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* Merge pull request #2278 in HDFFV/hdf5 from ↵Jerome Soumagne2020-01-187-18/+123
|\ | | | | | | | | | | | | | | ~JSOUMAGNE/hdf5:HDFFV-10992-fix-1_12 to hdf5_1_12 * commit '847c15691765b76beabf8f9abc89ee58a842a64e': Add test for reference shutdown issue H5R: set app ref when incrementing ref_count on location held by reference (fix HDFFV-10992)
| * Add test for reference shutdown issueJerome Soumagne2020-01-172-0/+84
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| * H5R: set app ref when incrementing ref_count on location held by referenceJerome Soumagne2020-01-175-18/+39
|/ | | | (fix HDFFV-10992)
* Merge pull request #2264 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-01-131-0/+1
|\ | | | | | | | | | | | | hdf5_1_12 * commit 'acdbf11c51ecf659b24eeb4bf743977b22e921be': Ignore ZLIB warnings
| * Ignore ZLIB warningsAllen Byrne2020-01-131-0/+1
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* Merge pull request #2262 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-01-13102-2821/+4081
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit '06f3c95c6ef68fdeff32569bc038ca3ba83b7aaa': Merge tools changes from develop Update file with changes from develop Fix CMake test macros and perform standalone tests Add MPI libs for standalone perf Fix autotools test scripts Add ref files to test script h5diff test script fixes Add new h5diff files Correct compile statement order Fix compile statement order HDFFV-10976,-10980 h5dump, h5ls, h5diff use new ref APIs
| * Merge tools changes from developAllen Byrne2020-01-1358-2417/+2424
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| * Update file with changes from developAllen Byrne2020-01-121-46/+39
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| * Fix CMake test macros and perform standalone testsAllen Byrne2020-01-1211-285/+469
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| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2020-01-0785-2102/+3784
| |\ | |/ |/| | | | | | | | | | | | | | | | | * 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
* | Merge pull request #2229 in HDFFV/hdf5 from vol_changes_to_1_12 to hdf5_1_12Quincey Koziol2020-01-0785-2102/+3784
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'fcdcc4beb18cfb6098ec2f0e0d45db38ee59178f': 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 Koziol2020-01-0442-537/+700
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| * | Cleanups from PR reviewsQuincey Koziol2020-01-044-102/+101
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| * | Remove unnecessary H5CX callQuincey Koziol2020-01-041-4/+0
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| * | Refactor H5Dvlen_get_buf_size to use optional dataset operation, with ↵Quincey Koziol2020-01-048-57/+258
| | | | | | | | | | | | generic fallback for VOL connectors that don't implement operation
| * | Refactor all the 'H5VL_*_optional' callbacks to move the type of operation outQuincey Koziol2020-01-0450-1583/+2904
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
| * | Update h5debug to retrieve file pointer through VOL frameworkQuincey Koziol2020-01-041-1/+7
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| * Add MPI libs for standalone perfAllen Byrne2019-12-221-2/+2
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| * Fix autotools test scriptsAllen Byrne2019-12-224-7/+45
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| * Add ref files to test scriptAllen Byrne2019-12-212-5/+18
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| * h5diff test script fixesAllen Byrne2019-12-212-1/+8
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| * Add new h5diff filesAllen Byrne2019-12-211-0/+3
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| * Correct compile statement orderAllen Byrne2019-12-201-2/+3
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| * Fix compile statement orderAllen Byrne2019-12-203-4/+5
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| * HDFFV-10976,-10980 h5dump, h5ls, h5diff use new ref APIsAllen Byrne2019-12-2052-471/+1484
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* Merge pull request #2168 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2019-12-201-0/+3
|\ | | | | | | | | | | | | hdf5_1_12 * commit '4e652fe75f600ed66d2870fc101cf8883c017cbb': Standalone doesn't use h5test implementation.
