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* Reclassify CMake messages - HDFFV-11144 (#253)Allen Byrne2021-01-131-1/+1
| | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages
* Add compiler flags for GCC 10, along with updating warnhist script to ↵Quincey Koziol2020-12-211-0/+3
| | | | accommodate them. (#217)
* Adds h5delete tool (#187)Dana Robinson2020-12-161-0/+1
| | | | | | | | | * Adds h5delete tool * Fixed MANIFEST * Added RELEASE.txt note * Fix typo in RELEASE.txt
* OESS-98 convert plugin option to FetchContent, add tests (#155)Allen Byrne2020-12-161-0/+1
| | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * Update other test machines * OESS-98 fix tools test for plugins * HDFFV-10865 performance improvement for java array
* Bring async branch to develop (#166)Quincey Koziol2020-12-141-0/+9
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Add H5Fwait, H5Dwait, and other changes for async vol connector * Revert temporary testing changes * Add H5Fwait to header file * Add H5VLreset_lib_state() routine. * Correct VOL wrap context when retrieving library state for file open & create. * Manage the API context's VOL connector state as part of the library state. * Set the 'VOL connector property valid' flag when restoring the library state. * Don't push new API context on stack when retrieving "current" one. * Check for NULL VOL wrap context before decrementing refcount on it, when freeing the API context state. * Manage recount of underlying connector for VOL wrap context. * Add H5TSmutex_acquire() and H5TSmutex_release() routines to acquire and release the global lock on the HDF5 library. * Update library with new functions related to library global lock * Add asynchronous token API * Add new lightweight FUNC_ENTER / LEAVE macros for helping to structure the threadsafety (H5TS*) routines. * Sync w/develop * Initial event set code framework. * Elaborate on the H5ES routines, starting to add API routines. Update the "close ID" callbacks to allow asynchronous request tokens to be passed in from an asynchronous close API call. Refactor current asynchronous API routines (H5Fopen/H5Fclose and H5Dread/H5Dread) to use event sets instead of directly working with request tokens from the application. Clean up a few other minor warnings & code style issues. * Implement H5EScreate, H5ESget_count, and H5ESclose. It should be possible to write a simple application that creates an event set and uses it with H5Fopen_async, H5Dread_async, H5Dwrite_async, and H5Fclose_async, then calls H5ESclose (which waits for all async events to complete). * Add source file for event set test. * Refactor sync & async API routines to call common routine. Move dataset API read / write routines to src/H5D.c, along with all the other API routines. Progress on "fake" async VOL connector, for testing. * Modify async implementation to wrap async requests in a H5VL_object_t struct so the VOL layer can find the connector when accessing the request at a later point. * Free the requests is H5ESclose. Remove comments implying that request wait, notify, and cancel callbacks should free the request. * Fix bug in error handling in H5Fclose. * Fix bugs in async file routines. Rename H5VL_create_object_generic to H5VL_create_object. * Add explicit async version of H5Fcreate. * Add more _async routines * Correct typo for return value from H5Awrite changes * Add H5EStest and H5ESwait routines * Updated with API tracing info * Fix NULL pointer dereference in H5ES__wait * Add H5is_library_terminating() routine, so that VOL connectors can detect when the library is shutting down. * Fix typo * Remove event from event set's linked list * Move block of code so that vol_obj is valid * Avoid setting properties in the DXPL when reseting the library state (and in the test code). * Refactor argument tracing to implement new capability for tracing arguments of non-API routines, with the H5ARG_TRACE macro. This macro is updated automatically with the bin/trace script that runs as part of the autogen.sh process. Major changes were in src/H5trace.c and bin/trace, with the other changes being cleanups to the argument lists, to improve their presentation in the tracing output. Also - added the "managed string" routines, which can dynamically allocate strings, appending printf-formatted output to the string efficiently. * Release memory for managed strings * Fix printf() formats. * More printf() format fixes. * Add H5Eappend_stack routine and regression tests * Clean up a few missed merge conflicts and update the error stacks. * Remove unnecessary fork() operations and ten second sleep(). * Restore commented out attribute out, to better enable tracking down the previous failure * Allow multiple H5ARG_TRACE macros within a routine to be updated * Switch to using "new" H5ES_insert (which takes the arguments for the caller