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* TRILAB-192 - merge changes from developAllen Byrne2020-04-071-3/+13
| | | | Single source, config files, for warnings for both autotools and CMake. Update CMake libraries, tools, tests to use correct flags.
* Merge pull request #2461 in HDFFV/hdf5 from ↵Vailin Choi2020-04-021-348/+388
| | | | | | | ~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().
* Was checking the wrong compiler macro.Quincey Koziol2020-03-251-1/+1
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* Correct failure when allocation tracking are disabled.Quincey Koziol2020-03-241-0/+12
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* Revise API for H5get_alloc_stats() to take a struct instead of separate values.Quincey Koziol2020-03-231-38/+30
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* Add routines to query the library's free list sizes and allocation stats.Quincey Koziol2020-03-231-0/+139
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* Merge changes from develop mostly cmake 3.12 minimum versionAllen Byrne2020-02-231-1/+1
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* Squashed commit of the following:David Young2020-01-3111-53/+53
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* Introduce new H5VL _by_value routinesJordan Henderson2020-01-292-17/+100
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* Merge pull request #2311 in HDFFV/hdf5 from ~KMU/hdf5:misc to developKimmy Mu2020-01-281-19/+19
| | | | | | | | | * 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
* Merge pull request #2300 in HDFFV/hdf5 from ~KMU/hdf5:squashed_cast to developKimmy Mu2020-01-287-47/+64
| | | | | | * commit 'af5c33afabdae2e39bb45eb1b3e9c8366da01145': remove unnecessary stuff squash cast warning fix
* Merge branch 'hdf5_1_12' of https://git.hdfgroup.org/scm/~kmu/hdf5 into ↵kmu2020-01-281-2/+1
|\ | | | | | | hdf5_1_12
| * Modify external_env.c to prevent deleting test file of external.c.Larry Knox2020-01-271-2/+1
| | | | | | | | Fix for HDFFV-10941.
* | Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to developKimmy Mu2020-01-2810-77/+66
|/ | | | | | | | | | | * 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
* Merge pull request #2238 in HDFFV/hdf5 from ~KMU/hdf5:hdf5_1_12 to hdf5_1_12Kimmy Mu2020-01-246-19/+19
|\ | | | | | | | | | | | | * 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 Mu2020-01-086-19/+19
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* | Improved CMake options for testsAllen Byrne2020-01-192-2/+4
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* | Squashed commit of the token_refactoring branch:Dana Robinson2020-01-1933-1534/+6434
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* | Add test for reference shutdown issueJerome Soumagne2020-01-171-0/+83
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* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2020-01-0716-372/+509
|\ \ | |/ | | | | | | | | | | | | | | | | | | * commit '7116d82f6b685261b5b4e64fada1a0a031cd7341': Remove mismerged code Cherry pick of 0225e6d5969 Cleanups from PR reviews Remove unnecessary H5CX call Refactor H5Dvlen_get_buf_size to use optional dataset operation, with generic fallback for VOL connectors that don't implement operation Refactor all the 'H5VL_*_optional' callbacks to move the type of operation out 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. Update h5debug to retrieve file pointer through VOL framework
| * Remove mismerged codeQuincey Koziol2020-01-071-4/+0
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| * Cherry pick of 0225e6d5969Quincey Koziol2020-01-0414-357/+478
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| * Refactor H5Dvlen_get_buf_size to use optional dataset operation, with ↵Quincey Koziol2020-01-041-3/+3
| | | | | | | | generic fallback for VOL connectors that don't implement operation
| * Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2020-01-043-12/+32
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* | Correct compile statement orderAllen Byrne2019-12-201-2/+3
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* Use HD prefix.David Young2019-12-191-8/+8
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* Fix HDFFV-10937: use a more reliable (and probably faster) scheme forDavid Young2019-12-191-32/+121
| | | | visiting all elements of a matrix in an arbitrary order.
* Follow longstanding execv convention for compatibility with NetBSD.David Young2019-12-191-1/+7
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* Adjust cache.c only variables.Allen Byrne2019-12-184-30/+27
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* Fix include to correct memory calls - big-endian issue.Allen Byrne2019-12-182-1/+1
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* Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-1624-112/+112
| | | | the Autotools and CMake.
* Fixed missing blob callbacks in test VOL connectors.Dana Robinson2019-12-162-0/+12
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* HDFFV-10979 cleanup global namesAllen Byrne2019-12-122-7/+5
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* HDFFV-10979 Merge global name fix from developAllen Byrne2019-12-114-718/+727
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* Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char toDavid Young2019-12-093-142/+139
| | | | | | | | | | | | | | | | | | | 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. An interesting side-effect that we probably should *not* rely on is that the struct-encapsulation changes the alignment so that some GCC warnings about casts that increase the alignment requirement of the operand go away. Warnings like that have to be taken seriously: I will add -Werror=cast-align to the default compiler flags so that they stop the build quickly. GCC warnings led me to some surprising casts in test/trefer.c. I found that it was possible to make many simplifications after introducing the struct-encapsulation that I described, above. In test objcopy_ref `same_file` is assigned but never used. Delete it.
