* Sync develop changes April 3 - April4 to hdf5_1_14_4 via hdf5_1_14 (#4324)
* Regenerate files generated by autogen.sh after configure changes.
Set workflows to run for the hdf5_1_14_4 branch.
* Take user block into account when returning chunk addresses (#4236)
Both H5Dchunk_iter() and H5Dget_chunk_info(_by_coord)() did not take
the size of the user block into account when reporting addresses. Since
the #1 use of these functions is to root around in the file for the raw
data, this is kind of a problem.
Fixes GitHub issue #3003
* Fix a minor warning in h5test.c (#4242)
* Turn on -Werror for Java in GitHub -Werror workflows (#4243)
* Update Windows CI to not install ninja (#4230)
* Rework Fortran macros to use the proper code. (#4240)
* Correct reference copy for 16 API (#4244)
* Determine MPI LOGICAL during build, used in tests. (#4246)
* Skip userblock test in chunk_info.c for multi-file VFDs (#4249)
* Match generators with real cmake -G output on Windows (#4252)
* Add Julia GitHub Actions. (#4123)
* Re-revert to using autoreconf in autogen.sh (#4253)
We previously tried removing the per-tool invocation of the Autotools
and instead simply invoked autoreconf (PR #1906). This was reverted
when it turned out that the NAG Fortran compiler had trouble with an
undecorated -shared linker flag.
It turns out that this is due to a bug in libtool 2.4.2 and earlier.
Since this version of libtool is over a decade old, we're un-reverting
the change. We've added a release note for anyone who has to build
from source on elderly platforms.
Fixes#1343
* Rewrite H5T__path_find_real for clarity (#4225)
* Move conversion path free logic to helper function
* Add tgz extensions on names (#4255)
* Remove an error check regarding large cache objects (#4254)
* Remove an error check regarding large cache objects
In PR#4231 an assert() call was converted to a normal HDF5 error
check. It turns out that the original assert() was added by a
developer as a way of being alerted that large cache objects
existed instead of as a guard against incorrect behavior, making
it unnecessary in either debug or release builds.
The error check has been removed.
* Update RELEASE.txt
* File format security issues (#4234)
* Add job timeout to cygwin workflow (#4260)
* Replace user-define with user-defined (#4261)
* Improve the CMake clang -fsanitize=memory flags (#4267)
-fsanitize=memory is almost useless without
using -fsanitize-memory-track-origins=2 and we shoud probably add
-fno-optimize-sibling-calls as well.
* Add documentation (H5M) (#4259)
* Add documentation (H5P) (#4262)
* MPI type correction (#4268)
* corrected type for MPI_*_f2c APIs
* fixed return type of callback
* reset compilation flags of logical test program
* Clean up test/cmpd_dtransform.c (#4270)
* Clean up test/cmpd_dtransform.c
* Fix uninitialized memory warning from sanitizers
* FAIL_STACK_ERROR --> TEST_ERROR
* Emit output
* Delete test file when done
* Fix typo
* H5Fdelete() --> remove()
* Fix uninitialized memory issues in packet table (#4271)
* replace deprecated CMAKE_COMPILER_IS_GNU** (#4272)
* Prevent stack overflows in H5E__push_stack (#4264)
* Minor fixes after merge of file format security fixes (#4263)
* Update H5_IS_BUFFER_OVERFLOW to account for 'size' of 0
* Invert a few checks to avoid function call
* CHECK --> CHECK_PTR in tmisc.c (#4274)
* Add release note for CVE-2017-17507 (#4275)
* Update Cygwin installation guide (#4265)
* Addresses configuration fortran testing flags (#4276)
* turn warnings to errors in fortran configure test
* Intel fortran test fix
* Merge julia workflows into standard ci format (#4273)
* Fix range check in H5_addr_overlap (#4278)
When the H5_addr_overlap macro was updated to use H5_RANGE_OVERLAP,
it failed to take into account that H5_RANGE_OVERLAP expects the
range to be inclusive. This lead to an assertion failure in
H5MM_memcpy due to a memcpy operation on overlapping memory.
This has been fixed by subtracting 1 from the calculated high
bound values passed to H5_RANGE_OVERLAP
* Fix potential buffer read overflows in H5PB_read (#4279)
H5PB_read previously did not account for the fact that the size of the
read it's performing could overflow the page buffer pointer, depending
on the calculated offset for the read. This has been fixed by adjusting
the size of the read if it's determined that it would overflow the page.
* Call memset before stat calls (#4202)
The buffers passed to stat-like calls are only partially filled in by
the call, leaving ununitialized memory areas when the stat buffers are
created on the stack.
This change memsets the buffers to 0 before the stat calls, quieting
the -fsanitze=memory complaints.
* Remove unused CMake configuration checks (#4199)
* Update link to Chunking in HDF5 page (#4203)
* Fix H5Pset_efile_prefix documentation error (#4206)
Fixes GH issue #1759
* Suggested header footer for NEWSLETTER (#4204)
* Suggested header footer for NEWSLETTER
* Updates
* Add NEWSLETTER.txt to h5vers script
* Fix grammar in README.md release template (#4201)
* Add back snapshot names (#4198)
* Use tar.gz extension for ABI reports (#4205)
* Fix issue with Subfiling VFD and multiple opens of same file (#4194)
* Fix issue with Subfiling VFD and multiple opens of same file
* Update H5_subfile_fid_to_context to return error value instead of ID
* Add helper routine to initialize open file mapping
* Reverts AC_SYS_LARGEFILE change (#4213)
We previously replaced local macros with AC_SYS_LARGEFILE, which is
unfortunately buggy on some systems and does not correctly set the
necessary defines, despite successfully detecting them.
This restores the previous macro hacks to acsite.m4
* Propagate group creation properties to intermediate groups (#4139)
* Add clarification for current behavior of H5Get_objtype_by_idx() (#4120)
* Addressed Fortran issues with promoted integers and reals via compilation flags (#4209)
* addressed issue wit promoted integers and reals
* added option to use mpi_f08
* Summarize the library version table (#4212)
Fixes GH-3773
* Fix URLs (#4210)
Also removed Copyright.html context because it's no longer valid.
* Fix 'make check-vfd' target for Autotools (#4211)
Changes Autotools testing to use HDF5_TEST_DRIVER environment
variable to avoid running tests that don't work well with several
VFDs
Restores old h5_get_vfd_fapl() testing function to setup a FAPL
with a particular VFD
Adds a macro for the default VFD name
* Revert "Addressed Fortran issues with promoted integers and reals via compil…" (#4220)
This reverts commit 06c42ff038.
* Backup and clear CMAKE_C_FLAGS before performing _Float16 configure checks (#4217)
* Fix broken links (#4224)
* Fix broken URLs in documentation (#4214)
Fixes GH-3881 partially. There are pages that need to be recreated.
* Avoid file size checks in C++ testhdf5 for certain VFDs (#4226)
* Fix an issue with type size assumptions in h5dumpgentest (#4222)
* Fix issue with -Werror cleanup sed command in configure.ac (#4223)
* Fix Java JNI warnings (#4229)
* Rework snapshots/release workflows for consistent args (#4227)
* Fixed a cache assert with too-large metadata objects (#4231)
If the library tries to load a metadata object that is above the
library's hard-coded limits, the size will trip an assert in debug
builds. In HDF5 1.14.4, this can happen if you create a very large
number of links in an old-style group that uses local heaps.
The library will now emit a normal error when it tries to load a
metadata object that is too large.
Partially addresses GitHub #3762
* Set DXPL in API context for native VOL attribute I/O calls (#4228)
* Initialize a variable in C++ testhdf5's tattr.cpp (#4232)
* Addressed Fortran issues with promoted integers and reals via compilation flags, part 2 (#4221)
* addressed issue wit promoted integers and reals
* fixed h5fcreate_f
* added option to use mpi_f08
* change the kind of logical in the parallel tests
* addressed missing return value from callback
* Use cp -rp in test_plugin.sh (#4233)
When building with debug symbols on MacOS, the cp -p commands in
test_plugin.sh will attempt to copy the .dSYM directories with
debugging info, which will fail since -r is missing.
Using cp -rp is harmless and allows the test to run
Fixes HDFFV-10542
* Clean up types in h5test.c (#4235)
Reduces warnings on 32-bit and LLP64 systems
* Fix example links (#4237)
* Fix links md files (#4239)
* Add markdown link checker action (#4219)
* Match minimum CMake version to 3.18 (#4215)
* Added new H5E with tests. (#4049)
Added Fortran H5E APIs:
h5eregister_class_f, h5eunregister_class_f, h5ecreate_msg_f, h5eclose_msg_f
h5eget_msg_f, h5epush_f, h5eget_num_f, h5ewalk_f, h5eget_class_name_f,
h5eappend_stack_f, h5eget_current_stack_f, h5eset_current_stack_f, h5ecreate_stack_f,
h5eclose_stack_f, h5epop_f, h5eprint_f (C h5eprint v2 signature)
Addresses Issue #3987
* Don't load toolchain file in CMake workflows (#4077)
* Add support for the new MSVC preprocessor (#4078)
Microsoft has added a new, standards-conformant preprocessor
to MSVC, which can be enabled with /Zc:preprocessor. This
preprocessor trips over our HDopen() function-like variadic
macro since it uses a hack that only works with the legacy
MSVC preprocessor.
This fix adds ifdefs to use the correct HDopen() macro
depending on the MSVC preprocessor selected.
