcheck, compile and run installed examples using the installed scripts. They were being compiled but not run.
Add Fortran2003 examples to the run-ex-fortran script when fortran2003 is enabled.
Set flag to -O3 in production mode for Intel compilers other than those with specified other settings.
Gentoo patches:
Remove unnecessary setting of LD_LIBRARY_PATH from configure.
Prevent potential array subscript out of bounds error in perform/pio_engine.c and sio_engine.c.
Tested with h5committest on jam, koala, ostrich and platypus, on emu and kite, and parallel tests on jam, koala and platypus with mpich built with gnu 4.8.2 and with intel compilers.
Adds write tracking to the core VFD, which can be configured
via the H5Pset/get_core_write_tracking() API call. When enabled
and writing to the backing store is enabled, this feature will
track writes and only write out the changed bytes on flush/close.
Tested on:
32-bit LE linux (jam) w/ Fortran and C++
64-bit BE linux (ostrich)
64-bit Darwin 12.5.0 (kite)
All were tested using the core VFD w/ paging on (core_paged
in the VFD list). Make check-vfd was also tested on jam.
AIX compiler complains that:
ex_ds1.f90, line 89.16: 1512-050 (W) Field separator is missing, in literal FMT specifier, after edit descriptor X. A comma is assumed.
Line 89:
WRITE(*,'(/,5X 3(A,1X),I0,A,L1)') 'Is',TRIM(DS_1_NAME),&
Solution:
Added the missing comma after "5X".
Tested:
AIX system.
- Added wrappers to H5Object for H5Iget_name() to get object's name
ssize_t getObjName(char *obj_name, size_t buf_size = 0) const;
ssize_t getObjName(H5std_string& obj_name, size_t len = 0) const;
H5std_string getObjName() const;
- Added tests tobject.cpp
- Added to various cleanup_* functions in tests to remove generated files
- Added an overload H5I_type_t getHDFObjType() to get object's type
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu) with gmake
and examples.
Platforms tested: Manual testing in place and using srcdir on jam, platypus, and emu with default and
PGI, Intel and new GNU compilers. ifort compiler was also tested with -i8 and -r8 flags
on jam. CMake tested on jam.
Fixes HDFFV-8518, HDFFV-8699
As a part of these changes, the thread-safe + static library options are declared unsupported since the solution relies on DllMain. A solution for the static library is probably doable, but requires much more complicated surgery and has been deferred to HDF5 1.8.14.
Tested on:
64-bit Windows 7 using VS 2012 (changes only affect Windows)
- Overloaded Atribute::getName to take a char* for the attribute name:
ssize_t Attribute::getName(char* attr_name, size_t buf_size)
- Switched the arguments in this function:
ssize_t getName(size_t buf_size, H5std_string& attr_name)
so it became:
ssize_t getName(H5std_string& attr_name, size_t buf_size)
The second argument is default to 0, and can be skipped.
- Removed this function:
H5std_string getName(size_t buf_size); it'll collide with the
first function when that function takes a NULL for the first
argument, and uses default value for the second argument.
- Added more tests
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
functions that return library-allocated memory. The test and tool
code were modified to use this new function where it's appropriate.
Fixes HDFFV-7710, HDFFV-8519, and HDFFV-8551
Tested on:
64-bit Windows 7 w/ VS2012
32-bit LE linux w/ parallel and fortran (jam)
32-bit LE linux w/ fortran and C++ (jam)
Description:
Added CompType::setSize(size_t size) to set size for compound data type
as H5Tset_size had been changed.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Clean up more compiler warnings, plus merge a few Coverity bug fixes from
the hdf5_1_8_coverity branch back to the trunk:
r20877:
Purpose: Fix coverity issue 1723
Description:
Modified test_generate in hl/test_image to close file "f" before exit, even if
an error occurs.
r20879:
Issue 63: change check of return of H5Tget_nmembers to <=0. No need to go
futher if call fails as well as empty.
r20881:
Coverity #659 in Run 46: I changed the Line 442 where it tries to check whether
FLAG_PRINTED is TRUE. But it had just been set to FALSE. I took out the
condition check in the print statement.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & Parallel
(too minor to require h5committest)
- Added a null terminator to the comment returned from the C call, in
getComment methods
- Some minor cleanup
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
Linux/64 2.6 (platypus)/PGI compilers
- Added another overload for char* argument:
ssize_t getComment(const char* name, const size_t buf_size, char* comment)
- Changed default value to 0 for the other two getComment methods
- Added HDmemset to after every char string allocation to clear the buffer
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
Linux/64 2.6 (platypus)/PGI compilers
Remove all traces of MPI-POSIX VFD and GPFS detection/code.
Remove remaining traces of stream VFD.
Remove testpar/t_posix_compliant test (it's not actually verifying anything).
Clean up H5D__mpio_opt_possible() further.
Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).
A few other small code cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
be found in the standard include and library paths.
Tested on:
32-bit LE linux (jam)
SunOS 5.11 (emu)
64-bit Darwin 12.5 (kite)
64-bit FreeBSD 8.2 (freedom)
Testing focused on making sure that Pthreads could be found on different
platforms and investigating the interaction of Fortran/C++/thread-safe
options.
Description:
Applied patch from user Jason Newton. JIRA issue HDFFV-8623, patch
9, improve c++ compatibility with exceptions. All additions of "throw()"
are included. Exception::what() is not added because it is not necessary.
It was suggested for the name, which follows stdlib.
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
Linux/64 2.6 (koala)/PGI compilers
KitWare recommendations: Change CMake commands to lower case.
Bump up CMake minimum versions.
Split test file into separate file for h5repack test.
Tested: local linux
KitWare recommendations: Change CMake commands to lower case.
Bump up CMake minimum versions.
Split test file into separate file for h5repack test.
Tested: local linux
Brought changes from Coverity branch back to trunk, and cleaned up misc.
other warnings & formatting issues:
r20833:
Fixed Coverity 667 and 668 with real integer overflow tests this time.
r20834:
Use HDstrncpy and HDstrncat. --gh
r20835:
Change to use strncpy - use base_len + 1 for line 156, use HDstrlen(path) + 1 for line 159
r20836:
Fixed coverity 585 by casting output of fgetc() to a char.
r20837:
Changed sprintf calls to snprintf with size 1 less than the allocated buffer to address coverity issue #967.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(too minor to require h5committest)
Rename GCC_DIAG_OFF/ON macros to H5_GCC_DIAG_OFF/ON and move from
src/H5private.h to src/H5public.h. Wrap typedef of hsize_t and hssize_t
in DIAG_OFF(long-long) macros.
Clean up a bunch of "macro '-' is unused" warnings.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/gcc 4.8.2, C++, FORTRAN, parallel
(too minor to require h5committest)
Check in Mohamad's changes to support collective I/O on point selections,
along with some other minor cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
(h5committest forthcoming)
assertion failure in fheap test (in test that is expected to fail cleanly).
Fix type in H5detect.c
Tested: ostrich, platypus (h5committest - jam and koala having issues)
h5committest failed in platypus because cmakehdf5 failed in installation because cmake generates
a install-tarball based on incomplete version number (subrelease string is missing).
Solution:
Fixed $HDF5_PACKAGE_VERSION to contain the subrelease string.
Fixed $HDF5_PACKAGE_VERSION_STRING to be the same as $HDF5_PACKAGE_VERSION.
Tested: jam and platypus in both trunk and v18 branches because the current
version number is trunk has a null sub-release and v18 has a non-null sub-release.
