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* Added skeletal version of H5FDsubfiling.c and H5FDsubfiling.h.inactive/develop_subfilingmainzer2020-07-165-3/+1396
| | | | | | | | | | | | | | | These are based on H5FDsec2, and will have to be re-worked heavily for sub-filing. Also added minimal test (based on existing sec2 tests) in test/vfd.c Since sub-filing is mostly a parallel feature, most testing will have to be moved to testpar. That said, a serial version of sub-filing will be neeced eventually, so it makes sense to retain at least a stub in the serial vfd tests. Tested serial and parallel on charis and jelly. Encountered errors in h5diff tests in the parallel builds, but am ignoring them as they also appear in the version prior to this checkin.
* Various bug fixes for the multi-threaded IO concentrator(s)Richard Warren2020-07-014-130/+280
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* Added support for vector I/O to the VFD layer, and associated test codemainzer2020-06-2916-0/+446
| | | | | | | | | | in test/vfd.c. Note that this test uses only sec2 and stdio at present. Since no VFDs support vector I/O at present, the vector I/O VFD calls are translated to regular read/write calls in the VFD layer. Tested serial and parallel, debug and production on charis, parallel debug on jelly. Some seemingly un-related issues, but after consultation with Richard, I'm proceeding with the checkin.
* Update Makefile.am files and fix issues unearthed by building with autotoolsRichard Warren2020-06-234-5/+18
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* Initial subfiling branchRichard Warren2020-06-2241-0/+8406
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* Merge pull request #2615 in HDFFV/hdf5 from ↵Jake Smith2020-06-151-0/+3
|\ | | | | | | | | | | | | ~JAKE.SMITH/hdf5:bugfix/splitter_valgrind_patch to develop * commit '6462c67b6578e48c1ef6d847be59c0b5e3598a50': Patch a few holes in the Splitter VFD implementation.
| * Patch a few holes in the Splitter VFD implementation.Jacob Smith2020-05-291-0/+3
| | | | | | | | | | * Missing logfile close on driver-open failure. * Initialize empty string in test/vfd (logfile path in W/O compat check).
* | Merge pull request #2635 in HDFFV/hdf5 from cache_last_id_info to developQuincey Koziol2020-06-101-2/+22
|\ \ | | | | | | | | | | | | * commit '0ef32f07fb9e8fb6063f3318425506047454d6f4': Remember the info for the last ID looked up for a given ID type.
| * | Remember the info for the last ID looked up for a given ID type.Quincey Koziol2020-06-091-2/+22
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* | | Merge pull request #2634 in HDFFV/hdf5 from opt_single_selection_io to developQuincey Koziol2020-06-101-27/+32
|\ \ \ | | | | | | | | | | | | | | | | * commit 'a8a4e9f27b67ae2e22970e42859225adcc2e5cbb': Eliminate allocating file & memory offset & length arrays when performing I/O on a single element.
| * | | Eliminate allocating file & memory offset & length arrays when performing ↵Quincey Koziol2020-06-091-27/+32
| |/ / | | | | | | | | | I/O on a single element.
* | | Remove redundant metadata cache tagging from some low-level internal chunk ↵Quincey Koziol2020-06-091-4/+4
|/ / | | | | | | functions. The metadata cache tagging has already been done by routines further up the call stack.
* | Merge pull request #2630 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-06-086-46/+38
|\ \ | | | | | | | | | | | | | | | | | | to develop * commit '87695c999ad7ea348ee6dc03b46b0bd345f7d7df': Minor normalizations with HDF5 1.10.
| * | Minor normalizations with HDF5 1.10.Dana Robinson2020-06-076-46/+38
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* | | Detect when there's the same-shaped selection of a single block of elements onQuincey Koziol2020-06-051-0/+9
|/ / | | | | | | | | | | both selections, but with different selection types (i.e. one selection defined as an 'all' type and the other as a hyperslab or point type), without falling into the generic selection iteration case.
* | Normalization of H5T.c with 1.10.Dana Robinson2020-06-041-24/+24
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* | Normalization of H5D.c with 1.10.Dana Robinson2020-06-041-11/+10
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* | Normalizations with 1.10 branch.Dana Robinson2020-06-023-16/+19
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* | Normalization with hdf5_1_10Dana Robinson2020-06-0124-473/+466
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* Replaced a few calls to HDmemcpy with H5MM_memcpy, which does overlapDana Robinson2020-05-152-8/+8
| | | | checking.
* Removed HDgets macros since gets was deprecated in C99 and removedDana Robinson2020-05-101-2/+5
| | | | in C11 (gets() is not used in our repo).
* Avoid allocating a chunk index for datasets with 0-sized dimensions, untilQuincey Koziol2020-05-012-3/+5
| | | | the dataset is extended.
* Merge pull request #2542 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:warning_fixes ↵Dana Robinson2020-04-271-15/+17
|\ | | | | | | | | | | | | to develop * commit 'c3367e6634d4dee88ff855da08e312f6685c23af': Moved -Woverlength-strings to the developer flags.
| * Moved -Woverlength-strings to the developer flags.Dana Robinson2020-04-261-15/+17
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* | Fix `src/H5FDdirect.c:1346:5: error: ISO C90 forbids mixed declarationsDavid Young2020-04-241-4/+1
|/ | | | and code [-Werror=declaration-after-statement]`.
