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* Revert "Switch ID code to use a hash table instead of a skip list (#52)" (#104)Dana Robinson2020-11-202-2/+0
| | | This reverts commit a50d211755cb272b2e468144e7d892a4c90813c4.
* Switch ID code to use a hash table instead of a skip list (#52)Dana Robinson2020-11-172-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brings hash table ID code over from Bitbucket branch * Includes reformatting via clang. * Excludes uthash.h from reformatting. * Still has the failing test issue in tid.c. This should only be a problem if a custom ID type is used and its free function deletes other IDs. * Fixes munged H5_GCC_DIAG_ON/OFF macros in H5I.c The H5_GCC_DIAG_ON/OFF macros used to turn off fallthrough warnings in uthash.h (external code) were munged when formatting with clang due to their lack of quotes. e.g.; H5_GCC_DIAG_OFF(implicit-fallthrough) was munged to: H5_GCC_DIAG_OFF(implicit - fallthrough) which compiles, but is useless. So, with quotes, this is now: H5_GCC_DIAG_OFF("implicit-fallthrough") which survives reformatting with clang. * Fixes issues with user callbacks in the ID hash tables The skip lists (previously) used to handle IDs use a mark-and-sweep scheme to deal with user-defined ID delete callbacks which themselves delete other IDs in the list. The uthash hash table implementation used to manage the IDs in this feature branch does not have this ability. This commit restores the skip lists for non-library ID types in lieu of significantly modifying the uthash code. The hash tables are used to manage the library IDs as those do not delete other IDs when they are closed. * Adds uthash.h to MANIFEST * Removes implicit-fallthrough diagnostic disable Removing -Wimplicit-fallthrough=5 means that the uthash code no longer raises warnings so the H5_GCC_DIAG_OFF/ON macros that disabled those warnings have been removed from H5I.c. * Adds a test to ensure you can delete IDs in the H5Iiterate() callback
* HD prefix updates in src/ and test/Dana Robinson2020-10-241-4/+87
| | | | | | | Adds missing HD prefixes to API calls in src and test. Adds some extra processing to bin/checkposix to keep the noise levels down when running the script (not comprehensive).
* Update reformatting settings, trace wrapping, and printf-format strings (#22)Quincey Koziol2020-10-064-13/+80
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Add BEGIN_FUNC / CATCH / END_FUNC to macros * Remove incorrect trailing '{' * Update trace script to wrap H5TRACE macros at 110 characters and improve comments for code that performs this operation. * Clean up printf-formatting in H5public.h and correct some oversights in the code. * Reformat with BEGIN_FUNC / END_FUNC handled correctly by clang-format * Run clang-format on changes. * Correct H5_SIZEOF_HSIZE_T/H5_SIZEOF_HSSIZE_T macros to match typedef. * And make the undef value match also. * Update comment * Update clang-format actions to exclude generated files. * Post-process generated H5LTparse.h file as well as H5LTparse.c file. * Fix formatting * Update version of github clang-format action
* Fix VFD h5repacktest (#20)Allen Byrne2020-10-061-8/+14
| | | | | | | | | | | | | | * h5repacktest VFD fix and formatting changes * Fix memory leak in H5PL__find_plugin_in_path When encountering a directory, the current loop iteration was skipped without freeing the memory allocated for the path. * Refactor parser GCC diagnostic statements * genparser on jelly with default bison/flex Co-authored-by: Michael Kuhn <michael.kuhn@ovgu.de>
* Change to executableAllen Byrne2020-09-242-0/+0
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* CMake and script changes for clang-formatAllen Byrne2020-09-042-0/+20
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* Removes staff email addresses from the repositoryDana Robinson2020-08-073-3/+3
| | | | Removes redundant C library headers from hl library
* Minor normalizations with 1.12 branchDana Robinson2020-08-011-108/+108
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* OESS-65 add option to use AEC library in place of SZipAllen Byrne2020-04-221-139/+139
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* Trim trailing whitespaceQuincey Koziol2020-04-202-13/+13
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* Merge pull request #2452 in HDFFV/hdf5 from ↵Jake Smith2020-04-111-0/+2
|\ | | | | | | | | | | | | | | | | | | | | | | ~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 Smith2020-04-071-0/+1
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into feature/vfd_splitter_mirror_a
| * | Add Splitter VFD to library.Jacob Smith2020-03-131-0/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * "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).
* | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Larry Knox2020-03-241-0/+1
|\ \ \ | | |/ | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'd3ef866a2963ce93d0b95184534a70849b6fa11d': Revise API for H5get_alloc_stats() to take a struct instead of separate values. Move the GNU warnings configuration under config/gnu-warnings/ and trim the filename prefixes. Update config/gnu-flags to suit. Fixed the RELEASE.txt note for HDFFV-11057 Fix shutdown errors when using the HDF5_VOL_CONNECTOR environment variable to set a dynamically loaded plugin as the default VOL connector. Fixes HDFFV-11057 Fix threadsafe for new test 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 Very minor comment change in H5VLconnector.h. Add routines to query the library's free list sizes and allocation stats. By default, demote warnings promoted to errors back to warnings. Incorporate the H5_ECFLAGS into the library CFLAGS. Now a bunch of errors will occur. Next commit will demote the warnings promoted to errors back to warnings again. Break out warnings into more files that autoconf and CMake can share. This change temporarily disables the warnings that were promoted to errors, but I will add those warnings back as warnings, not errors, in the next commit. Avoid a crash, don't check if we're flushing when the file is closing: 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.
| * | Revise API for H5get_alloc_stats() to take a struct instead of separate values.Quincey Koziol2020-03-201-0/+1
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* | Add \d to list of characters allowed after '-' in versions.Larry Knox2020-03-121-1/+1
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* Update examples and fix old version references.Allen Byrne2020-02-261-3/+3
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* Filter all of the new _USED / _UNUSED type modifiers.David Young2020-02-181-0/+4
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* Merge pull request #2297 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-01-231-1/+1
|\ | | | | | | | | * commit '30fa2606b45e789ba36f3193130cdea2c12b68a6': Max Library "index" should be 7.
| * Max Library "index" should be 7.Larry Knox2020-01-221-1/+1
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* | Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to developKimmy Mu2020-01-231-0/+1
|\ \ | |/ |/| | | | | | | | | | | | | | | | | * 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 and fixkmu2020-01-212-12/+35
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| * | merge and fix conflictkmu2020-01-191-0/+1
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* | | Remove duplicate lines noted on forum by Eric BavierLarry Knox2020-01-211-7/+0
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* | | Add v111 version for H5O functions to enable version1 default for HDF5Larry Knox2020-01-211-2/+16
| |/ |/| | | | | | | 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 Robinson2020-01-162-12/+35
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* Merge pull request #2071 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/intel_warnings ↵Kimmy Mu2020-01-061-4/+15
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
| * fix intel compile warningskmu2019-12-041-4/+15
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| * Revert "fix warnings from Intel compiler"kmu2019-11-261-13/+4
| | | | | | | | This reverts commit 8b9338ab57eec0cc8fa5a36c44d7b28e52e9a466.
| * Revert "using a different MACRO"kmu2019-11-261-2/+0
| | | | | | | | This reverts commit fc61b7a9f3a38331809ebcb6247482943947cdb8.
| * using a different MACROkmu2019-11-251-0/+2
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| * Merge branch 'develop' of https://git.hdfgroup.org/scm/~kmu/hdf5 into developkmu2019-11-0712-12/+26
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| * | fix warnings from Intel compilerkmu2019-11-071-4/+13
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* | | Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2019-12-201-0/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* | | Make this script work on hosts where PERL is not installed atDavid Young2019-11-131-1/+2
| |/ |/| | | | | /usr/bin/perl.