That covers both grounds.
Revert change of sprintf -> snprintf, due to failures on Windows. We'll
need to figure out the correct course of action in the future.
Tested on:
MacOSX/64 10.9.1 (amazon) w/C++, FORTRAN
(too minor to require h5committest)
Revert some earlier usage of strncpy, which was incorrect.
Bring Coverity changes from branch back to trunk:
r20821:
Use HDstrncpy. --gh
(Fixed already, with strdup)
r20822:
(Not merged, incorrect use of HDstrncpy())
r20823:
(Not merged, incorrect use of HDstrncpy())
r20824:
Maintenance: Bug fix: addressed CID 666.
Value stored at *expression_len should be used in the call to
HD5packFstring to avoid overflow (and unnecessary arithmetic
calculation and casting)
r20825:
Issue 642: Added check for error and handler with print to stderr and exit.
r20826:
Undo revision 20818, as that issue has already been fixed in the 1.8 branch
and trunk (but not coverity branch)
r20827:
(Not merged, incorrect use of HDstrncpy())
r20828:
Use HDstrncpy. --gh
(Corrected use of strncpy())
r20829:
Check return of H5Lget_val(print_udata->fid, path, targbuf,
linfo->u.val_size + 1, H5P_DEFAULT) and if error set trgbuf[0] to 0.
Check if H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL,
&filename, &objname) was successful and allow print. Otherwise filename
and objname are not created. (init those to NULL)
r20830:
resolved coverity issues 939, 940, 941, 944, and 947.
all were complaints about use of sprintf, and in all cases, the
buffers used were large enough for all eventualities.
Resolved issue by replacing calls to sprintf with calls
to snprintf.
r20831:
Maintenance: Addressed CID 852
Replaced sprintf with snprintf
r20832:
Purpose: Fix valgrind issues with hl/examples/ex_image2
Description:
Modified hl/examples/ex_image2 to free global "gbuf" before exit.
Tested on:
Mac OSX/64 10.9.1 (amaon) w/C++, FORTRAN & Threadsafety
(too minor to require h5committest)
view objects. The addition of view objects in the fastforward project
is expected to be brough into the trunk sometimes in the future, which
is why we need to make this change.
Tested Manually on Jam and Ostrich.
Tested with h5commitest - Koala with intel compilers failed, but nothing had to do with those changes.
error on Koala: error while loading shared libraries: libirng.so
Fix for HDF5/HDFFV-8620 H5Rget_name with NULL name parameter fails.
The name parameter now excepts NULL, in which case the length of then
name is returned.
Tested: jam (intel and gnu)
or 2 processes.
First bug is in testpar/t_mdset.c, where the test reports an error in
addition to skipping the test if there are less than three procs. Fix
to just skip the test.
Second bug is in testpar/t_dset.c in actual_io_mode tests, where
incorrect expected value for IO mode was set if the number of procs
running the test is 1.
tested with h5committest.
Changed to use the quick steps described in INSTALL_CMake.txt.
Previous version is available by --old.
Added a help page to explain how to use.
Added a fix to figure out the current HDF5 version and use that to find the
correct file for install. (Still need to figure out the platform name.)
Tested: Jam and Koala
Bring r24479 from 1.8 branch to trunk:
Fix ph5diff worker command handling so it can correctly respond to
situations where there's no work to perform. Also, a few minor code cleanups.
Tested on:
Mac OSX/64 10.9.0 (amazon) w/parallel
(too minor to require h5committest)
Remove duplicate "intent" flags from top & shared file structures, leaving
them only in the shared file structure.
Tested on:
Mac OSX/64 10.9.0 (amazon) w/gcc 4.8, both parallel & serial
(too minor to require h5committest)
The h5dump tests only looked at headers and never the data. Data reads would fail with invalid number of params (7 expected 20).
Regenerated file and replacement ddls updated.
New h5dump test will be added to read the data.
behind by "make distclean" (see below); modified appropriate Makefile.am files and ran
bin/reconfigure to create Makefile.in to fix the problem.
Here is the list of the files "make disclean" doesn't remove:
tools/h5dump/testfiles
tools/h5repack/testfiles/h5diff_attr1.h5
tools/h5repack/testfiles/tfamily00000.h5
tools/h5repack/testfiles/tfamily00010.h5
tools/h5repack/testfiles/tfamily00002.h5
tools/h5repack/testfiles/tfamily00004.h5
tools/h5repack/testfiles/tfamily00006.h5
tools/h5repack/testfiles/tfamily00008.h5
tools/h5repack/testfiles/tfamily00001.h5
tools/h5repack/testfiles/tfamily00003.h5
tools/h5repack/testfiles/tfamily00005.h5
tools/h5repack/testfiles/tfamily00007.h5
tools/h5repack/testfiles/tfamily00009.h5
tools/h5jam/testfiles/h5jam-ub-nohdf5.txt.err-sav
tools/h5jam/testfiles/h5jam-help.txt.err-sav
tools/h5jam/testfiles/h5unjam-help.txt.err-sav
tools/h5jam/testfiles/h5jam-ub-nohdf5.txt.out-sav
tools/h5jam/testfiles/h5jam-help.txt.out-sav
tools/h5jam/testfiles/h5unjam-help.txt.out-sav
hl/fortran/test/dsetf5.h5
c++/test/tattr_multi.h5
c++/test/tattr_scalar.h5
c++/test/tfattrs.h5
c++/test/tattr_basic.h5
c++/test/tattr_compound.h5
c++/test/tattr_dtype.h5
Tested on jam and emu in place and using srcdir with the svn stat command.
This fix doesn't address two problems:
tool/h5dump/testfiles directory is not removed by "make distclean" and it should be
tools/misc/testfiles directory is removed by "make distclean" and it shouldn't be
exclusively.
Part of the preparation for a fix for HDFFV-8551.
Tested on:
32-bit LE linux (jam) w/ parallel and Fortran.
There are no behavior changes, so testing was minimal.
Prep work for adding a memory free function, part of HDFFV-8551.
Tested on:
32-bit LE linux (jam)
* with C++, Fortran
* with thread safety on
These are minor changes (almost entirely renaming foo functions
to HDfoo) that don't change functionality. This should not
require a full commit test.
receiving review comments from people. I put the safeguard in both H5F_get_objects and H5F_get_objects_cb to prevent
overfill the list.
tested with h5committest.
The previous behavior was to execute a sec2, stdio, and family
test everytime it ran, which was very inefficient under check-vfd.
Tested on:
32- and 64-bit LE linux (jam and koala)
64-bit BE linux (ostrich)
64-bit OS-X 10.6 (fred)
- Added a lot of documentation to classes for Reference Manual.
- Fixed some format inconsistencies
Platforms tested:
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
Linux/64 2.6 (koala)/PGI compilers
Correct H5I use of skip list to acquire the 'next' pointer in the skip
list after the ID's 'free' callback has been called, since it occasionally
deletes the 'next' node.
Also a little bit of code cleanup in other modules.
Tested on:
FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode
FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.11 (emu) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (ostrich) w/C++ & FORTRAN, w/threadsafe, in debug mode
Switch H5I internal data structure from using hash table to skip lists.
Tested on:
Mac OSX 10.8.4 (amazon) w/C++ & FORTRAN
FreeBSD, Linux, etc. forthcoming
- Appended h5tutr_ to names of data files to avoid name clashing with
existing examples.
