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* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)David Young2022-04-161-74/+20
| | | | | | | | | | | | | | | | | * Do not conditionally compile code that uses a pointer dereference and assignment to copy a potentially unaligned variable to aligned automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s. Disassembling the generated code reveals that the `memcpy(3)`s optimize (`-O3`) to a single `mov` instruction for x86_64, which is not strict about alignment. This change reduces the size of code and scripts by 143 lines, eases our way to cross-compilation, and avoids invoking undefined behavior. * Committing clang-format changes * Per discussion, use HD and add comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes the STATIC flavor of FUNC_ENTER macros (#1622)Dana Robinson2022-04-081-18/+18
| | | | | * Removes the STATIC flavor of FUNC_ENTER macros
* Combo set of async and other changes (#161)Quincey Koziol2021-06-021-14/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* develop revert source to clang-format version 11 (#293)Allen Byrne2021-01-291-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction
* Jan ws changes (#282)Allen Byrne2021-01-271-1/+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 * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Whitespace fixes except for H5Tprivate.h typo fix
* Fix problems with vlens and refs inside compound using H5VLget_file_type() ↵hdf5-1_13_0-rc5Neil Fortner2021-01-221-1/+12
| | | | | | | | | | | | (#274) * Fixed problems with vlens and refs inside compound using H5VLget_file_type() * Fix date in RELEASE.txt * Add assertions * Move some manipulation of H5VL_object_t struct fields into the H5VL package.
* 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
* Basic alignment with async branch (#115)Quincey Koziol2020-11-231-2/+2
| | | | | | | * 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 Byrne2020-09-301-187/+162
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* Minor refactoring based on 1.10 normalization workDana Robinson2020-08-171-0/+1
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* Move H5T_vlen_reclaim to package scopeQuincey Koziol2020-08-071-4/+4
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* Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2019-12-201-2/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* Implement H5VLget_file_type() to return a copy of a datatype with theNeil Fortner2019-11-081-112/+64
| | | | | | | | | | | 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 Soumagne2019-10-081-93/+34
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info.Quincey Koziol2019-10-081-5/+2
| | | | Remove "by address" location for VOL operations. (Switching to "by token")
* Fix H5VL_blob_get to return size of blobJerome Soumagne2019-10-081-8/+61
| | | | | | | | | | | | | | | | | | | | Fix const in blob API Add H5HG_HEAP_ID_SIZE macro to return native blob size Add maximum size for blobs Fix blob API callbacks to pass VOL file object Add public wrappers for blob VOL API Implement passthrough blob callbacks Update H5Tvlen after callback changes Update trace information for H5VL blob routines Fix public header inclusion in native and passthru headers
* Add 'blob' callbacks to VOL, along with a native implementation to store themQuincey Koziol2019-10-081-350/+407
| | | | | | | in the global heap, and changed the VL datatype conversion code to use blobs. Move encode/decode of sequence lengths into VL datatype callbacks, from native VOL blob routines.
* Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-17/+17
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* Squashed commit of private branch changes to support stackable VOL plugins.Quincey Koziol2018-10-251-3/+3
| | | | modified: test/dsets.c
* Normalization with vol_integration (misc internal and datatype)Dana Robinson2018-09-201-9/+15
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* Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-110/+42
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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-r30219] Description:Quincey Koziol2016-07-221-5/+5
| | | | | | | | | More warning cleaups: down to 770 warnings (from ~940) in 134 files (from 148), with 28 unique kinds of warnings (from 31). Tested on: MacOSX/64 10.11.5 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28761] Description:Quincey Koziol2016-01-011-4/+4
| | | | | | | | | | | | Clean up many mismatches between malloc/free and H5MM_malloc/H5MM_xfree in the library and tests (and use of H5free_memory and H5Dvlen_reclaim). Also make H5Ocopy use a private version of H5Lexists, which doesn't internally throw (and suppress) errors when an object (or the path to it) isn't found in the destination. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28646] Minor normalization with revise_chunks.Dana Robinson2015-12-141-12/+0
| | | | | | | | | Also purged obsolete /*ARGSUSED*/ from the library. Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* [svn-r27768] Description:Quincey Koziol2015-09-141-28/+4
| | | | | | | | | | | | | | | | | | | | | | 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-r27626] Various minor warning fixes before major SWMR and VDS merges.Dana Robinson2015-08-311-4/+22
| | | | | | | | | | | gcc 4.9.2 was used to create the warning list - implicit casts - shadowed variables - various enum issues - other minor fixes (comments, unused macros, etc.) Tested on: h5committest
* [svn-r27133] - Add a new attribute function characterstic for format:Mohamad Chaarawi2015-06-011-12/+12
| | | | | | | | * H5_ATTR_FORMAT(X,Y,Z) __attribute__((format(X, Y, Z))) - Rename UNUSED attribute characterstic to H5_ATTR_UNUSED. - Rename NORETURN attribute characterstic to H5_ATTR_NORETURN tested with h5committest.
