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* Combo set of async and other changes (#161)Quincey Koziol2021-06-021-24/+31
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Apply patch for dynamically registering optional VOL operations * (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. * Remove H5Dwait & H5Fwait (moved to the async connector). Added H5atclose routine. Updated 'optional op' operations. * Fix missed merge marker, and reformatted line * Update API tracing infrastructure for H5atclose callback * Clean up some warnings * Normalize against develop branch * Correct level of indirection * Add doxygen info for H5is_library_terminating and regression tests for it and H5atclose * Relocate prototype (and doxygen info) for H5Aclose * Align w/changes on develop * Move group package initialization code to H5Gint.c, and update tracing macros * Change non-static function declarations to be static * Correct GCC diagnostic macro * Ensure that H5TSpublic.h header gets installed (#129) * Finish moving API routines that invoke VOL framework to main source files. * Fix position of H5Fmount and H5Funmount * Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information. * Add wrappers for dynamically registered optional operations * Fix typo * Update doxygen comment for H5atclose with additional detail. * Add H5VL\*_vararg versions of H5VL routines that use va_list parameters * Implement and test H5S_BLOCK * 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 * Finish another iteration on public H5ES routines, along with running the code reformatter * Another round of reformatting * 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) * Remove H5Dwait and H5Fwait calls, which were incorrectly brought back in * Tiny cleanup of H5Lcreate_hard_async * Run source formatter * Allow for canceled operation in wait_cb * Attempt to fix switch on string value * Re-run source formatter * Add H5S_BLOCK testfile to CMake clean target * Add H5Pset_vol_async API routine and 'get_cap_flags' VOL introspection callback * Clean up warnings * Add H5P(set\|get)_vol_implicit_async API routines to allow \/ disallow implicit asynchronous operations (default is disallowed) * Run formatting script * Remove H5VL_REQUEST_WAIT\* * Warning cleanup * Eliminate strdup()s on statically allocated strings * Warning cleanup * Split H5VLrestore_lib_state into H5VLstart_lib_state and H5VLrestore_lib_state, and rename H5VLreset_lib_state to H5VLfinish_lib_state. * Duplicate strings when building err_info to return to applicatin * Move connector author routines into seperate header files, all included in the new hdf5dev.h header * Run bin/trace to add TRACE macros * Allow H5ES_NONE as a valid, but no-op, parameter to all H5ES API routines that accept an event set ID * Clean up formatting * Remove H5Pset/get_vol_implicit_async * Clean up warning * Remove H5Pget_vol_async and replace with more generic H5Pget_vol_cap_flags * Clean up warnings * Add H5ESfree_err_info convenience routine * Fix typo * Correct matching for cached VOL plugins * Add developer header file * Update for C99 compatibility * Add missing trace macro * Stop clang-format from messing with the trace macros. Don't set up VOL wrappers for 'infrastructure' objects like requests and blobs * Fix warning about formatting a directory * Clean up formatting for H5E_BEGIN_TRY / H5E_END_TRY * Reduce scope of H5ES__close * Enable CMake checks for various types on MacOS * Clean up properly when H5CX_retrieve_state() fails. Also clean up many compiler warnings. * Committing clang-format changes * Merge from develop * Fix mis-placed assert * Remove commented-out code * Re-add macro for unsetenv on Windows (I think it accidentally was merged out) * Strengthen sanity check from error report to assertion * Committing clang-format changes * Add units to the comments for a few fields * Switch 'get execution time' operation for async request tokens to be an optional operation and query if connector supports operation before retrieving it. * Committing clang-format changes * Remove H5ESget_time_estimate * Committing clang-format changes * Create developer header for datatype routines and move type conversion register/unregister routines there. * Simplify internal H5VL_setup_name_args and H5VL_setup_idx_args routines * Add H5VLlink_optional_op, allowing dynamicly registered optional operations for the link VOL subclass, also added H5VL_loc_params argument to the link 'optional' callback to allow them to work correctly. * Run bin/format_source on current code * Add H5VLobject_optional_op, allowing dynamicly registered optional operations for the object VOL subclass, also added H5VL_loc_params argument to the object 'optional' callback to allow them to work correctly. * Run bin/format_source on current code * Committing clang-format changes * Revert "Switch 'get execution time' operation for async request tokens to be an optional operation and query if connector supports operation before retrieving it." This reverts commit 5ac92014da2682bdba62d7a2524b8d90e38f6b19. * Committing clang-format changes * Convert attribute 'get' operation to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Update tracing macros * Convert attribute 'specific' operation to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Convert dataset 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also, minor tweaks to attribute 'get' and 'specific' operation parameters. * Convert datatype 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also, minor