Fixes a few issues created in #3580:
* Fixes a problem where committed tools test files were deleted when cleaning after an in-source build
* Fixes issues with test file paths in Autotools tools test scripts
* Strip HD prefix from string/char C API calls
* HD(f)(put|get)(s|c)
* HDstr*
* HDv*printf
* HD(s)(print|scan)f
* HDperror
But NOT:
* HDstrcase*
* HDvasprintf
* HDstrtok_r
* HDstrndup
As those are not C99 and have portability work-around
implementations. They will be handled later.
* Fix th5_system.c screwup
* Adds semicolons to function-like macros
* Adds a do..while(0) loop to some macros
* Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END
* Remove duplicate code
Signed-off-by: Egbert Eich <eich@suse.com>
* Add test case for CVE-2021-37501
Bogus sizes in this test case causes the on-disk data size
calculation in H5O__attr_decode() to overflow so that the
calculated size becomes 0. This causes the read to overflow
and h5dump to segfault.
This test case was crafted, the test file was not directly
generated by HDF5.
Test case from:
https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.md
* Correct concurrency bugs when running tests, along with a bugfix & small
warning cleanup.
* Committing clang-format changes
* Allow spaces (and tabs) in VOL connector info string from environment variable.
* Parse connector name from HDF5_PLUGIN_PATH environment variable better
* Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an
error message to the failure return value from not finding a plugin.
* Play nice with existing plugin paths
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal>
Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Updated source file copyright headers to remove "Copyright by the Board of Trustees
of the University of Illinois", which is kept in the top-level COPYING file.
* Fix typos found in the rest of the hdf5 code-base
* Typo in tool.cmake
* Revert "Typo in tool.cmake"
This reverts commit 06b8403d99.
* Fix clang-format styling
* Onion VFD feature
* Fixes onion VFD errors with non-sec2 backing store VFDs
* Disables the onion VFD tests w/ ph5diff
* Disables non-sec2 VFDs as onion VFD backing stores
* Committing clang-format changes
* Formatted source
* Typo
* Adds onion VFD tools tests to CMake
* Fixes for v16 API compatibility
* Memset structs to avoid bad frees on errors
* H5Dwrite() calls now use H5T_NATIVE_INT as the memory type vs LE
* Properly decodes checksums on BE machines
* Be more careful about uint64_t to haddr_t/hsize_t conversions
* Another fix for BE data comparison
* Removed double underscores from onion constants
* Replace hard-coded onion header string w/ constant
* Fixes cleanup paths in H5FD__onion_ingest_history()
* Fixed use of size_t revision numbers
* Fix h5dump revision count format string
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Added support for vector I/O calls to the VFD layer, and
associated test code. Note that this includes the optimization
to allow shortened sizes and types arrays to allow more space
efficient representations of vectors in which all entries are
of the same size and/or type. See the Selection I/o RFC for
further details.
Tested serial and parallel, debug and production on Charis.
serial and parallel debug only on Jelly.
* ran code formatter
quick serial build and test on jelly
* Add H5FD_read_selection() and H5FD_write_selection(). Currently only
translate to scalar calls. Fix const buf in H5FD_write_vector().
* Format source
* Fix comments
* Add selection I/O to chunk code, used when: not using chunk cache, no
datatype conversion, no I/O filters, no page buffer, not using collective
I/O. Requires global variable H5_use_selection_io_g be set to TRUE.
Implemented selection to vector I/O transaltion at the file driver
layer.
* Fix formatting unrelated to previous change to stop github from
complaining.
* Add full API support for selection I/O. Add tests for this.
* Implement selection I/O for contiguous datasets. Fix bug in selection
I/O translation. Add const qualifiers to some internal selection I/O
routines to maintain const-correctness while avoiding memcpys.
* Added vector read / write support to the MPIO VFD, with associated
test code (see testpar/t_vfd.c).
Note that this implementation does NOT support vector entries of
size greater than 2 GB. This must be repaired before release,
but it should be good enough for correctness testing.
As MPIO requires vector I/O requests to be sorted in increasing
address order, also added a vector sort utility in H5FDint.c This
function is tested in passing by the MPIO vector I/O extension.
In passing, repaired a bug in size / type vector extension management
in H5FD_read/write_vector()
Tested parallel debug and production on charis and Jelly.