Fixes#2515
* Increased H5FD_ROS3_MAX_SECRET_TOK_LEN to 4096 to accommodate long AWS secret tokens (#4064)
ros3: increased H5FD_ROS3_MAX_SECRET_TOK_LEN to 4096; stratified the debugging statements so there is more control over the output
* Close and reopen file during dset vlen IO API tests (#4050)
- Close/reopen file and file objects to prevent cache from being used instead of actual I/O.
- Moved vlen io test datasets under the dset container group instead of the root group
- Moved the PASSED() invocation to after individual test cleanup in case an error occurs during H5Treclaim
* New option for building with static CRT in Windows (#4062)
* addressed compilation errors with gfortran 4.8 (#4082)
* Fix bin/trace script w/ out params (#4074)
The bin/trace script adds TRACE macros to public API calls in the main
C library. This script had a parsing bug that caused functions that
were annotated with /*out*/, etc. to be labeled as void pointers
instead of typed pointers.
This is mainly a developer feature and not visible to consumers
of the public API.
The bin/trace script now annotates public API calls properly.
Fixes GH #3733
* Use H5T_STD_I32LE to create datatype in vds examples (#4070)
Fixes issues when VDS examples are tested on BE systems
* Remove printf debugging in H5HL code (#4086)
* Fixed asserts due to H5Pset_est_link_info() values (#4081)
* Fixed asserts due to H5Pset_est_link_info() values
If large values for est_num_entries and/or est_name_len were passed
to H5Pset_est_link_info(), the library would attempt to create an
object header NIL message to reserve enough space to hold the links in
compact form (i.e., concatenated), which could exceed allowable object
header message size limits and trip asserts in the library.
This bug only occurred when using the HDF5 1.8 file format or later and
required the product of the two values to be ~64k more than the size
of any links written to the group, which would cause the library to
write out a too-large NIL spacer message to reserve the space for the
unwritten links.
The library now inspects the phase change values to see if the dataset
is likely to be compact and checks the size to ensure any NIL spacer
messages won't be larger than the library allows.
Fixes GitHub #1632
* Fix copy-paste comments
* update macOS support statement (#4084)
* fixes compilation failures due to H5E additions (#4090)
* Remove extra whitespaces from nvhpc-cmake action. (#4091)
* Remove printf debugging in H5I package (#4088)
* Add subfiling for h5dump filedriver option help message (#3878)
* Merge HDF4 release workflow changes to hdf5 (#4093)
* Update long double test with correct values (#4060)
Update long double test with correct values
* virtual creates must use the same datatype as the main file (#4092)
* Fixed -Wdeprecated-copy-dtor warnings by implementing a copy assignment operator (#3306)
Example warning was:
warning: definition of implicit copy assignment operator for 'Group' is deprecated because it has a user-declared destructor [-Wdeprecated-copy-dtor]
* Expand check for variable-length or reference types when clearing datatype conversion paths (#4085)
When clearing out datatype conversion paths involving variable-length or reference datatypes
on file close, also check for these datatypes inside compound or array datatypes
* Remove H5B debug checks (#4089)
The H5B (version 1 B-tree) package would add some computationally
expensive integrity checks when H5B_DEBUG was defined. Due to their
negative effects on performance, this option was rarely turned on,
making the H5B__assert() check function stale, if not dead, code.
This change:
* Builds H5B__assert() when NDEBUG is not defined (the function
relies on assert()) so it gets compiled more often.
* Removes some printf debugging statements in the B-tree code
* Removes all H5B "extra debug" checks that are leftover from
past debugging sessions. Maintainers can add H5B__assert()
selectively to perform integrity checks when debugging.
* Removes the HDF5_ENABLE_DEBUG_H5B CMake option
H5B_DEBUG now has no effect
* Fix the last C++ stack size warning (#4099)
* Clean up off_t usage (#4095)
* Add comments to C++ and Fortran API calls that use off_t
* Remove noise casts for small integers
* Correct missing change of source path for S3 build (#4100)
* Remove leading / from relative path. (#4101)
* msvc: don't declare `HAVE_TIMEZONE` for older MSVC (#3956)
It was introduced in MSVC 15 (Visual Studio 2017).
* Remove a few H5O printf debugging statements (#4096)
These were in H5Oint.c, were protected by H5O_DEBUG, and only dumped
to stdout if the HDF5_DEBUG environment variable were set to do so.
* Remove H5DEBUG() calls from H5Dmpio.c (#4103)
Just use stdout when a stream is needed.
* Remove printf debugging from H5Smpio.c (#4098)
* Change how stats are printed in H5Z (#4097)
H5Z used the soon-to-be-removed HDEBUG macro to decide if stats
would be dumped and to what stream. This is now handled by a
DUMP_DEBUG_STATS_g variable and the output is always sent to
stdout.
This is an internal change, not normally visible to users.
* Refactor datatype conversion code to use pointers rather than IDs (#4104)
The datatype conversion code previously used IDs for the source and
destination datatypes rather than pointers to the internal structures
for those datatypes. This was mostly due to the need for an ID for these
datatypes that can be passed to an application-registered datatype
conversion function or datatype conversion exception function. However,
using IDs internally caused a lot of unnecessary ID lookups and hurt
performance of datatype conversions in general. This was especially
problematic for compound datatype conversions, where the ID lookups were
occuring on every member of every compound element of a dataset. The
code has now been refactored to use pointers internally and only create
IDs for datatypes when necessary.
Fixed a test issue in dt_arith where a library datatype conversion
function was being cast to an application conversion function. Since the
two have different prototypes, this started failing after the parameters
for a library conversion function changed from hid_t to H5T_t * and an
extra parameter was added. This appears to have worked coincidentally in
the past since the only different between a library conversion function
and application conversion function was an extra DXPL parameter at the
end of an application conversion function
Fixed an issue where memory wasn't being freed in the h5fc_chk_idx test
program. Even though the program exits quickly after allocating the
memory, it still causes failures when testing with -fsanitize=address
* Minimize use of abort() (#4110)
The abort() call is used at several places where it probably shouldn't.
* Clean up a few things in H5T.c (#4105)
* remove (size_t) noise casts
* replace (hid_t)FAIL with H5I_INVALID_HID
* Convert H5B__assert to use error checks (#4109)
Switches assert() calls to HGOTO_ERROR in H5B__assert() so it can be
used in production mode. Also renames it to H5B__verify_structure()
to better reflect what it checks.
* Move common variables out of cache test blocks (#4108)
Fixes a stack size warning w/ XCode
* Remove lint comments (#4107)
* Change compression tests reference files to use masking for compression ratios (#4083)
Rework TEST_FILTER tests to handle slightly different compression ratios
* Add Doxygen for HDFS VFD (#4106)
* Add Doxygen for HDFS VFD
* Fix Doxygen warning
* Update H5FDhdfs.h
* long double tests has problems setting precision with offset (#4102)
* long double tests has problems setting precision with offset
* Disable long double until more development fixes issues
* Fix up dsets test for some platforms with different long double format (#4114)
* Adjust aocc workflow to fit the autotools/cmake pattern of other callable workflows. (#4115)
* Implement ID creation optimization for container datatype conversions (#4113)
Makes the datatype conversion context object available during both the
initialization and conversion processes for a datatype conversion
function, allowing the compound, variable-length and array datatype
conversion functions to avoid creating IDs for the datatypes when they
aren't necessary
Adds internal H5CX_pushed routine to determine if an API context is
available to retrieve values from
Also adds error checking to several places in H5T.c and H5Tconv.c where
the code had previously assumed object close operations would succeed
* Handle IBM long double issues in dsets.c test_floattypes test (#4116)
* Handle IBM long double issues in dsets.c test_floattypes test
* Remove old cmake check (#4117)
* Use AC_SYS_LARGEFILE on Autotools (#4119)
We previously used a hack introduced in 1.8.5 to paper over differences
in off_t and off64_t when determining the type sizes. We no longer explicitly
support off64_t in the library and AC_SYS_LARGEFILE works fine.
* Initialize selection type in chunk struct (#4087)
* Overhaul CMake LFS support (#4122)
Externally visible:
* The HDF_ENABLE_LARGE_FILE option (advanced) has been removed
* We no longer run a test program to determine if LFS works, which
will help with cross-compiling
* On Linux we now unilaterally set -D_LARGEFILE_SOURCE and
-D_FILE_OFFSET_BITS=64, regardless of 32/64 bit system. CMake
doesn't offer a nice equivalent to AC_SYS_LARGEFILE and since
those options do nothing on 64-bit systems, this seems safe and
covers all our bases. We don't set -D_LARGEFILE64_SOURCE since
we don't use any of the POSIX 64-bit specific API calls like
ftello64, as noted above.
* We didn't test for LFS support on non-Linux platforms. We've added
comments for how LFS should probably be supported on AIX and Solaris,
which seem to be alive, though uncommon. PRs would be appreciated if
anyone wishes to test this.
