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| * Add Autotools and CMake checks for big I/O MPI-3 functionsJordan Henderson2018-07-311-0/+1
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| * Add configure check for MPI_Mprobe and MPI_Imrecv functionsJordan Henderson2018-07-265-22/+78
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add line to libhdf5settings file for status of Parallel writes to filtered datasets status Surround Parallel Compression code in MPI_VERSION >= 3 checks Add disabled message for Parallel Compression built w/ MPI-2 Modify Parallel Compression tests to only run the parallel filtered read tests when parallel filtered writes are disabled Update big I/O code to handle being built with MPI-2 Add checks to CMakeLists.txt for MPI_Mprobe and MPI_Imrecv
* | Add quotes to places where MPI_C_LIBRARIES are linked againstJordan Henderson2018-07-271-4/+4
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* Fix for HDFFV-9277: update the ainfo message after removing an attribute.Vailin Choi2018-07-201-3/+6
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* Merge branch 'develop' of ↵Larry Knox2018-07-1883-356/+481
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
| * Removed white spaceBinh-Minh Ribler2018-07-171-1/+2
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| * Fixed HDFFV-10476, HDFFV-10478, HDFFV-10480Binh-Minh Ribler2018-07-173-4/+11
| | | | | | | | | | | | | | | | | | Description: Fixed potential out of bound read and NULL pointer dereferences. Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
| * Merge pull request #1134 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp4:develop ↵Binh-Minh Ribler2018-07-163-24/+36
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop Fixed HDFFV-10481 and HDFFV-10477 * commit '83ca39ba9a2d6852dd7754b533f7839e9d2a0107': Combined macro lines as Dana commented Platforms tested: Linux/64 (jelly) (very minor) Fixed division-by-zero issues Description: Fixed HDFFV-10481 and HDFFV-10477, division by 0. Fixed another occurrence beside what were reported. Also, changed a local variable to avoid an unnecessary cast. Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
| | * Combined macro lines as Dana commentedBinh-Minh Ribler2018-07-163-6/+3
| | | | | | | | | | | | | | | Platforms tested: Linux/64 (jelly) (very minor)
| | * Fixed division-by-zero issuesBinh-Minh Ribler2018-07-163-24/+39
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: Fixed HDFFV-10481 and HDFFV-10477, division by 0. Fixed another occurrence beside what were reported. Also, changed a local variable to avoid an unnecessary cast. Platforms tested: Linux/64 (jelly) Linux/32 (jam) Darwin (osx1010test)
| * | Fix evaluation of __has_attribute(no_sanitize_address) on older GCC versionsJerome Soumagne2018-07-161-3/+7
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| * | Merge pull request #1112 in HDFFV/hdf5 from ↵Jerome Soumagne2018-07-161-7/+5
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | ~JSOUMAGNE/hdf5_fork:gcc_sanitize to develop * commit '5afeefe1bae62fa5faf06c0c6f240e10863a2693': Fix H5detect to use no_sanitize_address attribute and support GCC sanitizers
| | * | Fix H5detect to use no_sanitize_address attribute and support GCC sanitizersJerome Soumagne2018-06-151-7/+5
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| * | | Merge pull request #1127 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to developJordan Henderson2018-07-162-53/+133
| |\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'a8d6f100cdddbfc42d0c4abfeb4ceb8788b1b087': Add note about single chunk caching and serial library Add check for actually using the MPI file driver when caching one chunk Fix error message mentioning wrong MPI function used Fix for HDFFV-10509 Revise H5D__mpio_array_gatherv() to not allocate memory needlessly Add test to continually grow and shrink chunks Changes to test with checksum filter as well as deflate filter Eliminate warning about signed to unsigned conversion Remove unused local variable Fix bug in parallel reads of compressed data Add data verification to parallel filtered compound write tests Add seven of fourteen parallel filtered data partial read tests
| | * | | Add note about single chunk caching and serial libraryJordan Henderson2018-07-131-1/+7
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| | * | | Add check for actually using the MPI file driver when caching one chunkJordan Henderson2018-07-131-1/+15
| | | | | | | | | | | | | | | Better explain rationale behind chunk caching issue fix
| | * | | Fix error message mentioning wrong MPI function usedJordan Henderson2018-07-131-1/+1
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| | * | | Fix for HDFFV-10509Jordan Henderson2018-07-041-2/+15
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| | * | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Jordan Henderson2018-07-0348-1909/+1952
| | |\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'b6fcbf4bb0f693fd6a0517f0ff3f74d52b329d1e': (400 commits) Fix ptr arith Correct function call Remove writeVL option Region reference in compounds need class check Correct cast formatting Correct var name Need to cast from void ptr Update Java util lib, Refactor H5D write VL to match read Fix attribute Read Correct "," handling Revert "Merge pull request #1116 in HDFFV/hdf5 from ~HDFTEST/hdf5_hft:hdf5_1_10 to develop" Snapshot version 1.10 release 3 (snap3) Remove debug statements Split/fix utility for vl types fix whitespace HDFVIEW compound vlen needed vlen_t size Update documents Update document Update document HDFFV-10433 Update file with fix for issues ...