* Ran source code formatter
* Add support for independent parallel I/O with selection I/O. Add
HDF5_USE_SELECTION_IO env var to control selection I/O (default off).
* Implement parallel collective support for selection I/O.
* Fix comments and run formatter.
* Update selection IO branch with develop (#1215)
Merged branch 'develop' into selection_io
* Sync with develop (#1262)
Updated the branch with develop changes.
* Implement big I/O support for vector I/O requests in the MPIO file
driver.
* Free arrays in H5FD__mpio_read/write_vector() as soon as they're not
needed, to cut down on memory usage during I/O.
* Address comments from code review. Fix const warnings with
H5S_SEL_ITER_INIT().
* Committing clang-format changes
* Feature/subfiling (#1464)
* Initial checkin of merged sub-filing VFD.
Passes regression tests (debug/shared/paralle) on Jelly.
However, bugs and many compiler warnings remain -- not suitable
for merge to develop.
* Minor mods to src/H5FDsubfile_mpi.c to address errors reported by autogen.sh
* Code formatting run -- no test
* Merged my subfiling code fixes into the new selection_io_branch
* Forgot to add the FindMERCURY.cmake file. This will probably disappear soon
* attempting to make a more reliable subfile file open which doesn't return errors. For some unknown reason, the regular posix open will occasionally fail to create a subfile. Some better error handling for file close has been added.
* added NULL option for H5FD_subfiling_config_t in H5Pset_fapl_subfiling (#1034)
* NULL option automatically stacks IOC VFD for subfiling and returns a valid fapl.
* added doxygen subfiling APIs
* Various fixes which allow the IOR benchmark to run correctly
* Lots of updates including the packaging up of the mercury_util source files to enable easier builds for our Benchmarking
* Interim checkin of selection_io_with_subfiling_vfd branch
Moddified testpar/t_vfd.c to test the subfiling vfd with default configuration.
Must update this code to run with a variety of configurations -- most particularly
multiple IO concentrators, and stripe depth small enough to test the other IO
concentrators.
testpar/t_vfd.c exposed a large number of race condidtions -- symtoms included:
1) Crashes (usually seg faults)
2) Heap corruption
3) Stack corruption
4) Double frees of heap space
5) Hangs
6) Out of order execution of I/O requests / violations of POSIX semantics
7) Swapped write requests
Items 1 - 4 turned out to be primarily caused by file close issues --
specifically, the main I/O concentrator thread and its pool of worker threads
were not being shut down properly on file close. Addressing this issue in
combination with some other minor fixes seems to have addressed these issues.
Items 5 & 6 appear to have been caused by issue of I/O requests to the
thread pool in an order that did not maintain POSIX semantics. A rewrite of
the I/O request dispatch code appears to have solved these issues.
Item 7 seems to have been caused by multiple write requests from a given
rank being read by the wrong worker thread. Code to issue "unique" tags for
each write request via the ACK message appears to have cleaned this up.
Note that the code is still in poor condtition. A partial list of known
defects includes:
a) Race condiditon on file close that allows superblock writes to arrive
at the I/O concentrator after it has been shutdown. This defect is
most evident when testpar/t_subfiling_vfd is run with 8 ranks.
b) No error reporting from I/O concentrators -- must design and implement
this. For now, mostly just asserts, which suggests that it should be
run in debug mode.
c) Much commented out and/or un-used code.
d) Code orgnaization
e) Build system with bits of Mercury is awkward -- think of shifting
to pthreads with our own thread pool code.
f) Need to add native support for vector and selection I/O to the subfiling
VFD.
g) Need to review, and posibly rework configuration code.
h) Need to store subfile configuration data in a superblock extension message,
and add code to use this data on file open.
i) Test code is inadequate -- expect more issues as it is extended.
In particular, there is no unit test code for the I/O request dispatch code.
While I think it is correct at present, we need test code to verify this.
Similarly, we need to test with multiple I/O concentrators and much smaller
stripe depth.
My actual code changes were limited to:
src/H5FDioc.c
src/H5FDioc_threads.c
src/H5FDsubfile_int.c
src/H5FDsubfile_mpi.c
src/H5FDsubfiling.c
src/H5FDsubfiling.h
src/H5FDsubfiling_priv.h
testpar/t_subfiling_vfd.c
testpar/t_vfd.c
I'm not sure what is going on with the deletions in src/mercury/src/util.