Internal:
* Drops off64_t size checks since this is unused (as in Autotools)
* Remove HDF_EXTRA_FLAGS, which is now unused
* Remove hack around deprecated LINUX_LFS
Fixes#2395
* Update CMake comment about _POSIX_C_SOURCE (#4124)
Was missng the 2008 pread/write info
* Deprecate bin/cmakehdf5 (#4127)
* Deprecate bin/cmakehdf5
* Add reference text
* Don't set the rpath when linking statically (#4125)
* Remove invalid compile flag (#4129)
* Fix segfault in vlen io API test (#4130)
* Update URLs in RELEASE.txt (#4132)
* Add cygwin CI and update yaml files for consistency and accuracy (#4131)
* Add cygwin CI
* add cygwin packages
* Correct option names
* Cleanup yaml file and synch look and feel
* Synch CI look and feel and correct path issues
* Upgrade oneapi version
* pwsh needs env: for vars
* No continuation char for pwsh
* restore correct pwsh step
* Run subset of tests for cygwin workflow
* Remove space chars in regex
* restore full tests
* Remove ros3 and hdfs VFDs from Autotools VFD list (#4142)
These will never pass `make check` and would require a custom test
suite for more comprehensive testing.
* Skip part of dsets.c test for IBM long double type (#4136)
* Capitalize option message for consistency. (#4141)
* Fixed misc. H5E fortran failures due to previous PR (#4138)
* fixed promotion of integers and reals tests and check-passthrough-vol failure
* fixed cygwin issue
* Fix Autotools -Werror cleanup (#4144)
The Autotools temporarily scrub -Werror(=whatever) from CFLAGS, etc.
so configure checks don't trip over warnings generated by configure
check programs. The sed line originally only scrubbed -Werror but not
-Werror=something, which would cause errors when the '=something' was
left behind in CFLAGS.
The sed line has been updated to handle -Werror=something lines.
Fixes one issue raised in #3872
* Fix doxygen link to example function usage (#4133)
* Remove useless headers (#4145)
Removes unnecessary headers from C library source files.
* Clean up some hbool_t/TRUE/FALSE stragglers (#4143)
It looks like most of these snuck in via selection I/O work
* Fix error when overwriting an indirectly nested vlen with a shorter sequence (#4140)
* defined CMAKE_H5_HAVE_DARWIN (#4146)
* Make the newsletter scheme work like HDF4 (#4149)
* Remove at the end of list item. (#4151)
* Fix buffer size calculation in the deflate filter (#4147)
* Remove H5O header and friend status from H5A.c (#4150)
* Remove HDF from Fortran 2003 configuration check message. (#4157)
* Suppress H5Dmpio debugging output unless HDF5_DEBUG=d is set (#4155)
* Header cleanup in C library (#4154)
* Ensure H5FL header is included everywhere
* Ensure H5SL header is included everywhere
* Ensure H5MM header is included everywhere
* Add Doxygen to H5FDmirror.h (#4158)
* Remove lseek64 and stat64 symbols from CMake (#4163)
We don't use these in the library.
* Remove HAVE_IOEO checks from CMake (#4160)
This was intended to check for thread-safety functionality on Windows.
The required functionality has been standard since Windows Vista, so
these checks can be removed.
* Fix some minor warnings (#4165)
* Bump the size of the mirror VFD IP field (#4167)
The IP address string isn't big enought to hold an IPv4-mapped IPv6
address.
* Fix mirror VFD script (#4170)
This had directory problems when running locally.
* Fix an issue where the Subfiling VFD's context cache grows too large (#4159)
* Address code page issues w/ Windows file paths (#4172)
On Windows, HDF5 attempted to convert file paths passed to open() and
remove() to UTF-16 in order to handle Unicode file paths. This scheme
does not work when the system uses code pages to handle non-ASCII
file names.
As suggested in the forum post below, we now also try to see if we
can open the file with open(), which should handle systems where
non-ASCII code pages are in use.
https://forum.hdfgroup.org/t/open-create-hdf5-files-with-non-utf8-chars-such-as-shift-jis/11785
* Add Doxygen to API calls in H5VLnative.h (#4173)
* Allow H5Soffset_simple to accept NULL offsets (#4152)
The reference manual states that the offset parameter of H5Soffset_simple()
can be set to NULL to reset the offset of a simple dataspace to 0. This
has never been true, and passing NULL was regarded as an error.
The library will now accept NULL for the offset parameter and will
correctly set the offset to zero.
Fixes HDFFV-9299
* Add filter plugin user guide text. Fix registered URL in docs (#4169)
* Add support for _Float16 16-bit floating point type (#4065)
Fixed some conversion issues with Clang due to problematic undefined
behavior when casting a negative floating-point value to an integer
Fixed a bug in the library's software integer to floating-point
conversion function where a user's conversion exception function
returning H5T_CONV_UNHANDLED in the case of overflows would result in
incorrect data after conversion
Added configure checks for functions and macros related to _Float16
usage since some compilers expose the datatype but not the functions or
macros
Fixed a dt_arith test failure when H5_WANT_DCONV_EXCEPTION isn't defined
Fixed a few warnings from not explicitly casting some _Float16 variables
upwards
* Remove some H5T_copy calls that are now unnecessary (#4164)
Removes some datatype copying calls that are now unnecessary after
refactoring the datatype conversion code to use pointers internally
rather than IDs
Rewrites the enum conversion function so that it uses cached copies
of the source and destination datatypes in order to avoid modifying
the datatypes passed in
Adds a 'recursive' field to the datatype conversion context which
allows the conversion functions for members of a container datatype
to skip unnecessary repetitive conversion setup code
Changes internal datatype conversion callback functions so that the
source and destination datatype structure pointers are const
Removes some unused and unnecessary internal IDs registered with
H5I_register
* Add RELEASE.txt note for cmpd segfault fix (#4175)
RELEASE notice for the fix in #3842
* Clean up CMake direct VFD handling (#4161)
There's no need to build and run programs, or even check the operating
system. We just need to check for O_DIRECT and posix_memalign().
* Capitalize linux for consistency (#4178)
* Reworked H5Epush_f (#4153)
* Add const to new _Float16 conversion routine parameters (#4181)
* Update Release Specific Information link. (#4179)
* Filter plugins updates for registration URL (#4180)
* Update filter plugin URL to new location
* Adjust test array size
* Add daily VFD CI workflow (#4176)
Adds testing of Subfiling VFD
* Exclude shell tests from sanitizers (#4186)
* Add a missing period at the end of sentence. (#4184)
* last-file.txt should not be created for release workflow (#4185)
* Skip part of dtypes.c _Float16 file size check for certain VFDs (#4182)
* Fixes several MinGW + Autotools issues (#4190)
* Fixes detection of various Windows libraries, etc.
* Corrects alarm(2) configure checks
* Uses Win32 threads by default w/ Pthreads override, if desired
* Set _WIN32_WINNT correctly for MinGW
* Fix setenv(3) wrapper for MinGW, which does not have getenv_s()
MinGW Autotools support is still not Amazing, but this at least
allows the library and tools build and is better about thread-safety
* Add semicolons to the end of HSYS_GOTO_ERROR (#4193)
Looks like we forgot these when we did the other macros.
* Remove broken links (#4187)
* Skip vlen IO API test for cache VOL (#4135)
* Fix cache VOL segfault in vlen io test
* Skip vlen IO API test
* Handle certain empty subfiling environment variables (#4038)
* h5diff compares attribute data like dataset data (#4191)
Updates tools docs to indicate that dataset and attribute data are compared in the same way
* A path component may include a dot with other characters (#4192)
* Add RELEASE.txt note for recent datatype conversion improvements (#4195)
* Add NEWSLETTER item about _Float16 support (#4197)
* Correct download link for develop doxygen (#4196)
* Update version in new .yml files.
* Do not enable szip for sanitizer runs (#4057)
* Add note to H5Tset_fields about needing to set datatype precision first (#4059)
* Offset of a floating-point type also needs to be accounted for
* Clarify ordering of H5Tset_precision and H5Tset_fields
* Fix issue where H5Tset_fields does not account for datatype offsets (#4061)
H5Tset_fields did not account for any offset in a floating-point datatype,
causing it to fail when a datatype's precision is correctly set such that
it doesn't include the offset bits.
* Ignore UserPresets and Use only C compiler for sanitizers (#4066)
* Remove user presets file
* Only use C compiler for sanitzers
* Rename incorrectly named option (#4067)
* Rename incorrectly named option
* Restore the correct uses of USING_MEMCHECKER
* Update release note
* Fix a memory leak in the cmpd_dset test (#4071)
This was due to not freeing a test buffer. It was not a core
library memory leak.
* Fix uninitialized bytes in cmpd_dset test (#4072)
Compound fill values were set to the integer -1, causing valgrind
to flag 'uninitialized bytes' errors.
This is just a problem with the cmpd_dset test and not a core
library problem.
* Update INSTALL files (#4052)
* Add NEWSLETTER and merge abi reports and add sha256sums (#4055)
* Fix uninitialized bytes in selection I/O test (#4073)
This was due to a complex type fill value being set to -1 instead
of a proper complex value. This was a test problem and not a core
library issue.
* fix path for S3 build path in CI (#4076)
* Correct paths for 1.14 and add lines missing from release_docs/INSTALL_CMake.txt.
---------
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Remove oneapi return value warning. (#4028)
* Replaced last sprintf with snprintf (#4007)
* Replaced last sprintf with snprintf
To have the size of the buffer, it was required to change a function signature, and change all users of it.
In most cases, determining the buffer size wasn't trivial and so SIZE_MAX is passed. But at least this improves the infrastructure. Someone can later figure out the correct sizes.
* Test vlen sequence IO in API tests (#4027)
* Check argument for CMake REGEX FCMangle.h. (#4029)
* Replace deprecated Fortran 'include mpif.h' with 'USE mpi' (#4031)
With MPI 4.1 the use of the mpif.h include file has been deprecated. Codes
should transition to USE mpi or USE mpi_f08.
