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* Fix for jira issue HDFFV-11080:vchoi2020-07-141-1/+1
| | | | | (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads
* Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-261-67/+86
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| * Align contents of CMake and autotools testfile cleanup lists.Quincey Koziol2020-05-031-8/+9
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| * Avoid allocating a chunk index for datasets with 0-sized dimensions, untilQuincey Koziol2020-05-011-1/+2
| | | | | | | | the dataset is extended.
| * Add Splitter VFD to library.Jacob Smith2020-03-131-6/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * "Simultaneous and equivalent" Read-Write and Write-Only channels for file I/O. * Only supports drivers with the H5FD_FEAT_DEFAULT_VFD_COMPATIBLE flag for now, preventing issues with multi-file drivers. Add Mirror VFD to library. * Write-only operations over a network. * Uses TCP/IP sockets. * Server and auxiliary server-shutdown programs provided in a new directory, `utils/mirror_vfd`. * Automated testing via loopback ("remote" of localhost).
| * Replace pthread_self_ulong() with H5TS_thread_id(). The POSIX ThreadsDavid Young2020-02-031-1/+1
| | | | | | | | | | implementation ought to be portable to any system that has POSIX Threads. On Windows, I use the same API call as before.
| * Revert "Make a squash commit of 'Quiet some warnings by adjusting warnings ↵David Young2019-11-271-7/+1
| | | | | | | | level and fixing some code.' (commit 5c911d8baf3)"
| * Undo accidental test deletion.David Young2019-11-131-1/+1
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| * Straggler from previous commit: build and link the new .c files where IDavid Young2019-11-131-1/+7
| | | | | | | | | | moved some previously-static variables and functions that were causing unused-variable/function warnings.
| * Change some GCC warnings to errors. Fix code to quiet some warnings.David Young2019-11-051-1/+1
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| * Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Also support references to external files Add new H5T_REF type and type conversion routines Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF Add H5Treclaim() API to reclaim memory of vlen/reference types Deprecate H5Dvlen_reclaim() Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback Add H5T_ref_reclaim() Move previous H5R APIs to H5Rdeprec.c Clean up H5Ocopy Separate H5O_copy_expand_ref() to H5Ocopy_ref() Add support for copying new reference types Clean up deprecated routines to go through VOL and same code path Fix return codes in existing trefer.c test Rename trefer.c to trefer_deprec.c trefer.c is for new references Add performance test for trefer Add additional obj_copy_ref test Make use of tokens and blobs to store references Skip blob encoding for object references Start adding new reference examples
| * HDFFV-10677 and HDFFV-10661Binh-Minh Ribler2019-08-281-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: - Added functions to query chunk information: H5Dget_num_chunks(dset_id, fspace_id, *nchunks) Gets the number of written chunks that intersect with the given dataspace. However, in this version, the intersection is not yet completed. Thus, the number of all written chunks will be returned. H5Dget_chunk_info_by_coord(dset_id, *offset, *filter_mask, *addr, *size) Given a chunk's logical coordinates, returns the chunk's filter, address, and size. H5Dget_chunk_info(dset_id, fspace_id, index, *offset, *filter_mask, *addr, *size) Given a chunk's index, returns the chunk's logical coordinates, filter, address, and size. The chunk belongs to a set of chunks that have nonempty intersection with the specified dataspace. However, in this version, the intersection is not yet completed, and the index is of all the written chunks. These functions comply with VOL. - Fixed some oversights found in the library for the tests in chunk_info.c to work correctly. The returned value from a callback function was not checked in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate(). This oversight caused a callback function to continue iterating even though it's supposed to stop. Platforms tested: Linux/64 (jelly) Linux/64 (platypus) Darwin (osx1011test)
| * Mostly whitespace in testpar, addl changes for tmp dirAllen Byrne2019-08-151-1/+2
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| * Update COPYING file.Larry Knox2019-07-301-1/+1
| | | | | | | | Remove hdfs from list of vfds for check-vfd testing as it is read-only.
| * Squashed commit of the following:Larry Knox2019-07-251-8/+8
| | | | | | | | | | | | | | | | | | | | | | Merge changes from update_merged_S3_HDFS branch into develop. commit d5034315aea88629929ac0c9c59ebfafd5f21a31 Merge: 9c48823 d3fdcd8 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jul 25 08:24:53 2019 -0500 Merge branch 'develop' into update_merged_S3_HDFS
| * Some coding style changes.Songyu Lu2019-04-111-2/+2
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| * HDFFV-10658 - setting and getting properties in API context:Songyu Lu2019-04-091-2/+2
| | | | | | | | | | 1. switched to use the existing H5F_prefix_open_t for enum type; 2. put the common private function used by external.c and external_env.c into external_common.c
| * This commit basically has the following changes:Songyu Lu2019-04-041-7/+11
| | | | | | | | | | | | 1. restored the datatype, dataspace, and LCPL of the dataset for VOL connector back to the properties. 2. splitted external.c and vds.c because they called HDsetenv in the program, instead using shell scripts to set the environment variables. 3. changed H5CX_get_vds_prefix and H5CX_get_ext_file_prefix to use H5P_peek instead of H5P_get.
| * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Vailin Choi2019-01-021-11/+13
| |\ | | | | | | | | | | | | | | | | | | | | | develop Resolve conflicts: Conflicts: test/Makefile.am
| | * Merge pull request #1413 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:yay_plugins ↵Dana Robinson2018-12-311-9/+10
| | |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '3ca19cca5395d79be69209f8d7d0a2b06834a648': Flipped swapped testing strings. Added test_vol_plugin.sh to the list of scripts to clean Fixed a CMake build issue (CMake still doesn't run the VOL plugin tests) Added more sub-tests to the VOL plugin test. Added a simple test for registration of VOL connector plugins. Autotools only for right now, but this will be fleshed out in future work.
| | | * Added test_vol_plugin.sh to the list of scripts to cleanDana Robinson2018-12-281-1/+2
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| | | * Added a simple test for registration of VOL connector plugins.Dana Robinson2018-12-271-8/+8
| | | | | | | | | | | | | | | | | | | | Autotools only for right now, but this will be fleshed out in future work.
| | * | Move H5Fset_dset_no_attrs_hint VOL operations to native.Jacob Smith2018-12-181-1/+1
| | | | | | | | | | | | | | | | | | | | Move minimzied object header tests from separate file to test/ohdr.c Some formatting changes.
| | * | Merge branch 'develop' into dset_ohdr_minimizeJacob Smith2018-12-121-3/+15
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| | * | change test file name and apply 'h5_fixname' to itJacob Smith2018-12-111-1/+1
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| | * | Add presumptive test for external links.Jacob Smith2018-09-121-2/+2
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| | * | Stash work on object header reduction code and tests.Jacob Smith2018-09-111-7/+8
| | | | | | | | | | | | | | | | CMake stuff is not verified.
| * | | Fix for HDFFV-10659: The library abort with "infinite loop closing library"Vailin Choi2018-12-281-7/+9
| | |/ | |/| | | | | | | | | | | | | | | | | | | after deleting attributes in densed storage. The fix: When deleting attribute nodes from the name index v2 B-tree, if an attribute is found in the intermediate B-tree nodes, which may be merged/redistributed in the process, we need to free the dynamically allocated spaces for the intermediate decoded attribute.
| * | Correct "make check-vol" regression test target.Quincey Koziol2018-11-291-0/+2
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| * | Add support for "make check-vol", along with a few minor cleanups, etc.Quincey Koziol2018-11-291-0/+3
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| * | VOL FEATUREDana Robinson2018-10-101-3/+10
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| * | HD prefix and whitespaceAllen Byrne2018-08-281-5/+5
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| * Apply Cygwin pathches from Marco Atzeri.Larry Knox2018-07-181-0/+2
| | | | | | | | Commit Joe Lee's typo corrections for src/H5MF.c.
| * Merge branch 'develop' into h5do_direct_chunk_hl_to_srcDana Robinson2018-04-301-1/+1
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| | * Fix errors in Makefile.am files that cause "make check" to repeat test, evenQuincey Koziol2018-04-291-1/+1
| | | | | | | | | | | | | | | when there are no changes to source files. (Also add a ggenerated script to the list of files cleaned up on 'make distclean')
| * | First stage of moving H5DOread/write_chunk() to src/ and makingDana Robinson2018-04-301-6/+7
| |/ | | | | | | | | | | | | | | | | | | 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.
| * Added gen_bounds.cBinh-Minh Ribler2018-02-011-1/+1
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| * Fixed the problems with LDFLAGS and AM_LDFLAGS in filter plugins.Dana Robinson2017-11-131-4/+4
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| * Plugin test reworkDana Robinson2017-11-091-30/+19
| | | | | | | | Cleanup of plugin test code. Renames many files. Prep for VOL branch merge.
| * Add "-rpath /nowhere" to *_la_LDFLAGS for plugin test libraries. Thislrknox2017-10-091-16/+14
| | | | | | | | | | | | 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.
* | Changes to make timers within the library monotonic.Quincey Koziol2017-09-031-1/+2
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* Fix for HDFFV-10216 segfault in H5G_node_cmp3 with corrupt h5 fileVailin Choi2017-08-221-1/+1
| | | | | 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 for HDFFV-10160Vailin Choi2017-06-291-5/+7
| | | | Modifications to fix the assertion/abort failure when the application does not close the file.
* Comment out install-exec-hooks to remove libdynlib* files. Allen didlrknox2017-04-281-2/+2
| | | | | | | 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.
* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * 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.
* Our best effort to build dynamic plugin tests and not install them withlrknox2017-04-211-16/+14
| | | | | "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.lrknox2017-04-201-1/+15
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* HDFFV-10170 undo patchAllen Byrne2017-04-181-7/+6
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* Add plugin options for libsAllen Byrne2017-04-181-0/+4
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* HDFFV-10170 fix command syntaxAllen Byrne2017-04-171-1/+1
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