- Added example dependencies to Makefile.*
(pointed out by Allen)
Platforms tested:
SunOS 5.11 (emu) with gmake
Linux/ppc64 (ostrich)
Linux/32 2.6 (jam)
Linux/64 2.6 (koala)/PGI compilers
The reason was typo in the index variable in the newly added test_get_obj_ids().
Solution: fixed the typo.
Tested: AIX machine. (Did not run h5committest because the fix is in a remote
machine and the fix is quite obvious.)
Mailing lists instructions are incorrect.
Fix by removing hdf5dev which has long retired (2009). Subscription requests
should be sent to new address due to server change.
Tested: tried to subscribe myself and it worked.
Description:
There is a bug in the current big.c tests. In a nut-shell,
the writing part randomly picks 50 locations and write 4KB
from that location. Random location range is from byte 0
to end of dataset. There is the problem--if the random location
is greater than (end of dataset - 4KB), then error.
Solution:
Adjust the random number to be at least 4KB less than the end of the
dataset. That allows it write 4KB more from the generated starting
position.
Tested: h5comittest plus jam serial build and test.
Description:
Changed header guards from single underscore to double underscore.
Platforms tested:
Linux/32 2.6 (jam) - very minor
Linux/64 2.6 (koala)/PGI compilers
Description:
- The failure in daily test was caused by missing initialization of member
"id" in a few constructors. This is now fixed.
- Added two overloaded H5Location::setComment
- Improved some error reporting in H5Location
- Improved error reporting in tests
Platforms tested:
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Linux/64 2.6 (koala)/PGI compilers
Description:
Added tutorial examples that Barbara made following the C tutorial examples.
They will be configured for daily test.
Platforms tested:
Linux/32 2.6 (jam) - tested by running a script that compiled them with
h5c++ and executing the examples; output are checked manually
Description:
With optimization enabled, gcc 4.8 inserts garbage into the padding bytes of
floating point types when assigning from a literal constant. This caused
problems when H5detect.c scanned the bits in floating point types to determine
their properties.
Modified H5detect.c to scan for padding before further analyzing the type, and
to ignore all information in the padding areas. Also removed code that
temporarily disabled optimization.
Tested: jam, koala, ostrich, platypus (h5committest)
Description:
- Improved the changes in revisions r22836 and r23438, mainly on the
wrappers of reference, dereference, get region, and set/getcomment.
- Added more tests.
Platforms tested:
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Linux/ppc64 (ostrich)
Description:
- Completed the changes in revisions r22836 and r23438 with improvement
on wrappers such as reference, dereference, get region, and set/getcomment.
- Added more tests.
Platforms tested:
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Linux/ppc64 (ostrich)
Description:
- Passing the c_str() of an std string into a C function caused failure
on OpenVMS. Added a work around using temporary string. (th5s.cpp)
- Passing incorrect file access property list caused test_datasize() to
fail. Fixed.
- Close a group in test_dset, before the file can be properly closed.
This should fix the problem on OpenVMS.
Platforms tested:
Linux/32 2.6 (jam)
SunOS 5.11 (emu)
Linux/ppc64 (ostrich)
Description:
H5Fis_hdf5 uses H5F_locate_signature to check if the file is hdf5. If it does
not locate the signature, H5F_locate_signature would issue an error and return
HADDR_UNDEF. H5Fis_hdf5 does not consider it an error if the signature is not
found, so it does not issue an error or clear the stack. The filled stack could
then cause issues later on.
Changed H5F_locate_signature to return herr_t, not issue an error if the
signature is not found, and added a parameter for a pointer to the signature
address that the function fills in.
Tested: jam, koala, ostrich (h5committest)
Reduce warnings w/gfortran in FORTRAN build by declaring interface for
utility test routines.
Tested on:
Mac OSX/64 10.8.4 (amazon) w/gcc/g++/gfortran 4.8
Clean up warnings, enable new compiler warning flag(s) and bring back
changes from Coverity branch:
r20813:
Remove the dead code as listed for coverity bug #1722. h5committested.
r20814:
Issue 69: Check return value and throw error if negative return. Also free datatype id on error
r20815:
Use HDstrncpy. --gh
r20816:
Replaced one last HDstrcat call with HDstrncat to resolve coverity issue 832.
r20817:
Use HDstrncpy and HDstrncat. --gh
r20818:
Purpose: Fix valgrind issues with h5jam
Description:
Modified h5jam to free strings strdup'd in parse_command_line before exit. Note
that they may still not be freed in case of error, due to the widespread use of
exit().
r20819:
Issue 80: change loop to use int as loop index.
r20820:
Maintenance: Fixed the bug found by coverity CID 788
There were two problems with this function:
1) it tried to unnecessary free NULL pointer
2) it tried to allocate c_name buffer that is done by H5Pget_class_name
Tested on:
Mac OSX 10.8.4 (amazon) w/gcc 4.8.1, C++ & FORTRAN
(too minor to require h5committest)
problem in H5detect.c (uninitialized buffer) and provided the solution. I checked it in yesterday. But it
turned out to be a false fix. So I'm back it out.
Tested on jam - reverse of changes.
problem in H5detect.c (uninitialized buffer) and provided the solution. Allen and I verified it.
Tested with h5committest and CMake on jam, koala, ostrich, playtus, and Allen's virtual machine.
This is needed to avoid a conflict with the Read Context object to be
introduced in another Project.
No impact on users, since this is a private module, and low for
developers as the RC module use is very sparse in the library.
Tested with h5committest.
The new gcc v4.8.* compilers does not work well with dt_arith which failed
in production mode.
Solution:
A temporary patch by removing any optimization (-O*) from the PROD_CFLAGS
so that dt_arith will pass for now. A more through investigation is needed.
Tested: Jam and Koala where it failed and now passes.
Tested: jam, koala, ostrich (h5committest)
Log from r23939:
Fix unused variables warnings in trunk
Rename static functions in H5Adense.c, H5B2cache.c, H5Bcache.c
Switch these functions to use FUNC_ENTER_STATIC* macros
Tested: koala
Changes applied to eliminate several compiler warnings in the test directory in
files:
dt_arith.c
filter_fail.c
big.c
dynlib2.c
dynlib3.c
Also an HDassert(0 && "Unknown type"); statement was added to all 29 combination
s of
case OTHER:
default:
See crucible review HDF5-145 for more details.
Tested with h5committest.
A) Fix for HDFFV-1238:
--Add 3 new options to allow users in setting threshold for small groups/datasets/attributes (tools/h5stat/h5stat.c)
--Generate new test file for testing the new options (tools/h5stat/h5stat_gentest.c)
--Add tests for the new options (tools/h5stat/testh5stat.sh.in)
--Update expected output files (tools/h5stat/testfiles/*.ddl)
B) Fix a bug in determining maximum dimension size for 1-D dataset in dataset_stats() (tools/h5stat/h5stat.c)
dt_arith.c
filter_fail.c
big.c
dynlib2.c
dynlib3.c
Also an HDassert(0 && "Unknown type"); statement was added to all 29 combinations of
case OTHER:
default:
See crucible review HDF5-145 for more details.
tools/h5diff/testh5diff.sh is run in every "make check", even after it
has passed in the previous run.
The error was in the previous change made to Makefile.am
when testh5diff.sh.in was created. The mistake was in the
SCRIPT_DEPEND=h5diff$(EXEEXT) $(H5PDIFF) $(srcdir)/testh5diff.sh
$(srcdir)/testh5diff.sh no longer existed. It is now generated in the
current built directory from $(srcdir)/testh5diff.sh.in (which configure
takes care of).