Tested parallel/debug on Charis and Jelly
* subfiling with selection IO (#1219)
Merged branch 'selection_io' into subfiling branch.
* Subfile name fixes (#1250)
* fixed subfiling naming convention, and added leading zero to rank names.
* Merge branch 'selection_io' into selection_io_with_subfiling_vfd (#1265)
* Added script to join subfiles into a single HDF5 file (#1350)
* Modified H5FD__subfiling_query() to report that the sub-filing VFD supports MPI
This exposed issues with truncate and get EOF in the sub-filing VFD.
I believe I have addressed these issues (get EOF not as fully tested as it should be), howeer,
it exposed race conditions resulting in hangs. As of this writing, I have not been able
to chase these down.
Note that the tests that expose these race conditions are in testpar/t_subfiling_vfd.c, and
are currently skipped. Unskip these tests to reproduce the race conditions.
tested (to the extent possible) debug/parallel on charis and jelly.
* Committing clang-format changes
* fixed H5MM_free
Co-authored-by: mainzer <mainzer#hdfgroup.org>
Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com>
Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org>
Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Move Subfiling VFD components into H5FDsubfiling source directory
* Update Autotools build and add H5_HAVE_SUBFILING_VFD macro to H5pubconf.h
* Tidy up CMake build of subfiling sources
* Merge branch 'develop' into feature/subfiling (#1539)
Merge branch 'develop' into feature/subfiling
* Add VFD interface version field to Subfiling and IOC VFDs
* Merge branch 'develop' into feature/subfiling (#1557)
Merge branch 'develop' into feature/subfiling
* Merge branch 'develop' into feature/subfiling (#1563)
Merge branch 'develop' into feature/subfiling
* Tidy up merge artifacts after rebase on develop
* Fix incorrect variable in mirror VFD utils CMake
* Ensure VFD values are always defined
* Add subfiling to CMake VFD_LIST if built
* Mark MPI I/O driver self-initialization global as static
* Add Subfiling VFD to predefined VFDs for HDF5_DRIVER env. variable
* Initial progress towards separating private vs. public subfiling code
* include libgen.h in t_vfd tests for correct dirname/basename
* Committing clang-format changes
* removed mercury option, included subfiling header path (#1577)
Added subfiling status to configure output, installed h5fuse.sh to build directory for use in future tests.
* added check for stdatomic.h (#1578)
* added check for stdatomic.h with subfiling
* added H5_HAVE_SUBFILING_VFD for cmake
* fix old-style-definition warning (#1582)
* fix old-style-definition warning
* added test for enable parallel with subfiling VFD (#1586)
Fails if subfiling VFD is not used with parallel support.
* Subfiling/IOC VFD fixes and tidying (#1619)
* Rename CMake option for Subfiling VFD to be consistent with other VFDs
* Miscellaneous Subfiling fixes
Add error message for unset MPI communicator
Support dynamic loading of subfiling VFD with default configuration
* Temporary fix for subfile name issue
* Added subfile checks (#1634)
* added subfile checks
* Feature/subfiling (#1655)
* Subfiling/IOC VFD cleanup
Fix misuse of MPI_COMM_WORLD in IOC VFD
Propagate Subfiling FAPL MPI settings down to IOC FAPL in default
configuration case
Cleanup IOC VFD debugging code
Change sprintf to snprintf in a few places
* Major work on separating Subfiling and IOC VFDs from each other
* Re-write async_completion func to not overuse stack
* Replace usage of MPI_COMM_WORLD with file's actual MPI communicator
* Refactor H5FDsubfile_mpi.c
* Remove empty file H5FDsubfile_mpi.c
* Separate IOC VFD errors to its own error stack
* Committing clang-format changes
* Remove H5TRACE macros from H5FDioc.c
* Integrate H5FDioc_threads.c with IOC error stack
* Fix for subfile name generation
Use number of I/O concentrators from existing subfiling configuration file, if one exists
* Add temporary barrier in "Get EOF" operation to prevent races on EOF
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for retrieval of machine Host ID
* Default to MPI_COMM_WORLD if no MPI params set
* added libs rt and pthreads (#1673)
* added libs rt and pthreads
* Feature/subfiling (#1689)
* More tidying of IOC VFD and subfiling debug code
* Remove old unused log file code
* Clear FID from active file map on failure
* Fix bug in generation of subfile names when truncating file
* Change subfile names to start from 1 instead of 0
* Use long long for user-specified stripe size from environment variable
