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* Merge pull request #2173 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2019-12-211-0/+25
|\ | | | | | | | | | | | | | | | | | | * commit '576e713924b1802a64ae2f6655d2389d70fadfd1': Add new h5diff files Fix compile statement order HDFFV-10976,-10980 Init obj_type before calling H5Rget_obj_type3 Add unknown define for h5dump ref objects Standalone doesn't use h5test implementation. HDFFV-10980 - h5diff uses new ref APIs
| * Add new h5diff filesAllen Byrne2019-12-211-0/+3
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| * HDFFV-10980 - h5diff uses new ref APIsAllen Byrne2019-12-191-0/+22
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* | Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2019-12-201-0/+1
|/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | of the va_list, so it's at least possible for another connector to know what the operation is and decide whether to implement it or not. Added a new VOL sub-class called "introspect" where callbacks that report information about the connector or container can be placed. Added an 'opt_query' callback to this sub-class, for a connector to report back to the library whether a particular optional callback operation is supported. Also added a 'get_conn_cls' introspection callback, to retrieve the H5VL_class_t of a connector (either the "current" connector, H5VL_GET_CONN_LVL_CURR, or the terminal connector, H5VL_GET_CONN_LVL_TERM). Moved the "post open" operation from a file 'specific' operation to a file 'optional' operation, now that it's possible to detect (with the 'opt_query' introspection callback) whether a VOL connector implements an optional operation, without just returning an error. Added new internal VOL helper routines: H5VL_object_is_native, to determine if an object is in (or is a) native file, and H5VL_file_is_same, to determine if two objects are in (or are) the same terminal VOL connector's container. (And moved the special handling for FILE_IS_EQUAL operation out of internal VOL callback routine into H5VL_file_is_same) Made new dataset 'get' operation for H5Dvlen_get_buf_size, aligning it better with other 'get' operations in API. Fixed several issues with pass-through connectors, which are now passing the 'make check-passthrough-vol' tests again. A bunch of warning and style cleanups as well.
* TRILABS-135 Add clang analyzersAllen Byrne2019-12-111-0/+7
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* Add missing filenamesAllen Byrne2019-12-091-2/+3
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* Add new test referenceAllen Byrne2019-12-081-0/+2
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* Apparently, + has no special meaning, and neither does \+, in so-calledDavid Young2019-11-121-0/+1
| | | | | | | | "obsolete" / POSIX "basic" regular expressions. Also, not every version of `sed` out there supports the `-E` option. So delete the -E flag and use the regex `[^/][^/]*` instead of `[^/]+`. Add config/netbsd to the MANIFEST.
* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-2/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Add 'blob' callbacks to VOL, along with a native implementation to store themQuincey Koziol2019-10-081-0/+1
| | | | | | | in the global heap, and changed the VL datatype conversion code to use blobs. Move encode/decode of sequence lengths into VL datatype callbacks, from native VOL blob routines.
* Add new toolchain fileAllen Byrne2019-10-011-0/+1
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* Merge branch 'develop' of ↵Jacob Smith2019-09-231-0/+34
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage
| * Merge pull request #1908 in HDFFV/hdf5 from ~BMRIBLER/hdf5-bmr:develop to ↵Binh-Minh Ribler2019-09-031-0/+1
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop - Added new chunk query functions: H5Dget_num_chunks(), H5Dget_chunk_info(), and H5Dget_chunk_info_by_coord() - Fixed iterator issue in H5EA_iterate(), H5FA_iterate(), and H5D__none_idx_iterate() * commit '96dab622e3bbe75d85b0cef3ca2bd5288cf4ac32': Fixed error code and error messages Tested on Jelly (very minor) Changed H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COOR to H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COORD per a review comment. Updated comments Updated based on reviews and refactored test code Code cleanup and refactor Re-ordered items w.r.t. date. Fixed typo Added notes about HDFFV-10677 and HDFFV-10661 HDFFV-10677 and HDFFV-10661
| | * HDFFV-10677 and HDFFV-10661Binh-Minh Ribler2019-08-281-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
| * | Add 32-bit cross-compile toolchainAllen Byrne2019-08-291-0/+1
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| * Some refactoring prior to implementing new H5P MPI functions.Dana Robinson2019-08-141-0/+1
| | | | | | | | | | | | * Macro cleanup and obvious warning fixes in parallel code. * Moved H5FD comm and info dup/free wrapper code to a new H5mpi.c file and separated it to deal with each MPI type separately.
