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* TRILAB-192 - merge changes from developAllen Byrne2020-04-072-7/+3
| | | | Single source, config files, for warnings for both autotools and CMake. Update CMake libraries, tools, tests to use correct flags.
* Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2020-04-051-2/+12
|\ | | | | | | | | * commit 'db3f89ce9dc7eae17cb15d39e402112c3fbd2955': Merge pull request #2461 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/dtype_close_on_error to develop
| * Merge pull request #2461 in HDFFV/hdf5 from ↵Vailin Choi2020-04-021-2/+12
| | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/dtype_close_on_error to develop * commit 'afdcac28b85d690eebc80ab568fa5266081baaaa': A fix in the cleaning up code for datatype when datatype initialization via H5D__init_type() fails. This is triggered by the tests for revised references when the libver bounds setting does not allow version 4 datatype message to be created. The test failure is abort core dumped. This is due to the datatype initialization fails before the datatype ID is registered. The datatype cleanup code should provide for the above situation. The code to fix the problem is the same as what is done in H5D__open_oid().
* | TRILAB-192 merging warnings changes from developAllen Byrne2020-03-301-0/+6
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* Remove VCS merge conflictQuincey Koziol2020-03-241-6/+0
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* Revise API for H5get_alloc_stats() to take a struct instead of separate values.Quincey Koziol2020-03-234-61/+33
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* Add routines to query the library's free list sizes and allocation stats.Quincey Koziol2020-03-238-211/+472
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* Merge pull request #2451 in HDFFV/hdf5 from ↵Vailin Choi2020-03-165-5/+23
| | | | | | | ~VCHOI/my_third_fork:bugfix/develop_seg_fault_sel_compat to develop * commit '81b1ed4e1724b8a6a731ab2b8fb03234a8b49d15': Fix issues when deserializing point/all/none selection with version beyond the library's supported version: (1) Verify the decoded version before proceeding further with deserialization (2) Close the dataspace if errors occurred after opening the dataspace
* Merge pull request #2425 in HDFFV/hdf5 from ~JAKE.SMITH/hdf5:hdf5_1_12 to ↵Jake Smith2020-03-011-2/+2
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit '46f0de82c7674a28b08e4da3b0149c793b762203': Fix improper signing key null check. (HDFFV-11015) Add updates from develop, PR 1958.
| * Fix improper signing key null check. (HDFFV-11015)Jacob Smith2020-02-281-2/+2
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* | Switch the 'get offset' operation from a dataset 'get' callback to a [native]Quincey Koziol2020-02-285-37/+21
| | | | | | | | dataset 'optional' operation.
* | Merge pull request #2325 in HDFFV/hdf5 from ~DYOUNG/werror:h5t_copy to developDavid Young2020-02-2515-194/+480
| | | | | | | | | | | | | | | | | | | | | | Merged per discussion with Elena. * commit '3f903a441ad84001ea66589728bd8b036b6fdfca': Take out the temporary performance tests. Make calls through a function pointer. Use the same number of arguments, always. Increase iterations, provide a baseline for no-op, simplify the overhead case a bit. Temporarily add some code that measures the time to run the simplest possible H5T__copy_all()-like routine 10 million times and then measures the version with FUNC_ENTER_STATIC/_LEAVE_NOAPI and a HGOTO_ERROR() statement. H5T_copy() constification plus Quincey's contributions.