* Skip 0-sized I/Os in low-level IOC I/O routines
* Don't update EOF on read
* Convert printed warning about data size mismatch to assertion
* Don't add base file address to I/O addresses twice
Base address should already be applied as part of H5FDwrite/read_vector calls
* Account for 0-sized I/O vector entries in subfile write/read functions
* Rewrite init_indep_io for clarity
* Correction for IOC wraparound calculations
* Some corrections to iovec calculations
* Remove temporary barrier on EOF retrieval
* Complete work request queue entry on error instead of skipping over
* Account for stripe size wraparound for sf_col_offset calculation
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Re-write and fix bugs in I/O vector filling routines (#1703)
* Rewrite I/O vector filling routines for clarity
* Fix bug with iovec_fill_last when last I/O size is 0
* added subfiling_dir line read (#1714)
* added subfiling_dir line read and use it
* shellcheck fixes
* I/O request dispatch logic update (#1731)
Short-circuit I/O request dispatch when head of I/O queue is an
in-progress get EOF or truncate operation. This prevents an issue where
a write operation can be dispatched alongside a get EOF/truncate
operation, whereas all I/O requests are supposed to be ineligible for
dispatch until the get EOF/truncate is completed
* h5fuse.sh.in clean-up (#1757)
* Added command-line options
* Committing clang-format changes
* Align with changes from develop
* Mimic MPI I/O VFD for EOF handling
* Initialize context_id field for work request objects
* Use logfile for some debugging information
* Use atomic store to set IOC ready flag
* Use separate communicator for sending file EOF data
Minor IOC cleanup
* Use H5_subfile_fid_to_context to get context ID for file in Subfiling
VFD
* IOVEC calculation fixes
* Updates for debugging code
* Minor fixes for threaded code
* Committing clang-format changes
* Use separate MPI communicator for barrier operations
* Committing clang-format changes
* Rewrite EOF routine to use nonblocking MPI communication
* Committing clang-format changes
* Always dispatch I/O work requests in IOC main loop
* Return distinct MPI communicator to library when requested
* Minor warning cleanup
* Committing clang-format changes
* Generate h5fuse.sh from h5fuse.sh.in in CMake
* Send truncate messages to correct IOC rank
* Committing clang-format changes
* Miscellaneous cleanup
Post some MPI receives before sends
Free some duplicated MPI communicator/Info objects
Remove unnecessary extra MPI_Barrier
* Warning cleanup
* Fix for leaked MPI communicator
* Retrieve file EOF on single rank and bcast it
* Fixes for a few failure paths
* Cleanup of IOC file opens
* Committing clang-format changes
* Use plan MPI_Send for send of EOF messages
* Always check MPI thread support level during Subfiling init
* Committing clang-format changes
* Handle a hang on failure when IOCs can't open subfiles
* Committing clang-format changes
* Refactor file open status consensus check
* Committing clang-format changes
* Fix for MPI_Comm_free being called after MPI_Finalize
* Fix VFD test by setting MPI params before setting subfiling on FAPL
* Update Subfiling VFD error handling and error stack usage
* Improvements for Subfiling logfiles
* Remove prototypes for currently unused routines
* Disable I/O queue stat collecting by default
* Remove unused serialization mutex variable
* Update VFD testing to take subfiling VFD into account
* Fix usage of global subfiling application layout object
* Minor fixes for failure pathways
* Keep track of the number of failures in an IOC I/O queue
* Make sure not to exceed MPI_TAG_UB value for data communication messages
* Committing clang-format changes
* Update for rename of some H5FD 'ctl' opcodes
* Always include Subfiling's public header files in hdf5.h
* Remove old unused code and comments
* Implement support for per-file I/O queues
Allows the subfiling VFD to have multiple HDF5 files open simultaneously
* Use simple MPI_Iprobe over unnecessary MPI_Improbe
* Committing clang-format changes
* Update HDF5 testing to query driver for H5FD_FEAT_DEFAULT_VFD_COMPATIBLE
flag
* Fix a few bugs related to file multi-opens
* Avoid calling MPI routines if subfiling gets reinitialized
* Fix issue when files are closed in a random order
* Update HDF5 testing to query VFD for "using MPI" feature flag
* Register atexit handler in subfiling VFD to call MPI_Finalize after HDF5
closes
* Fail for collective I/O requests until support is implemented
* Correct VOL test function prototypes