Signed-off-by: Christoph Niethammer <niethammer@hlrs.de>
* Fix H5F_get_access_plist to copy file locking settings (#4030)
H5F_get_access_plist previously did not copy over the file locking settings
from a file into the new File Access Property List that it creates. This would
make it difficult to match the file locking settings between an external file
and its parent file.
* Fix missing NOT from if check in HL folder (#4036)
* Fix the datatype passed to H5*exists_async APIs in tests. (#4033)
Add a new testing function to verify C_BOOL values.
* Add deb and rpm binaries to snapshots (#4035)
* Update and Add general INSTALL (#4016)
* Improve performance of flushing single objects (#4017)
Improve performance of flushing a single object, and remove metadata
cache flush markers
* Fix memory leak in H5LTopen_file_image when H5LT_FILE_IMAGE_DONT_COPY flag is used (#4021)
When the H5LT_FILE_IMAGE_DONT_COPY flag is passed to H5LTopen_file_image, the internally-allocated
udata structure gets leaked as the core file driver doesn't have a way to determine when or if it
needs to call the 'udata_free' callback. This has been fixed by freeing the udata structure when
the 'image_free' callback gets made during file close, where the file is holding the last reference
to the udata structure.
* Fix allocating too much memory in dset API test (#4041)
* Don't try to load general-19 warnings file for icc (#4042)
The Autools Classic Intel compiler configuration attempts to load a file
named `general-19` from the intel-warnings/classic directory, which does
not exist.
This removes the attempted load of the file.
* Remove unused AIX cross-compile cache overrides (#4043)
The ibm-aix Autotools config file had some unmaintained and unnecessary
Autoconf cache overrides. These have been removed.
* Consolidate Autotools linux files (#4044)
There are many architecture-specific linux files in the config
directory, all of which simply redirect to linux-gnulibc1.
This change renames linux-gnulibc1 to linux-gnu and deletes the more
specific files.
* Remove check for gettimeofday + tz in CMake (#4045)
This is not used in the library
* Remove limitations on preset generators (#4051)
* Fix issue with FAPL file locking setting inheriting test (#4053)
Fixes an issue where the HDF5_USE_FILE_LOCKING environment variable being
set can interfere with the file locking setting that the test expects to
be returned.
* Bump the github-actions group with 2 updates (#4054)
Bumps the github-actions group with 2 updates: [actions/download-artifact](https://github.com/actions/download-artifact) and [github/codeql-action](https://github.com/github/codeql-action).
* Fix VOL-compatibility issues in External Link API test (#4039)
Fix link API tests with incorrect filename
* Add upddated cmake tools from source location (#4040)
* Add options to allow tools type selection and naming (#4046)
* Improve error messages when tools attempt to use non-enabled S3 and HDFS VFDs. (#4047)
* Correct several 1.15/1.15.0 references to 1.14/1.14.4.
* Ignore HDF5Examples/CMakeUserPresets.json
off_t is a 32-bit signed value on Windows, so we should use HDoff_t
(which is __int64 on Windows) internally instead.
Also defines HDftell on Windows to be _ftelli64().
* Fix build error on freebsd (#3883)
Fixes:
checking for config freebsd12.1... no
checking for config freebsd... found
compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpicc' is GNU gcc-9.2.0
compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpif90' is GNU gfortran-9.2.0
stdout: .: cannot open ./config/classic-fflags: No such file or directory
* Correct CMake command and example packaging (#3888)
* Feat: Hashpin sensitive dependencies on GitHub Actions and enable Dependabot to update them monthly (#3892)
* feat: hashpin sensitive dependencies on GHAs
Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>
* feat: enable dependabot for monthly updates on GHA
Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>
---------
Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>
* Some changes to portal links when they could be found on docs.hdfgroup.org, and changed the helpdesk link to help.hdfgroup.org (#3893)
* Updated some portal links to go directly to docs.hdfgroup.
* Fixed some portal and help desk links
* Add variable option syncing for examples (#3885)
* Add period(.) at the end of the sentence for consistency. (#3897)
* Remove redundant backslash character from comment. (#3899)
* Disable doxygen as errors for netcdf (#3900)
* disable building doxygen for netcdf test
* Doc versions (#3903)
* Added missing \since tags to H5D.
* Committing clang-format changes
* Fixed H5T version info.
* Committing clang-format changes
* Added missing version info to H5E.
* Committing clang-format changes
* Added version info to H5F public APIs.
* Committing clang-format changes
* Added missing H5Z public API version info.
* Added missing version info to H5G public APIs
* Added missing version info to H5I public API.
* Added missing version info to H5 public APIs
* Committing clang-format changes
* Added missing version info to H5P public APIs
* Added missing version info to H5R public APIs
* Fix comment error.
* Committing clang-format changes
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Change Trouble Shooting to Troubleshooting (#3905)
* Implement optimized support for vector I/O in Subfiling VFD (#3896)
Vector I/O requests are now processed within a single
set of I/O call batches, rather than each I/O vector
entry (tuple constructed from the types, addrs, sizes
and bufs arrays) being processed individually. This allows I/O to be
more efficiently parallelized among the I/O concentrator processes
during large I/O requests.
* Fixed some calculations and add test cases for issues spotted from review
* Removed a variable that was compensating for previous miscalculations
* Add 'warning density' computation to the warnhist script (#3910)
* Add 'warning density' computation to the warnhist script, along with several
cleanups to it. Add "--enable-show-all-warnings" configure (and CMake)
option to disable compiler diagnostic suppression (and therefore show all the
otherwise suppressed compiler diagnostics), disabled by default. Clean up
a buncn of misc. warnings.
Signed-off-by: Quincey Koziol <qkoziol@amazon.com>
* Added H5Fdelete_f with test (#3912)
* New Fortran Examples added (#3916)
* added subfiling example
* Added filtered writes with no selection example
* Version and space corrections.
* Restore H5_VERSION definition in configure.ac.
* renamed defined H5_VERS* to avoid conflicts (#3926)
* Preserve MPI-I/O file hints when fapl is closed (#3755)
* Fix for issue #3025: Save the MPI info in the file struct so H5Fget_access_plist() can retrieve it from there.
* Add compression tests for subfiling (#3769)
* Fix typo in comment (#3775)
* Fixed a file handle leak in the core VFD (#3779)
When opening a file with the core VFD and a file image, if the file
already exists, the file check would leak the POSIX file handle.
Fixes GitHub issue #635
* Fix a format string warning in the C++ examples (#3776)
* Cancel running GitHub workflows on push to same PR (#3772)
* Cancel running GitHub workflows on push to same PR
* Remove github.sha from workflow concurrency groups
* Print some messages in parallel tests on MPI rank 0 only (#3785)
Avoids overly verbose output from all processes emitting progress, etc. info.
* Avoid attempted use of NULL pointer in parallel compression code (#3786)
The parallel compression test code tests for the case where all MPI ranks have no selection in a dataset when writing to it. Add an early exit to the code to avoid attempting to use a NULL pointer due to there being no work to do.
* Don't install h5tools_test_utils test program on system (#3793)
* Add Doxygen to H5FDsplitter.h (#3794)
* H5FD_CURR_SPLITTER_VFD_CONFIG_VERSION
* H5FD_SPLITTER_PATH_MAX
* H5FD_SPLITTER_MAGIC
* H5FD_splitter_vfd_config_t
* H5Pset_fapl_splitter()
* H5Pget_fapl_splitter()
* Update Doxygen initializers & identifiers in VFDs (#3795)
* Add Doxygen for all H5FD_<VFD> initializers
* Add Doxygen for all H5FD_<VFD>_VALUE values
* Mark H5FD_<vfd>_init() calls private in Doxygen
* Fix memory corruption in 'MPI I/O FAPL preserve' test (#3806)
* Fix usage of h5_clean_files in t_pflush2.c (#3807)
* Fix parallel driver check in h5_fixname_real (#3808)
* Fix a couple usages of MPI_Info_get (#3809)
* Remove H5system.c warning on Windows oneAPI. (#3812)
* Add processing of NVHPC flags in linux-gnulibc1 file (#3804)
* Disable testing as tests are failing the same as in CMake
* Use the current toolchain for examples as default (#3810)
* Fix misc. warnings from GCC when compiling with -fsanitize=undefined (#3787)
* Set NVHPC maximum optimization level to -O1 for now (#3800)
* Set NVHPC maximum optimization level to -O1 for now
Compiling HDF5 with NVHPC 23.5 - 23.9 results in test failures in
4 different test files that need to be resolved. Since those tests
pass with an optimization level of -O1 (and -O0) and it is currently
unclear whether the test failures are due to issues in HDF5 or issues
in the 'nvc' compiler, set the maximum optimization level for NVHPC
to -O1 until the test failures are resolved.
* Disable nvhpc Java testing in CMake and amend known issues
* Re-enable testing of Autotools nvhpc
* Update some doxygen links to local refs (#3814)
* Rework MPI Info FAPL preserve PR to use VFD 'ctl' operations (#3782)
* Removed the use of C wrappers from H5P APIs. (#3824)
* fix seg fault on frontier/cray
* fix seg fault on frontier/cray
* fix seg fault on frontier/cray
* removed the use of h5pclose_c
* removed the use of h5pclose_c
* Fortran Wrappers H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f (#3801)
* Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f
* Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f tests
* Create test for H5Pget_dxpl_mpio (#3825)
* Create test and add to testphdf5
* Renamed h5fuse.sh to h5fuse (#3834)
* provide an alternative to mapfile for older bash
* Disable FP exceptions in H5T init code (#3837)
The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization.
Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore.
Fixes#3831
* Add intel oneapi windows build to CI CMake (#3836)
* Remove printf format warning on Windows oneAPI. (#3838)
* Correct ENV variables (#3841)
* Remove Autotools sed hack (#3848)
configure.ac contains a sed line that cleans up incorrect library
flags which was added to paper over some bugs in earlier versions
of the Autotools. These issues are not a problem with the current
versions of the Autootols.
The sed line causes problems on MacOS, so it has been removed.
Fixes#3843
* Make filter unregister callbacks safe for VOL connectors (#3629)
* Make filter callbacks use top-level API functions
When using VOL connectors, H5I_iterate may not provide
valid object pointers to its callback. This change keeps
existing functionality in H5Zunregister() without using
potentially unsafe pointers.
* Filter callbacks use internal API
* Skip MPI work on non-native VOL
* Add extra space in comments for consistency (#3852)
* Add extra space in comments for consistency
* uncomment tfloatsattrs test
* Update Actions badges to link to relevant workflow (#3850)
* Add CMake long double cross-compile defaults (#3683)
HDF5 performs a couple of checks at build time to see if long double
values can be converted correctly (IBM's Power architecture uses a
special format for long doubles). These checks were performed using
TRY_RUN, which is a problem when cross-compiling.
These checks now use default values appropriate for most non-Power
systems when cross-compiling. The cache values can be pre-set if
necessary, which will preempt both the TRY_RUN and the default.
Affected values:
H5_LDOUBLE_TO_LONG_SPECIAL (default no)
H5_LONG_TO_LDOUBLE_SPECIAL (default no)
H5_LDOUBLE_TO_LLONG_ACCURATE (default yes)
H5_LLONG_TO_LDOUBLE_CORRECT (default yes)
H5_DISABLE_SOME_LDOUBLE_CONV (default no)
Fixes GitHub #3585
* Updates for building and testing VOL connectors
* Fix issue with HDF5_VOL_ALLOW_EXTERNAL CMake variable
* Initialize parallel testing with MPI_THREAD_MULTIPLE when testing API
* Add CMake variable to allow specifying a VOL connector's package name
* Remove call to MPI_Init in serial API tests
While previously necessary, it now interferes with VOL connectors that
may need to be initialized with MPI_THREAD_MULTIPLE
* Fixes for CI and presets (#3853)
* Change dest for doxygen (#3856)
* Implement selection vector I/O with collective chunk filling (#3826)
* Changes for ECP-344: Implement selection vector I/O with collective chunk filling.
Also fix a bug in H5FD__mpio_write_vector() to account for fixed size optimization
when computing max address.
* Fixes based on PR review comments:
For H5Dchunk.c: fix H5MM_xfree()
For H5FDmpio.c:
1) Revert the fix to H5FD__mpio_write_vector()
2) Apply the patch from Neil on the proper length of s_sizes reported by H5FD__mpio_vector_build_types()
* Put back the logic of dividing up the work among all the mpi ranks similar to the
original H5D__chunk_collective_fill() routine.
* Add a test to verify the fix for the illegal reference problem in H5FD__mpio_write_vector().
* Do not publish compression headers or docs (#3865)
* Fix typo: look -> loop (#3866)
* Moved the README to markdown and expanded its overview of the files, file generation, and other Fortran wrapper development practices as mentioned in the HDF5 architectural document. I added a new figure and included the SVG file and the original xfig file it was generated from. (#3862)
* Add HDF5_DISABLE_TESTS_REGEX option to skip tests (#3859)
* Fix typo in error message for `MPI_Type_dup`. (#3867)
* Complete the `if command line option` sentence. (#3868)
* Fix h5dump segmentation fault when --vfd-value option is used (#3873)
* Updated URL in funding.yml (#3882)
Using new shortened URL, might look better.
* Remove unused variable from unmerged changes
* Update src/H5Tinit_float.c
* Sync fixes for CI and presets
* Sync the Fortran build changes
* Update fortran test file
* Sync hl/fortran files
* Merge the nvidia compiler flag changes
* Update link
* Update links to doxygen refs for 1.14
* Add missing test files to distclean target (#3734)
Cleans up new files in Autotools `make distclean` in the test directory
* Add tools/libtest to Autotools builds (#3735)
This was only added to CMake many years ago and tests the tools
library.
* Clean up onion VFD files in tools `make clean` (#3739)
Cleans up h5dump and h5diff *.onion files in the Autotools when
runing `make clean`.
* Clean Java test files on Autotools (#3740)
Removes generated HDF5 and text output files when running `make clean`.
* Clean the flushrefresh test dir on Autotools (#3741)
The flushrefresh_test directory was not being cleaned up w/
`make clean` under the Autotools
* Fix file names in tfile.c (#3743)
Some tests in tfile.c use h5_fileaccess to get a VFD-dependent file
name but use the scheme from testhdf5, reusing the FILE1 and FILE8
names. This leads to files like test1.h5.h5 which are unintended
and not cleaned up.
This changes the filename scheme for a few tests to work with h5test,
resulting in more informative names and allowing the files to
be cleaned up at the end of the test. The test files have also
been added to the `make clean` target for the Autotools.
* Clean Autotools files in parallel tests (#3744)
Adds missing files to `make clean` for parallel, including Fortran.
* Add native VOL checks to deprecated functions (#3647)
* Add native VOL checks to deprecated functions
* Remove unneeded native VOL checks
* Move native checks to top level calls
* Fix buffer overflow in cache debugging code (#3691)
* update stat arg for apple (#3726)
* update stat arg for apple
* use H5_HAVE_DARWIN for Apple ifdef
* fix typo
* removed duplicate H5_ih_info_t
* added fortran async test to cmake
* Fix windows cpack error in WiX package. (#3747)
* Add a simple cache to the ros3 VFD (#3753)
Adds a small cache of the first N bytes of a file opened with the
read-only S3 (ros3) VFD, where N is 4kiB or the size of the file,
whichever is smaller. This avoids a lot of small I/O operations
on file open.
Addresses GitHub issue #3381
* Update Autotools to correctly configure oneAPI (#3751)
* Update Autotools to correctly configure oneAPI
Splits the Intel config files under the Autotools into 'classic'
Intel and oneAPI versions, fixing 'unsupported option' messages.
Also turns off `-check uninit` (new in 2023) in Fortran, which kills
the H5_buildiface program due to false positives.
* Enable Fortran in oneAPI CI workflow
* Turn on Fortran in CMake, update LD_LIBRARY_PATH
* Go back to disabling Fortran w/ Intel
For some reason there's a linking problem w/ Fortran
error while loading shared libraries: libifport.so.5: cannot open shared object file: No such file or directory
* Add h5pget_actual_selection_io_mode fortran wrapper (#3746)
* added h5pget_actual_selection_io_mode_f test
* added tests for h5pget_actual_selection_io_mode_f
* fixed int_f type conversion
* Update fortran action step (#3748)
* Added missing DLL for H5PGET_ACTUAL_SELECTION_IO_MODE_F (#3760)
* add missing H5PGET_ACTUAL_SELECTION_IO_MODE_F dll
* Bump the ros3 VFD cache to 16 MiB (#3759)
* Fix hangs during collective I/O with independent metadata writes (#3693)
* Fix some issues with collective metadata reads for chunked datasets (#3716)
Add functions/callbacks for explicit control over chunk index open/close
Add functions/callbacks to check if chunk index is open or not so
that it can be opened if necessary before temporarily disabling
collective metadata reads in the library
Add functions/callbacks for requesting loading of additional chunk
index metadata beyond the chunk index itself
* Fix failure in t_select_io_dset when run with more than 10 ranks (#3758)
* Fix H5Pset_evict_on_close failing regardless of actual parallel use (#3761)
Allow H5Pset_evict_on_close to be called regardless of whether a parallel build of HDF5 is being used
Fail during file opens if H5Pset_evict_on_close has been set to true on the given File Access Property List and the size of the MPI communicator being used is greater than 1
* Correct ld in format strings in cmpd_dset.c (#3697)
Removes clang warnings
* Clean up comments. (#3695)
* Add NVidia compiler support and CI (#3686)
* Work around Theta system issue failure in links test (#3710)
When the Subfiling VFD is enabled, the links test may
try to initialize the Subfiling VFD and call MPI_Init_thread.
On Theta, this appears to have an issue that will cause
the links test to fail. Reworked the test to check for
the same conditions in a more roundabout way that doesn't
involved initializing the Subfiling VFD
* Fix issue with unmatched messages in ph5diff (#3719)
* provide an alternative to mapfile for older bash (#3717)
* Attempt to quiet some warnings with cray compilers. (#3724)
* Fix CMake VOL passthrough tests by copying files to correct directory (#3721)
* Develop intel split (#3722)
* Split intel compiler flags into sub-folders
* Update Intel options for warnings
* Mostly CMake, Autotools needs additional work
* Fixes and adjustments to t_filters_parallel (#3714)
Broadcast number of datasets to create in multi-dataset I/O cases
so that interference with random number generation doesn't cause
mismatches between ranks
Set fill time for datasets to "never" by default and adjust on a
per-test basis to avoid writing fill values to chunks when it's
unnecessary
Reduce number of loops run in some tests when performing multi-dataset
I/O
Fix an issue in the "fill time never" test where data verification
could fill if file space reuse causes application buffers to be
filled with chosen fill value when reading from datasets with
uninitialized storage
Skip multi-chunk I/O test configurations for multi-dataset I/O
configurations when the TestExpress level is > 1 since those
tests can be more stressful on the file system
Disable use of persistent file free space management for now
since it occasionally runs into an infinite loop in the library's
free space management code
* Suppress cast-qual warning in H5TB Fortran wrapper (#3728)
This interface is fundamentally broken, const-wise.