| | * | | | Revise H5D__mpio_array_gatherv() to not allocate memory needlesslyJordan Henderson2018-06-061-38/+61
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| | * | | | Eliminate warning about signed to unsigned conversionJordan Henderson2018-05-171-4/+4
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| | * | | | Remove unused local variableJordan Henderson2018-05-171-7/+4
| | | | | | | | | | | | | | | | | | Ensure frees are done in a more heap-fragmentation friendly order
| | * | | | Fix bug in parallel reads of compressed dataJordan Henderson2018-05-171-7/+34
| | | | | | | | | | | | | | | | | | Add remaining parallel compound dataset partial read tests
| * | | | | Merge pull request #1133 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp4:develop ↵Binh-Minh Ribler2018-07-1479-253/+252
| |\ \ \ \ \ | | | |_|_|/ | | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop Fixed HDFFV-10404 * commit 'ec31438afdaf575368938e930eb3af0865a342b3': Fixed HDFFV-10404 Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
| | * | | | Fixed HDFFV-10404Binh-Minh Ribler2018-07-1379-253/+252
| | | |/ / | | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
| * | | | Merge pull request #1129 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to ↵Vailin Choi2018-07-134-15/+39
| |\ \ \ \ | | |/ / / | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop * commit '08de02c838c05993fea5febb9c320a679e7f841a': Changes based on feedback from pull request. Fix test_misc33() in test/tmisc.c Open the test file read-only so that it can be accessed for testing. Modifications made based on feedback from pull request. Fix for HDFFV-10333: 1) Check for valid object header version for a refcount messge 2) Check for invalid fill value size 3) Check for invalid dimension size in a layout message 4) Add --enable-error-stack option to h5stat 5) Add error checks to h5stat.c 6) Add tests to h5stat and h5dump Fix daily test failure.
| | * | | Changes based on feedback from pull request.Vailin Choi2018-07-121-3/+1
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| | * | | Fix for HDFFV-10333:Vailin Choi2018-07-114-15/+41
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 1) Check for valid object header version for a refcount messge 2) Check for invalid fill value size 3) Check for invalid dimension size in a layout message 4) Add --enable-error-stack option to h5stat 5) Add error checks to h5stat.c 6) Add tests to h5stat and h5dump
* | | | | Apply Cygwin pathches from Marco Atzeri.Larry Knox2018-07-181-9/+9
|/ / / / | | | | | | | | | | | | Commit Joe Lee's typo corrections for src/H5MF.c.
* | | | Revert "Merge pull request #1116 in HDFFV/hdf5 from ↵hdftest2018-06-2434-719/+287
| | | | | | | | | | | | | | | | | | | | | | | | | | | | ~HDFTEST/hdf5_hft:hdf5_1_10 to develop" This reverts commit e9f476dad47ce593f13dacb77b1cc664d1f24e7b, reversing changes made to 2ff00b1b937ebe36ac6ddf590c16a4c27fc0b053.
* | | | Snapshot version 1.10 release 3 (snap3)hdftest2018-06-241-2/+2
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* | | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_10)hdftest2018-06-1645-1859/+1902
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '87829e06189cd9b29583b5ca8065b52b1f4cd523': (30 commits) HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly Cleaned up H5Fmount/unmount code. Normalization with vol_integration branch. Add fortran MPI to test and example Add mpi include folders for fortran C objects Normalization with the vol_integration branch. Fixed MANIFEST Fix usage of compression lib in shared tests Fix jni function call version Fix the error found after earlier checkin. H5O_info fixes for java and examples Added a RELASE.txt entry for HDFFV-10505. Changed 'deprecated' to indicate 'no longer supported' in the --enable-debug/production configure flags. (1) Made the change according to the pull request feedback. (2) Removed the performance test form test/th5o.c: will decide on what needs to be done to show speedup via HDFFV-10463. Normalize with vol_integration. Removed unused H5MF functions and updated FUNC_ENTER macros and naming in H5MFsection.c. Restored some unused #defines to the deprecated section of H5Dpublic.h. Changes made based on feedback from pull request #1039. ...