tweaks to H5O_refresh_metadata arguments. * Reduce warnings * Reduce warnings * Track change to datatype 'get' callback * Fix bug with file pointer getting invalidated when object closed * Reformat source * Convert file and group VOL classes 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also small cleanup to the attribute get name operation. Also moved 'mount' and 'unmount' operations to be group specific operations, instead of file specific, to better align with their behavior (mounted files are on groups, so a group is what is operated on). * Remove remainder of merge conflict marking * Convert link VOL class 'create' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Remove some unused local variables * Convert link VOL class 'get' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also refactor 'get name by idx' routines to return actual length of name with a parameter instead of the return value, and move some callback context structs for the link interface from the private header file into the source code module, to reduce their visibility scope. * Update tracing macros * Convert link VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Convert object VOL class 'get' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Convert object VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also refactor H5G_loc_exists, et al, to return 'exists' flag in a parameter and errors with the function return value, instead of overloading both into the return value. And, corrected logic error in test/links.c around non-existant objects in a file. * Convert request VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. * Convert blob VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also removes the H5VL_BLOB_GETSIZE operation, as it's unused in the library and the blob ID size for a container is now returned with H5VL_FILE_GET_CONT_INFO. * Add 'const' to several parameters that are only queried. * Convert all VOL classes' 'optional' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Convert several 'get' routines to return the length of an array in a parameter instead of combining it into the return value. Move several routines to be in less public namespace. Correct direct_chunk test to verify that parameters aren't modified on error. * Switch get/specific/optional VOL callback argument structures to be 'async-friendly'. Also other minor cleanups and bug-fixes. * Add H5Pset_dataset_io_hyperslab_selection / H5S_PLIST feature, to allow skipping H5Dget_space + H5Sselect_hyperslab for async operation * Add dynamic optional operations for request objects * Update dynamic operation test for optional request operations * Update a comment for an operation argument * Run trace and format_source scripts * Committing clang-format changes * Committing clang-format changes 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> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 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/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Enhance API tracing (#120)Quincey Koziol2020-11-261-116/+53
| | | 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.
* Basic alignment with async branch (#115)Quincey Koziol2020-11-231-44/+3
| | | | | | | * 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 Byrne2020-09-301-305/+280
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-39/+39
| | | | | | 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.
* Minor normalization with 1.10.Dana Robinson2020-07-201-14/+9
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* Squashed commit of the token_refactoring branch:Dana Robinson2020-01-161-27/+37
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* Small changes from the token_refactoring branch, to reduce the delta to developQuincey Koziol2020-01-041-3/+3
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* Added the map (H5M) APIDana Robinson2019-08-131-0/+6
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* Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-211-0/+1
| | | | clean up warnings.
* Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-1/+1
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* Removed H5I_REFERENCE from the library. It has always been unusedDana Robinson2018-12-081-1/+0
| | | | and has been marked 'deprecated' since 1.10.0. Fixes HDFFV-10252.
* Squashed commit of private branch changes to support stackable VOL plugins.Quincey Koziol2018-10-251-17/+4
| | | | modified: test/dsets.c
* VOL FEATUREDana Robinson2018-10-101-0/+1
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* Remainder of vol_normalization changes (dataset, attribute, files, objects).Dana Robinson2018-09-241-1/+1
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* Normalization with vol_integration (property lists, file drivers,Dana Robinson2018-09-211-22/+24
| | | | other misc).
* Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-1/+1
| | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-12/+7
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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.
* [svn-r27768] Description:Quincey Koziol2015-09-141-6/+6
| | | | | | | | | | | | | | | | | | | | | | 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-r24285] Eliminate several "passing argument ... with different width ↵Larry Knox2013-10-101-2/+2
| | | | | | due to prototype" warnings by casting constants to size_t where expected by string functions. Tested on jam, koala,ostrich and platypus with h5committest.