I updated the dependance to
SCRIPT_DEPEND=h5diff$(EXEEXT) $(H5PDIFF) testh5diff.sh
and that fixes the error.
Reviewed: HDF5-149
Tested: h5committested.
Merge changes from Coverity branch to trunk:
r20768:
Switch to snprintf, HDstrncat, HDstrncpy to address coverity issue 832.
r20812:
Use HDstrncpy. --gh
Tested on:
Mac OSX/64 10.8.4 (amazon) w/debug
Linux/32 2.4 (jam) w/debug
Found and removed two more "//" comments.
Tested: in Koala by
$ env CFLAGS="-ansi" ../hdf5/bin/buildhdf5 -fortran -cxx -config # enable fortran and cxx, configure only
$ make AM_CFLAGS=-ansi # compile all source file by setting HDF5 build CFLAGS as "-ansi" only
Description:
Failure to write fill values to the user's buffer when reading unallocated
chunks from datasets that have a fill value set to H5D_FILL_VALUE_DEFAULT.
A consequence of this was the reporting of spurious data values in h5dump
and h5diff output.
Solution:
Added check for fill value of H5D_FILL_VALUE_DEFAULT whenever fill value
setting was checked to decide whether or not to fill. This effectively
treats H5D_FILL_VALUE_DEFAULT the same as H5D_FILL_VALUE_USER rather than
H5D_FILL_VALUE_UNDEFINED.
Tested:
h5committest (platypus, ostrich, jam-pp, koala) ran successfully
(fillval test was modified to reveal and check for this error)
Note: RELEASE.txt was previously changed to reflect this fix. This
checkin was of a cleaner version of the code, but mostly to get this
full log message entered.
-This line, and those below, will be ignored--
M H5Dchunk.c
Clean up warnings, switch library code to use Standard C/POSIX wrapper
macros, remove internal calls to API routines, update checkapi and checkposix
scripts.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
Big-Endian Linux/64 (ostrich)
Revert r23695, which breaks big-endian tests on ostrich, etc. Will
investigate and submit correction later.
Tested on:
BE & LE Linux systems (ostrich, koala, jam, emu)
Clean up warnings in H5Tconv.c (down to _only_ 9000 lines of output now!)
Merge changes from Coverity branch back to trunk:
r20684:
Fix for coverity bug #1721 which was due to the fix for coverity bug #943.
r20685:
Use HDstrncpy. --gh
r20761:
Purpose: Fix valgrind issues
Description:
Free image_data and data as appropriate in test_image.
r20762:
Purpose: Fix coverity issue 600
Description:
Add check for return value of H5O_close in H5Ocopy. Also cleaned up various
warnings.
r20763:
Purpose: Fix valgrind issues with h5stat
Description:
Modified h5stat to free "iter" before exit, and free "hand" before exit if
parse_command_line exits directly.
r20764:
fixed coverity issues:
69, 327, 614, 684, 685, 696, 697, 1681, 967, 826, 660, 80
r20765:
Fixed coverity bug 668
Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning.
No actual integer overflow tests are performed since it's just a test program but I did add a check that n_elements is >= 1.
I also changed an error condition from doing its own close and returning -1 to "goto out;" like the rest of the program.
r20766:
Fixed coverity bug 667
Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning.
No actual integer overflow tests are performed since it's just a test program.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
(h5committest upcoming)
reviewed my previous commit and suggested me to use H5I_iterate to iterate through
all opened objects in H5Z_unregister. I changed it in this commit.
Tested with h5committest.
Some files are not distributed when release tarball is created by bin/release
according to MANIFEST. But --enable-build-all compiles them in test/.
Solution:
Distributed those missing files for now. Need to resolve if these files
should be distributed or not. And if not, fix --enable-build-all NOT to
compile them.
Tested: use bin/release to generate the tarball and run --enable-build-all with
it. Error is gone and all passed.
1. The file states that:
NOTE:
We are no longer actively supporting MinGW as of 1.8.5.
2. It is not tested for v1.8.11.
3. If we ever supports it again, it can be "restored" from previous
release (e.g. v1.8.10).)
Threadsafe works in v1.8.10 release. But it fails v1.8.11-pre1 tarball in
configure stage now. There was a typo in the configure around the checking
of pthread library. Fixed it.
Tested: AIX and also h5committested.
Daily test failed in koala with parallel and v16compat API from the previous
commit r22735.
Descriptoin:
Changed to use H5Dopen2() instead of H5Dopen().
Tested: koala --enable-parallel --with-default-api-version=v16.
No h5committest test since this is limited to parallel test program.
Bring r20683 from Coverity branch back to trunk:
Isues 1309-1333: Changed strcpy/strcat to strncpy/strncat with maximum size expected.
Tested on:
Max OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
The previous change set exec_prefix, libdir and includedir to actual values.
That removed the option for user to hand edit just the first prefix=...
to make "everything" to work.
Changed h5redeploy to do this by default:
## Installation directories: ##
## prefix architecture-independent files. ##
## exec_prefix architecture-dependent files, default is <prefix>. ##
## libdir libraries, default is <exec_prefix>/lib. ##
## includedir header files, default is <prefix/include>. ##
############################################################################
This allows users to just change the first line of prefix=<...> and the
effect will change libdir and includedir too.
This was also try to accommodate the -prefix option of h5XX. Unfortunately,
after changing h5redeploy, I found out the h5XX code to support -prefix
actually does not provide the stated efffect. This will be fixed in the
release.
Tested: h5committested plus hand test.
Bring r23542 from desy_1_8 branch to trunk:
Further revisions to dynamic library loading code, to clean it up.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/parallel
Stop aliasing property to indicate internal collective metadata operations
with property to perform collective raw data operations from the application.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/paralllel
to copy library file names in the form of libdynlib{123].*.
Another problem: Even when copy failed in copying the libray files (was in the form of *.so*),
the test still passed. That was because .libs was included in $HDF5_PLUGIN_PATH and the needed
plug in libraries were generated there.
Fixed by copying the plug in library files to separate directories and seetup HDF5_PLUGIN_PATH
to include them but NOT .libs.
Tested: used desycommittest (duck, emu, jam, koala, ostrich) plus cmakehdf5 in jam.
The cmakehdf5 in jam reported a failure in
Test #594: H5REPART-h5repart_test ....................................***Failed
Since this failure could not be caused by my change in test_plugin.sh, I reported it to Allen
and proceed to check this in.
delete the removed multi dxpl function names from the class.
Tested on: jam w/ fortran & C++
I did not test on other platforms (h5committest) since there is nothing
even remotely platform-specific here.
were removed in HDF5 1.8.11.
Tested on: jam w/ fortran & C++, tested with check-vfd
I did not test on other platforms (h5committest) since there is nothing
even remotely platform-specific here.
Change h5redeploy to change all 4 lines, prefix=..., exec_prefix=...,
libdir=..., and includedir=... This way, it reset all 4 lines. Should work
for both version of h5cc created by configure or by rpm.
Tested: hand tested in jam.
Test was not checking error result. It basically return succeess to make check
all the time.
Fixed it so that it does check the return code of the test (plugin) and set
nerror accordingly. It then exit 1 if there is any error detected.
Test: use the desy committest to pass on jam, koala, ostrich, duck and emu.
Also hand test by "rm test/.lib/libdynlib1* to verify the test script can
indeed response to errors properly.
Change h5diff_exit() routine to always return a zero exit code when running
in parallel, since returning a non-zero exit code can cause MPI implementations
to print output and that can throw off our "expected output" comparisons.