* [svn-r23695] Description:Quincey Koziol2013-05-111-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Clean up warnings in H5Tconv.c (down to _only_ 9000 lines of output now!) Merge changes from Coverity branch back to trunk: r20684: Fix for coverity bug #1721 which was due to the fix for coverity bug #943. r20685: Use HDstrncpy. --gh r20761: Purpose: Fix valgrind issues Description: Free image_data and data as appropriate in test_image. r20762: Purpose: Fix coverity issue 600 Description: Add check for return value of H5O_close in H5Ocopy. Also cleaned up various warnings. r20763: Purpose: Fix valgrind issues with h5stat Description: Modified h5stat to free "iter" before exit, and free "hand" before exit if parse_command_line exits directly. r20764: fixed coverity issues: 69, 327, 614, 684, 685, 696, 697, 1681, 967, 826, 660, 80 r20765: Fixed coverity bug 668 Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning. No actual integer overflow tests are performed since it's just a test program but I did add a check that n_elements is >= 1. I also changed an error condition from doing its own close and returning -1 to "goto out;" like the rest of the program. r20766: Fixed coverity bug 667 Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning. No actual integer overflow tests are performed since it's just a test program. Tested on: Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN (h5committest upcoming)
* [svn-r22287] Description:Quincey Koziol2012-04-161-10/+10
| | | | | | | | Clean up more FUNC_ENTER/FUNC_LEAVE macros and move H5D & H5T code toward the final design (as exemplified by the H5EA & H5FA code). Tested on: Mac OSX/64 10.7.3 (amazon) w/debug & parallel
* [svn-r21919] Description:Quincey Koziol2012-02-091-26/+26
| | | | | | | | 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-r19272] Description:Quincey Koziol2010-08-201-119/+52
| | | | | | | | | | | | Close out various resource leaks and usages of uninitialized memory that were flagged by valgrind. [There's still some more valgrind warnings, but it's better now... :-/ ] Also clean up warnings and code formatting. Tested on: Mac OS X/32 10.6.4 (amazon) w/debug & valgrind (h5committest forthcoming)
* [svn-r18804] Purpose:Mike McGreevy2010-05-141-0/+41
| | | | | | | | | | | | | Fix memory leaks Description Added a routine to free memory which addresses a memory leak when variable length strings are used as fill values. Tested: h5committest and valgrind (on jam/amani) to confirm freed memory.
* [svn-r18212] Description:Quincey Koziol2010-02-051-2/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring revisions from Coverity fixing branch to trunk: r18184: Fixed Coverity issue 373. Allocated memory freed in line 762 in case of error. r18185: Fixed Coverity issues 357 & 358. Added check for NULL pointer before use. r18186: Fix coverity item 65. Added code to h5unjam to correctly handle failures in read() and write, and also to correctly handle writes that write less than requested. r18187: Fix coverity items 115 and 116. Added code to H5Tenum.c to correctly close opened datatypes in case of failure. r18188: Fixed Coverity issue 46. Check that dataset->shared is not null when freeing memory after error. r18190: Fix coverity item 95. Added code to H5T_create_vlen to correctly close allocated datatype in case of failure. r18191: Fixed Coverity error 59. Checked sfirst for -1 value before use in line 10533. r18192: Fix Coverity items 121 and 28 Added Asserts: 121: assert that all dimensions of count have values greater than zero. 28: assert curr_span pointer is not null before dereference. Note: still need too add checks in hyperslab APIs that fail when count values are zero, and appropriate tests. r18194: Fixed Coverity issues 61 & 62. Checked variable snpoints for value < 0 in line 218. Tested on: Mac OS X/32 10.6.2 (amazon) w/debug & production (already daily tested on coverity branch)
* [svn-r18197] Description:Quincey Koziol2010-01-301-2/+2
| | | | | | | | | Trim trailing whitespace from source code files with this command: find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//' Tested on: None - eyeballed only
* [svn-r17177] In H5Odtype.c, the decoding function used to mark the datatype ↵Raymond Lu2009-07-131-1/+7
| | | | | | | | | | as on disk (see bug #1585). I changed it to undefined and let the caller functions decide the location of the datatype. For H5Tdecode, it should mark the datatype as in memory. For other callers like H5Dopen or H5Aopen, they should makr it as on disk. Tested it on jam, smirom, linew.