* Minor cleanup of old code and comments
* Update mercury dependency
* Cleanup of subfiling configuration structure
* Committing clang-format changes
* Build system updates for Subfiling VFD
* Fix possible hang on failure in t_vfd tests caused by mismatched
MPI_Barrier calls
* Copy subfiling IOC fapl in "fapl get" method
* Mirror subfiling superblock writes to stub file for legacy POSIX-y HDF5
applications
* Allow collective I/O for MPI_BYTE types and rank 0 bcast strategy
* Committing clang-format changes
* Use different scheme for subfiling write message MPI tag calculations
* Committing clang-format changes
* Avoid performing fstat calls on all MPI ranks
* Add MPI_Barrier before finalizing IOC threads
* Use try_lock in I/O queue dispatch to minimize contention from worker threads
* Use simple Waitall for nonblocking I/O waits
* Add configurable IOC main thread delay and try_lock option to I/O queue dispatch
* Fix bug that could cause serialization of non-overlapping I/O requests
* Temporarily treat collective subfiling vector I/O calls as independent
* Removed unused mercury bits
* Add stubs for subfiling and IOC file delete callback
* Update VFD testing for Subfiling VFD
* Work around HDF5 metadata cache bug for Subfiling VFD when MPI Comm size
= 1
* Committing clang-format changes
Co-authored-by: mainzer <mainzer#hdfgroup.org>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com>
Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org>
Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
* Fixes a stack overflow in the h5dump test generator
The opaque type size was declared to be the size of the "buffer of two
opaque elements", causing a memcpy call in H5Dwrite to read outside
the buffer, dumping garbage into the file.
Note that this only affected the test generator and not h5dump itself.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Straightforward conversion of sprintf to the safer snprintf
* Trickier conversion of sprintf to safer snprintf
This involved minor changes to private function signatures to take the size of the buffer.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Remove const from the argv tools/tests main sig.
* also remove const from H5_get_option and parse_command_line.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Create 2D arrays on the heap by malloc'ing `struct { TYPE arr[ROWS][COLS];
}`. This avoids the double-indirection through pointers and the
additional memory of H5TEST_ALLOCATE_2D_ARRAY().
This change will safely quiet the cast warning that PR #1129 was
intended to fix.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Move test utilities to utils/test folder
* Fix makefile assignment
* Add new dir
* add new folder
* Correct copied makefile
* Fix dir typo
* Add missing include dir
* Remove unnecessary lib link
* Correct dependent dirs
* Fix conditional checks
* Disable test if not built
* fix path to executable
* Use fixture for swmr_vfd check
* Add release note
* Correct shell tests and c++ flag warning
* Update autotools c++ warning
* Fix typo
* Pacify clang-analyzer-unix.cstring.NullArg
* Apply some bugprone-suspicious-string-compare
* Apply some readability-simplify-boolean-expr
* Apply some readability-make-member-function-const
* Apple some bugprone-macro-parentheses
* Changed an f suffix to L for `long double`
* Applied some readability-uppercase-literal-suffix automatically
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
* Correct VAR used to find configure time file
* Set the path correctly
* Update missing release note info.
* Update code owners
* Correct JIRA note
* add known problem.
* Use only core library for testing dynamic plugins.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Update API tracing for new H5VL_request_status_t typedef
* Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure
* Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation
* Remove 'canceled' event status from Java constants
* Be safer about releasing resources when inserting a newly opened/created object or file into an event set
* Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate".
* Remove H5ES_STATUS_CANCELED from Java wrappers also
* Apply patch for dynamically registering optional VOL operations
* (a) Add async APIs for H5O module as listed in jira issue ID-283.
(b) Remove verification of name parameter in async related routines for H55A and H5L modules
because it is checked in H5VL_setup* routine.
(c) Modify h5dump expected output due to the async changes.
* Corrections based on PR feedback.