* | Merge pull request #2391 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-02-241-1/+1
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit '5b5ff6ee094033f2ecd974b8e0bdaac2b0c7e617': Correct usage of add_compile_definitions Merge changes from develop mostly cmake 3.12 minimum version Merge changes from develop for CMake and Java
| * | Merge changes from develop mostly cmake 3.12 minimum versionAllen Byrne2020-02-231-1/+1
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* | | Partial fix for HDFFV-10792Jordan Henderson2020-02-211-4/+45
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* | Merge pull request #2338 in HDFFV/hdf5 from ~JHENDERSON/hdf5:hdf5_1_12 to ↵Jordan Henderson2020-02-1715-117/+102
|\ \ | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit '2dbcd87fcddfb519369a368a00acbe8826d5a0eb': Fix some places where H5P_DEFAULT gets passed down to a VOL connector
| * | Fix some places where H5P_DEFAULT gets passed down to a VOL connectorJordan Henderson2020-02-0115-117/+102
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* | | Squashed commit of the following:David Young2020-01-3122-201/+195
|/ / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | commit ff7a9a34de2fcd78f5d32a1532f3d0e224b20d94 Author: Kimmy Mu <kmu@hdfgroup.org> Date: Wed Jan 29 14:12:18 2020 -0600 Merge pull request #2324 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12 * commit '781fa57f6ee816e037dd12fff02d37ff7ec9c2b1': pick up missing piece from merge Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop remove redundent definition Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2315 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop missing prototype warning prototype issue Merge pull request #2306 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to develop Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized to develop Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to develop Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to develop Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to develop commit 9f3d808c05d2a3b308f32c958c6671fcac0a432c Author: David Young <dyoung@hdfgroup.org> Date: Wed Jan 29 11:43:55 2020 -0600 testpar/t_2Gio.c: Fix a typo that I think was introduced by a previous warnings PR. An array element was assigned to itself---shape[2]Â =Â shape[2];---instead of being assigned to chunk[2]. fortran/src/H5Pf.c: move conditional compilation controlled by H5_NO_DEPRECATED_SYMBOLS outside of a function for readability. fortran/src/H5match_types.c: put a variable's declaration under the same conditional compilation (H5_FORTRAN_HAVE_C_LONG_DOUBLE) as its use. For now, skip compilation of some unused debug dump routines in the JNI. While I'm in the JNI, delete a set-but-unused variable. src/H5Z.c: condition a variable declaration on H5_NO_DEPRECATED_SYMBOLS so that it's not declared but unused or vice versa. test/cache_common.h: add an #include in to get some symbols we need to avoid implicit declaration warnings. test/dsets.c: use a more conventional conditional-compilation syntax. test/dt_arith.c, test/fillval.c: initialize a bunch of uninitialized variables before use. test/vfd.c: pass the expected type of `void **` to posix_memalign(3) instead of `int **`. testpar/t_bigio.c: explicitly compare with 0 instead of using ! when "equal to 0?" is the question not "is false?" Repair some indentation while I'm here. testpar/testpar.h: repair misaligned line-continuation backslashes in a macro that probably should be a function so that we don't have to fiddle with the line continuation to begin with. tools/src/h5repack/h5repack_main.c: fix some compiler fussing about enums. tools/test/perform/pio_engine.c: the compiler fusses if you cast a function call returning double directly to off_t. It's ok if you cast a variable that's a double to off_t, however. Write and use a new function, sqrto(), to avoid the cast warnings. commit 43a4b80b21c0329fbc1f9a0e2854795189f0bb50 Author: David Young <dyoung@hdfgroup.org> Date: Wed Jan 29 10:47:30 2020 -0600 Reduce casts of HDcalloc()/HDmalloc() that -Wc++-compat required. Reduce gratuitous casts---e.g., (size_t)1. Use the right format string for a pointer. In the H5C sanity checks, change a "size increase" variable from ssize_t (too narrow) to int64_t (wide enough). Parenthesize every appearance of `storage` in the macro `H5D_CHUNK_STORAGE_INDEX_CHK(storage)` so that you can pass in an expression like &sc and it works properly. Disallow re-assignment of the `dset` parameter to H5D__chunk_init() because it helped assure me that it's safe to replace the repeating expression `&dset->shared->layout.storage.u.chunk` with `sc` throughout. Replace lengthy expressions such as `&dset->shared->layout.storage.u.chunk` with `sc` throughout several functions in H5Dchunk.c ISTR that the compiler warned that `sc` was declared but unused in a couple of functions, and then I found that `sc` could be used in many places. Maybe the disused `sc` appeared because a bunch of code was copied and pasted, I don't know. Anyway, it's a lot tighter code now that I use `sc`. In H5D__chunk_update_old_edge_chunks() and H5D__chunk_delete() I actually expand `sc` and another temporary variable, `pline`, because they're used only in !defined(NDEBUG) code. This squashes unused-variable warnings in the defined(NDEBUG) configuration. Don't drop the `volatile` qualification with a cast in tools/src/h5import/h5import.c. commit 035bfa0769a4012881fc659b673bacf44d146537 Author: David Young <dyoung@hdfgroup.org> Date: Tue Jan 28 20:35:28 2020 -0600 Reduce differences between my -Werror branch and `develop`: Rename index -> idx, fileno -> fnumber, fileno -> fno to avoid GCC shadowed declaration warnings about index(3). Convert #pragma GCC diagnostic push/pop/ignored to the HDF5 library's H5_GCC_DIAG_OFF()/H5_GCC_DIAG_ON() macros.