* [svn-r15656] Purpose: fix bug 1286Neil Fortner2008-09-181-49/+154
| | | | | | Description: Added configure test to see if pointer alignment restrictions are enforced (as in dereferencing an unaligned pointer causes an error). Added code in H5Tvlen.c to avoid dereferencing unaligned pointers, conditionally compiled based on the configure test. Added test case in dtypes.c which would previously cause such machines to fail. Tested: kagiso, smirom, linew (h5committest); linew64
* [svn-r15609] Description:Quincey Koziol2008-09-101-34/+32
| | | | | | | | Omnibus compiler warning cleanup & some reformatting also. Tested on: Mac OS X/32 10.5.4 (amazon) Too minor to require h5committest
* [svn-r15485] Purpose: Allow library to shut down properly when objects have ↵Neil Fortner2008-08-191-1/+1
| | | | | | | | | | | | | | | | 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-r14004] Description:Quincey Koziol2007-07-241-9/+12
| | | | | | | | | | | | Fix problem with datatype messages where the version of the format for a datatype message could depend on the "use the latest format" flag from the file after it was initially created. Tested on: FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (kagiso) Mac OS X/32 10.4.10 (amazon)
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
* [svn-r13068] Ran bin/reconfigure. Some of the scripts have been changed or ↵James Laird2006-12-181-1/+1
| | | | | | | | | haven't been run in a while, so many of the source files were updated with tracing macros, etc. No code changes by me. Tested on kagiso and smirom.
* [svn-r12842] Description:Quincey Koziol2006-11-021-4/+4
| | | | | | | | | | | | | | | | Refactor generic property list initialization code to put property list specific routines in property list modules, instead of scattered to the four winds. Also, introduce property list class initialization objects, to make adding new property list classes in the library easier. Fix daily test failure by using H5Pget_elink_prefix() API routine instead of looking at the "raw" generic property list information. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) w/threadsafe Linux/32 2.4 (heping) w/C++ & FORTRAN Linux/64 2.4 (mir) w/build-all & 1.6 compat
* [svn-r12680] Description:Quincey Koziol2006-09-251-1/+1
| | | | | | | | | Review, revise & checkin in Peter's latest round of object copy changes, which add basic support for datasets & attributes with reference datatypes. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r11899] Purpose:Quincey Koziol2006-01-281-1/+1
| | | | | | | | | | | | | | | | Bug fix & new feature Description: Support variable-length datatypes in compact data storage and chunked data storage, along with attributes. Bug fix on the H5T_vlen_set_loc to allow for changing the file on a variable-length datatype on disk. Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Can't h5committest right now, due to missing cache files.
* [svn-r11758] Purpose:Quincey Koziol2005-12-041-0/+1
| | | | | | | | | | | | | New feature Description: Add in a combination of Peter's & my code to support copying variable-length data from one file to another, although currently only supported with contiguous data storage. Platforms tested: FreeBSD 4.11 (sleipnir) h5committest
* [svn-r11712] Purpose:Quincey Koziol2005-11-151-5/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | New feature Description: Check in baseline for compact group revisions, which radically revises the source code for managing groups and object headers. WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! This initiates the "unstable" phase of the 1.7.x branch, leading up to the 1.8.0 release. Please test this code, but do _NOT_ keep files created with it - the format will change again before the release and you will not be able to read your old files!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! Solution: There's too many changes to really describe them all, but some of them include: - Stop abusing the H5G_entry_t structure and split it into two separate structures for non-symbol table node use within the library: H5O_loc_t for object locations in a file and H5G_name_t to store the path to an opened object. H5G_entry_t is now only used for storing symbol table entries on disk. - Retire H5G_namei() in favor of a more general mechanism for traversing group paths and issuing callbacks on objects located. This gets us out of the business of hacking H5G_namei() for new features, generally. - Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t - Lots more... Platforms tested: h5committested and maybe another dozen configurations.... :-)
* [svn-r11384] Purpose:Quincey Koziol2005-09-121-6/+1
| | | | | | | | | | | | | | | | | | | | | Code cleanup Description: Merge back changes from "compact group" work that improve the infrastructure of the library and may impact others. In this round of merging, that includes: - Move datatype allocation into single internal routine, instead of duplicated code that was spread out in a dozen or so places. - Clean up guts of object header routines (H5O_*) to allow for some of the fancieroperations that need to be performed on groups, along with some general improvements. - Added a new error code - Some minor cleanups in other code.... Platforms tested: FreeBSD 4.11 (sleipnir) Linux 2.4 Mac OS X
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-17/+17
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Trim trailing whitespace, which is making 'diff'ing the two branches difficult. Solution: Ran this script in each directory: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
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