* Further changes to make based on PR feedback.
* Remove H5Dwait & H5Fwait (moved to the async connector). Added H5atclose
routine. Updated 'optional op' operations.
* Fix missed merge marker, and reformatted line
* Update API tracing infrastructure for H5atclose callback
* Clean up some warnings
* Normalize against develop branch
* Correct level of indirection
* Add doxygen info for H5is_library_terminating and regression tests for it and H5atclose
* Relocate prototype (and doxygen info) for H5Aclose
* Align w/changes on develop
* Move group package initialization code to H5Gint.c, and update tracing macros
* Change non-static function declarations to be static
* Correct GCC diagnostic macro
* Ensure that H5TSpublic.h header gets installed (#129)
* Finish moving API routines that invoke VOL framework to main source files.
* Fix position of H5Fmount and H5Funmount
* Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information.
* Add wrappers for dynamically registered optional operations
* Fix typo
* Update doxygen comment for H5atclose with additional detail.
* Add H5VL\*_vararg versions of H5VL routines that use va_list parameters
* Implement and test H5S_BLOCK
* Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value. Make the corresponding changes through most of the v1 and v2 B-tree code. Clean up warnings in H5public.h and cmpd_dtransform.c.
* Add H5Iregister_future routine and tests.
* Correct return value for H5Lexists_async
* Add H5_DLL macro to public H5ES API routines
* Update supported -> flags parameter for introspect_query callback
* Remove my email address. Update passthrough VOL connector ID.
* Fix comment for post_open_api_common
* Remove unused non-blocking VOL connector
* Minor cleanup in async branch in preparation for merge to develop
* Update CMake and the Autotools to use the new pass-through VOL ID
* Finish another iteration on public H5ES routines, along with running the code reformatter
* Another round of reformatting
* Fix for SWMR daily test failures (#160)
The H5I_register_using_existing_id() call did not initialize the future
ID callbacks, causing the library to segfault when it tried to
resolve those function pointers.
* Added selective async APIs (#150)
* Added selective async APIs
Description:
Added the following APIs:
H5Ropen_attr_async
H5Ropen_object_async
H5Ropen_region_async
H5Mcreate_async
H5Mopen_async
H5Mput_async
H5Mget_async
H5Mclose_async
H5Tcommit_async
H5Topen_async
H5Tcopy_async
H5Tclose_async
- Updated an expected output file to include a new internal function
in the error stack for the failure case.
* Updated async APIs per reviews, including removing async version of
H5Tcopy.
* Removed statements that were added by mistake in the previous commit.
* Fix compile issues in H5M and warnings elsewhere
* Reformat code
* Brings VOL_LIST changes from develop. (#163)
* Remove H5Dwait and H5Fwait calls, which were incorrectly brought back in
* Tiny cleanup of H5Lcreate_hard_async
* Run source formatter
* Allow for canceled operation in wait_cb
* Attempt to fix switch on string value
* Re-run source formatter
* Add H5S_BLOCK testfile to CMake clean target
* Add H5Pset_vol_async API routine and 'get_cap_flags' VOL introspection callback
* Clean up warnings
* Add H5P(set\|get)_vol_implicit_async API routines to allow \/ disallow implicit asynchronous operations (default is disallowed)
* Run formatting script
* Remove H5VL_REQUEST_WAIT\*
* Warning cleanup
* Eliminate strdup()s on statically allocated strings
* Warning cleanup
* Split H5VLrestore_lib_state into H5VLstart_lib_state and H5VLrestore_lib_state, and rename H5VLreset_lib_state to H5VLfinish_lib_state.
* Duplicate strings when building err_info to return to applicatin
* Move connector author routines into seperate header files, all included in the new hdf5dev.h header
* Run bin/trace to add TRACE macros
* Allow H5ES_NONE as a valid, but no-op, parameter to all H5ES API routines that accept an event set ID
* Clean up formatting
* Remove H5Pset/get_vol_implicit_async
* Clean up warning
* Remove H5Pget_vol_async and replace with more generic H5Pget_vol_cap_flags
* Clean up warnings
* Add H5ESfree_err_info convenience routine
* Fix typo
* Correct matching for cached VOL plugins
* Add developer header file
* Update for C99 compatibility
* Add missing trace macro
* Stop clang-format from messing with the trace macros. Don't set up VOL wrappers for 'infrastructure' objects like requests and blobs
* Fix warning about formatting a directory
* Clean up formatting for H5E_BEGIN_TRY / H5E_END_TRY
* Reduce scope of H5ES__close
* Enable CMake checks for various types on MacOS
* Clean up properly when H5CX_retrieve_state() fails. Also clean up many compiler warnings.