* | Merge pull request #2331 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-01-312-0/+9
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit 'a29f9e8451ffa391c8395db1142bd003f40f3aaa': Merge changes from develop to fix various issues Remove commented flags Revert accidental change Chnage tools debug macros to not use the error stack Create common warnings for build systems
| * | Merge changes from develop to fix various issuesAllen Byrne2020-01-302-0/+9
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* | | Introduce new H5VL _by_value routinesJordan Henderson2020-01-295-25/+227
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* | Merge pull request #2324 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12Kimmy Mu2020-01-2954-241/+250
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '781fa57f6ee816e037dd12fff02d37ff7ec9c2b1': pick up missing piece from merge Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop remove redundent definition Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to develop Merge pull request #2315 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop missing prototype warning prototype issue Merge pull request #2306 in HDFFV/hdf5 from ~KMU/hdf5:develop to develop Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to develop Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized to develop Merge pull request #2295 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/float to develop Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to develop Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to develop
| * | Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to developKimmy Mu2020-01-281-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '406330addf45529ecdd088f4d22e9aab9a03661d': rename macro change condition pick up from Dave's fix leave Wswitch-default for later fix fix Wredundant-decls, Wswitch-default, Wdeclaration-after-statement, Wsign-compare, Wmisleading-indentation, Wshadow
| * | prototype issuekmu2020-01-281-1/+1
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| * | Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to developKimmy Mu2020-01-2811-91/+93
| | | | | | | | | | | | | | | | | | * commit 'af5c33afabdae2e39bb45eb1b3e9c8366da01145': remove unnecessary stuff squash cast warning fix
| * | Merge pull request #2291 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/uninitialized ↵Kimmy Mu2020-01-281-2/+2
| | | | | | | | | | | | | | | | | | | | | to develop * commit '2de0ce0d8ba2fb58fadefc5d718a3c0fedab25c8': fix uninitizlized warning
| * | Merge pull request #2292 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/prototype to ↵Kimmy Mu2020-01-281-1/+2
| | | | | | | | | | | | | | | | | | | | | develop * commit '9f80ffa1f1908975b3100814b2529bf779521e13': fix missing prototype warning
| * | Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to developKimmy Mu2020-01-2843-145/+151
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '145ef3ceee20c28a443bd11507c58858bea3f889': more cleanup change it back pick up missing piece fix unused related warnings removed unused parameter more fix and address comments remove unsed var,function,macro, etc
* | | Update version to 1.12.1-snap0 for hdf5_1_12 branch.Larry Knox2020-01-281-3/+3
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* | Merge pull request #2238 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12Kimmy Mu2020-01-2428-55/+63
|\ \ | | | | | | | | | | | | | | | | | | * commit '48cc850199901c5b67a40183262f4ead975b884f': fix test assert fail error Merge pull request #2071 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings to develop Merge pull request #2234 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings to develop
| * | Merge pull request #2071 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings ↵Kimmy Mu2020-01-0827-55/+62
