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* Replace H5E_ATOM major error category with H5E_ID (#121)Dana Robinson2020-11-301-7/+7
| | | | | | | | | | * Renames H5I_ATOM to H5I_ID, among other related changes * Java has been updated. * Fortran is failing on my VM, even though I don't touch that. * Adds a RELEASE.txt note for H5E_ATOM to H5E_ID changes * Fixes typos in comments
* Basic alignment with async branch (#115)Quincey Koziol2020-11-231-9/+4
| | | | | | | * Basic alignment with async branch - trivial changes to reduce clutter in overall diff. * Update minor error code to reflect change within library * Update the error output to match library
* Clang-format of source filesAllen Byrne2020-09-301-946/+944
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* File changes to affect formattingAllen Byrne2020-09-041-51/+51
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* Fixed HDFFV-10933Binh-Minh Ribler2020-08-141-13/+21
| | | | | | | | | | | Description: Updated the original fix by Kent Y. in commit 200a77d8c3e51663c375aafffff607ae9b438f4e - used internal functions instead of public API - moved some code into the subroutine for a cleaner look. - added test to dsets.c Platforms tested: Linux/64 (jelly)
* Switch H5VM inline routines back to single underscope and put a comment in ↵Quincey Koziol2020-08-061-3/+3
| | | | their header about this naming
* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-8/+10
| | | | | | header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* Normalizations with 1.10 branch.Dana Robinson2020-06-021-13/+16
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* Avoid allocating a chunk index for datasets with 0-sized dimensions, untilQuincey Koziol2020-05-011-1/+1
| | | | the dataset is extended.
* Fix according to PR feedback.vchoi2020-04-071-1/+1
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* Fix an error in previous merge: should use NULL instead of FAIL.vchoi2020-04-071-2/+2
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* Merge branch 'develop' into tools_vol_updateDana Robinson2020-04-021-2/+15
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| * Merge pull request #2461 in HDFFV/hdf5 from ↵Vailin Choi2020-04-021-2/+12
| |\ | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/dtype_close_on_error to develop * commit 'afdcac28b85d690eebc80ab568fa5266081baaaa': A fix in the cleaning up code for datatype when datatype initialization via H5D__init_type() fails. This is triggered by the tests for revised references when the libver bounds setting does not allow version 4 datatype message to be created. The test failure is abort core dumped. This is due to the datatype initialization fails before the datatype ID is registered. The datatype cleanup code should provide for the above situation. The code to fix the problem is the same as what is done in H5D__open_oid().
| | * A fix in the cleaning up code for datatype when datatype initialization via ↵vchoi2020-03-231-2/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | H5D__init_type() fails. This is triggered by the tests for revised references when the libver bounds setting does not allow version 4 datatype message to be created. The test failure is abort core dumped. This is due to the datatype initialization fails before the datatype ID is registered. The datatype cleanup code should provide for the above situation. The code to fix the problem is the same as what is done in H5D__open_oid().
| * | Changed default dataset shared struct to initialize hid_t IDs toDana Robinson2020-04-021-0/+3
| |/ | | | | | | H5I_INVALID_HID.
* | Misc changes for h5dump VOL changes.Dana Robinson2020-03-301-1/+1
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* Merge pull request #2325 in HDFFV/hdf5 from ~DYOUNG/werror:h5t_copy to developDavid Young2020-02-171-2/+2
|\ | | | | | | | | | | | | | | | | | | | | Merged per discussion with Elena. * commit '3f903a441ad84001ea66589728bd8b036b6fdfca': Take out the temporary performance tests. Make calls through a function pointer. Use the same number of arguments, always. Increase iterations, provide a baseline for no-op, simplify the overhead case a bit. Temporarily add some code that measures the time to run the simplest possible H5T__copy_all()-like routine 10 million times and then measures the version with FUNC_ENTER_STATIC/_LEAVE_NOAPI and a HGOTO_ERROR() statement. H5T_copy() constification plus Quincey's contributions.
| * H5T_copy() constification plus Quincey's contributions.David Young2020-01-291-2/+2
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* | Reduce differences between my -Werror branch and `develop`:David Young2020-01-291-3/+2
|/ | | | | | | | Rename index -> idx, fileno -> fnumber, fileno -> fno to avoid GCC shadowed declaration warnings about index(3). Convert #pragma GCC diagnostic push/pop/ignored to the HDF5 library's H5_GCC_DIAG_OFF()/H5_GCC_DIAG_ON() macros.