Note that this change only changes the exit code for situations where an
incorrect command-line parameter was given - ph5diff was already returning a
zero exit code for all "normal" executions, including those where a serial
h5diff would return a non-zero exit code.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/parallel
(Too minor to require h5committest)
Reversed it to use gcc/g++ as the default C and CXX compilers for Darwin 10.X
systems.
Tested: duck (darwin 11), wren (darwin 12) and fred (darwin 10).
Use Clang as the compiler for the Mac platform.
Changed all Mac to use clang/clang++ as the default C and CXX compilers if
not provided by the user. Still use gfortran as the default fortran
compiler since Apple does not provide any fortran compiler.
Tested: passed all three macs OS, snow leapord (fred), lion (duck) and
mountain lion (wren). Also passed test using Apple gcc, Gnu gcc, Intel
as the C compilers and all corresponding CXX compilers fits in.
Did not run h5committest or other non-mac platform since this change
affect Apple platforms only.
Compile scripts will add paths for external libraries linked to executable files that they create.
Eliminates need for LD_LIBRARY_PATH for szip in locations not known to ld.
Teted on platypus and emu (64bit) in addition to h5committest.
Changes default value for USE_SHARED_LIB in compile scripts to yes when static is disabled.
Comments in scripts about the order of flag variables containing library paths was also corrected.
Tested with h5committest on duck, jam, koala, and ostrich in addition to specific testing for the
compile script change.
Description:
+ The C++ test failed with the new PGI compilers versions 12.4 and 12.5
+ An exception thrown by an internal function, which was called by
a constructor, was not propagating to the test program during the stack
unwinding, so it couldn't be caught by the test and the program terminated.
+ Various trials and errors indicated that the problem is where an STD string
converted to a char* being passed to the internal function, but confirmation
has not been found yet. It could be a compiler bug.
Solution:
+ Added a try/catch in the constructor around the internal function and
re-throw the exception when it is caught. This is a workaround.
+ Unrelated minor fixes: removed unused variables and MESSAGE's; commented
out tvlstr.cpp/test_read_vl_string_attribute because it may be redundant,
and commented out H5Tpkg.h inclusion because TEST_ALIGNMENT is not added
yet and probably not necessary in the C++ API.
Platforms tested:
Linux/32 2.6 (jam) with PGI compilers
Linux/32 2.6 (jam) with GNU compilers
Linux/64 2.6 (koala)
during variable-length type conversion. All variable-length type conversion
buffers are now initialized to contain 0s on allocation.
Tested on: jam(w/ fortran, C++, parallel, parallel fortran)
ostrich
This is a very small change (basially changing malloc to calloc) and
is unlikely to cause issues on other platforms.
This turned out being an issue with configure. The reporter submitted a patch which fixed the fact that we should not be
setting AM_FCFLAGS (an automake variable) with FFLAGS (a user variable).
I removed this, and we now only set FFLAGS if the environment variable is set, otherwise we don't.
Tested: jam (gnu)
HDFFV-8214 - h5repack failed converting small chunked dataset (size < 1K) to contiguous layout.
Description:
h5repack failed converting small chunked dataset (size < 1K) to contiguous layout.
The first case was when chunk dim is bigger than the dataset dim (at leat one), h5repack failed with displaying error stacks.
The other case is when chunk dim is smaller than the dataset dim, h5repack failed to change layout.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), emu (solaris-BE),fred (mac64-LE), Windows (32-LE cmake), cmake (jam)
library. The intended functionality for them was never fully implemented
and they are fundamentally broken.
The functions were removed from the C and C++ interfaces. They were not
exported in the Fortran interface.
Tested on: jam(c++/fortran/hl)
I tested using check-vfd to ensure the multi VFD still works properly.
There is no reason to test this on other machines or on parallel.
Some systems, like Mac, strings inspect library files and older versions
of strings maybe know newer library format, resulting in errors.
Make it read the file as stdin, avoiding this problem.
Tested: h5committest. all passed.
------------
Fix for:
HDFFV-8149: h5pset_external_f API - the offset is declared integer which can cause problem if use 64-bit integer
Added new type off_t, modified source files and added a new test.
Tested (jam, intel, gnu)
Bring changes from Coverity branch to the trunk:
r20612:
Changed string functions to versions with string length to fix coverity issues
922, 942 and 943.
r20614:
Use HDsnprintf. --gh
r20675:
Fix for coverity #1714 due to the fix for #810.
Use HDfree() instead of H5MM_xfree().
r20678:
Repaired coverity issue #598 -- failure to check return value from a
call to fstat(), or to tidy up in the event of failure.
r20679:
Use HDstrncpy. --gh
r20681:
Use HDstrncat and HDstrncpy. --gh
Tested on:
Mac OSX/64 10.8.2 (amazon) w/Debug, etc.
(too minor to require h5committest)
HDFFV-7643 - h5diff - incorrect exit-code returns for extra attribute exist
Description:
h5diff: Fixed to return correct exit code 1 when detect unique
attribute. Prior to this fix, h5diff returned exit code 0 indicating
two files are identical.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE), emu (solaris-BE), Windows (32-LE cmake), cmake (jam)
Fortran2003 option does not work under windows; Need to manage .def files more efficiently
Changed the comment notes from adding to the 'hdf5_fortrandll.def' to instead adding
to the 'hdf5_fortrandll.def.in' file.
Since this is a testing code error that does not affect the function of the
library or tools, I started a new "Testing" section for this sort of changes.
The ERROR macro had a typo of missing a separator comma. When used, it seg.
fault. Added the comma back in.
Fix is reviewed in Crucible HDF5-107.
Tested: h5committest passed. Also tested using the ERROR macro in the
Mac (Owl) platform. Before fix, it seg. fault. After fix, it prints the
message as intended.
Bring changes from Coverity branch to trunk:
r20528:
Purpose: Fix coverity issue 1372
Description: Rewrite file open secition of H5FD_stdio_open to avoid TOCTUO
condition. No longer calls access, and uses a tentative open in "rb" or "rb+"
mode to check for existence of the file.
r20609:
Use HDstrncpy and HDstrncat. --gh
r20611:
Use HDstrncpy. --gh
Tested on:
Mac OSX/64 10.8.2 (amazon) w/debug, C++ & FORTRAN
(h5committest not required, already tested on branch)
Description:
Adds 2 new API functions, H5Dscatter and H5Dgather. H5Dscatter retrieves data
from a specified callback function and scatters it into a selection, defined by
a supplied dataspace, within a supplied memory buffer. H5Dgather gathers data
from a selection within a supplied memory buffer and passes it in a contiguous
form to a supplied callback function. Added tests for these functions
Tested: jam, ostrich, koala (h5committest); ummon
Description:
Adds 2 new API functions, H5Dscatter and H5Dgather. H5Dscatter retrieves data
from a specified callback function and scatters it into a selection, defined by
a supplied dataspace, within a supplied memory buffer. H5Dgather gathers data
from a selection within a supplied memory buffer and passes it in a contiguous
form to a supplied callback function. Added tests for these functions
Tested: jam, ostrich, koala (h5committest); ummon
Revert back one of the coverity updates from previous checkin. "r20457: Coverity issue 691" in previous svn log. Only revert the change about using "STDOUT_FILENO".