routine) for all event set operations. Renames H5ES_insert_new to H5ES_insert and removes the previous H5ES_insert. * Merge "managed" string routines into "ref-counted" strings, and refactor code to use them. * Add missing file. * Add caller's name and arguments to event, for error reporting * Refactor event set setup for "API common" internal routines * Checkin async API routines for H5A* and H5G* modules as listed in ID-283. Fix couple h5dump expected output files due to the changes. * Add some of the error query routines needed for event sets. * Refactor to make async setup / teardown and "common" routines cleaner * (1) Add async APIs to H5L, H5F, and H5D modules (2) Fix errors in previous checkins of async APIs in H5A and H5G modules (3) h5dump expected output changes * Enhance event info, for better error handling * Change name of temporary vol_obj variable, to help reduce coding errors * Fix oversight with vol_obj pointer * Minor code cleanup * Add missing \'valid\' flag for VOL wrapper context, when restoring the library\'s state * Run source formatter * Change H5TSmutex lock and release to include a lock count * Update error reporting ideas * Minor updates to improve sanity checking for retrieving / restoring library state * Updated with feedback from h5py team members * Refactor internal event set list and event handling, add implementation for H5ESget_err_info * Change the VOL request subclass callbacks that switch from using "H5ES_status_t" to "H5VL_request_status_t", and also add a H5VL_request_status_t* parameter to the 'cancel' callback in the request subclass. Also more code quality cleanups to add iterator callbacks to internal event set routines. * Update API tracing for new H5VL_request_status_t typedef * Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure * Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation * Remove 'canceled' event status from Java constants * Be safer about releasing resources when inserting a newly opened/created object or file into an event set * Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate". * Remove H5ES_STATUS_CANCELED from Java wrappers also * (a) Add async APIs for H5O module as listed in jira issue ID-283. (b) Remove verification of name parameter in async related routines for H55A and H5L modules because it is checked in H5VL_setup* routine. (c) Modify h5dump expected output due to the async changes. * Corrections based on PR feedback. * Further changes to make based on PR feedback. * Fix missed merge marker, and reformatted line * Clean up some warnings * Correct level of indirection * Relocate prototype (and doxygen info) for H5Aclose * Change non-static function declarations to be static * Ensure that H5TSpublic.h header gets installed (#129) * Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information. * Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value. Make the corresponding changes through most of the v1 and v2 B-tree code. Clean up warnings in H5public.h and cmpd_dtransform.c. * Add H5Iregister_future routine and tests. * Correct return value for H5Lexists_async * Add H5_DLL macro to public H5ES API routines * Update supported -> flags parameter for introspect_query callback * Remove my email address. Update passthrough VOL connector ID. * Fix comment for post_open_api_common * Remove unused non-blocking VOL connector * Minor cleanup in async branch in preparation for merge to develop * Update CMake and the Autotools to use the new pass-through VOL ID * Fix for SWMR daily test failures (#160) The H5I_register_using_existing_id() call did not initialize the future ID callbacks, causing the library to segfault when it tried to resolve those function pointers. * Added selective async APIs (#150) * Added selective async APIs Description: Added the following APIs: H5Ropen_attr_async H5Ropen_object_async H5Ropen_region_async H5Mcreate_async H5Mopen_async H5Mput_async H5Mget_async H5Mclose_async H5Tcommit_async H5Topen_async H5Tcopy_async H5Tclose_async - Updated an expected output file to include a new internal function in the error stack for the failure case. * Updated async APIs per reviews, including removing async version of H5Tcopy. * Removed statements that were added by mistake in the previous commit. * Fix compile issues in H5M and warnings elsewhere * Reformat code * Brings VOL_LIST changes from develop. (#163) Co-authored-by: Houjun Tang <htang4@lbl.gov> Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org> Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <derobins@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Add Makefile.ins in utils directory to MANIFEST. (#152)Larry Knox2020-12-101-0/+2
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* (fix) Segmentation fault when using a compound type. (#143)Jan-Willem Blokland2020-12-021-0/+1