* merge and fix conflictkmu2020-01-191-4/+3
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* \ merge and fix conflictskmu2020-01-141-22/+313
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| * Remove unnecessary H5CX callQuincey Koziol2019-12-211-4/+0
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| * Refactor H5Dvlen_get_buf_size to use optional dataset operation, with ↵Quincey Koziol2019-12-211-26/+219
| | | | | | | | generic fallback for VOL connectors that don't implement operation
| * Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2019-12-201-40/+142
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* | fix unused related warningskmu2020-01-131-1/+1
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* Implement support for using H5Dvlen_get_buf_size withNeil Fortner2019-12-051-1/+1
| | | | non-native VOL connectors.
* Merge pull request #2049 in HDFFV/hdf5 from ~CHOGAN/hdf5:chogan/issue_10934 ↵Chris Hogan2019-12-021-15/+62
|\ | | | | | | | | | | | | | | | | to develop * commit '3664cea5d6f87a7e8e708191f9cea36077424a80': Fix failing test and retain semantics for chunk cache properties in non-chunked datasets Add two missing calls to H5I_dec_ref for new dapl_id Community-proposed fix
| * Fix failing test and retain semantics for chunk cache properties in ↵Chris Hogan2019-11-251-4/+34
| | | | | | | | non-chunked datasets
| * Add two missing calls to H5I_dec_ref for new dapl_idChris Hogan2019-11-211-4/+7
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| * Community-proposed fixChris Hogan2019-11-181-7/+21
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* | Implement H5VLget_file_type() to return a copy of a datatype with theNeil Fortner2019-11-081-2/+2
|/ | | | | | | | | | | location set to be in a file. Only meant to be used by VOL connectors. Implement H5VLpeek_connector_id() to support connectors querying their own IDs. Fix app_ref with connector IDs in a couple places (external VOLs registered as default through ENV should be visible to the application). Modify vlen and reference interfaces to work with arbitrary VOL connectors. Implement file "post open" specific callback, to enable connectors to update their file structs after a wrap context has been set.
* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-45/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Progress toward moving the dataset routines to using the 'shared' file pointerQuincey Koziol2019-08-211-1/+1
| | | | instead of the 'top' file pointer.
* Add support for GCC9, update warnhist script, and clean up warnings.Quincey Koziol2019-07-031-2/+3
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* Updated configure & CMake compiler flags for GCC 8.x, along with correspondingQuincey Koziol2019-06-281-21/+21
| | | | | changes to warnhist script (and some extra improvements for condensing C++ and Java warnings), and fixed a bunch of warnings.
* Updated H5Tcopy() to get the dataset's datatype through the VOL whenDana Robinson2019-06-241-24/+0
| | | | that is passed in as the object ID.
* Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-211-1/+0
| | | | clean up warnings.
* Merge pull request #1600 in HDFFV/hdf5 from ↵Ray Lu2019-04-181-28/+38
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~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. ...
| * Changing the prefix of external file and VDS from empty string to null for ↵Songyu Lu2019-04-171-19/+16
| | | | | | | | performance improvement.
| * Improving the condition checking of empty string.Songyu Lu2019-04-171-8/+8
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| * Replacing string operation strdup with assignment for empty string.Songyu Lu2019-04-171-11/+18
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| * HDFFV-10658 - setting and getting properties in API context:Songyu Lu2019-04-091-14/+8
| | | | | | | | | | 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
| * Merge branch 'develop' of ↵Songyu Lu2019-04-041-8/+9
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~songyulu/hdf5_ray into HDFFV-10658-performance-drop-from-1-8
| * | This commit basically has the following changes:Songyu Lu2019-04-041-4/+4
| | | | | | | | | | | | | | | | | | 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: 1. moving HDgetenv to dataset initialization stage to reduce ↵Songyu Lu2019-03-221-14/+26
| | | | | | | | | | | | 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.
| * | HDFFV-10658: setting and getting properties in API context:Songyu Lu2019-03-131-18/+18
| | | | | | | | | | | | | | | 1. external file prefix and VDS prefix. 2. the datatype, dataspace, and LCPL of the dataset for VOL connector.
* | | Correct set extent operation on VDS to iterate over # of used sub-datasetsQuincey Koziol2019-04-161-1/+1
| |/ |/| | | | | instead of # of allocated sub-datasets.
* | Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-7/+7
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* | Fix issue with direct chunk write not updating the "last chunk" indexNeil Fortner2019-03-061-1/+2
|/ | | | | cache. Fix issues involving datasets being "no allocated" when they contain cached raw data.
* Move 'minimize dataset object header flag' into API contextQuincey Koziol2019-03-051-6/+6
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