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* Fixed configure issue when building HDF5 with NAG Fortran 7.0.M. Scot Breitenfeld2020-02-281-0/+6
| | | | | | | HDF5 now accounts for the addition of half-precision floating-point in NAG 7.0 with a KIND=16. (MSB - 2020/02/28, HDFFV-11033)
* Merge branch 'hdf5_1_12' of ↵M. Scot Breitenfeld2020-02-281-215/+3
|\ | | | | | | ssh://bitbucket.hdfgroup.org:7999/~brtnfld/hdf5_msb into hdf5_1_12
| * Merge pull request #2418 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_12 to ↵Larry Knox2020-02-281-215/+3
| |\ | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit 'ec6162f7bbd77b411bbefe66f5cc6a06e6094e0f': One more change to RELEASE.txt. Clear RELEASE.txt HDF5 1.12.0 entries.
| | * One more change to RELEASE.txt.Larry Knox2020-02-281-9/+1
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| | * Clear RELEASE.txt HDF5 1.12.0 entries.Larry Knox2020-02-281-207/+3
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* | Fixed issue building HDF5 with NAG Fortran 7.0.M. Scot Breitenfeld2020-02-281-6/+19
|/ | | | | | Accounted for the additon of half precision floating-point with a KIND=16. HDFFV-11033
* Merge pull request #2416 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_12 to ↵Larry Knox2020-02-282-2/+2
|\ | | | | | | | | | | | | hdf5_1_12 * commit '2c43125dbe01e2c3c1f8a05ba38d65aad0e9d229': Modify expression to match mpicc built with Intel as intel compiler, not gcc.
| * Modify expression to match mpicc built with Intel as intel compiler, notLarry Knox2020-02-272-2/+2
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* Merge pull request #2413 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-02-271-2/+3
|\ | | | | | | | | | | | | hdf5_1_12 * commit 'b551bee9cb2440d4b32d0a58e87e8047b7fef7f4': Add java version and reference libsettings
| * Add java version and reference libsettingsAllen Byrne2020-02-271-2/+3
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* Merge pull request #2410 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Larry Knox2020-02-2716-267/+256
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit '1e5d4257c4e88a9368899798672bf3e3cc37971b': Update examples and fix version references Move MODEL check to before usage in CTestScript.cmake.
| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2020-02-2615-194/+480
| |\ | |/ |/| | | | | * commit '6bf98769c1f264ad414c949c917ff61cdb16f35a': Merge pull request #2325 in HDFFV/hdf5 from ~DYOUNG/werror:h5t_copy to develop
* | Merge pull request #2403 in HDFFV/hdf5 from ~DYOUNG/werror:h5t_copy-for-1.12 ↵David Young2020-02-2615-194/+480
|\ \ | | | | | | | | | | | | | | | | | | to hdf5_1_12 * commit 'a3462bf164ef3b00e863de64a2a547c76f7adcd4': Merge pull request #2325 in HDFFV/hdf5 from ~DYOUNG/werror:h5t_copy to develop
| * | 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.
| | * Update examples and fix version referencesAllen Byrne2020-02-2615-258/+248
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| | * Move MODEL check to before usage in CTestScript.cmake.Allen Byrne2020-02-262-9/+8
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* | Merge pull request #2406 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Larry Knox2020-02-253-37/+78
|\ \ | |/ |/| | | | | | | | | | | | | hdf5_1_12 * commit '44003b135f9530f929ff7d2b30c79092704e32a8': Change to dynamic allocation for buffer Copy generated files instead of creating twice Fix standalone link in perform tools
| * Change to dynamic allocation for bufferAllen Byrne2020-02-251-1/+17
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| * Copy generated files instead of creating twiceAllen Byrne2020-02-251-8/+32
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| * Fix standalone link in perform toolsAllen Byrne2020-02-252-28/+29
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* Merge pull request #2399 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-02-254-16/+12
|\ | | | | | | | | | | | | hdf5_1_12 * commit '6b1e2d835fbbdbea242443837b3694f48e89591a': Fix Fortran macro use and jni comment
| * Fix Fortran macro use and jni commentAllen Byrne2020-02-254-16/+12
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* Merge pull request #2395 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-02-245-19/+129
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit 'ab88352ac262e3b8240c30711b9243e5bdcc5462': Update Windows platforms HDFFV-11036 - Corrected CMake test by adding file compare script
| * Update Windows platformsAllen Byrne2020-02-241-5/+1
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| * HDFFV-11036 - Corrected CMake test by adding file compare scriptAllen Byrne2020-02-244-14/+128
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* Merge pull request #2391 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-02-2494-378/+517
|\ | | | | | | | | | | | | | | | | 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
| * Correct usage of add_compile_definitionsAllen Byrne2020-02-231-3/+1