Description:
Using "STDOUT_FILENO" caused error on Windows. On unix it's defined in <unistd.h>, but not in Windows. After a little discussion with Allen, he remembered how the similar case were handled for h5dump redirecting those streams. (in h5dump.c) However it would requires more attention to apply, so this issue is entered as a separate task in jira HDDFV-8306.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE)
Revert use of snprintf() for sprintf(), as it is not supported on Windows.
(And file a bug, http://jira.hdfgroup.uiuc.edu/browse/HDFFV-8302, for the
general problem)
Tested:
Mac OSX/64 10.8.2 (amazon)
Bring reviewed changes from Coverity branch back to trunk (QK & JK):
r20457:
Coverity issue 691: return of H5duo could be negative. Fixed by using
STDOUT_FILENO and redesign parse_command_line and main to cleanup file
allocations. The output_file var is null when using stdout. In cleanup do not
close output_file if NULL.
r20510:
Initialize ufid = -1 and predicate HDclose call on ufid != -1
r20511:
Purpose: Fix coverity issue 1715
Description: Free "file" and nested data on failure in H5FD_core_open.
r20512:
Initialize ifid = -1 and predicate HDclose call on ifid != -1
r20514:
Initialize h5fid = -1 and predicate HDclose call on h5fid != -1
r20516:
Added else branch to the if (ret_value < 0) check.
r20522:
Addressed coverity issues 930-933, 850, 836, 835, 1307. All minor
potential buffer overwrite bugs, or coverity errors. Fixed by replacing
strcpy and sprintf with strncpy and snprintf.
r20523:
fixed coverity issues 68, 1120, 1116i
r20524:
Check H5Z_SZIP->encoder_present < 1 assuming 0 represents absence.
r20601:
Purpose: Fix coverity issues 1703-1705
Description: Modified the cleanup code in test_free in accum.c to reset
allocated buffers to NULL after they are freed, and modified the error cleanup
code to check if these buffers are NULL before freeing them. Also fixed some
unrelated warnings in accum.c.
r20602:
Use HDsnprintf and HDstrncat
r20603:
Purpose: Fix coverity issues 808-809
Description: Modified test_core in vfd.c to check the returns from malloc, and
keep track of whether points and check are allocated by setting them to NULL
when they are not. Added code to free points and check on error if they are
not NULL. Also fixed unrelated warnings in vfd.c.
r20604:
Use HDstrncpy.
r20605:
Use HDstrncpy and HDstrncat.
r20606:
Purpose: Fix coverity issue 807
Description: Modified long_compact in stab.c to keep track of whether objname is
allocated by setting it to NULL when it is not. Added code to free objname on
error if it is not NULL.
r20607:
Changed string function calls to use versions that specify the string length
to fix coverity issues 832 and 839.
Tested on:
Mac OSX/64 10.8.2 (amazon)
(Too minor to require h5committest)
to the standout. This keeps command output terse and easier to tell if it
passes or not.
Added time stamps printing.
Added exit code and command executation summary.
All these will make it easier for user to tell if the command succeeds or not.
Tested: {jam,koala,ostrich} all passed. {Linew,fred,duck,owl} failed.
The failure is the cmake process, not cmakehdf5 itself.
Fixes for HDF5 1.8.10 p1
HDFFV-7975
Changed the max single I/O operation size on Darwin/Mac OS X.
HDFFV-8124 and HDFFV-8158
Fixed a core VFD bug when large blocks of data are read.
HDFFV-8246
Added more fields to the VFD read/write error messages.
Tested on:
64-bit Windows 7, Visual Studio 2010, CMake
64-bit Mac OS X Snow Leopard (Fred), Fortran, C++
64-bit BE Linux (Ostrich), Fortran, C++
32-bit LE Linux (jam), Fortran, C++ (also parallel w/ Fortran)
testh5stat.sh fails in LLNL uDawn. The test actually ran as expected
but it did not prepare for the extra error messages from the MPI
process.
Solution:
This sort of problem has been fixed by using the output filters in
output_filter.sh. testh5stat.sh is updated to use the output filters.
Tested:
uDawn.
Removed example grpit.f90 which used undocumented/obsolete APIs, The equivalent and up-to-date example
to transverse through a file would be the example h5ex_g_traverse_F03.f90 in hdf5-examples.
Clean up warnings and bring changes from Coverity branch back to trunk:
r20451:
Fixed coverity 810
r20454:
Purpose: Fix coverity issue 816
Description: Modified various file drivers to always check the return value from
H5P_get_driver_info.
r20455:
Purpose: Cleanup fix for coverity issue 816
Description: Removed redundant check for "fa" in H5FD_core_open.
Tested on:
Mac OSX/64 10.8.2 (amazon) w/debug
(Too minor to require h5committest)
HDFFV-8146 - Remove "multi-chunk IO without optimization" sub-feature from MPI I/O optimization for chunked dataset feature
Description:
The “multi-chunk IO without optimization” feature is removed and made the related xfer property (H5FD_MPIO_CHUNK_MULTI_IO) go directly to “multi-chunk-io” feature.
Also update/fix/cleanup testings (chunk collective IO and actual chunk opt mode) accordingly.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE), Windows (32-LE cmake), cmake (jam)
Clean up a few warnings and minor code issues during review of enum ->
int/float conversion changes.
Tested on:
Mac OSX/64 10.8.2 (amazon) w/debug
(too minor to require h5committest)
HDFFV-8145 h5diff slowness with version >= 1.8.7
Description:
Improved speed when comparing HDF5 files with lots of attributes. Much slower performance was identified with release version from 1.8.7 to 1.8.10 compared to 1.8.6.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), Windows (32-LE cmake), cmake (jam)
Review Coverity changes and bring them back to trunk. (QK & JK)
r20402:
Added #includes for h5tools.y or h5tools_utils.h as required to remedy implicit
function declarations which caused compiler warnings and coverity issues 703-4
and 708-11.
r20414:
This is related to the previous checkin r20399. There were incorrect updates
which caused incorrect behavior when no file was given. Also possible segfault
when handling hyperslab options. Simplify the code changes.
r20449:
Description: Modified H5E_walk2_cb to check return value of H5I_object_verify.
r20450:
fixed coverity 813
Tested on:
Mac OSX/64 10.8.2 (amazon) w/C++, FORTRAN, debug & threadsafe
(too minor to require h5committest)
Bring Coverity changes back to trunk:
r20399:
Change parse_command_line to free hand structure on error and only "leave()" at end of main.
r20400:
Purpose: Fix coverity issue 592
Description: Added void cast to call to H5F_sfile_assert_num() in
H5F_term)interface(). There is no need to check the return value of this
function in general, and there would be nothing to do even if it did fail.
r20401:
Added free(src_sizes) and free(src_offset). --gh
Tested on:
Mac OSX/64 10.8.2 (amazon) w/C++, FORTRAN, threadsafe
(too minor for h5committest)
dt_arith would fail in Lion and Mountain Lion system when GCC version 4.2.1
is used with --enable-production. Somehow the -O optimization will fail some of
the hard conversion code.
Solution:
This is just a temporary patch by detecting if this is a Lion or Mountain Lion
system using GCC 4.2.1, then just remove the any -O option from the PROD_CFLAGS.
A better fix should be deviced later.
Tested: Duck(lion) and Owl (mountain lion) tested with --enable-production.
Also tested in Fred and Tejeda, both Snow Leopard systems to verify there is
no undesired side effect.
Correct use of 'uint8_t' parameter type in public header file (which was
causing Windows builds to fail).
Tested on:
Mac OSX/64 10.7.5 (amazon) w/debug
(too minor to require h5committest)
benchpar.c is compiled when configure --enable-build-all --enable-paralllel.