* Committing clang-format changes
* Merge from develop
* Fix mis-placed assert
* Remove commented-out code
* Re-add macro for unsetenv on Windows (I think it accidentally was merged out)
* Strengthen sanity check from error report to assertion
* Committing clang-format changes
* Add units to the comments for a few fields
* Switch 'get execution time' operation for async request tokens to be an optional operation and query if connector supports operation before retrieving it.
* Committing clang-format changes
* Remove H5ESget_time_estimate
* Committing clang-format changes
* Create developer header for datatype routines and move type conversion register/unregister routines there.
* Simplify internal H5VL_setup_name_args and H5VL_setup_idx_args routines
* Add H5VLlink_optional_op, allowing dynamicly registered optional operations for the link VOL subclass, also added H5VL_loc_params argument to the link 'optional' callback to allow them to work correctly.
* Run bin/format_source on current code
* Add H5VLobject_optional_op, allowing dynamicly registered optional operations for the object VOL subclass, also added H5VL_loc_params argument to the object 'optional' callback to allow them to work correctly.
* Run bin/format_source on current code
* Committing clang-format changes
* Revert "Switch 'get execution time' operation for async request tokens to be an optional operation and query if connector supports operation before retrieving it."
This reverts commit 5ac92014da.
* Committing clang-format changes
* Convert attribute 'get' operation to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Update tracing macros
* Convert attribute 'specific' operation to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert dataset 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also, minor tweaks to attribute 'get' and 'specific' operation parameters.
* Convert datatype 'get' and 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also, minor tweaks to H5O_refresh_metadata arguments.
* Reduce warnings
* Reduce warnings
* Track change to datatype 'get' callback
* Fix bug with file pointer getting invalidated when object closed
* Reformat source
* Convert file and group VOL classes 'get' and 'specific' operations to use
struct-of-tagged-union pattern for VOL callback arguments, instead of using
varargs. Also small cleanup to the attribute get name operation. Also moved
'mount' and 'unmount' operations to be group specific operations, instead of
file specific, to better align with their behavior (mounted files are on
groups, so a group is what is operated on).
* Remove remainder of merge conflict marking
* Convert link VOL class 'create' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Remove some unused local variables
* Convert link VOL class 'get' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also refactor 'get name by idx' routines to return actual length of name with a parameter instead of the return value, and move some callback context structs for the link interface from the private header file into the source code module, to reduce their visibility scope.
* Update tracing macros
* Convert link VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert object VOL class 'get' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert object VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also refactor H5G_loc_exists, et al, to return 'exists' flag in a parameter and errors with the function return value, instead of overloading both into the return value. And, corrected logic error in test/links.c around non-existant objects in a file.
* Convert request VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs.
* Convert blob VOL class 'specific' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Also removes the H5VL_BLOB_GETSIZE operation, as it's unused in the library and the blob ID size for a container is now returned with H5VL_FILE_GET_CONT_INFO.
* Add 'const' to several parameters that are only queried.
* Convert all VOL classes' 'optional' operations to use struct-of-tagged-union pattern for VOL callback arguments, instead of using varargs. Convert several 'get' routines to return the length of an array in a parameter instead of combining it into the return value. Move several routines to be in less public namespace. Correct direct_chunk test to verify that parameters aren't modified on error.
* Switch get/specific/optional VOL callback argument structures to be 'async-friendly'. Also other minor cleanups and bug-fixes.
* Add H5Pset_dataset_io_hyperslab_selection / H5S_PLIST feature, to allow skipping H5Dget_space + H5Sselect_hyperslab for async operation
* Add dynamic optional operations for request objects
* Update dynamic operation test for optional request operations
* Update a comment for an operation argument
* Run trace and format_source scripts
* Committing clang-format changes
* Committing clang-format changes
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <derobins@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* GH #359 implement and fix tools 1.6 API usage
* remove excessive comments
* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