* Add new API function H5Pget_actual_select_io_mode() (#2974)
This function allows the user to determine if the library performed selection I/O, vector I/O, or scalar (legacy) I/O during the last HDF5 operation performed with the provided DXPL. Expanded existing tests to check this functionality.
* Test scripts now execute in-source with creation of tmp dir (#3723)
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
* Add -h and --help as flags in h5cc & h5fc (#3729)
Adds these common help flags in addition to -help
* Update the library version matrix for H5Pset_libver_bounds() (#3702)
* Fixed#3524
Added 1.12, 1.14, and 1.16 to the table for libver bounds in the H5Pset_libver_bounds docs.
* Remove references to LIBVER_V116
---------
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Neil Fortner <fortnern@gmail.com>
Co-authored-by: Glenn Song <43005495+glennsong09@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Address nagfor exceptions stoppage. (#3658)
* added cmake ieee flag for nagfor
* generalized determining the nag compiler
* fixing some misc. NAG warnings
* Simplify. (#3659)
* Address @jhendersonHDF review
* Add expedited testing support to t_filters_parallel (#3665)
* Remove clang warnings (#3656)
* Fixes test failure for gfortran -O2 and -O3, -fdefault-real-16 (#3662)
* added cmake ieee flag for nagfor
* fixes gfortran -O2 and -O3, -fdefault-real-16
* fixed sync
* updated release notes
* Fix link error on clang17/gfortran13/macOS-13 (#3666) (#3671)
* Correct fortran CMake generator expressions (#3670)
* Add AOCC GitHub Action (#3504) (#3657)
* Fix uninitialized subfiling test variable (#3675)
Picked up by gcc 10 on skybridge. Probably spurious, but no harm in
initializing it to a "bad" value.
* Add support for AOCC & Flang w/ the Autotools (#3674)
* Adds a config/clang-fflags options file to support Flang
* Corrects missing "-Wl," from linker options in the libtool wrappers
when using Flang, the MPI Fortran compiler wrappers, and building
the shared library. This would often result in unrecognized options
like -soname.
* Enable -nomp w/ Flang to avoid linking to the OpenMPI library.
CMake can build the parallel, shared library w/ Fortran using AOCC
and Flang, so no changes were needed for that build system.
Fixes GitHub issues #3439, #1588, #366, #280
* Fix a strncpy call to use dest size not src (#3677)
A strncpy call in a path construction call used the size of the src
buffer instead of the dest buffer as the limit n.
This was switched to use the dest size and properly terminate the
string if truncation occurs.
* Remove CANBE_UNUSED() from subfiling VFD (#3678)
This macro was an attempt to quiet warnings about release mode unused
variables that only appear in asserts. It resolves to a void cast, which
doesn't quiet warnings when an assignment has already taken place.
* Suppress MPI_Waitall warnings w/ MPICH (#3680)
MPICH defines MPI_STATUSES_IGNORE (a pointer) to 1, which raises warnings
w/ gcc. This is a known issue that the MPICH devs are not going to fix.
See here:
https://github.com/pmodels/mpich/issues/5687
This fix suppresses those issues w/ gcc
* Fix a possible NULL pointer dereference in tests (#3676)
The dtypes test could dereference a NULL pointer if a strdup call
failed.
* Fix printf warnings in t_mpi (#3679)
* Fix printf warnings in t_mpi
The type of MPI_Offset varies with implementation. In MPICH, it's long,
which raises warnings when we attempt to use long long format
specifiers. Casting to long long fixes the warnings.
* Fix invalid memory access in S3 comms (#3681)
In the ros3 VFD, passing an empty string parameter to an internal
API call could result in accessing the -1th element of a string.
This would cause failures on big-endian systems like s390x.
This parameter is now checked before writing to the string.
Fixes GitHub #1168
* Add Doxygen for H5Pset_fapl_sec2() (#3685)
*
* switch to using time function instead of date function (#3690)
* Initialize API context MPI types to MPI_BYTE (#3688)
* Add test info output to t_filters_parallel (#3696)
* Suppress format string warnings in subfiling test (#3699)
* Fix unused variable in tselect.c (#3701)
* Fix unused variable warning in H5F_sfile_assert_num (#3700)
* Restore floating-point suffixes in tests (#3698)
A prior commit removed too many F suffixes. This restores the suffixes
for float variables.
* Sync with changes from develop
---------
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Rework tools.cmake and add C flags (#3110)
* Fix gh pages so that the doxygen files are uploaded (#3102)
* Add workspace path
* add debug
* Make one job so workspace files are available
* Put doxygen docs under docs folder in gh-pages
* Fix a misc warning in test/vol.c (#3112)
The compiler complains about using integers instead of size_t
for some sizes.
* Remove H5detect and H5make_libsettings (#3104)
Removes H5detect and H5make_libsettings from the build and replaces
their functionality with things that don't affect cross-compiling.
H5detect --> floating-point types are now detected on library load
H5make_libsettings --> Moved functionality to a new H5build_settings.c template file
* clang-tidy clang-analyzer-core issues addressed (#3113)
src/H5system.c:1293:13: warning: Dereference of null pointer
[clang-analyzer-core.NullDereference]
src/H5trace.c:4048:17: warning: Passed-by-value struct argument contains
uninitialized data (e.g., via the field chain: 'initial.user')
[clang-analyzer-core.CallAndMessage]
* Add note for issue 3056 (#3117)
* Use 1.14 toolchain (#3116)
* Remove the checkposix script (#3122)
This script was used to ensure that all non-HDF5 calls were prefixed
with 'HD'. We are removing this scheme so this script is no longer
needed.
* Remove unused HD macros (#3120)
* Remove unused HD macros
The library prefixes most C and POSIX API calls with 'HD'. We are
going to start removing these so the code looks like normal C.
This PR removes most of the unused HD markup macros.
* Replace ntohl/ntohs
* Adds an optional version arg to bin/format_source (#3119)
* Clean up mirror VFD code in utils dir (#3121)
* Remove dead code
* Replace mybzero with memset
* Replace hbool_t/TRUE/FALSE with bool/true/false
* Fix spelling issues flagged by codespell (#3130)
* Make autogen.sh output message consistent (#3128)
* Add Python for HDF-EOS zoo description (#3129)
* Fix function name in comment in ros3 VFD (#3131)
* Revert long double checks (#3133)
* Revert "Remove long double conversion work-arounds (#3097)"
This reverts commit 1e1dac1dac.
* Update comments to reflect newer systems
* Add java options to build scripts (#3127)
* Add java options to build scripts
Previously, cmakehdf5 turned on compiling of the java interface
by default due to a value set in cacheinit.cmake.
Now, consistent with how Fortran and CPP interfaces are handled,
the script overwrites this default value to disable the libraries,
fixing #2958.
I also implemented the --enable-java/--disable java options for
cmakehdf5, and -java for buildhdf5.
Allen said these scripts should mention that
compilers are to be specified in environment variables, but missing
compilers causes errors at the CMake level, and
CMake's error messages are already pretty informative (See the one
in #2958 about JAVA_COMPILER).
* Removed .lnt linter files (#3143)
These were last usefully modified in 2004
* Fix path to libhdf5.settings in cmakehdf5 (#3140)
* Many clang -Wextra-semi-stmt fixes (#2537)
* 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 HD prefix from network calls (#3142)
HDsocket(), etc. Only affects the mirror VFD and its test code.
* Remove hbool_t/TRUE/FALSE from java (#3145)
Replaces with bool/true/false
* CMake: (feature) ROS3 and cmake config file. (#3146)
- Added a cmake variable to the hdf5-config.cmake file which
indicate if the library has been build with or without the
read-only S3 functionality.
* Define minimal permissions for new GitHub workflows (#3147)
* Track s3 i/o when S3COMMS_DEBUG enabled (#3139)
* Track s3 i/o when S3COMMS_DEBUG enabled
* Fix the snapshots workflow (#3148)
* Add upload url as artifact
* Change doxygen path and comment log-url upload
* zip doxygen files for upload
* add workspace var
* chore: fix grammar (#3150)
* chore: fix grammar
* Removes the HD prefix from java C99 calls (#3149)
POSIX calls (HDstrndup, etc.) are unchanged
* Correct the zip usage (#3153)
* Many fixes to various compiler warnings (#3124)
* Fixed various -Wmissing-variable-declarations by adding static keyword
* In a few cases, renamed the variable suffix from _g to _s.
* Fixed some -Wmissing-variable-declarations by using different declaration macros
* Fixed various -Wconditional-uninitialized warnings by just initializing variable to zero
* Fixed various -Wcomma warnings
* Fixed clang -Wstrict-prototypes warnings
* Fixed various -Wunused-variable warnings
* Updated some casts to fix the only 3 -Wcast-qual warnings
* Fixed the only -Wsometimes-uninitialized warning
* Create Security Policy (#3152)
* Fix#1978 h5vers usage message. (#3162)
Update Platforms Tested in RELEASE.txt.
* speed-up building HDF5 (#3087)
Disables building the tests when building the netCDF, etc.
