| Commit message (Collapse) | Author | Age | Files | Lines |
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* Enable the Onion VFD to support H5Pset_driver_by_name and added a test case for it.
* Committing clang-format changes
* Revised a private function to return an error if it fails.
* Committing clang-format changes
* Refactored some code in the previous commit.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Struct cleanup
* More renaming
* Minor cleanup
* Removed aspirational code from the feature
* Revert "Removed aspirational code from the feature"
This reverts commit 0b162d16a175a08565089f829014d0d93e171a23.
* Split header code into new files, history_header --> header
* In-memory things are size_t now
* Minor renaming
* More encode/decode functions use size_t instead of uint64_t
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* Removes the user info from the onion VFD revision entries
* Formatted source
* Fixed codespell issue
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* Sync with develop. h5dump is broken, so I can't test the tools.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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h5dump. (#1726)
* Removes unused definitions from module headers (#1624)
* Fix these Doxygen warnings #1581 (#1589)
* Fixes a typo in H5.c (#1639)
* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)
* free MPI_Group/MPI_Comm/MPI_Datatype objects
* fix clang-format style
* Adds build and license shields to README.md (#1641)
* First stab at a Github status bar
* Adds a .tokeignore file for counting lines of code accurately
* Yanks lines of code calculation since it wildly overcounts
* not depend on doIO to free an MPI_Comm object (#1642)
* free MPI datatypes previously created (#1637)
* Retrieve MPI-IO hints used by MPI library after file open (#1636)
H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.
* OESS-168: Remove clang warnings. (#1309)
* OESS-168: Remove clang warnings.
* OESS-168: Address @lrknox review.
* OESS-168: Remove clang warnings. (#1376)
* Added the support to get the revision count for the onion file into the h5dump.
* Committing clang-format changes
* Changed the function from H5FDget_onion_revision_count to H5FDonion_get_revision_count for better name.
* Fixed compiler warnings.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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(#1692)
* Removes unused definitions from module headers (#1624)
* Fix these Doxygen warnings #1581 (#1589)
* Fixes a typo in H5.c (#1639)
* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)
* free MPI_Group/MPI_Comm/MPI_Datatype objects
* fix clang-format style
* Adds build and license shields to README.md (#1641)
* First stab at a Github status bar
* Adds a .tokeignore file for counting lines of code accurately
* Yanks lines of code calculation since it wildly overcounts
* not depend on doIO to free an MPI_Comm object (#1642)
* free MPI datatypes previously created (#1637)
* Retrieve MPI-IO hints used by MPI library after file open (#1636)
H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.
* OESS-168: Remove clang warnings. (#1309)
* OESS-168: Remove clang warnings.
* OESS-168: Address @lrknox review.
* OESS-168: Remove clang warnings. (#1376)
* Adding a new API function to get the number of revisions for an onion file. This function uses H5FD_ctl().
* Committing clang-format changes
* Removed a few unused variables.
* Modified the way that the API function H5FDget_onion_revision_count is organized and added Doxygen comments for the three API functions.
* Committing clang-format changes
* Minor changes: modified some Doxygen comments.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Removes unused definitions from module headers (#1624)
* Fix these Doxygen warnings #1581 (#1589)
* Fixes a typo in H5.c (#1639)
* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)
* free MPI_Group/MPI_Comm/MPI_Datatype objects
* fix clang-format style
* Adds build and license shields to README.md (#1641)
* First stab at a Github status bar
* Adds a .tokeignore file for counting lines of code accurately
* Yanks lines of code calculation since it wildly overcounts
* not depend on doIO to free an MPI_Comm object (#1642)
* free MPI datatypes previously created (#1637)
* Retrieve MPI-IO hints used by MPI library after file open (#1636)
H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.
* OESS-168: Remove clang warnings. (#1309)
* OESS-168: Remove clang warnings.
* OESS-168: Address @lrknox review.
* OESS-168: Remove clang warnings. (#1376)
* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)
* Do not conditionally compile code that uses a pointer dereference
and assignment to copy a potentially unaligned variable to aligned
automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s.
Disassembling the generated code reveals that the `memcpy(3)`s optimize
(`-O3`) to a single `mov` instruction for x86_64, which is not strict
about alignment.
This change reduces the size of code and scripts by 143 lines, eases
our way to cross-compilation, and avoids invoking undefined behavior.
