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* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories.
* Bring async branch to develop (#166)Quincey Koziol2020-12-141-0/+21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Expand ID dec_ref and close callbacks to allow for asynchronous close ↵Quincey Koziol2020-12-011-8/+40
| | | | | | | | | | | operations (#135) * Expand ID dec_ref and close callbacks to allow for asynchronous close operations. * Fix typo * Rename token -> request, remove programmer name * H5E_ATOM to H5E_ID
* Replace H5E_ATOM major error category with H5E_ID (#121)Dana Robinson2020-11-301-13/+13
| | | | | | | | | | * 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
* Clang-format of source filesAllen Byrne2020-09-301-350/+297
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* Updates H5Sset_extent_none() to set H5S_NULLDana Robinson2020-07-281-2/+5
| | | | | | | | The API call used to set the internal H5S_NO_CLASS value which produced errors when such a dataspace was passed to many other API calls. Fixes HDFFV-11027
* Minor changes from normalization with 1.10Dana Robinson2020-07-091-322/+323
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* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-3/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Update versioning to next major versionAllen Byrne2019-09-251-314/+315
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* New hyperslab selection routines and new public selection iterator routines.Quincey Koziol2019-06-161-0/+21
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* Fixed a memory issue where unfreed shared attribute dataspace memoryDana Robinson2019-06-111-3/+7
| | | | | | tripped an assert in our memory sanity checks. Fixes HDFFV-10774.
* HDFFV-10365: Changes as described in the RFC: H5Sencode/H5Sdecode Format Change.Vailin Choi2019-04-061-7/+15
| | | | This also addresses HDFFV-10255: H5Sencode/decode performance issue.
* Set V112 as the latest format and extend the arrays of version bounds.Vailin Choi2019-04-041-0/+1
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* - Added H5MMprivate.h #includes where neededDana Robinson2019-03-161-0/+1
| | | | | - Added casts to quiet H5MM_memcpy warnings - Removed char * casts from HDmemcpy
* Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-1/+1
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* Align develop with incoming hyperslab_updates branch changes.Quincey Koziol2019-02-131-270/+121
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* Delta reduction against hyperslab_updates branch.Quincey Koziol2019-01-111-8/+7
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* H5S adjust callbacks now return an herr_t instead of void.Dana Robinson2018-09-241-2/+2
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* Revert "Merge pull request #1116 in HDFFV/hdf5 from ↵hdftest2018-06-241-7/+7
| | | | | | | ~HDFTEST/hdf5_hft:hdf5_1_10 to develop" This reverts commit e9f476dad47ce593f13dacb77b1cc664d1f24e7b, reversing changes made to 2ff00b1b937ebe36ac6ddf590c16a4c27fc0b053.
* Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-06-041-1/+52
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| * * Fixed the error testsDana Robinson2018-05-021-1/+52
| | | | | | | | * Moved common functionality into helper functions
* | Merge branch 'develop' into hdf5_1_10.syncM. Scot Breitenfeld2018-05-081-74/+8
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| * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-04-291-87/+39
| |\ | | | | | | | | | merge_hyperslab_updates
| | * Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-13/+32
| | |\ | | | | | | | | | | | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| | | * Fix for HDFFV-10355 (CVE-2017-17506).Dana Robinson2018-02-271-2/+2
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| | | * Changes made based on code reviews.Vailin Choi2018-01-121-6/+9
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| | | * (1) Merge branch 'develop' into bugfix/version_boundsVailin Choi2017-11-251-6/+6
| | | |\ | | | | | | | | | | | | | | | | | | | | | | | | | (2) Add two new options to h5repack for low and high bounds as in H5Pset_libver_bounds. (3) Modify message pre_copy callbacks so that H5Ocopy can handle version bounds check. (4) Add version bounds check for cache image feature.
| | | * | Initial checkin for library version boundsVailin Choi2017-10-031-9/+25
| | | |/ | | | | | | | | | | | | Code changes to provide versioning support when adding to the enumerated defines for H5F_libver_t.
| | * | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-72/+7
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| | * Added missing casts for the return value of H5I_object_verify().Dana Robinson2017-05-241-1/+1
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| | * 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.
| * | Checkpoint normalization against incoming hyperslab / selection / dataspaceQuincey Koziol2017-03-281-2/+1
| |/ | | | | | | improvements.
