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* Fix for daily test failureVailin Choi2017-08-241-1/+1
| | | | Fix for the compilation error from the PGI compiler.
* Modifications based on comments from pull request reviewVailin Choi2017-08-234-47/+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 Choi2017-08-226-415/+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.
* Moved H5PL diagnostic pragmas to comply with old gcc requirements that theyDana Robinson2017-08-022-17/+19
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* Minor tweaks in response to code review.Dana Robinson2017-08-011-6/+2
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* Merge branch 'develop' into h5pl_commitDana Robinson2017-08-014-19/+24
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| * Skip test in test/fheap.c when:Vailin Choi2017-07-181-1/+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 Choi2017-07-184-18/+23
| | | | | | | | Test the changes in a branch via daily testing.
* | Major rework of H5PL package code before bringing VOL changesDana Robinson2017-07-1413-817/+1856
|/ | | | | | | | over. Brings coding standards in line with the rest of the library, enforces better software engineering principles, and makes everything more maintainable.
* Merge pull request #596 in HDFFV/hdf5 from GreaterThan-2GB-MPIO to developRichard Warren2017-07-131-46/+458
|\ | | | | | | | | | | | | | | | | * 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
| * Include code fixes and additional modifications pointed out by code reviewersRichard Warren2017-07-101-6/+6
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| * Commited changes to the development branch here to allow a pull request to ↵Richard Warren2017-07-051-46/+458
| | | | | | | | be published
* | Fix for HDFFV-10217 infinite loop in H5VM_power2up().Vailin Choi2017-07-104-6/+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.
* More minor whitespace cleanupDana Robinson2017-07-031-3/+3
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* Fixed a minor comment typo in H5R.cDana Robinson2017-07-031-1/+1
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* * Reverted removal of H5I_REFERENCE to avoid breaking binaryDana Robinson2017-07-0315-5/+100
| | | | | | compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19() in tmisc.c.
* Purged the unused H5I_REFERENCE from the library.Dana Robinson2017-07-0114-115/+22
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* Added a test for VFD IDs to testhdf5.Dana Robinson2017-07-012-243/+70
| | | | | | | This required adding some code to generate a fake VFD class to pass to H5FDregister(). Also, a bunch of whitespace and comment tidying.
* Fix for HDFFV-10160Vailin Choi2017-06-293-0/+36
| | | | Modifications to fix the assertion/abort failure when the application does not close the file.
* Fix for HDFFV-7853 H5Ocopy doesn't work with open identifiersVailin Choi2017-06-115-88/+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.
* Revert "Merge pull request #567 in HDFFV/hdf5 from ↵Dana Robinson2017-06-098-395/+230
| | | | | | | ~DEROBINS/hdf5_der:develop to develop" This reverts commit 4242753848c44ab3b5d226e66225eac2f64db314, reversing changes made to b0e79fe6dd20ec7aa1b3e5f0f8b370639a4ef5bd.
* * Made STATIC free lists EXTERN for H5O_layout_t.Dana Robinson2017-06-077-170/+251
| | | | * Made all non-global instances of H5O_layout_t in H5Pdcpl.c dynamic.
* Updated H5O_layout_t dynamic work to use the H5FL interface.Dana Robinson2017-06-077-28/+79
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* Made some H5O_layout_t stack allocations dynamic (quiets warnings).Dana Robinson2017-06-066-53/+86
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* Merge branch 'develop' into windows_openDana Robinson2017-05-3130-1674/+1755
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| * Merge branch 'develop' into compat_feature_flagDana Robinson2017-05-2611-137/+145
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| | * Merge pull request #538 in HDFFV/hdf5 from ↵Dana Robinson2017-05-267-128/+131
| | |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:may_dev_warnings to develop * 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.
| | | * More minor warning fixes.Dana Robinson2017-05-251-1/+1
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| | | * Fixed many minor warnings.Dana Robinson2017-05-256-127/+130
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| | * | Merge pull request #534 in HDFFV/hdf5 from ↵Frank Willmore2017-05-251-0/+5
| | |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~FRANK.WILLMORE/hdf5:fix-set-mpi-err-handler to develop * commit '1ee90786196c10c2c616a9fb4b8b1f92ebefa1f2': updated MPI error handling call for MPICH2 standard cleanup enabled MPI error handling added test file
| | | * | updated MPI error handling call for MPICH2 standardFrank Willmore2017-05-241-1/+1
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| | | * | enabled MPI error handlingFrank Willmore2017-05-231-0/+5
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| | * | | Added missing casts for the return value of H5I_object_verify().Dana Robinson2017-05-243-9/+9
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| * | | * Added new public H5FDdriver_query() API call.Dana Robinson2017-05-244-7/+48
| | | | | | | | | | | | | | | | | | | | | | | | * 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.Dana Robinson2017-05-244-39/+40
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
| * | | Fixed HDFFV-10214:Dana Robinson2017-05-198-17/+28
| |/ / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
| * | Incorporate additional code changes for the H5DOread_chunk patch from GE ↵Vailin Choi2017-05-151-21/+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.
| * | Merged HDFFV-10187 direct chunk overwrite bugfix to develop from 1.10 branch.Dana Robinson2017-05-121-5/+11
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| * | HDFFV-10186 Add endianess to bitfield and fix testsAllen Byrne2017-05-101-8/+21
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| * | Fix for HDFFV-10051Vailin Choi2017-05-091-0/+1
| | | | | | | | | | | | | | | Fix missing declaration for H5D__layout_compact_dirty_test(). Tested on mayll and osx1010test.
| * | Merge pull request #494 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to ↵Vailin Choi2017-05-093-4/+55
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop * 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.
| | * | Fix for the two issues reported in HDFFV-10051Vailin Choi2017-05-092-1/+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 Choi2017-05-072-3/+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.
| * | | HDFFV-10186 Whitespace changesAllen Byrne2017-05-091-1441/+1389
| |/ / | | | | | | | | | Mostly replacing tabs with spaces Removed empty mod sections
| * | 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
* | | Rework of the POSIX file open permissions and macros to clean upDana Robinson2017-04-287-28/+18
| | | | | | | | | | | | | | | | | | HDopen() calls. Also fixed a minor const warning in the core VFD.
* | | Changed the Windows POSIX open() file permissions to be correctDana Robinson2017-04-287-9/+28
|/ / | | | | | | according to MSDN. Partial fix for HDFFV-9630.
* | 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 Choi2017-04-256-70/+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.
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