| | | | | | | | | | | | | | | | | | | | | | | * (fix) Segmentation fault when using a compound type. In the case when a compounded attribute is written to dataset followed by writing the data with a data transform function to the dataset will result in a segmentation fault. It turns out the data is classified as compounded while it is not. Now, the state is always reset first to not compounded followed by the existing check if the variable is compounded. * (fix) Removed undesired comment lines. * (fix) Segmentation fault when using a compound type: added test. * (fix) Added the missing cmpd_transform.c file to MANIFEST. * (fix) cmpd_dtransform test: autotools and source header. Added the cmp_dtransform test to the autotools configuration and updated the HDF Group copyright header. Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
* Replace H5E_ATOM major error category with H5E_ID (#121)Dana Robinson2020-11-301-1/+1
| | | | | | | | | | * 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
* Enhance API tracing (#120)Quincey Koziol2020-11-261-0/+1
| | | Enhance API tracing to handle more types, and to put tracing info in a string, allowing it to be used when reporting errors. Also refactor ref-counted strings (H5RS) module to add capabilities needed for the tracing. Refactored H5Gname.c routines to use new H5RS routines also. Added /*out*/ tags to API routines that are returning information to the application. Updated H5TRACE macros from running updated trace script over library code. Added tests for new H5RS routines.
* Add else choice to error flags option (#128)Allen Byrne2020-11-251-0/+6
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* Update release text files (#109)Allen Byrne2020-11-231-1/+3
| | | | | | | * Update release text files * spelling correction * Update list
* Basic alignment with async branch (#115)Quincey Koziol2020-11-231-31/+31
| | | | | | | * 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
* Full set of current H5F documentation. (#105)Gerd Heber2020-11-211-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.
* Minor/id code cleanup (#114)Dana Robinson2020-11-211-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | * Revert "Switch ID code to use a hash table instead of a skip list (#52)" This reverts commit a50d211755cb272b2e468144e7d892a4c90813c4. * H5I_id_type_t and H5I_class_t are no longer managed via free lists * Fixed commenting issues * Naming and commenting cleanup in H5I.c * H5I cleanup * Header cleanup * Commenting * More uniform naming * Renames H5I_id_type_t and related in H5I.c * Adds gcc pragmas to ignore H5I const casting * Split H5I code into multiple files * Rename id_type to simply type in H5I code * Minor typo in H5Itest.c
* Revert "Switch ID code to use a hash table instead of a skip list (#52)" (#104)Dana Robinson2020-11-201-2/+1
| | | This reverts commit a50d211755cb272b2e468144e7d892a4c90813c4.
* Add new files to CMake and MANIFEST (#100)Allen Byrne2020-11-191-0/+2
| | | | | * Add new header file * Add missing file
* Switch ID code to use a hash table instead of a skip list (#52)Dana Robinson2020-11-171-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brings hash table ID code over from Bitbucket branch * Includes reformatting via clang. * Excludes uthash.h from reformatting. * Still has the failing test issue in tid.c. This should only be a problem if a custom ID type is used and its free function deletes other IDs. * Fixes munged H5_GCC_DIAG_ON/OFF macros in H5I.c The H5_GCC_DIAG_ON/OFF macros used to turn off fallthrough warnings in uthash.h (external code) were munged when formatting with clang due to their lack of quotes. e.g.; H5_GCC_DIAG_OFF(implicit-fallthrough) was munged to: H5_GCC_DIAG_OFF(implicit - fallthrough) which compiles, but is useless. So, with quotes, this is now: H5_GCC_DIAG_OFF("implicit-fallthrough") which survives reformatting with clang. * Fixes issues with user callbacks in the ID hash tables The skip lists (previously) used to handle IDs use a mark-and-sweep scheme to deal with user-defined ID delete callbacks which themselves delete other IDs in the list. The uthash hash table implementation used to manage the IDs in this feature branch does not have this ability. This commit restores the skip lists for non-library ID types in lieu of significantly modifying the uthash code. The hash tables are used to manage the library IDs as those do not delete other IDs when they are closed. * Adds uthash.h to MANIFEST * Removes implicit-fallthrough diagnostic disable Removing -Wimplicit-fallthrough=5 means that the uthash code no longer raises warnings so the H5_GCC_DIAG_OFF/ON macros that disabled those warnings have been removed from H5I.c. * Adds a test to ensure you can delete IDs in the H5Iiterate() callback
* Merge pull request #84 from byrnHDF/developLarry Knox2020-11-131-0/+1
|\ | | | | Downgrade m4 doxygen macros.