But it failed to compile. It is decided to retire or move it to example.
I removed it from the PARA_BUILD_ALL list so that --enable-build-all will
not fail. The program file still need to be moved.
Tested: Koala using --enable-build-all --enable-parallel.
--in parallel mode.This line, and those below, will be ignored--
M perform/Makefile.in
M perform/Makefile.am
Description:
Fixed miscellaneous inconsistencies and typos, which also took
care of the failure in Packet Table test on daily test today.
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (koala)
Mac Lion (duck)
Description:
In this bug, H5File doesn't have the ability to create attribute. The
following changes will provide that functionality and several others that
were also missing:
- Added an abstract class H5Location in between IdComponent and H5Object.
- New class structure of IdComponent, H5Location, H5Object, H5File
IdComponent
|
H5Location
/ \
H5Object H5File
- Wrappers in H5Object were moved to H5Location because the related C
functions take either file, group, dataset, or named datatype ID.
- Added wrapper for H5Rget_obj_type2
- Added tests for file attributes and H5Rget_obj_type2 wrapper
Platforms tested:
Linux/32 2.6 (jam)
Linux/64 2.6 (koala)
SunOS 5.10 (linew)
Description: The Fortran compiler flags were all set to "-O". They should be
different setting for different situations. E.g, "-g" for debug and
"-pg" for profile, etc.
Fix: set them to appropriate different values.
Tested: in Remote ADA AIX machines using 3 different settings:
configure --enable-fortran --enable-cxx # default to --disable-production
configure --enable-fortran --enable-cxx --enable-production
configure --enable-fortran --enable-cxx --disable-production
Larry mentioned that intel compiler was used on Mac for testing.
Allen requested comment it out.
"It is not scheduled for 1.8, I created the file for Java testing. Actually I
have to create windows versions because of the use of floating point." - Allen
It goes down to the error handling branch and prints "FAILED". The fix is adding "return 0;" in the end of the function.
Tested on jam - simple change.
HDFFV-8012 - h5repack changes max dims and cause failure if only "-f none" is used without changing layout for chunked dataset when a chunk dim is bigger than a dataset dim
Description:
"h5repack -f <obj>:NONE <file.h5> out.h5" command failed if source file contains chunked dataset and a chunk dim is bigger than a dataset dim.
Another issue is that the command changed max dims if chunk dim is smaller than the dataset dim.
These issue occurred when dataset size is smaller than 64k (compact size limit)
Fixed them.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
distribute by the author. It was an example program showing how to measure
parallel IO speed. Since then, we have created h5perf to do I/O performanace
measurement. This example is not needed any more.
mpi-perf.c:
Removed.
Makefile.am:
Makefile.in:
Removed the entry of mpi-perf.c so that "configure --enable-build-all ..."
will not build it.
The change is trivial that I got permission to skip the code review step.
Tested: h5committest plus "--enable-parallel --enable-build-all" in koala.
Use
LT_PREREQ([2.2])
LT_INIT([dlopen])
instead of
AC_LIBTOOL_DLOPEN
AM_PROG_LIBTOOL
Also add ALLOW_UNSUPPORTED on threadsafe check
Both from 1.8 configure
Propogate Coverity changes to trunk, also fix compiler warnings and
other minor code cleanups. (QK & JK)
r20393: (Not directly propogated, since trunk also had a similar fix)
Move initialization ocrt_info.new_obj = NULL; before FUNC_ENTER_NOAPI -- gh
r20397:
Added free(src_sizes) --gh
r20398:
Added free(src_offset). --gh
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug, parallel, FORTRAN & C++
(h5committest forthcoming)
HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Fixed Daily test failed from the previous commit r22735. (ember)
Also changed H5Pget_mpio_no_collective_cause() parameter type from
H5D_mpio_no_collective_cause_t to uint32_t due to change to return
combined bitmap value which can be not emun defined value.
Tested:
jam (linux32-LE), koala-pp (linux64-LE), ember, h5committest
Bring generic improvements from encode/decode property list branch to
the trunk. This includes a better version of the property list comparison
routine, cleaned up compiler warnings, and some cleaned up property list
callbacks. Also, started on changes to clean up parallel test output, so that
it doesn't report successful tests from each process.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug, GCC 4.7.x, FORTRAN, C++, threadsafe and parallel
Linux 2.6/32 (jam) w/debug
Solaris 2.7/64 (linew) w/debug
HDFFV-5919 - GMQS: h5diff - The number of object difference is not consistent between dataset and group/type when attribute(s) have differences
Description:
Object differences are not consistent between dataset and group/datatype when their attribute(s) have differences. This is because attribute(s) differences is not accumulated to group or datatype object’s difference, but accumulated to dataset difference.
To fix, do not accumulate attribute difference to dataset difference. This is referred to h5diff’s default behavior and also past report from users that users were confused by the accumulated behavior. (also can’t figure out only for dataset difference , also hard to spot dataset difference when it has lots of attributes or differences)
This also lead to fix inconsistent format indicating difference between dataset and group/datatype object.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
Fix for HDFFV-7959 H5Rdereference should check for default (HADDR_UNDEF) value and not continue processing and return so that ret value can be checked and handled properly.
Added fix and test, reviewed:
Tested: jam (gnu, intel)
HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Daily test failed from the previous commit r22735. (ember)
Skip tests not to disrupt other tests while finding a solution for ember.
HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Daily test failed from the previous commit r22735. (ember)
Follow actual_io function to sync before go futher as this is similar
function.
Tested:
jam (linux32-LE), koala-pp (linux64-LE), ember
HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Daily test failed from the previous commit r22735. (koala , ember)
Fixed failure due to not be able to read external-storage file from external test.
Tested:
jam (linux32-LE), koala-pp (linux64-LE)
HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Added H5Pget_mpio_no_collective_cause() function that retrive reasons why the collective I/O was broken during Read/Write IO access.
Reasons to break collective I/O:
- SET_INDEPENDENT
- DATATYPE_CONVERSION
- DATA_TRANSFORMS
- MPIPOSIX
- NOT_SIMPLE_OR_SCALAR_DATASPACES (NULL Space)
- POINT_SELECTIONS
- NOT_CONTIGUOUS_OR_CHUNKED_DATASET (Compact or External-Storage)
- FILTERS
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
Bring back some more cleanups from the plist_encode_decode branch, clean up
some formatting and compiler errors, and add a few more property comparison
routines that we've skipped implementing in the past.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug
(Too minor to require h5committest)
Minor refactoring to extract managed object length determination.
This makes the tiny, managed, and huge code work alike.
Tested on:
jam (very minor change, no need for full commit test)
HDFFV-7942 - h5diff: incorrect result for comparing attribute data with different type size in same class
Description:
This is additional fix due to daily build fail against previous r22684.
Refer to the svn -r22684 log for previous details
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), cmake (jam)
Address HDFFV-7942 - h5diff: incorrect result for comparing attribute data with different type size in same class
Description:
When comparing attribute data values with same type class but different size, the result was incorrect. It was due to the size difference and got truncated.