| * \ \ \ Merge pull request #1111 in HDFFV/hdf5 from hdf5_1_10.sync to hdf5_1_10Scot Breitenfeld2018-06-1545-1859/+1902
| |\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '57f64b92d19fed2879ee9bafe1d29bfac865d54c': (30 commits) HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly HDFFV-10405: Using h5fget_obj_count_f with a file id of H5F_OBJ_ALL_F does not work properly Cleaned up H5Fmount/unmount code. Normalization with vol_integration branch. Add fortran MPI to test and example Add mpi include folders for fortran C objects Normalization with the vol_integration branch. Fixed MANIFEST Fix usage of compression lib in shared tests Fix jni function call version Fix the error found after earlier checkin. H5O_info fixes for java and examples Added a RELASE.txt entry for HDFFV-10505. Changed 'deprecated' to indicate 'no longer supported' in the --enable-debug/production configure flags. (1) Made the change according to the pull request feedback. (2) Removed the performance test form test/th5o.c: will decide on what needs to be done to show speedup via HDFFV-10463. Normalize with vol_integration. Removed unused H5MF functions and updated FUNC_ENTER macros and naming in H5MFsection.c. Restored some unused #defines to the deprecated section of H5Dpublic.h. Changes made based on feedback from pull request #1039. ...
| | * \ \ \ Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-06-149-498/+507
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| | | * | | Cleaned up H5Fmount/unmount code.Dana Robinson2018-06-071-18/+40
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| | | * | | Normalization with vol_integration branch.Dana Robinson2018-06-076-252/+232
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| | | * | | Normalization with the vol_integration branch.Dana Robinson2018-06-063-235/+242
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| | * | | Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-06-0438-1365/+1399
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| | | * | Merge pull request #1043 in HDFFV/hdf5 from ↵Dana Robinson2018-05-318-584/+318
| | | |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:h5do_direct_chunk_hl_to_src to develop * commit '1da9c5545c013ebc540ba3044810889d4acfa5be': Restored some unused #defines to the deprecated section of H5Dpublic.h. Added deprecated symbol wrappers for the H5DOwrite/read_chunk wrappers. Updated commenting in the H5DO compat test. Stripped out most of the duplicated functionality in the H5DO compat test. * Added H5DO compatibility functions. * Changed the offset copy to use an array on the stack. * Yanked some unused #defines. * Fixed the error tests * Moved common functionality into helper functions Normalize with trunk prior to update merge Fixed a warning. Finished move of H5DOread/write_chunk calls to H5D. First stage of moving H5DOread/write_chunk() to src/ and making them H5D calls. * Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*. * Moved the hl/test/test_dset_opt test to test/ and renamed to direct_chunk. * Moved the hl/test/dectris_hl_perf test to tools/test/perform and renamed to direct_write_perf. * Updated autotools and CMake files.
| | | | * | Restored some unused #defines to the deprecated section of H5Dpublic.h.Dana Robinson2018-05-151-1/+13
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| | | | * | Merge branch 'develop' into h5do_direct_chunk_hl_to_srcDana Robinson2018-05-152-85/+78
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| | | | * | * Added H5DO compatibility functions.Dana Robinson2018-05-042-67/+51
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Changed the offset copy to use an array on the stack. * Yanked some unused #defines.
| | | | * | * Fixed the error testsDana Robinson2018-05-023-89/+136
| | | | | | | | | | | | | | | | | | | | | | | | * Moved common functionality into helper functions
| | | | * | Merge branch 'develop' into h5do_direct_chunk_hl_to_srcDana Robinson2018-04-3029-1863/+1832
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| | | | * | | Normalize with trunk prior to update mergeDana Robinson2018-04-301-16/+16
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| | | | * | | Fixed a warning.Dana Robinson2018-04-301-1/+1
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| | | | * | | Finished move of H5DOread/write_chunk calls to H5D.Dana Robinson2018-04-305-600/+142
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| | | | * | | First stage of moving H5DOread/write_chunk() to src/ and makingDana Robinson2018-04-302-5/+154
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | them H5D calls. * Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*. * Moved the hl/test/test_dset_opt test to test/ and renamed to direct_chunk. * Moved the hl/test/dectris_hl_perf test to tools/test/perform and renamed to direct_write_perf. * Updated autotools and CMake files.
| | | * | | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Vailin Choi2018-05-3117-412/+426
| | | |\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'e8ece625f223032db0d26cfffafc045e4ccdf37d': Normalize with vol_integration.
| | | | * | | | Normalize with vol_integration.Dana Robinson2018-05-2917-412/+426
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