* Merge pull request #2525 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-04-231-1/+1
|\ | | | | | | | | | | | | | | | | * commit '43424a1392b662a29542bb70014c253162ccfe48': Add missing ')'. Add C++ warnings treated as error for autotools builds. Move macro ADD_H5_CFLAGS to cmake_ext_mod/HDFMacros.cmake and remove duplicate versions. Address PR suggestions and add overlooked GCC compiler version flags. Don't add general warnings flags for unsupported old versions of gcc and g++ (older than gcc/g++ 4.2). Correct gnu-cxxflags to determine warnings flags to be added based on C++ compiler version instead of C compiler version.
| * Add C++ warnings treated as error for autotools builds.Larry Knox2020-04-231-1/+1
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* | Trim trailing whitespaceQuincey Koziol2020-04-20147-2473/+2473
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* Fixed some minor cmp callback bugs and cleaned warnings.Dana Robinson2020-04-171-3/+5
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* Fixed problems with S3 and HDFS VFDs.Dana Robinson2020-04-171-1/+6
| | | | | | * Updated info struct parameter to correct info_string * Fixed Makefile.am where the S3 VFD was listed twice, causing duplicated symbols errors.
* Merge pull request #2452 in HDFFV/hdf5 from ↵Jake Smith2020-04-1111-5/+4020
|\ | | | | | | | | | | | | | | | | | | | | | | ~JAKE.SMITH/hdf5:feature/vfd_splitter_mirror_a to develop Add Splitter VFD and Mirror VFD. * commit '664fc6af47e369152727ff66d68d8532feb0e210': Add enable-mirror-vfd flag to configure options. Tidying of Mirror VFD. Add function header comment for `mirror_writer:run_writer()`. Add Splitter VFD to library.
| * Merge branch 'develop' of ↵Jacob Smith2020-04-0721-370/+682
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into feature/vfd_splitter_mirror_a
| * | Tidying of Mirror VFD.Jacob Smith2020-04-072-8/+15
| | | | | | | | | | | | | | | | | | | | | * Rename server-stop utility to mirror_server_stop. * Remove external dependency on bzero(). * Modify test/use_common to use only the public API. * Rename internal bitswap macro to follow convention.
| * | Add Splitter VFD to library.Jacob Smith2020-03-1311-5/+4013
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * "Simultaneous and equivalent" Read-Write and Write-Only channels for file I/O. * Only supports drivers with the H5FD_FEAT_DEFAULT_VFD_COMPATIBLE flag for now, preventing issues with multi-file drivers. Add Mirror VFD to library. * Write-only operations over a network. * Uses TCP/IP sockets. * Server and auxiliary server-shutdown programs provided in a new directory, `utils/mirror_vfd`. * Automated testing via loopback ("remote" of localhost).
* | | Merge pull request #2502 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-04-093-20/+55
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '35c0d5cdfcfaa84f59e1c596ba1ccaeb28e3d83d': Fix for passthrough VOL not passing tools tests due to incorrect optional callback queries.
| * | | Fix for passthrough VOL not passing tools tests due to incorrectDana Robinson2020-04-083-20/+55
| | |/ | |/| | | | | | | optional callback queries.
* | | Merge pull request #2496 in HDFFV/hdf5 from ↵Vailin Choi2020-04-081-3/+3
|\ \ \ | |/ / |/| | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/dtype_close_on_error to develop * commit 'db9155c2f34bbf77a1cda01904805fe5c993b6d5': Fix according to PR feedback. Fix an error in previous merge: should use NULL instead of FAIL.
| * | Fix according to PR feedback.vchoi2020-04-071-1/+1
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| * | Fix an error in previous merge: should use NULL instead of FAIL.vchoi2020-04-071-2/+2
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* | | Update printf pointer syntax and revert fortran to f2003Allen Byrne2020-04-061-106/+106
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* | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-04-062-2/+2
|\ \ \ | |/ / | | | | | | | | | | | | | | | * commit '4830a1796441abbb5a4fbd2cff9a651f2a0d066e': Updated tools dump output when dataset offset is undefined. Added checks for native optional call support in some of the tools. Misc changes for h5dump VOL changes.
| * | Added checks for native optional call support in some of the tools.Dana Robinson2020-04-021-1/+1
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| * | Merge branch 'develop' into tools_vol_updateDana Robinson2020-04-022-41/+92
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| * | | Misc changes for h5dump VOL changes.Dana Robinson2020-03-301-1/+1
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* | | | TRILAB-192 add c++ and fortran warnings build systems one fileAllen Byrne2020-04-051-6/+2
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* | | 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().
| * | | A fix in the cleaning up code for datatype when datatype initialization via ↵vchoi2020-03-231-2/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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().
* | | | Changed default dataset shared struct to initialize hid_t IDs toDana Robinson2020-04-021-0/+3
| | | | | | | | | | | | | | | | H5I_INVALID_HID.
* | | | Merge pull request #2363 in HDFFV/hdf5 from ~DYOUNG/werror:thread_id to developDavid Young2020-04-011-39/+77
|\ \ \ \ | |_|/ / |/| | | | | | | | | | | | | | | * commit '63c95faf49559ea66e3066427961095b69fdb213': Remove tongue-in-cheek credit for Rusty Shackleford and Dale Alvin Gribble. Follow HDF5 conventions.
| * | | Remove tongue-in-cheek credit for Rusty Shackleford and Dale Alvin Gribble.David Young2020-02-101-21/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Delete the comment questioning whether pthread_mutex_lock is allowed in a key destructor, since pthread_key_create(3) provides the answer: There is no notion of a destructor-safe function. If an application does not call pthread_exit() from a signal handler, or if it blocks any signal whose handler may call pthread_exit() while calling async-unsafe functions, all functions may be safely called from destructors. Delete redundant comment.
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