* | Merge pull request #1984 in HDFFV/hdf5 from ~DYOUNG/netbsd:develop to developDavid Young2019-11-0512-12/+26
|\ \ | |/ |/| | | | | | | | | | | | | | | | | | | | | | | * commit '0b721858e46a317c370a24115032d5be41688f67': Make these scripts relocatable again: derive a relative path for the original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived. Get the path to prefix right: needs a ../ to back out of subdirectory c/. Make this script relocatable again: derive a relative path for the original installation prefix from the examples prefix. Use that relative path to locate the current installation prefix, always. Fall back to an absolute installation prefix if the relative path cannot be derived. Let us override the examples directory using --with-examplesdir=DIR. This is handy for NetBSD where HDF5 examples are installed by convention in $prefix/share/examples/hdf5/ rather than in ${prefix}/share/hdf5_examples/, which is the HDF5 default. Follow longstanding execv convention for compatibility with NetBSD. Under the examples directories, always find the installed HDF5 executables and scripts using @prefix@ instead of a relative path, because the number of ../ in the relative path will be different on NetBSD than on other systems. Make the HDF5 configure script grok NetBSD. For portability, insulate the HDF5 library from some system macros. Not every system has perl installed in /usr/bin/, so change the shebang (#!) line to `/usr/bin/env perl` to locate perl on the PATH. For portability, use the POSIX sh(1) string-comparison operator `=` instead of `==`.
| * Not every system has perl installed in /usr/bin/, so change the shebangDavid Young2019-10-0312-12/+26
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#!) line to `/usr/bin/env perl` to locate perl on the PATH. Everything after the first pathname in the shebang line is treated as a single argument to the command interpreter (/usr/bin/env "perl -w"), and there is not ordinarily any such program as "perl -w". So if the old shebang line used an option such as `-w`, add a `use warnings;` statement to the script---note that the semantics change slightly. `bin/destdep` uses a trick to pass `-p` to `/usr/bin/env perl`. It couldn't hurt to use the same trick to pass `-w`. With these changes, `sh autogen.sh` runs on NetBSD. It ought to still work on every other system HDF5 supports, too.
* | Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-1/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* | Fix H5VL_blob_get to return size of blobJerome Soumagne2019-10-081-0/+1
|/ | | | | | | | | | | | | | | | | | | | Fix const in blob API Add H5HG_HEAP_ID_SIZE macro to return native blob size Add maximum size for blobs Fix blob API callbacks to pass VOL file object Add public wrappers for blob VOL API Implement passthrough blob callbacks Update H5Tvlen after callback changes Update trace information for H5VL blob routines Fix public header inclusion in native and passthru headers
* Update versioning to next major versionAllen Byrne2019-09-252-5/+5
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* Added the map (H5M) APIDana Robinson2019-08-131-0/+1
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* Escape { and } in regex as required by sh in updated cori.nersc.gov.Larry Knox2019-08-071-3/+3
| | | | Tested change on jam, jelly, emu, ostrich and osx1011test.
* Squashed commit of the following:Larry Knox2019-07-251-0/+2
| | | | | | | | | | | Merge changes from update_merged_S3_HDFS branch into develop. commit d5034315aea88629929ac0c9c59ebfafd5f21a31 Merge: 9c48823 d3fdcd8 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jul 25 08:24:53 2019 -0500 Merge branch 'develop' into update_merged_S3_HDFS
* Updates to warnhist script, along with a few cleanups, and add some commentsQuincey Koziol2019-07-101-7/+18
| | | | to warning cleanups that are a bit obscure.
* Cleaned up code that genericizes warning output, and add "-u" option toQuincey Koziol2019-07-051-269/+65
| | | | | leave unique types in warnings (i.e. don't genericize output). Also fixed the '-S' option to work correctly.
* Add support for GCC9, update warnhist script, and clean up warnings.Quincey Koziol2019-07-032-63/+218
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* Updated configure & CMake compiler flags for GCC 8.x, along with correspondingQuincey Koziol2019-06-281-22/+57
| | | | | changes to warnhist script (and some extra improvements for condensing C++ and Java warnings), and fixed a bunch of warnings.
* Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-211-4/+34
| | | | clean up warnings.
* Added a warning summary script for gcc to binDana Robinson2019-06-171-0/+484
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