* [svn-r23713] Description:Quincey Koziol2013-05-211-7/+7
| | | | | | | | | | Clean up warnings, switch library code to use Standard C/POSIX wrapper macros, remove internal calls to API routines, update checkapi and checkposix scripts. Tested on: Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN Big-Endian Linux/64 (ostrich)
* [svn-r23238] Description:Quincey Koziol2013-02-081-1/+1
| | | | | | | | | | | | | | | | | | | | | | Bring changes from Coverity branch to trunk: r20528: Purpose: Fix coverity issue 1372 Description: Rewrite file open secition of H5FD_stdio_open to avoid TOCTUO condition. No longer calls access, and uses a tentative open in "rb" or "rb+" mode to check for existence of the file. r20609: Use HDstrncpy and HDstrncat. --gh r20611: Use HDstrncpy. --gh Tested on: Mac OSX/64 10.8.2 (amazon) w/debug, C++ & FORTRAN (h5committest not required, already tested on branch)
* [svn-r23219] Description:Quincey Koziol2013-02-021-20/+33
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring reviewed changes from Coverity branch back to trunk (QK & JK): r20457: Coverity issue 691: return of H5duo could be negative. Fixed by using STDOUT_FILENO and redesign parse_command_line and main to cleanup file allocations. The output_file var is null when using stdout. In cleanup do not close output_file if NULL. r20510: Initialize ufid = -1 and predicate HDclose call on ufid != -1 r20511: Purpose: Fix coverity issue 1715 Description: Free "file" and nested data on failure in H5FD_core_open. r20512: Initialize ifid = -1 and predicate HDclose call on ifid != -1 r20514: Initialize h5fid = -1 and predicate HDclose call on h5fid != -1 r20516: Added else branch to the if (ret_value < 0) check. r20522: Addressed coverity issues 930-933, 850, 836, 835, 1307. All minor potential buffer overwrite bugs, or coverity errors. Fixed by replacing strcpy and sprintf with strncpy and snprintf. r20523: fixed coverity issues 68, 1120, 1116i r20524: Check H5Z_SZIP->encoder_present < 1 assuming 0 represents absence. r20601: Purpose: Fix coverity issues 1703-1705 Description: Modified the cleanup code in test_free in accum.c to reset allocated buffers to NULL after they are freed, and modified the error cleanup code to check if these buffers are NULL before freeing them. Also fixed some unrelated warnings in accum.c. r20602: Use HDsnprintf and HDstrncat r20603: Purpose: Fix coverity issues 808-809 Description: Modified test_core in vfd.c to check the returns from malloc, and keep track of whether points and check are allocated by setting them to NULL when they are not. Added code to free points and check on error if they are not NULL. Also fixed unrelated warnings in vfd.c. r20604: Use HDstrncpy. r20605: Use HDstrncpy and HDstrncat. r20606: Purpose: Fix coverity issue 807 Description: Modified long_compact in stab.c to keep track of whether objname is allocated by setting it to NULL when it is not. Added code to free objname on error if it is not NULL. r20607: Changed string function calls to use versions that specify the string length to fix coverity issues 832 and 839. Tested on: Mac OSX/64 10.8.2 (amazon) (Too minor to require h5committest)
* [svn-r22219] Description:Quincey Koziol2012-03-311-4/+7
| | | | | | | | Merge "file image" changes from feature branch back to trunk. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug (h5committest upcoming)
* [svn-r21923] Description:Quincey Koziol2012-02-101-9/+107
| | | | | | | | | Add FUNC_ENTER macros for package-private routines and begin process of switching package routines to use them. All H5G routines are currently finished. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
* [svn-r21919] Description:Quincey Koziol2012-02-091-15/+15
| | | | | | | | Refactor function name macros and simplify the FUNC_ENTER macros, to clear away the cruft and prepare for further cleanups. Tested on: Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
* [svn-r21126] Description:Quincey Koziol2011-07-191-19/+53
| | | | | | | | | | | | | Clean up some compiler warnings, but mainly an interim checkin on the path of reducing code coupling in the library by removing most of the places which were accessing H5F package definitions. Tested on: Mac OS X/32 10.6.8 (amazon) w/debug FreeBSD/32 8.2 (loyalty) w/debug FreeBSD/64 8.2 (freedom) w/debug Linux/64 2.6 (heiwa) w/debug Linux/64 2.6 (ember) w/parallel
