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* Snapshot version 1.10 release 2 (snap2)HDF Tester2017-10-161-2/+2
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* Merge candidate for the 1_10 branchRichard Warren2017-09-202-46/+459
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* Fix for daily test failureVailin Choi2017-08-301-1/+1
| | | | Fix for the compilation error from the PGI compiler.
* Modifications based on comments from pull request reviewVailin Choi2017-08-304-47/+26
| | | | | (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 fileVailin Choi2017-08-306-415/+438
| | | | | 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.
* Snapshot version 1.10 release 2 (snap1)hdftest2017-08-091-2/+2
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* Snapshot 1.10.2-snap1hdftest2017-08-041-2/+2
| | | | (Committed 8/1/2017 but not pushed from fork)
* Skip test in test/fheap.c when:Vailin Choi2017-08-021-1/+1
| | | | | | 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 commentsVailin Choi2017-08-024-18/+23
| | | | Test the changes in a branch via daily testing.
* Fix for HDFFV-10217 infinite loop in H5VM_power2up().Vailin Choi2017-07-194-6/+26
| | | | | | 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.
* Fix for HDFFV-7853 H5Ocopy doesn't work with open identifiersVailin Choi2017-07-185-88/+155
| | | | 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.
* Marked H5I_REFERENCE as deprecated in H5Ipublic.h.Dana Robinson2017-07-051-1/+6
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* Merge of recent develop work to 1.10 branch.Dana Robinson2017-07-052-243/+70
| | | | | | | | | | Fixes for: * HDFFV-10247 (autotools Fortran long double bug) * HDFFV-10248 (autotools deprecated debug/production tweak) * HDFFV-10250 (-fno-omit-frame-pointer w/ symbols) * Disabled missing parameter warnings in Java constant code * Added H5I_VFL ID checks to tmisc.c * Added 'get a dummy VFD' call to h5test library
* Merge of recent develop work to 1.10 branch:Dana Robinson2017-05-3119-185/+241
| | | | | | | | | * H5FD_FEAT_DEFAULT_VFD_COMPATIBLE VFD feature flag (HDFFV-10214) * H5FDdriver_query() API call (HDFFV-10215) * Fix to skip SWMR tests that when the current VFD is not compatible with the default VFD (HDFFV-10197) * Removed obsolete compiler versions from config/gnu-flags (HDFFV-9937) * Many warning fixes
* Added missing casts for the return value of H5I_object_verify().Dana Robinson2017-05-253-9/+9
| | | | (cherry picked from commit 8807f918b9b00916efa822dda0301d3aa9debd80)
* merge from develop and apply HDFFV-8611Allen Byrne2017-05-242-1450/+1411
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* Incorporate additional code changes for the H5DOread_chunk patch from GE ↵Vailin Choi2017-05-161-21/+22
| | | | | | | | | | 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.
* Merge pull request #511 in HDFFV/hdf5 from ↵Dana Robinson2017-05-121-5/+11
|\ | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:h5do_overwrite_1_10 to hdf5_1_10 * commit '1d786206df53942a3a3dbd538b369c94a632050d': Removed redundant assignement. Fixes the chunk overwrite bug (HDFFV-10187) and adds a new H5DO HL test.
| * Removed redundant assignement.Dana Robinson2017-05-121-1/+0
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| * Fixes the chunk overwrite bug (HDFFV-10187) and adds a new H5DO HL test.Dana Robinson2017-05-091-5/+12
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* | Merge pull request #499 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:hdf5_1_10 to ↵Dana Robinson2017-05-101-1/+1
|\ \ | |/ | | | | | | | | | | hdf5_1_10 * commit '1a4bda1bd824df2da1e8c3441881fb7fca6a4413': Set the HDF5_GENERATE_HEADERS CMake option to default to ON and removed the option from the CMake cache init files.
| * Set the HDF5_GENERATE_HEADERS CMake option to default to ON and removedDana Robinson2017-04-271-1/+1
| | | | | | | | | | | | the option from the CMake cache init files. Fixes HDFFV-10184
* | Fix for HDFFV-10051Vailin Choi2017-05-101-0/+1
| | | | | | | | | | Fix missing declaration for H5D__layout_compact_dirty_test(). Tested on mayll and osx1010test.
* | Fix for the two issues reported in HDFFV-10051Vailin Choi2017-05-102-1/+44
| | | | | | | | | | 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:Vailin Choi2017-05-102-3/+11
|/ | | | | | | | | | | (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.