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '0a2bb11b248df6841daabca3970df5d8504adfc7': address problems from comments fix and address comments change according to previous comments add missing piece remove unnecessary check macro fix intel compile warnings Revert "fix warnings from Intel compiler" Revert "fix warnings and some text alignment" Revert "let hdf5 pick up the right compiler in Intel environment" Revert "fix issues from previous PR comments" Revert "using a different MACRO" using a different MACRO fix issues from previous PR comments let hdf5 pick up the right compiler in Intel environment fix warnings and some text alignment fix warnings from Intel compiler
| * | Merge pull request #2234 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings ↵Kimmy Mu2020-01-081-0/+1
| | | | | | | | | | | | | | | | | | | | | to develop * commit '30ac64d83aff5e022d51a17fd6c1d72903ae4f02': add new type support
* | | Merge pull request #2289 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-01-221-5/+14
| | | | | | | | | | | | | | | | | | | | | * commit 'a92cfed71e0da0ff61af2550640e38bf6d415fee': Remove irrelevant sentence from comment. Remove duplicate lines noted on forum by Eric Bavier Add v111 version for H5O functions to enable version1 default for HDF5 1.8-1.10 and version 3 default for HDF5 1.12. Version 2 functions are available (deprecated) but will not be the default for any version.
* | | Squashed commit of the token_refactoring branch:Dana Robinson2020-01-1966-998/+4065
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* | | H5R: set app ref when incrementing ref_count on location held by referenceJerome Soumagne2020-01-175-18/+39
|/ / | | | | | | (fix HDFFV-10992)
* | Cherry pick of 0225e6d5969Quincey Koziol2020-01-0422-148/+190
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* | Cleanups from PR reviewsQuincey Koziol2020-01-044-102/+101
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* | Remove unnecessary H5CX callQuincey Koziol2020-01-041-4/+0
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* | Refactor H5Dvlen_get_buf_size to use optional dataset operation, with ↵Quincey Koziol2020-01-047-54/+255
| | | | | | | | generic fallback for VOL connectors that don't implement operation
* | Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2020-01-0445-1571/+2860
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* | For portability, insulate the HDF5 library from some system macros.David Young2019-12-191-1/+18
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* | Minor tweaks noticed while going over VOL documentation.Dana Robinson2019-12-163-6/+6
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* | Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-168-51/+36
| | | | | | | | the Autotools and CMake.
* | Trivial parameter renaming in VOL API calls.Dana Robinson2019-12-164-23/+23
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* | Modify H5VL initialization routines to initialize all VOL-managed objectNeil Fortner2019-12-1311-2/+153
| | | | | | | | | | types. Modify H5VLwrap_register() to reject non-VOL-managed object types. Also fix overisights in h5trace.c from previous changes.
* | Update version to 1.12.0-alpha1.Larry Knox2019-12-121-2/+2
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* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2019-12-112-2/+2
|\ \ | | | | | | | | | | | | * commit '9b38aef978299a76b6b19586396bf626a1e58df6': Fix 2010 compile issue
| * | Fix 2010 compile issueAllen Byrne2019-12-112-2/+2
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* | | HDFFV-10876 Merge from developAllen Byrne2019-12-091-21/+17
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* | Merge pull request #2116 in HDFFV/hdf5 from ↵Jerome Soumagne2019-12-0919-180/+429
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | ~JSOUMAGNE/hdf5:hdf5-1_12-ref_token to hdf5_1_12 * commit '1aea46ce671daf2828ac65d0b8551b369f497922': Fix H5VL_token_t type and fix H5VL_loc_by_token to use H5VL_token_t * Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char to structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc. H5R: fix H5Tconv to check for null references Remove H5VL_NATIVE_FILE_GET_FILE_ID and add H5VL_OBJECT_GET_FILE
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