| * Added the map (H5M) APIDana Robinson2019-08-131-0/+7
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| * Merge reconciliation and VFD test fixesAllen Byrne2019-08-041-0/+1
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| * Reverts the removal of config/conclude_fc.am while keepingDana Robinson2019-08-011-0/+1
| | | | | | | | the changes to config/gnu-fflags.
| * Fixed the MANIFESTDana Robinson2019-07-301-1/+1
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| * Merge pull request #1808 in HDFFV/hdf5 from ↵Dana Robinson2019-07-291-1/+0
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:gnu-flags-work to develop * commit '7d291d059da6287f769951c4854c566da0b93ce8': Parallel Fortran tests now use the MPI module instead of including mpif.h. First stab at gfortran versions. Tested on gfortran 7-9 so far. Moved the -std=f2008 option to gfortran 9 for now. Updated gfortran options. * Removed conclude_fc.am, which was causing verbose builds. Need to investigate more, though. * Added gfortran 9 warnings and flags. This will need to be separated into other version blocks based on when the options first appeared. * The standard is now explicitly set at 2008.
| | * Updated gfortran options.Dana Robinson2019-07-171-1/+0
| | | | | | | | | | | | | | | | | | | | | | | | * Removed conclude_fc.am, which was causing verbose builds. Need to investigate more, though. * Added gfortran 9 warnings and flags. This will need to be separated into other version blocks based on when the options first appeared. * The standard is now explicitly set at 2008.
| * | Squashed commit of the following:Larry Knox2019-07-251-0/+22
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
| * | HDFFV-10845 add support for mingw toolchainAllen Byrne2019-07-171-0/+1
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* | Refactor h5repackgentest to have more modular internals, for easierJacob Smith2019-09-231-7/+13
| | | | | | | | | | addition of new tests. Update manifest and test script for new hdf5 external-storage .h5 files.
* | Merge branch 'develop' of ↵Jacob Smith2019-07-221-0/+2
|\ \ | |/ | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into bugfix/repack_external_storage
| * Add support for GCC9, update warnhist script, and clean up warnings.Quincey Koziol2019-07-031-0/+1
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| * HDFFV-9407 Add testAllen Byrne2019-06-241-0/+1
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* | Undo some formatting modifications.Jacob Smith2019-06-211-0/+13
| | | | | | | | Update MANIFEST.
* | Merge branch 'develop' into bugfix/repack_external_storageJacob Smith2019-06-201-5/+10
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| * HDFFV-10805 Add option to only build shared targetsAllen Byrne2019-06-181-2/+0
| | | | | | | | | | HDFFV-10805 Add ONLY_SHARED_LIBS option and prefer shared over static HDFFV-10803 Update FindSZIP.cmake find module Remove unneeded modules and update java modules
| * Added a warning summary script for gcc to binDana Robinson2019-06-171-0/+1
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| * Merge pull request #1729 in HDFFV/hdf5 from ↵Vailin Choi2019-06-171-0/+1
| |\ | | | | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/HDFFV-10800-h5ocopy-failure to develop * commit 'dfdc27b04b2e8bcd1985ba90ce6553d8b3805fda': Fix release notes based on feedback from pull request. Fix for HDFFV-10800 H5Ocopy failure: The value for the H5F_LIBVER_V18 index in H5O_fill_ver_bounds[], the format version bounds array for fill value message, should be version 3 not 2.
| | * Fix for HDFFV-10800 H5Ocopy failure:Vailin Choi2019-06-121-0/+1
| | | | | | | | | | | | | | | The value for the H5F_LIBVER_V18 index in H5O_fill_ver_bounds[], the format version bounds array for fill value message, should be version 3 not 2.
| * | Merge pull request #1738 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-06-151-2/+4
| |\ \ | | | | | | | | | | | | | | | | * commit '6c3f90ae222a8d4e8d8edf172a6745028209b75c': Update MANIFEST for move of h5cc.in and h5redeploy.in to bin directory.