* Change position of declaration to top of blockAllen Byrne2017-04-271-1/+2
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* Modifications based on pull request review.Vailin Choi2017-04-261-1/+1
| | | | Made couple changes based on the review comments.
* Incorporate patch from GE Healthcare (HDFFV-9934)Vailin Choi2017-04-266-70/+438
| | | | | 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.
* Change signature of H5PLget_sizeAllen Byrne2017-04-252-14/+16
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* Fixed problems that prevent bin/trace from marking up some functions.Dana Robinson2017-04-243-18/+12
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* bin/trace updates in H5PL.cDana Robinson2017-04-201-0/+4
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* The cache_image test shows a skipped message about EoC in parallel.Dana Robinson2017-04-201-1/+0
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* Added code to disable the evict-on-close feature inDana Robinson2017-04-201-2/+19
| | | | the parallel library.
* Reformat char * argsAllen Byrne2017-04-181-4/+4
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* Merge pull request #431 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10Larry Knox2017-04-171-118/+118
|\ | | | | | | | | | | | | | | * commit 'b67e626ba9095f35dd9a8f9e8ca906320f85914c': HDFFV-10173 remove hook for noinst libs HDFFV-10170 fix noinst for test libs HDFFV-10173 fix compile on VS2008 Due to HDFVIEW-19 add read VL as string function
| * HDFFV-10173 fix compile on VS2008Allen Byrne2017-04-171-118/+118
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* | Commit copyright header change for src/H5PLpkg.c which was added after ↵lrknox2017-04-151-6/+4
| | | | | | | | running script to make changes.
* | Add new files in release_docs to MANIFEST.lrknox2017-04-152-7/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Conflicts: README.txt c++/src/Makefile.in fortran/src/Makefile.in hl/c++/src/Makefile.in hl/fortran/src/Makefile.in hl/src/Makefile.in java/src/jni/Makefile.in release_docs/RELEASE.txt src/Makefile.in
* | Change copyright headers to replace url referring to file to be removedlrknox2017-04-14439-2646/+1764
|/ | | | | | | | and replace it with new url for COPYING file. Fix 2 lines in java error test expected output file where messages include line numbers changed by reducing the copyright header by 2 lines.
* Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771)Vailin Choi2017-04-122-3/+13
| | | | | 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.
* Merge pull request #408 in HDFFV/hdf5 from develop to hdf5_1_10Larry Knox2017-04-119-28/+297
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'ccb4e9ed9a5e0af27db9f1504a628e35d7f4cf92': (27 commits) Removed commeted out code from H5C_dump_coll_write_list() Checkin of fix for CGNS bug (https://jira.hdfgroup.org/browse/HDFFV-10055). HDFFV-10143 add missing javadoc param Add missing test status Fix CMake regex commands Modify test/fheap.c to run with various file space strategies and/or page buffering Modify test/fheap.c to run with different combinations of file space strategies and page buffering only when ExpressMode is 0 (HDF5TestExpress is 0). Tested on ostrich, platypus, mayll, emu, osx1010test, quail, kite, kituo. Updated the H5L.c error message after additional thought. Fix for HDFFV-10141. Updated an error message in H5L.c to be more helpful. Fixes HDFFV-10141. Re-enabled fixed array index testing in the test_random_rank4_vl() test in test/set_extent. This was fixed some time ago, but the test was never re-enabled for that index type. Fix typo deletion HDFFV-10143 Update new feature section. HDFFV-10143 clean up format and function return HDFFV-10143 Add plugin APIs to Java interface Update with checks for index bounds Update tools issues 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 ...
| * Removed commeted out code from H5C_dump_coll_write_list()mainzer2017-04-071-5/+0
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| * Checkin of fix for CGNS bugmainzer2017-04-068-26/+298
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (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.
| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2017-04-051-2/+4
| |\ | | | | | | | | | | | | | | | * 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.
| | * Updated the H5L.c error message after additional thought.Dana Robinson2017-04-051-1/+1
| | | | | | | | | | | | Fix for HDFFV-10141.
| | * Updated an error message in H5L.c to be more helpful.Dana Robinson2017-04-051-2/+4
| | | | | | | | | | | | Fixes HDFFV-10141.
| * | Update with checks for index boundsAllen Byrne2017-04-031-1/+10
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| * | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2017-04-035-34/+121
| |\ \ | | |/ | | | | | | | | | | | | | | | | | | | | | | | | * 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)
| * | HDFFV-10143 fix use before setAllen Byrne2017-03-301-1/+1
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| * | Fix code error and use H5PL_MAX_PATH_NUM in testAllen Byrne2017-03-301-2/+1
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