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* Modified page buffer to split entries only where necessary -- specificallymainzer2020-05-2110-273/+1443
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | when handling an I/O request on a metadata entry that has been sub-allocated from a larger file space allocation (i.e. fixed and extensible array), and that crosses at least one page boundary. . This required modifying the metadata cache to provide the type of the metadata cache entry in the current I/O request. For now, this is done with a function call. Once we are sure this works, it may be appropriate to convert this to a macro, or to add a flags parameter to the H5F block read/write calls. Also updated the metadata cache to report whether a read request is speculative -- again via a function call. This allowed me to remove the last address static variable in the H5PB_read() call, which is necessary to support multiple files opened in VFD SWMR mode. Also re-wrote the H5PB_remove_entries() call to handle release of large metadata file space allocations that have been sub-allocated into multiple metadata entries. Also modified the call to H5PB_remove_entries() in H5MF__xfree_impl() to invoke it whenever the page buffer is enabled and the size of the space to be freed is of page size or larger. Tested serial / debug on charis and Jelly. Found a bug in H5MF_xfree_impl(), in which the call to H5PB_remove_entries() is skipped due to HGOTO_DONE calls earlier in the function. While the obvious action is to move the call earlier in the function, best to consult with Vailin first, as there is much going on and it would be best to avoid making the situation worse. If nothing else, there are some error management issues.
* and `vfd_swmr_reader_did_increase_tick_to` declarations.David Young2020-05-201-0/+1
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* Rebase repair: do not list any VFD SWMR source files twice.David Young2020-05-201-2/+1
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* Reduce diffs with `develop`.David Young2020-05-201-1/+1
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* Reduce diffs with `develop`, where `H5C_move_entry` takes an `H5C_t *`David Young2020-05-203-13/+6
| | | | argument, first, not `H5F_t *`.
* Reduce diffs with `develop`.David Young2020-05-201-5/+1
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* Repair a bunch of H5_ATTR_SANITY_CHECK uses that should have beenDavid Young2020-05-2036-74/+72
| | | | | H5_ATTR_NDEBUG_UNUSED. This really makes me wonder what else I have screwed up in this merge....
* Move declarations before statements, ugh.David Young2020-05-201-6/+8
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* Replaced a few calls to HDmemcpy with H5MM_memcpy, which does overlapDana Robinson2020-05-202-8/+8
| | | | checking.
* Removed HDgets macros since gets was deprecated in C99 and removedDana Robinson2020-05-201-2/+5
| | | | in C11 (gets() is not used in our repo).
* Avoid allocating a chunk index for datasets with 0-sized dimensions, untilQuincey Koziol2020-05-202-3/+5
| | | | the dataset is extended.
* Moved -Woverlength-strings to the developer flags.Dana Robinson2020-05-201-15/+17
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* Fix `src/H5FDdirect.c:1346:5: error: ISO C90 forbids mixed declarationsDavid Young2020-05-201-4/+1
| | | | and code [-Werror=declaration-after-statement]`.
* Add C++ warnings treated as error for autotools builds.Larry Knox2020-05-201-1/+1
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* Trim trailing whitespaceQuincey Koziol2020-05-20147-2466/+2462
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* Fixed some minor cmp callback bugs and cleaned warnings.Dana Robinson2020-05-201-3/+5
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* Fixed problems with S3 and HDFS VFDs.Dana Robinson2020-05-201-1/+6
| | | | | | * Updated info struct parameter to correct info_string * Fixed Makefile.am where the S3 VFD was listed twice, causing duplicated symbols errors.
* Tidying of Mirror VFD.Jacob Smith2020-05-202-8/+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 Smith2020-05-2011-11/+4015
| | | | | | | | | | | | | | | * "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).
* Fix for passthrough VOL not passing tools tests due to incorrectDana Robinson2020-05-203-20/+55
| | | | optional callback queries.