* Remove dead code behind #ifdef OLD_WAY (#3163)
* Remove H5F_evict_tagged_metadata() (#3165)
The rest of the library just calls H5AC_evict_tagged_metadata()
directly.
* Add missing space in zip command (#3167)
* Fixed check for a VOL's async compatibility (#3164)
* cap flag fix in test
* added async comp. output
* Update Linux workflows (#3173)
* Consolidate environment setup
* Turn on ros3 VFD in CMake (Linux only)
* Add gh-pages doxygen link (#3175)
* Fix the doxygen to gh pages and artifact creation (#3176)
* Tidy the list of options in main.yml (#3181)
* Remove HD/hbool_t from fortran (#3182)
* Remove HD/hbool_t from high-level lib (#3183)
* Remove HDva_(arg|copy|end|start) (#3184)
* Drop HD prefix & hbool_t from H5TS (#3180)
* Remove HD from fork/exec*/wait* (#3190)
These are not C99 but are hidden behind ifdefs and are highly
unlikely to ever have non-POSIX equivalents.
* Fix assertion failure when attempting to use IOC VFD directly (#3187)
* Rename HDqsort() to qsort() (#3193)
* Rename HDqsort() to qsort()
* Committing clang-format changes
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Rename HDpipe() to pipe() (#3192)
Pipe is POSIX but implemented in Microsoft's CRT
* Rename HDassert() to assert() (#3191)
* Change HDassert to assert
* Fix bin/make_err
* Rename HD(f)printf() to (f)printf() (#3194)
* Add note about HDF5_VOL_CONNECTOR to tools usage (#3159)
* Rename HDsystem() to system() (#3197)
system() is only used in the iopipe test and the things it calls
(which are POSIX-y) are protected by an ifdef.
* Remove HD from HDposix_memalign() (#3196)
The posix_memalign call is only used in the direct VFD, which can only
be built if posix_memalign() is available.
* Remove HD from memory allocate/free calls (#3195)
* HDcalloc
* HDfree
* HDmalloc
* HDrealloc
* chore: fix grammar (#3207)
* docs: remove redundancy in Data Transfer section of user guide (#3208)
* Remove checks for setsysinfo, which is unused (#3205)
* Autotools
* CMake
* Remove HD from protected POSIX calls (#3203)
These calls are non-C99 but protected by ifdefs and have no Windows
equivalents:
* HDalarm
* HDasprintf
* HDclock_gettime
* HDfcntl
* HDgethostname
* HDgetrusage
* HDsymlink
* Rename HDato*() to ato*() (#3201)
* Remove some "Programmer" comments (#3209)
These are meaningless noise.
Removes the "Programmer" lines on comment start lines:
/* Programmer: John Smith
These complicate my sed script that will rip out the rest of
the comments.
* Rename HDexit() and related to exit(), etc. (#3202)
* HDatexit
* HDexit
* HD_exit
* Remove HD from strto* calls (#3204)
* HDstrtod
* HDstrtol
* HDstrtoll
* HDstrtoul
* HDstrtoull
* HDstrtoumax
* Remove HD from C std lib file ops (#3206)
* HDfclose
* HDferror
* HDfeof
* HDfflush
* HDfopen
* HDfread
* HDfwrite
* Remove programmer/date from comments (#3210)
* Removes Programmer: and Date: fields
* Fixes a few Modifications: fields leftover from previous work
* Remove HD from HDmem* calls (#3211)
* Remove HD from HDis* (e.g., isalpha) (#3212)
* HDisalnum
* HDisalpha
* HDiscntrl
* HDisdigit
* HDisgraph
* HDislower
* HDisprint
* HDispunct
* HDisspace
* HDisupper
* HDisxdigit
* Update actions for release option, fix branch for daily build (#3185)
* Update actions for release option, fix branch for daily build
* Scheduled workflows run on latest commit on the develop
* Add snapshots location
* docs: improve consistency in verb form (#3076) (#3188)
* fix gh action if statements (#3213)
* Adjust presets timeout and fix build script VS versions (#3215)
* Several ros3vfd logging improvements
* Committing clang-format changes
* Update COPYING (#3231)
Fixed old support URL.
* addresses compilation fortran warnings on Frontier (#3236)
* Fix doc for H5allocate_memory (#3240)
* merge bbrelease to release (#3232)
* merge bbrelease to release
* Fix pre-req workflow
* Replace support.hdfgroup.org URLs for alternative COPYING file (#3228)
* Replace support.hdfgroup.org URLs for alternative COPYING file
locations in copyright headers with https://www.hdfgroup.org/licenses.
Replace support.hdfgroup.org URL for alternative COPYING_LBNL_HDF5
with github URL.
Tweak chkcopyright script for change from UICOPYRIGHTSTR to
THGCOPYRIGHTSTR.
* Replace 1_10 reference with develop branch (#3227)
* Switch CI to use release script (#3242)
* Subfiling VFD source cleanup (#3241)
* Subfiling VFD source cleanup
Modularize Subfiling CMake code into separate CMakeLists.txt file
Update Mercury util code to latest version and update Copyright
Generate mercury_util_config.h header file instead of using
pre-generated file
Remove unnecessary Mercury functionality
Fix minor warning in Subfiling VFD code
* Remove Mercury headers from Autotools publicly-distributed header list
* install h5fuse.sh in bin dir. (#3244)
* Disable h5py until fixed properly without spack (#3243)
* ROS3: (feature) Temporary security credentials (#3030)
- Implemented support for AWS temporary security credentials.
For this kind of credentials also a session/security token
should be included in the request by adding the
x-amz-security-token header.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Avoid truncating at null byte when copying to std::string (#3083)
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix CMake builds when Subfiling VFD isn't enabled (#3250)
* Fix CMake builds when Subfiling VFD isn't enabled
* Add Subfiling VFD entry to hdf5-config.cmake.in
* Fix some warnings in developer builds (#3247)
* Fix some warnings in developer builds
* Switch approach to Winline flag
* Fixed more warnings about extra semicolons (#3249)
* Require semi-colon after H5_CHECK_OVERFLOW calls
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix warning in H5C__UPDATE_STATS_FOR_DIRTY_PIN macro (#3259)
Add braces to H5C__UPDATE_STATS_FOR_DIRTY_PIN macro to fix warning
causing Werror Release builds to fail
* Update DEFAULT_API_VERSION documentation for CMake (#3255)
* Update DEFAULT_API_VERSION documentation for CMake
* Fix hint
---------
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* changed the scope of #ifdef DOXYGEN to now include H5D multi-functions (#3254)
* Option changed but not all references (#3252)
* Option changed but not all references
* remove quotes from binary var
* Move 1.12.3 release to October (#3263)
* Fixed some -Wunused-variable warnings and one Wsometimes-uninitialized warning (#3260)
* removed the use of encoded single apostrophe (#3261)
* removed the use of encoded single apostrophe, and fix H5Dread_chunk from write to read
* updated sanitizer paragraph
* fixed brief description for H5Fget_info
* ROS3: (fix) Replaced HDfprintf (#3266)
- Replaced the HDfprintf() functions by fprintf() to be consistent
with other parts of the library.
* chore: make VRFY output consistent (#3268)
* CMake: (fix) Threads dependency (#3267)
- If the HDF5 library has been build with either thread-safety or
subfiling VFD feature on it will have an additional dependency
on a threading library. This dependency has been added to the
hdf-config.cmake.in file.
* chore: fix grammar - get hang -> get hung (#3272)
* Another round of fixing -Wextra-semi-stmt warnings (#3264)
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* chore: fix typo - persent -> present (#3273)
* Remove py-pip from h5py action (#3265)
* Update release schedule (#3317)
* Move 1.12.3 to November
* Add 1.14.3 in October
* Update README.md w/ 1.4.3 info (#3318)
* Switch parallel compression to use vector I/O (#3245)
Updates parallel compression feature to use vector I/O instead of
creating and passing down MPI derived types to VFD
* Fix incorrect error check in H5Ofill.c for undefined fill values (#3312)
* Fix H5Otoken_to_str call in h5dump and other minor cleanup (#3314)
* Fix loading plugin fails with missing directory GH issue #3248 (#3315)
* Made HGOTO_ERROR a do-while loop (#3308)
* Made HGOTO_ERROR a do-while loop
* Update files to skip list and ignore_words_list (#3321)
* Update files to skip list and ignore_words_list for codespell to not
check files generated by autotools. Autotools generate misspellings
that can't be fixed in HDF5 code.
* Windows runtime items go into the bin folder (#3320)
* A couple of documentation items to fix (#3332)
* Fix h5repack for variable-length datatyped datasets (#3331)
* Fix CVE-2018-11202 (#3330)
A malformed file could result in chunk index memory leaks. Under most
conditions (i.e., when the --enable-using-memchecker option is NOT
used), this would result in a small memory leak and and infinite loop
and abort when shutting down the library. The infinite loop would be
due to the "free list" package not being able to clear its resources
so the library couldn't shut down. When the "using a memory checker"
option is used, the free lists are disabled so there is just a memory
leak with no abort on library shutdown.
The chunk index resources are now correctly cleaned up when reading
misparsed files and valgrind confirms no memory leaks.