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| * Merge changes from develop mostly cmake 3.12 minimum versionAllen Byrne2020-02-2388-347/+481
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| * Merge changes from develop for CMake and JavaAllen Byrne2020-02-218-31/+38
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* | Merge pull request #2387 in HDFFV/hdf5 from ~JHENDERSON/hdf5:hdf5_1_12 to ↵Jordan Henderson2020-02-222-4/+60
|\ \ | |/ |/| | | | | | | | | hdf5_1_12 * commit '34e9f449cca2d03629e70efa1a12332f5e7660b7': Partial fix for HDFFV-10792
| * Partial fix for HDFFV-10792Jordan Henderson2020-02-212-4/+60
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* Merge pull request #2380 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:hdf5_1_12 to ↵Scot Breitenfeld2020-02-192-1/+7
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit 'e8285ad6b1ecbbe7159d2526277e5f0316932b2a': update HDFFV-11029 Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size
| * update HDFFV-11029M. Scot Breitenfeld2020-02-181-0/+6
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| * Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_sizeM. Scot Breitenfeld2020-02-181-1/+1
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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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* | Merge pull request #2373 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-02-111-3/+12
|\ \ | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit 'ec4da2d649726e8d0d2671201b1bb4c1f11f3e96': Update release note
| * | Update release noteAllen Byrne2020-02-111-3/+12
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* | | Merge pull request #2370 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:hdf5_1_12 to ↵Scot Breitenfeld2020-02-118-65/+133
|\ \ \ | |/ / |/| | | | | | | | | | | | | | hdf5_1_12 * commit '08737e596da4c4e3d9917c84be7fc2269e02f63c': HDFFV-11018 Add Fortran H5F_LIBVER_V*_F definitions
| * | HDFFV-11018 Add Fortran H5F_LIBVER_V*_F definitionsM. Scot Breitenfeld2020-02-118-65/+133
|/ / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Added ------ New Definitions: INTEGER :: H5F_LIBVER_ERROR_F INTEGER :: H5F_LIBVER_NBOUNDS_F INTEGER :: H5F_LIBVER_V18_F INTEGER :: H5F_LIBVER_V110_F INTEGER :: H5F_LIBVER_V112_F New API: h5pget_libver_bounds_f(fapl_id, low, high, hdferr) Removed: call to C wrapper h5pset_libver_bounds_c in h5pset_libver_bounds_f
* | Merge pull request #2365 in HDFFV/hdf5 from ~MYANG6/hdf5-develop:hdf5_1_12 ↵Muqun Yang2020-02-102-1/+23
|\ \ | | | | | | | | | | | | | | | | | | to hdf5_1_12 * commit '47fa9d17898fb6f9edec6e9642dc1853bb003417': HDFFV-11014, fix the h5repack issue that misses a few attributes during the repacking. The flag that checks the object reference attribute is not updated properly. The fix is trivial. Just need to move the flag update line into the inner loop. Tested at Jelly. Also update the release.txt.
| * | HDFFV-11014, fix the h5repack issue that misses a few attributes during the ↵Muqun Yang2020-02-102-1/+23
|/ / | | | | | | repacking. The flag that checks the object reference attribute is not updated properly. The fix is trivial. Just need to move the flag update line into the inner loop. Tested at Jelly. Also update the release.txt.
* | Merge pull request #2344 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-02-058-6/+434
|\ \ | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit '7541b6abb9b679c32dbba70bec51807ca4165cdc': HDFFV-11012 fix fortran include properties HDFFV-10996 merge java vol tests from develop
| * | HDFFV-11012 fix fortran include propertiesAllen Byrne2020-02-054-6/+48
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| * | HDFFV-10996 merge java vol tests from developAllen Byrne2020-02-044-0/+386
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* | Merge pull request #2334 in HDFFV/hdf5 from ↵David Young2020-02-0447-413/+430
|\ \ | |/ |/| | | | | | | | | ~DYOUNG/werror:hdf5_1_12-warnings-squashed to hdf5_1_12 * commit 'd42bee368850f0bf47ee3a708e3c5d8b7119a632': Squashed commit of the following:
| * Squashed commit of the following:David Young2020-01-3147-413/+430
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 #2337 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_12 to ↵Larry Knox2020-02-011-1/+1
|\ \ | |/ |/| | | | | | | | | hdf5_1_12 * commit '4475757f93a29ff5209f8ec3187f6ecbf1a67a08': Merge pull request #2312 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
| * Merge pull request #2312 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-02-011-1/+1
|/ | | | | * commit '1c812fcd5d475afb7e65ed28d84990f96eefa649': Restore fix of test assert fail eror undone by later commit.
* Merge pull request #2331 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-01-3139-572/+564
|\ | | | | | | | | | | | | | | | | | | | | 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
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