Fixed to match up the smaller type size to big type size like what dataset does.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
Clean up file driver property handling, along with some misc. warnings.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug, gcc 4.7.1, C++, FORTRAN & threadsafe
(h5committest upcoming)
Have free space manager use temporary address space for storing the
section info, until the file is flushed or closed.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug, gcc 4.7.x, C++, FORTRAN & threadsafe
(h5committest forthcoming)
Merge "flush me last" & "flush me collectively" feature from the
avoid_truncate branch back to the trunk. (To help enable allowing the
free space section info to reside in temporary address space)
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug, gcc 4.7.x, C++, FORTRAN & threadsafe
(h5committest forthcoming)
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)
Merge some of the changes on the plist_encode_decode branch back to the
trunk.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug
(Too minor to require h5committest)
Purpose:
HDFFV-8003 - ph5diff (parallel h5diff): daily test failure on ember intermittently during non comparable test file comparison
HDFFV-7755 - parallel h5diff : hanging on koala intermittently during non comparable test file comparison
Description:
non-comparable test intermittently hung on koala and ember, but not on jam. it didn't occur until -np reaches 4 or bigger. it occurred once out of many repeated attempts of the same test.
There was a incorrectly (mistakenly?) duplicated code in MPI section which caused such hang in a certain condition. The test used more processes than other tests, which increased chance to trigger more undone processes, and such process could enter the incorrect code section and wait for wrong pair of send. it explains why it occurred intermittently according to machine condition and using a certain feature.
Removed incorrect code which blocked correct code.
Tested: some manually repeated test performed
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE)
Fix for HDFFV-8107 testh5diff will fail if build/test in HDF5 source tree
Description:
This is sub-task for "HDFFV-8105 testh5diff.sh uses the wrong operator (-a) in an if statement."
From the HDFFV-8105's update, h5diff test failed if build&test is performed in HDF5 source tree because 'cp' try to copy test files to self dir.
It's addressed by skipping if cp's src dir and dest dir is same.
Also this applied for all other tools under src/tools dir.
No change to the CMakeLists.txt files because CMake cautions/demands that in-source builds be avoided.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), some manual tests as well
Switch propert list/class iteration from internal to external form of
iteration, cleaning up and simplifying the code a bit.
Bring other general improvements from plist_encode_decode branch back to
trunk.
Clean up many warnings.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/gcc 4.7, debug and C++ & FORTRAN
(too minor to require h5committest)
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
Description:
The test command in COPY_TESTFILES_TO_TESTDIR used the wrong operator -a which
means and. It is not sufficient to test mere existence as $tstfile could have
been a directory or other non-file things. If the file is not readable, the
$CP command would fail but its return code was not checked.
Solution:
Get rid of the test command and go ahead to $CP it and then check its returned
code and report errors if detected.
Tested; committested. (note that ostrick still failed on errors committed by
other staff).
Refactor ID class registration to be more like how other "class"s in the
library are registered, and clean up compiler warnings.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug
(Too minor to require h5comittest)
Create setters for indexing options in h5trav.c to be set before the obj table is created.
Revert h5trav_print to remove now duplicated parameters.
Added test and testfiles.
Tested: local linux with cmake
Create setters for indexing options in h5trav.c to be set before the obj table is created.
Revert h5trav_print to remove now duplicated parameters.
Added test and testfiles.
Tested: local linux with cmake
HDFFV-7602 - GMQS: HDF5 command tools: Provide framework for reusable test files among tools
Stage2 working for h5dump tool.
Description:
Update cmake script to fetch test files from any tools to a test directory
and run test in organized manner.
Also keep the apperance similiar to shell script for better maintainance.
Tested:
CMake (Windows and jam)
Added static local variables in h5trav to hold the index_by and index_order values. Defaults are set.
H5dump only use of the trav_print function, added two parameters and passed in the sort_by and sort_order variables.
Tested: local linux
See HELPDESK-643 issue in JIRA.
NAG Fortran compiler doesn't like the current tH5E_F03.f90 file that has only comments
and no executable statements. Removed tH5E_F03.f90 from the list of modules to build.
Tested on jam with Intel compiler using --enable-fortran2003 flag.
Copy the file image test file from the source directory to the build
directory, instead of trying to open the [in-memory] file R/W.
Also, clean up a few other test files that were left lying around from
other tests.
Tested on:
MacOSX/64 10.7.4 (amazon) w/debug
Too minor to require h5committest
- Fixed a typo in return value of the nh5dread_f_c function ( was 1
instead of 0 on success); fixed the return value to make it consistent
with other Fortran functions; cleaned the code from debug statements.
Platforms tested: jam with GNU and Intel compilers, fortran 2003 feature.
(2) fix to extend into the aggregator based on threshold
(3) fix for the "flavor" logging problem
(4) fix for test failures due to the above fixes
(5) bug fix for h5stat when h5stat against a non-existing file
HDFFV-7602 - GMQS: HDF5 command tools: Provide framework for reusable test files among tools
Stage2 working for h5diff tool.
Description:
Update cmake script to fetch test files from any tools to a test directory
and run test in organized manner.
Also keep the apperance similiar to shell script for better maintainance.
Tested:
CMake (Windows and jam)
Fix h5repacktst (test file generating binary) to address HDFFV-8016 h5repacktst failed in AIX 32bit mode
Description:
Segmentation fault occurred when h5repacktst try to generate a dataset when
system memory is limited to 256MB.
Add error handling to display apporiate message to exit and adjust the test
dataset according to the original size which didn't causing out of memory.
Tested: test was done by limit memory in csh.
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE)
Change name of MPE log file produced from "cpilog" (which was the name
used in the example code we were referencing) to "h5log".
Tested on:
None, too trivial, eyeballed only...
The ph5diff (parallel h5diff) can intermittently hang in parallel mode
when comparing the two HDF5 files that contains common name objects with
different object types. (HDFFV-8003)
Skip only the specific test for parallel until the fix has made.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
Fix for HDFFV-7998-h5diff: incorrect behavior and output for comparing symbolic dangling links without following-symlinks option
Description:
Fix not to check and display dangling link status without --follow-symlinks option.
Berfor the fix, when comparing symbolic link to symbolic link without follow-symlinks option, h5diff followed to check if those links are dangling or not. It caused to display output incorrectly (dangling link instead of symbolic link).
The fix also improved performance when comparing lots of symbolic links without the --follow-symlinks option.
Test cases were added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
Correct error reported by user (Martin Otte) where we weren't using
realloc'ed buffer in MPI datatype code.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/parallel
Fix for HDFFV-8001 - h5unjam: segfault when used -V (show version) option
Description:
h5unjam has an option '-V' to display version information.
"h5unjam -V" caused segfulat for 1.8.9 pre-release.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward
the final design (as exemplified by the H5EA & H5FA code).
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug & parallel
Fix for HDFFV-7993 - h5repack fails with error "chunk size must be <= maximum dimension size for fixed-sized dimensions"
Description:
Fixed a failure when change the chunk size of a specified chunked dataset with unlimited max dims.
Also took care of converting to contiguous and compact from the dataset.
Test cases were added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
2012-04-11 15:57:10 -05:00
3536 changed files with 621422 additions and 548071 deletions
set(CPACK_RPM_PACKAGE_SUMMARY"HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.")
set(CPACK_RPM_PACKAGE_DESCRIPTION
"The HDF5 technology suite includes:
* A versatile data model that can represent very complex data objects and a wide variety of metadata.
* A completely portable file format with no limit on the number or size of data objects in the collection.
* A software library that runs on a range of computational platforms, from laptops to massively parallel systems, and implements a high-level API with C, C++, Fortran 90, and Java interfaces.
* A rich set of integrated performance features that allow for access time and storage space optimizations.
* Tools and applications for managing, manipulating, viewing, and analyzing the data in the collection.
The HDF5 data model, file format, API, library, and tools are open and distributed without charge.
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