* Committing clang-format changes
* Per discussion, use HD and add comments.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t (#1651)
* Cleans up some HL library code that inappropriately returns
htri_t values cast to herr_t
* Committing clang-format changes
* Formatted source
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Mirror vfd test fixes (#1629)
* Use the FAPL that was created earlier in the test (and delete an unused
variable). This allows 'make check-vfd' to pass with --enable-mirror-vfd.
* Check for testing directory before creating, to avoid warning from bash.
Clean out .libs directory before re-using it (after a failed test), to
remove any files generated by libtool.
* Committing clang-format changes
* Increment error count on failed file open and skip tests for VFDs that need
modified filenames.
* Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking
configuration parameters and can't be provided for an automated test that
is configured with an environment variable.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes HDF Group paths, adds shellcheck fixes (#1656)
For more information:
https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti...
https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...
* HDFFV-11306 Fixed (#1657)
* HDFFV-11306,
* Fixed it so both h5open_f and h5close_f can be called multiple times.
* Fixed an issue with open objects remaining after h5close_f was called.
* Added additional tests.
* comments clean-up
* Develop clang format java (#1653)
* added HDFFV-11306 entry (#1662)
* Adds the -q flag to all swmr test programs, quieting noisy output (#1665)
* Adds paths-ignore to the Github pull request workflow (#1663)
* Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666)
So the PR action name is not the same as the one in main.yml
* Replace H5detect's build-time detection of C99 integer properties with a (#1400)
* Replace H5detect's build-time detection of C99 integer properties with a
table-driven routine, `H5T__init_native_int()`, that is run at library
initialization time.
* Improve handling of copying of dynamic libraries and clean them up after (#1681)
test finishes.
* Warnings fixes (#1680)
* Clean stack size warnings in sio_engine (#1687)
* Fixes stack size warnings in tcoords.c (#1688)
* Minor things noticed while bringing VFD SWMR in line with develop (#1691)
* Removed dead code, weird formatting, and other badness
* Fixed remaining stack size warnings in onion VFD
* Committing clang-format changes
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
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* Removes unused definitions from module headers (#1624)
* Fix these Doxygen warnings #1581 (#1589)
* Fixes a typo in H5.c (#1639)
* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)
* free MPI_Group/MPI_Comm/MPI_Datatype objects
* fix clang-format style
* Adds build and license shields to README.md (#1641)
* First stab at a Github status bar
* Adds a .tokeignore file for counting lines of code accurately
* Yanks lines of code calculation since it wildly overcounts
* not depend on doIO to free an MPI_Comm object (#1642)
* free MPI datatypes previously created (#1637)
* Retrieve MPI-IO hints used by MPI library after file open (#1636)
H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.
* OESS-168: Remove clang warnings. (#1309)
* OESS-168: Remove clang warnings.
* OESS-168: Address @lrknox review.
* OESS-168: Remove clang warnings. (#1376)
* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)
* Do not conditionally compile code that uses a pointer dereference
and assignment to copy a potentially unaligned variable to aligned
automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s.
Disassembling the generated code reveals that the `memcpy(3)`s optimize
(`-O3`) to a single `mov` instruction for x86_64, which is not strict
about alignment.
This change reduces the size of code and scripts by 143 lines, eases
our way to cross-compilation, and avoids invoking undefined behavior.
* Committing clang-format changes
* Per discussion, use HD and add comments.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t (#1651)
* Cleans up some HL library code that inappropriately returns
htri_t values cast to herr_t
* Committing clang-format changes
* Formatted source
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Mirror vfd test fixes (#1629)
* Use the FAPL that was created earlier in the test (and delete an unused
variable). This allows 'make check-vfd' to pass with --enable-mirror-vfd.
* Check for testing directory before creating, to avoid warning from bash.
Clean out .libs directory before re-using it (after a failed test), to
remove any files generated by libtool.
* Committing clang-format changes
* Increment error count on failed file open and skip tests for VFDs that need
modified filenames.
* Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking
configuration parameters and can't be provided for an automated test that
is configured with an environment variable.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes HDF Group paths, adds shellcheck fixes (#1656)
For more information:
https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti...
https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...
* HDFFV-11306 Fixed (#1657)
* HDFFV-11306,
* Fixed it so both h5open_f and h5close_f can be called multiple times.
* Fixed an issue with open objects remaining after h5close_f was called.
* Added additional tests.