* | Needs to sync with lib version and Sencode.M. Scot Breitenfeld2018-03-071-13/+32
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* | Fix for HDFFV-9947 H5SencodeVailin Choi2017-11-281-7/+7
| | | | | | | | Modifications to fix H5Sencode bug when num points selected is > 2^32.
* | Added missing casts for the return value of H5I_object_verify().Dana Robinson2017-05-251-1/+1
| | | | | | | | (cherry picked from commit 8807f918b9b00916efa822dda0301d3aa9debd80)
* | Change copyright headers to replace url referring to file to be removedlrknox2017-04-141-6/+4
|/ | | | | | | | and replace it with new url for COPYING file. Fix 2 lines in java error test expected output file where messages include line numbers changed by reducing the copyright header by 2 lines.
* [svn-r29372] minor error reporting fix.Mohamad Chaarawi2016-03-091-2/+2
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* [svn-r27956] Description:Quincey Koziol2015-10-051-2/+3
| | | | | | | | Minor code cleanups, preparing to merge to trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r27916] Re-merge of r27884-27891 from the trunk + bugfix for a fewDana Robinson2015-09-301-18/+22
|\ | | | | | | | | | | | | | | H5S recursive functions where an aliased pointer was incorrectly set too early. Tested on: Ubuntu 15.04 (Linux 3.19 x86_64) w/ gcc 4.9.2 serial and parallel (w/ MPICH 3.1.4)
* | [svn-r27912] Revert of r27887, which caused failures in the vds test. TheseDana Robinson2015-09-291-22/+18
| | | | | | | | | | | | | | | | changes will be merged more carefully so we can more easily identify any errors that arise. Tested on: Ubuntu 15.04 (Linux 3.19 x86_64) w/ gcc 4.9.2 serial and parallel (w/ MPICH 3.1.4)
* | [svn-r27887] Description:Quincey Koziol2015-09-271-18/+22
|\ \ | |/ | | | | | | | | | | | | Merge changes from trunk to the branch. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
| * [svn-r27884] Description:Quincey Koziol2015-09-261-18/+22
| | | | | | | | | | | | | | | | | | Update dataspace selection encode/decode routines to avoid type aliasing errors. Tested on: Linux/64 2.6.x (platypus) w/production (h5committest forthcoming)
| * [svn-r27851] Description:Quincey Koziol2015-09-221-32/+63
| | | | | | | | | | | | | | | | | | Normalization changes that wouldn't otherwise be necessary if the VDS branch wasn't coming in shortly. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest forthcoming)
* | [svn-r27835] Description:Quincey Koziol2015-09-211-42/+87
|\ \ | |/ | | | | | | | | | | | | Sync w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
| * [svn-r27768] Description:Quincey Koziol2015-09-141-42/+87
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* | [svn-r27632] Description:Quincey Koziol2015-08-311-3/+3
| | | | | | | | | | | | | | | | | | | | Revert changes to pass file pointer to selection serialize/deserialize routines. Also patch back in some changes that were merged out in the previous merge w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial (h5committest not required on this branch)
* | [svn-r27606] Merge revisions 27593 through 27605 from trunk to vds branch.Neil Fortner2015-08-281-1/+1
|\ \ | |/ | | | | Tested: ummon
| * [svn-r27605] Fix potential memory error when using a dataspace that was ↵Neil Fortner2015-08-281-1/+1
| | | | | | | | | | | | | | | | created with H5Screate and had its extent set by H5Sextent_copy. Tested: jam, ostrich (h5committest)
* | [svn-r27598] Description:Quincey Koziol2015-08-271-15/+1
| | | | | | | | Check in misc. minor code cleanups, found during code review
* | [svn-r27479] Add checking for invalid inputs to H5Dset_virtual: point ↵Neil Fortner2015-08-071-6/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | selections, incorrect numbers of elements selected, incorrect "slice" through limited dimensions, incorrect number of printf substitutions. Patch source selection space extent with bounds of selection if extent is unknown before returning via H5Pget_virtual_srcspace. Write updated VDS dataspace to file when it changes due to unlimited selections. Other minor fixes/cleanup. Tested: ummon
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