| * Standalone doesn't use h5test implementation.Allen Byrne2019-12-201-0/+3
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* Merge pull request #2160 in HDFFV/hdf5 from ~DYOUNG/netbsd:hdf5_1_12 to ↵David Young2019-12-1934-76/+401
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit '471df15556025fd211351ad54183fa196b2fd341': In portable shell scripts (using #!/bin/sh) we have to use single square brackets, [ ], instead of the bash-ism double square brackets, [[ ]]. Make this script work on hosts where PERL is not installed at /usr/bin/perl. Use HD prefix. Fix HDFFV-10937: use a more reliable (and probably faster) scheme for visiting all elements of a matrix in an arbitrary order. Apparently, + has no special meaning, and neither does \+, in so-called "obsolete" / POSIX "basic" regular expressions. Also, not every version of `sed` out there supports the `-E` option. So delete the -E flag and use the regex `[^/][^/]*` instead of `[^/]+`. 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 `==`.
| * In portable shell scripts (using #!/bin/sh) we have to use single squareDavid Young2019-12-192-2/+2
| | | | | | | | brackets, [ ], instead of the bash-ism double square brackets, [[ ]].
| * Make this script work on hosts where PERL is not installed atDavid Young2019-12-191-1/+2
| | | | | | | | /usr/bin/perl.
| * 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.
| * Apparently, + has no special meaning, and neither does \+, in so-calledDavid Young2019-12-196-5/+6
| | | | | | | | | | | | | | | | "obsolete" / POSIX "basic" regular expressions. Also, not every version of `sed` out there supports the `-E` option. So delete the -E flag and use the regex `[^/][^/]*` instead of `[^/]+`. Add config/netbsd to the MANIFEST.
| * Make these scripts relocatable again: derive a relative path for theDavid Young2019-12-194-4/+97
| | | | | | | | | | | | | | 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 subdirectoryDavid Young2019-12-191-1/+1
| | | | | | | | c/.
| * Make this script relocatable again: derive a relative path for theDavid Young2019-12-191-2/+25
| | | | | | | | | | | | | | 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.David Young2019-12-1913-18/+40
| | | | | | | | | | | | | | | | | | 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. Place hdf5_examples/ under ${datarootdir} which on most systems will be ${prefix}/share/, anyway.
| * Follow longstanding execv convention for compatibility with NetBSD.David Young2019-12-191-1/+7
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| * Under the examples directories, always find the installed HDF5David Young2019-12-196-6/+6
| | | | | | | | | | | | | | | | | | | | 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. Examples on NetBSD are installed at ${prefix}/share/examples/hdf5/ instead of at ${prefix}/share/hdf5_examples/, by convention. It may be the same on other BSDs, I'm not sure.
| * Make the HDF5 configure script grok NetBSD.David Young2019-12-192-0/+59
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| * For portability, insulate the HDF5 library from some system macros.David Young2019-12-191-1/+18
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| * Not every system has perl installed in /usr/bin/, so change the shebangDavid Young2019-12-1912-12/+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.
| * For portability, use the POSIX sh(1) string-comparison operator `=`David Young2019-12-191-2/+2
|/ | | | instead of `==`.
* Merge pull request #2154 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2019-12-194-31/+28
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit 'dd6b6ce61ca1a6af8e872ad09ef5da6ca437e9bc': Adjust cache.c only variables. Fix include to correct memory calls - big-endian issue.
| * 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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* Merge pull request #2147 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2019-12-172-8/+2
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit '1b4957c585e255850b711edb08903d99204c7a61': Minor Whitespace Remove duplicate instance
| * Minor WhitespaceAllen Byrne2019-12-171-2/+2
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| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2019-12-1750-205/+5154
| |\ | |/ |/| | | | | | | | | | | | | | | * commit '1097ac60c2b95a2b958a3150b537c75f512cacca': Merge t_2Gio test into hdf5_1_12. This will eventually be refactored out after merging the test functionality into the testphdf5 test. Merge t_2Gio test into hdf5_1_12. This will eventually be refactored out after merging the test functionality into the testphdf5 test. Minor tweaks noticed while going over VOL documentation. Yanked -Wc++-compat from the flags used to build the C library in both the Autotools and CMake. Fixed missing blob callbacks in test VOL connectors. Trivial parameter renaming in VOL API calls.
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