| * Add missing entries, remove m4 referenceAllen Byrne2020-11-121-0/+1
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* | Merge pull request #60 from bmribler/developLarry Knox2020-11-121-0/+1
|\ \ | |/ |/| Fix HDFFV-10590
| * Miscellaneous updateBinh-Minh Ribler2020-11-111-0/+1
| | | | | | | | | | - added test for CMake - renamed new input file to conform to the existing files
* | Doxygen add new files and update docsAllen Byrne2020-11-031-0/+24
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* Remove obsolete fileAllen Byrne2020-10-071-1/+0
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* OESS-98 merge with clang-format changesAllen Byrne2020-09-251-0/+2
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* Fix manifestAllen Byrne2020-09-241-1/+2
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* Add code owners fileAllen Byrne2020-09-241-0/+1
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* Update actions - split push/pull-request commitsAllen Byrne2020-09-241-0/+3
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* CMake and script changes for clang-formatAllen Byrne2020-09-041-0/+2
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* Add testfilesAllen Byrne2020-08-151-0/+7
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* TRILABS-277 Use JIRA number as #ifdefAllen Byrne2020-08-151-0/+1
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* HDFFV-9984 Add options to merge/prune external links during repackAllen Byrne2020-08-141-0/+19
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-0/+1
| | | | | | 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.
* Correct h5diff filenamesAllen Byrne2020-07-291-4/+4
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* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-07-171-0/+1
|\ | | | | | | | | | | * commit '9d3ea366d4bf3278e8260f4d5cdcc88cb4b61c56': Update MANIFEST. Add new test to Cmake. Fix for jira issue HDFFV-11080: (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads
| * Update MANIFEST.vchoi2020-07-161-0/+1
| | | | | | | | Add new test to Cmake.
* | Tools refactorAllen Byrne2020-07-151-0/+3
|/ | | | | | Move error_stack setup to tools library Add structure for h5dump properties Eliminate duplicated h5diff functions Use properties structure in place of argument lists.
* Clean up warningsQuincey Koziol2020-06-281-0/+2
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* Fix MANIFESTDana Robinson2020-06-101-0/+2
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* Update MANIFEST for removal of older warnings files.Larry Knox2020-05-201-19/+1
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* Correct pathAllen Byrne2020-05-071-1/+1
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* Add github actionsAllen Byrne2020-05-061-0/+2
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* TRILAB-244 separate CXX warnings and errors from CAllen Byrne2020-04-231-0/+3
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* TRILAB-192 - cleanup edits and match CMake CXX to autotoolsAllen Byrne2020-04-131-0/+1
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* Merge branch 'develop' of ↵Jacob Smith2020-04-071-4/+51
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into feature/vfd_splitter_mirror_a
| * Move intel warnings to subfolder, update autotools filesAllen Byrne2020-04-061-2/+2
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| * Flag construction must be after compiler detectionAllen Byrne2020-04-051-0/+1
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| * TRILAB-192 add c++ and fortran warnings build systems one fileAllen Byrne2020-04-051-0/+11
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| * TRILAB-192 add comparable clang flagsAllen Byrne2020-03-271-0/+4
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| * Update the MANIFEST for the autoconf/cmake shared warnings files.David Young2020-03-241-3/+34
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* | Tidying of Mirror VFD.Jacob Smith2020-04-071-1/+1
| | | | | | | | | | | | | | * Rename server-stop utility to mirror_server_stop. * Remove external dependency on bzero(). * Modify test/use_common to use only the public API. * Rename internal bitswap macro to follow convention.
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