* [svn-r20885] Description:Quincey Koziol2011-05-201-2/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes back to trunk: r20340: Address coverity issue 248. Set freed pointer to NULL if realloc fails, then check for NULL before attempting to close array of handles stored in memory addressed by pointer. r20341: Added initialization udata.path = NULL; udata.visited = NULL; to prevent unintialized use after done: label. Do C-style initialization AFTER all variable definitions. r20342: Fix valgrind error in H5DUMP-XML-tall.h5 r20343: Addressed Coverity issue 591 - check the return value of H5S_SELECT_ITER_RELEASE. r20344: Added initialization udata.path = NULL; to prevent uninitialized used after done: label r20347: Purpose: Fix memory leak in overhead.c Description: Fixed leak in test() in overhead.c where array "had" was never freed. r20348: Addressed Coverity issue 705 - added prototype for resize_configs_are_equal to cache_common.h. r20392: Purpose: Fix coverity issues 1677 and 1678 Description: Added return value checking for 4 funciton calls in H5tools_get_symlink_info(). r20394: Purpose: Fix coverity issues 1674 and 1675 Description: Modified H5Epush2() and H5E_printf_stack() to keep track of whether va_start() has been called, and to call va_end() at the end if so. r20395: Should be H5MM_calloc(count * sizeof(void*)). Fixed --gh r20396: Should be H5MM_calloc(count * sizeof(void*)). Fixed. --gh Tested on: Mac OSX/32 10.6.7 (amazon) w/debug & production (h5committested on branch)
* [svn-r19398] Descriptino:Quincey Koziol2010-09-161-2/+2
| | | | | | | | | | | | | | | | | | | | | | | Clean up the internal usage H5I_dec_ref() to eliminate the sequence of flags that has been creeping in. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.4 (amazon) in debug mode Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
* [svn-r19363] When mandatory filter failed to write data chunks, the datasetRaymond Lu2010-09-091-2/+2
| | | | | | | couldn't close (bug 1260). The fix releases all resources and closes the dataset but returns a failure. Tested with h5committest - jam, heiwa, amani.
* [svn-r19133] Description:Quincey Koziol2010-07-281-32/+40
| | | | | | | | | | | | | | | | | | | | | | | | | | | | Correct traversal of user-defined links (including external links) to retain path information of object, allowing H5Iget_name() queries to work quickly (without searching entire destination file). This required some refactoring and addition of a mechanism to detect if a "fast" query was performed (for the tests). Minor code cleanups, etc. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.4 (amazon) in debug mode Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
* [svn-r18616] Description:Quincey Koziol2010-04-221-0/+19
| | | | | | | | Clean up compiler warnings. Tested on: Mac OS X/32 10.6.3 (amazon) w/debug (too minor to require h5committest)
* [svn-r16560] Description:Quincey Koziol2009-03-101-2/+0
| | | | | | | | | | Remove another call to H5E_clear_stack() from within the library. Clean up lots of compiler warnings. Tested on: Mac OS X/32 10.5.6 (amazon) (followup on other platforms forthcoming)
* [svn-r16279] Description:Quincey Koziol2009-01-081-3/+1
| | | | | | | | | | | | | | Bring revision 16278 back from revise_chunks branch: Update layout information in DCPL to unify all information in one underlying property and switch to using H5O_layout_t for storing it, which simplifies things considerably. Also, fix many compiler warnings. Tested on: FreeBSD/32 6.3 (duty) in debug mode (Original patch tested on many machines)
* [svn-r15796] Purpose: Close bug #1322Neil Fortner2008-10-071-3/+3
| | | | | | | | | Description: Fixes a possible datatype id leak that could occur during compound datatype conversion, or more precisely, when unregistering those conversions. Datatype ids normally registered by the library are no longer visible to the application via H5Fget_obj_ids and H5Fget_obj_count. Tested: kagiso, linew, smirom (h5committest)
* [svn-r15628] Description:Quincey Koziol2008-09-161-8/+8
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r15485] Purpose: Allow library to shut down properly when objects have ↵Neil Fortner2008-08-191-3/+3
| | | | | | | | | | | | | | | | reference count > 1. Description: Added a new field 'app_count' to H5I_id_info_t struct, to track the reference count on an id due to the application. the old 'count' field tracks the total. Generally any id visible to the application gets placed in app_count. Added app_ref boolean parameter to H5I_inc_ref, H5I_dec_ref, H5I_register, H5I_clear_type, and a few other functions, to specify whether the operation(s) being performed on the id(s) are due to the application (TRUE) or not (FALSE). Test added for this case. Tested: kagiso, smirom, linew (h5committest)
* [svn-r15451] Purpose: Fix various problems that were occurring when using ↵Neil Fortner2008-08-071-6/+6
| | | | | | | | | | | | | | | | mounted files. Description: Moved mount table from top file structure to shared file structure. Moved parent out of mount table and back into top file structure. Mounted files can now be accessed from any handle of the parent file. Changes to how files are closed. Stricter cycle checking on mounted files. Removed unused function H5F_has_mount(). Tested: committest in 1.8 branch. Committing now due to the urgency of the fix. No changes here are specific to the trunk, but I will keep an eye on the daily tests.