* H5R: fix H5Tconv to check for null referencesJerome Soumagne2019-12-091-4/+4
| | | | | | Valid for both deprecated and non-deprecated references Update test
* Revert "Merge branch 'hdf5_1_12' of ↵Jerome Soumagne2019-12-0923-310/+133
| | | | | | | https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12" This reverts commit 9f9336a5bd541752f472bab4c93da8de89f862cd, reversing changes made to 437a1919e7ba60fe75a33a466d264183a0255319.
* Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 ↵Richard Warren2019-12-062-43/+43
|\ | | | | | | into hdf5_1_12
| * Merge pull request #2080 in HDFFV/hdf5 from ↵Vailin Choi2019-12-061-1/+1
| |\ | | | | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/112_hyper_ver to hdf5_1_12 * commit '0f1be317c37ca04db263680e6f1fe4d97b937b39': More fixes for the PR: (1) Set the version for reference datatype message to H5O_DTYPE_VERSION_4. (2) The tests for the new reference types should work for V112 and beyond. Verify the decoded version for hyperslab selection.
| | * More fixes for the PR:Vailin Choi2019-12-061-1/+1
| | | | | | | | | | | | | | | (1) Set the version for reference datatype message to H5O_DTYPE_VERSION_4. (2) The tests for the new reference types should work for V112 and beyond.
| * | Add OAPL parameter to H5Rcreate_ APIsJordan Henderson2019-12-062-42/+42
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* | Merged HDFFV-10929_2GB_testing to hdf5_1_12Richard Warren2019-12-0623-133/+310
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* Merge pull request #2001 in HDFFV/hdf5 from ↵Dana Robinson2019-10-111-2/+7
|\ | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:1_12_alpha_merges to hdf5_1_12 * commit '75f2ed6167b094431fce2b4b700b3cf9da564c51': Fixed a bug (HDFFV-10899) where the behavior of the deprecated H5Gget_objinfo() call had changed and passing in a non-existing soft link with a statbuf of NULL passed instead of failed (as it should as per the RM). The HDF5 1.8 and 1.10 behavior was restored and H5Gget_objinfo() will now fail and return -1 as before. Fixed the java assert issue with H5O cache corking calls. Corrected missing parallel #ifdefs. Converted H5O MD cache cork calls to use the VOL. Marked up H5Fget/set_mpi_atomicity() to use the VOL.
| * Fixed a bug (HDFFV-10899) where the behavior of the deprecatedDana Robinson2019-10-111-2/+7
| | | | | | | | | | | | | | | | H5Gget_objinfo() call had changed and passing in a non-existing soft link with a statbuf of NULL passed instead of failed (as it should as per the RM). The HDF5 1.8 and 1.10 behavior was restored and H5Gget_objinfo() will now fail and return -1 as before.
* | Merge pull request #1959 from develop to 1.12.Vailin Choi2019-10-111-6/+5
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* Merge pull request #1990 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:references_1_12 ↵Larry Knox2019-10-0920-766/+5371
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to hdf5_1_12 * commit '5d2545ee26d4b7013ed363545705f16a67087549': Fix func enter macro in H5T_ref_reclaim() Update RELEASE.txt for reference changes Fix reference type comparison in h5dump Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim() Add new H5R API that abstracts object, region and attribute reference types Remove ability to loc by ref from H5VL layer Add support for retrieving object name by token Add H5VL_OBJECT_GET_TYPE to get object type Add H5VL_MAX_TOKEN_SIZE and H5VL_token_t Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info. Fix H5VL_blob_get to return size of blob Add 'blob' callbacks to VOL, along with a native implementation to store them in the global heap, and changed the VL datatype conversion code to use blobs.
| * Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()Jerome Soumagne2019-10-0813-185/+185
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| * Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-087-581/+5186
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* | Merge pull request #1962 in HDFFV/hdf5 from ↵Vailin Choi2019-10-091-0/+162
|\ \ | |/ |/| | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/112_HDFFV-10585-investigate-slowness-of-regular to hdf5_1_12 * commit 'bffa18b684de83359f4ad25e11f4ad0b15f34040': Merge pull request #1957 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop Merge pull request #1934 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/HDFFV-10585-investigate-slowness-of-regular to develop
| * Merge pull request #1957 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2019-09-301-1/+1
| | | | | | | | | | * commit '3fb711e0ff2516cba7a0cb34f2d8ca38241b06a7': Number of arguments requires H5Dopen2.
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