| | * | Update MANIFEST for move of h5cc.in and h5redeploy.in to bin directory.Larry Knox2019-06-151-2/+4
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| * | | Merge branch 'develop' into vol_dev_headersDana Robinson2019-06-141-2/+3
| |\ \ \ | | |/ / | | | | | | | | | | | | Also moved the wrapper functions from the H5VLconnector.h to H5VLconnector_passthru.h
| | * | Merge pull request #1708 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:H10621 to developScot Breitenfeld2019-06-121-1/+2
| | |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '0742c15fca95965ed4eb87c6d54f41bb07bd4526': makefile clean-up move the vol_info to an optional parameter added H5Pset_vol added vol connector added test for vol_connector removed H5VL constants removed VOLL NULL connector and replaced it with native VOL added connector_name test added missing files add tests added more tests added missing files Implemented VOL APIs and C constants, no tests Implemented VOL APIs and C constants, no tests initial API impl.
| | | * | removed VOLL NULL connector and replaced it with native VOLM. Scot Breitenfeld2019-05-161-1/+1
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| | | * | Merge branch 'develop' into H10621M. Scot Breitenfeld2019-04-241-2/+10
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| | | * \ \ Merge branch 'develop' into H10621M. Scot Breitenfeld2019-03-071-44/+115
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| | | * | | | Implemented VOL APIs and C constants, no testsScot Breitenfeld2018-12-071-0/+1
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| | * | | | | Modified Makefile.ams for h5repack, h5watch and gif2h5 to allowLarry Knox2019-06-121-1/+1
| | | |_|_|/ | | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | disabling tests. Moved h5cc.in from tools/src/misc to src directory to always create h5cc whether or not tools are enabled. Added configuration status of tools and tests to libhdf5.settings.
| * | | | | Split VOL connector routines into separate headers:Dana Robinson2019-05-241-0/+2
| |/ / / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * H5VLconnector.h for terminal connector things * H5VLconnector_passthru.h for passthrough connector things Note that these headers are arranged such that they are included in hdf5.h so VOL connectors only need to include that. The separation into multiple headers is mainly for readability.
* | | | | Add initial failing test for h5repack copying external data into new file.Jacob Smith2019-05-301-0/+1
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* | | | added -M HPC to ctest commandM. Scot Breitenfeld2019-05-101-4/+0
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* | | | Adding cross-compilation for theta (ANL) and qsub (COBALT) batch controls.M. Scot Breitenfeld2019-05-091-0/+2
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* | | Merge pull request #1600 in HDFFV/hdf5 from ↵Ray Lu2019-04-181-0/+6
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~SONGYULU/hdf5_ray:HDFFV-10658-performance-drop-from-1-8 to develop * commit 'b5ef82a1786605ae86502bc82086047720b7d4ca': (21 commits) Moving the handling of null prefix into H5_combine_path. Changing the prefix of external file and VDS from empty string to null for performance improvement. Improving the condition checking of empty string. Replacing string operation strdup with assignment for empty string. Adding back links_env.out which I accidentally removed in my previous commit. Taking out two unnecessary diff output files. Taking out unnecessary diff files for output. Adding some comments. Some coding style changes. Adding the standard output files for the external_env.c and vds_env.c tests. Small correction for my previous commit. Forgot to add external_common.c and external_common.h. Updated CMake for the splitting of external.c and vds.c. Minor fix: removal of unnecessary enum values. Minor fixes: updating the test vds_env.c according to the set up of vds.c. Left out this file in previous commit. HDFFV-10658 - setting and getting properties in API context: 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: 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. HDFFV-10658: I left out this file in my previous commit. HDFFV-10658: 1. moving HDgetenv to dataset initialization stage to reduce the overhead; 2. restoring the retrieval of three vol properties to H5P_get instead of using API context to prepare for Quincey's upcoming refactoring work. ...
| * | | Some coding style changes.Songyu Lu2019-04-111-0/+2
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| * | | Merge branch 'develop' of ↵Songyu Lu2019-04-091-0/+1
| |\ \ \ | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~songyulu/hdf5_ray into HDFFV-10658-performance-drop-from-1-8
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