* [svn-r15290] H5Tpack didn't act correctly with nested compound datatype. ↵Raymond Lu2008-06-271-1/+0
| | | | | | | | The new size of the type in the inner nest wasn't passed to the outer nest. This has been fixed. Tested on kagiso, linew, smirom.
* [svn-r15131] Description:Quincey Koziol2008-06-031-3/+0
| | | | | | | | | | | | | | | | | | | | | | Finish omnibus chunked dataset I/O refactoring, to separate general actions on chunked datasets from actions that are specific to using the v1 B-tree index. Cleaned up a few bugs and added some additional tests also. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.5.2 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14973] Purpose: Fix bug in H5G_get_name_by_addr where buffer size is ↵Scott Wegner2008-05-121-1/+1
| | | | | | | | | | | less than size of name Description: In the new tests merged from the fortran_1_8 branch, there is a test that fetches a dataset name in a small buffer. The call to H5G_get_name_by_addr wrote an extra byte off the end of the buffer. A simple and sufficient fix is to decrease the buffer size passed to strncmp by 1. This bug was only caught by Visual Studio 2005 with extra debug checks on. Tested: VS2005 on WinXP kagiso
* [svn-r14284] Description:Quincey Koziol2007-11-241-188/+94
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Add H5Lvisit_by_name() API routine to library. Eliminated all (five!) other group traversal routines and changed them all to use the new API routine. Cleaned up output of h5ls & h5stat: - Issue error when requesting recursive traversal of a file with the "group info" flag, but no group given - Print info about root group in all(?) appropriate situations - Don't print "verbose" information about root group until the root group is in the list of objects to display (mostly because h5ls & h5stat had a different twist on traversing the groups in a file that the other utilities) Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14224] Description:Quincey Koziol2007-10-301-4/+7
| | | | | | | | | | | | | | | | | | | Change H5Literate -> H5Literate_by_name and add simpler form of H5Literate, to bring this routine into alignment with the other new API routines. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14175] Description:Quincey Koziol2007-10-021-2/+8
| | | | | | | | Minor fixes to avoid memory leaks when 'realloc' fails. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r14154] Description:Quincey Koziol2007-09-251-87/+92
| | | | | | | | | | | | | | | | | | | | Finish deprecating last H5G symbol (H5G_obj_t) - yay! Lots of misc. library fixes to remove confusion between links and objects. The tools could still use another pass, to remove h5trav_type_t type and make the correct distinction between links & objects. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode
* [svn-r14122] Description:Quincey Koziol2007-08-281-1/+1
| | | | | | | | | | | | | Move H5Gmove() to deprecated code section, replacing with H5Lmove() in source files. Tested on: FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (kagiso) Linux/64 2.6 (smirom) Solaris/32 5.10 (linew) Mac OS X/32 10.4.10 (amazon)
* [svn-r13986] Description:Quincey Koziol2007-07-171-1/+1
| | | | | | | | | Add flag to bypass (expensive) B-tree & heap size retrieval for internal calls to H5O_get_info(). Teted on: Mac OS X/32 10.4.10 (amazon) FreeBSD/32 6.2 (duty)
generated by cgit v0.12 at 2024-07-09 14:31:10 (GMT)