* Fix according to PR feedback.vchoi2020-05-201-1/+1
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* Fix an error in previous merge: should use NULL instead of FAIL.vchoi2020-05-201-2/+2
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* Update printf pointer syntax and revert fortran to f2003Allen Byrne2020-05-201-106/+106
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* Added checks for native optional call support in some of the tools.Dana Robinson2020-05-201-1/+1
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* Misc changes for h5dump VOL changes.Dana Robinson2020-05-201-1/+1
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* TRILAB-192 add c++ and fortran warnings build systems one fileAllen Byrne2020-05-201-6/+2
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* A fix in the cleaning up code for datatype when datatype initialization via ↵vchoi2020-05-201-2/+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 Robinson2020-05-201-0/+3
| | | | H5I_INVALID_HID.
* Remove tongue-in-cheek credit for Rusty Shackleford and Dale Alvin Gribble.David Young2020-05-201-21/+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.
* Follow HDF5 conventions.David Young2020-05-201-30/+89
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* TRILAB-192 restrict extensive warnings to librariesAllen Byrne2020-05-201-0/+6
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* Revise API for H5get_alloc_stats() to take a struct instead of separate values.Quincey Koziol2020-05-204-61/+33
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* Add routines to query the library's free list sizes and allocation stats.Quincey Koziol2020-05-208-212/+467
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* Incorporate the H5_ECFLAGS into the library CFLAGS. Now a bunch of errors willDavid Young2020-05-201-1/+1
| | | | | occur. Next commit will demote the warnings promoted to errors back to warnings again.
* Fix shutdown errors when using the HDF5_VOL_CONNECTOR environmentDana Robinson2020-05-203-2/+16
| | | | | variable to set a dynamically loaded plugin as the default VOL connector. Fixes HDFFV-11057
* Very minor comment change in H5VLconnector.h.Dana Robinson2020-05-201-1/+1
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* Fix issues when deserializing point/all/none selection with version beyond ↵Vailin Choi2020-05-205-5/+23
| | | | | | | 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
* Avoid a crash, don't check if we're flushing when the file is closing:David Young2020-05-201-5/+5
| | | | | | | | there's no need to check if the metadata cache is flushing if we already know the file is closing, because the condition we rely on is "closing OR flushing." Further, the cache may have already gone away, so sometimes calling into the cache to see if it's flushing will crash the program.
* Use a naked pthread_self() call in the HDF5 thread wrappers.David Young2020-05-202-6/+2
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* Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG).Jacob Smith2020-05-202-3/+3
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* Switch the 'get offset' operation from a dataset 'get' callback to a [native]Quincey Koziol2020-05-205-37/+21
| | | | dataset 'optional' operation.
* TRILAB-142 Change minimum CMake version to 3.12Allen Byrne2020-05-201-1/+1
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* Replace the old H5F_DECODE_LENGTH() implementation with one thatDavid Young2020-05-201-1/+1
| | | | initializes the variable it's loading on every path.
* H5_HAVE_PARALLEL, _DEBUG_API, etc. Add attributes to some variables andDavid Young2020-05-208-23/+53
| | | | parameters that are unused under some configurations.
* Delete unhelpful comment per Jordan's question.David Young2020-05-201-3/+0
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* Make sure that H5TS_thread_id() is available as either a function or a macro inDavid Young2020-05-202-12/+5
| | | | | | | | | all configurations. Previously it was neither declared nor defined in --disable-threadsafety builds. The compiler's warning got lost in the noise---I first saw the issue because my -Werror branch stopped compiling cold---and the tests still linked and ran.
* Provide C99/POSIX.1 format strings PRI[doux]{8,16,32,64,MAX,PTR} on systemsDavid Young2020-05-201-1/+39
| | | | that are missing <inttypes.h>.
* H5T_copy() constification plus Quincey's contributions.David Young2020-05-2015-194/+480
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* Fix improper S3 signing key null check (HDFFV-11015).Jacob Smith2020-05-201-2/+2
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* If H5_HAVE_THREADSAFE is not #defined, define nothing but a stub implementationDavid Young2020-05-201-0/+7
| | | | of H5TS_thread_id().
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