* comments clean-up
* Develop clang format java (#1653)
* added HDFFV-11306 entry (#1662)
* Adds the -q flag to all swmr test programs, quieting noisy output (#1665)
* Adds paths-ignore to the Github pull request workflow (#1663)
* Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666)
So the PR action name is not the same as the one in main.yml
* Replace H5detect's build-time detection of C99 integer properties with a (#1400)
* Replace H5detect's build-time detection of C99 integer properties with a
table-driven routine, `H5T__init_native_int()`, that is run at library
initialization time.
* Improve handling of copying of dynamic libraries and clean them up after (#1681)
test finishes.
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
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* Trivial comment change
* Misc refactoring in the onion test
* Committing clang-format changes
* Fix unused parameter warning
* Removed printf debugging statements
* checkposix fixes
* Cleaned up some function headers
* Remove useless casts
* Fixes most warnings in the onion VFD test code
(exception: stack size warnings)
* Make TEST_ERROR semicolons consistent
* Much tidying in the onion VFD tests
* Formatted source
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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'revision_num' for better description (#1650)
* Changed the field name 'revision_id' of H5FD_onion_fapl_info_t to 'revision_num' for better description.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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FUNC_ENTER_STATIC to FUNC_ENTER_PACKAGE to follow the changes in the develop branch.
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raylu_onion_vfd_7
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* Removes the STATIC flavor of FUNC_ENTER macros
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(version, subversion) (#1556)
* Fix MPI version check for MPI_Aint_diff usage
* Add H5_CHECK_MPI_VERSION macro
Adds new H5_CHECK_MPI_VERSION macro to check for MPI library version/subversion pair of at least the specified pair
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* Unnecessary extern C guards in cache headers
* Non-existent H5Xpublic.h includes hidden behind NOT_YET symbols
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From Vailin:
Fix the FSM bug when setting the FSM threshold to a non-default value.
Check for smaller or larger section size after merging and shrinking a
section, for this case is the section that is smaller than threshold
(see H5MF_xfree() in H5MF.c). It is possible for the section to be
smaller after merging/shrinking (see H5MF__sect_large_shrink() in
H5MFsection.c).
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to MANIFEST (#1460)
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Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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* Committing clang-format changes
* Spelling of preceed was corrected to proceed, but should have been
corrected to precede.
* Correct spelling correction of 'preceed' incorrectly to 'proceed'. It should be 'precede'.
* OESS-168: Remove clang warnings.
* OESS-168: Address @lrknox and @gnuoyd reviews.
* Eliminate clang warnings listed in PR #1310 without adding new ssize_t
variables.
* Committing clang-format changes
* Add H5_ATTR_UNUSED to wait_for_child call.
Remove unneeded casts in mirror_log calls.
* Keep ssize_t in mirror_server.c line 479.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Hyo-Kyung Lee <hyoklee@hdfgroup.org>
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* Fix issue with copying null new references. Fix assertion failure when
reference copying fails.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Implement big I/O support for independent reads. Add test for this.
* Committing clang-format changes
* Update big I/O code in H5FD__mpio_write() to match that in
H5FD__mpio_read().
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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(#1358)" (#1437)
This reverts commit 01092658a3095c31d7dc1ed1beebbd965095c244.
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* Implement H5ESget_requests() to retrieve request pointers and
corresponding connector IDs from an event set. Add tests for this
function.
* Add "order" parameter to H5ESget_requests, to allow the user to specify
the order in which requests are returned.
* Fix bugs with H5ESinsert_request()
* Change H5ESget_requests() API to have separate input and output
parameters for the allocated array length(s) (in) and the number of events in
the event set (out).
* Fix issue with H5_now_usec() with 32 bit systems. Also improve event
set test.
* Committing clang-format changes
* Add comments to H5_now_usec() explaining rationale for uint64_t casts.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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When resizing a pinned/protected cache entry, the metadata
cache code previously would wait until after resizing the
entry to attempt to log the newly-dirtied entry. This would
cause H5C_resize_entry to mark the entry as dirty and make
H5AC_resize_entry think that it doesn't need to add the
newly-dirtied entry to the dirty entries skiplist.
Thus, a subsequent H5AC__log_moved_entry would think it
needs to allocate a new entry for insertion into the dirty
entry skip list, since the entry doesn't exist on that list.
This causes an assertion failure, as the code to allocate a
new entry assumes that the entry is not dirty.
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