* Fix CVE-2018-13867 (#3336)
* Fixes the last of the -Wextra-semi-stmt warnings (#3326)
* Fixed extra semi warning by adjusting alternative macro definitions
* Find-replace H5E_END_TRY; -> H5E_END_TRY
* Made H5Epush_goto a do-while loop, fixed indentation
* Made GOTOERROR and ERRMSG do-while loops
* Made Hgoto_error and Hgoto_done do-while loops
* Made vrfy_cint_type and vrfy_ctype do-while loops
* Made TEST_TYPE_CONTIG and others do-while loops
* Removed extraneous semi-colons
* Committing clang-format changes
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix a typo in RELEASE.txt
* Fix assertion failure in H5D__mpio_collective_filtered_vec_io (#3340)
* Make h5dump spacing consistent when printing VLEN datatype (#3351)
* Fix for the bug exposed from running test/set_extent.c when selection… (#3319)
* Fix for the bug exposed from running test/set_extent.c when selection I/O is enabled.
This is a fix from Neil.
The test/set_extent.c is modified to test for selection I/O enabled.
* Add Fortran ES module to deploy list (#3341)
* Add Fortran ES module to deploy list
* Change fortran mod file export to use a list of names
* test(parallel): verify FALSE case (#3356)
* Implementation of the mpio driver with selection I/O. (#3222)
* This changes the default selection I/O to on for MPIO.
* Work around a testphdf5 failure on Cray MPICH machines (#3361)
* set H5_PAC_C_MAX_REAL_PRECISION default to 0 when cross sompiling with (#3364)
CMake to fix Fortran build failures.
* Add RELEASE.txt notes for recent selection I/O work. (#3374)
* Fix possible performance regression introduced with in-place type conversion in 1.14.2 (#3376)
* Correct script (#3377)
* Correct CI settings (#3384)
* Correct CI settings
* Correct plugin file name
* restore CI tarball name prefix to match bin/release (#3385)
* Fix assertion failure during file close on error (#3387)
* Fix compile failures with H5C_DO_MEMORY_SANITY_CHECKS enabled (#3388)
* Fix valgrind warning about write of uninitialized bytes (#3389)
* Fix valgrind warning about write of uninitialized bytes in ScaleOffset filter (#3390)
* Update presets, examples uncompress, szip cache (#3391)
* Fix serial to parallel chunked dataset file space allocation bug (#3394)
* chore: fix typo (#3405)
* Fix for CVE-2016-4332 (#3406)
This CVE issue was previously listed as fixed (via HDFFV-9950) back in
2016, but with no confirmation test. Now that test files exist for
the 2016 Talos CVE issues, we found that CVE-2016-4332 can raise an
assert in debug builds.
This fix replaces the assert with pointer checks that don't raise
errors or asserts. Since the function is in cleanup code, we do our
best to close and free things, even when presented with partially-
initialized structs.
Fixes CVE-2016-4332 and HDFFV-9950 (confirmed via the cve_hdf5 repo)
* Fix ph5diff tests for MPIEXEC_MAX_NUMPROCS=1 (#3407)
* Enable szip by default in Autotools (#3412)
Since libaec is so prevalent and BSD-licensed for both encode and
decode, we build the szip filter by default when the szip or aec
libraries are found.
* Re-enable SZIP default to ON in CMake (#3414)
The Autotools were handled in a separate commit
* Fix Heap-buffer-overflow WRITE in H5MM_memcpy (#3368)
* Add Intel oneAPI actions (#2949) (#2977)
* ci: add Intel oneAPI actions (#2949)
* ci: fix CMake installation
* ci: use absolute paths for libtool installation
* ci(oneAPI): update compiler versions and use cron
* Add RELEASE.txt entry for compound performance regression fix (#3376) (#3416)
* chore: remove gubbins comment (#3420)
* Add other types and full type to enum/str/vlen dataformat for structblock[begin/end] (#3353)
* Avoid H5Ocopy in h5repack for variable-length string types (#3419)
* Skip atomicity tests for OpenMPI major versions < 5 (#3421)
* Fix an issue with use of uninitialized memory in trefer_deprec.c test (#3422)
* Add parallel examples in doxygen (#3413)
* Fix use of uninitialized value in testpar/t_dset.c test (#3423)
* Remove extraneous "33" in RELEASE.txt (#3425)
* Revise file close assertion failure fix (#3418)
* Remove intel oneapi warning (#3426)
* Fix for CVE-2018-15671. h5stat -S $POC will result in a crash with segmenetation fault. (#3427)
It is because the object in the testfile points back to the root group.
When the tool tries to traverse the object, it goes back to the root group and then back again.
* chore: match function call and VRFY() output (#3428)
* Fix the Fortran extension used in example links (#3430)
* Put H5T_CONV_ab macros in do..while loops (#3432)
Ever since a recent round of macro cleanup, bin/trace and clang-format
have been bickering over what H5Tconv.c should look like and neither
produces readable code.
This change puts the top-level H5T_CONV_ab macros in do..while loops,
adds appropriate semicolons, and adds the missing H5_CLANG_DIAG_ON|OFF
and H5_GCC_CLANG_DIAG_ON|OFF macros to the list of statement macros
clang-format recognizes. H5Tconv.c is now readable and both bin/trace
and clang-format are happy.
* Convert some H5MM calls to standard C equivalents (#2382)
* H5MM_calloc and malloc are now mapped to stdlib C calls
* H5MM_memcpy now maps directly to memcpy in release builds
* H5MM_memcpy is still implemented as a separate function that
checks for buffer overlap when H5MM_DEBUG is defined
(default w/ debug builds)
* Switches many library memcpy calls to use H5MM_memcpy
* Fixes a possible zero allocation in H5Olayout.c
* Add 1.14.4 to the release schedule (#3434)
* Output stderr file in CMake testing on failure (#3431)
* Add Intel oneAPI badges (#3433)
* Add a CVE regression test action (#3445)
*
* Disable SZIP for Intel oneAPI Action (#3449)
* Disable SZIP for Intel oneAPI Action
* Disable Fortran and parallel
* Update VOL CMake for REST VOL (#3450)
* Update VOL CMake for REST VOL
* Prevent linking static libs to VOLs
* Add an h5py badge to README.md (#3477)
* Removed all the ranks printing out testing information (#3457)
* Fix Subfiling VFD IOC assignment bug (#3456)
* Correct java test dimension (#3482)
* Support CMake VOL builds with FetchContent from local directory (#3455)
* Update VOL CMake for REST VOL
* Prevent linking static libs to VOLs
* index on fetch_local: 5c5c3f1505 Prevent linking static libs to VOLs
* index on (no branch): 9a36d3e7b1 On fetch_local: WIP:add source dir fetch option for vols
* Allow building of VOL from local source
* Move LOCAL_DIR option to HDF5_VOL_ALLOW_EXTERNAL
* Fix the Fortran include dir in install config files (#3454)
* Convert hbool_t --> bool in examples (#3492)
* Fix some minor formatting for consistency (#3499)
* Create scorecard.yml (#3508)
Bring in OSSF Scorecard code scanner as a GitHub action
* Convert hbool_t --> bool in testpar (#3495)
* hbool_t/TRUE/FALSE --> bool/true/false in tools (#3491)
* Convert hbool_t --> bool in test (#3494)
* Convert hbool_t --> bool in src (#3496)
* hbool_t --> bool in src
* Does not remove TRUE/FALSE
* Public header files are unchanged
* Public API calls are unchanged
* TRUE/FALSE --> true/false in src
* Add deprecation notice for hbool_t
* Added new Fortran API wrappers (#3511)
* Added new wrappers for
h5get_free_list_sizes_f
H5Sselect_intersect_block_f
H5Sselect_shape_same_f
h5pget_no_selection_io_cause_f
h5pget_mpio_no_collective_cause_f
H5Lvisit_by_name_f
H5Lvisit_f
H5Fget_info_f
h5dwrite_chunk_f
h5dread_chunk_f
* added h5pget_file_space_page_size_f, h5pset_file_space_page_size_f, h5pget_file_space_strategy_f, h5pset_file_space_strategy_f, h5info tests
* added fortran tests
* Update tH5F.F90
* misc. fortran fixes for failing CI dailty tests (#3523)
* fixed H5Lvisit* interface
* changed integer type for direct write
* Consistent initialization of hid_t in the tests (#3521)
* Fix windows cpack with debug (#3525)
* Add missing row for the ROS3 VFD in table #3415 (#3517)
* fixed nvidia compiler issue (#3527)
* Identify functions in a subgroup (#3530)
* quiet warning on sunspot (gcc 11.2.0) (#3534)
* Add API examples doxygen page (#3500)
* removed C_INT32_T from Fortran APIs (#3537)
* Add NVHPC 23.7 GitHub Actions (#3509)
* Add NVHPC 27.3 GitHub Actions
* Address @derobins review
* Remove HD prefix from math functions (#3538)
* Remove HD prefix from HDlog10 calls (#3539)
Was missed in a previous commit and causes building subfiling to
fail.
* fixed arg to C H5Dwrite_chunk (#3541)
* Strip HD prefix from string/char C API calls (#3540)
* 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
* Convert main.yml CI into callable workflows (#3529)
* Fix broken URL. (#3546)
* Fix grammar (#3545)
* Update oneAPI-C/A badge yml links. (#3564)
* Check return values from HDF5 API calls. (#3556)
* Adds link to h5fuse.sh in testpar for autotools (#3557)
* Make the h5fuse.sh utility available to parallel subfiling tests so h5fuse testing is not skipped.
* Some minor formatting and text changes (#3563)
* Fix typos and grammar in t_pread. (#3565)
* Fix typo (givin->given) in test/testframe.c. (#3567)
* Fix ifx unused variable hdferr warning. (#3568)
* Correct comments about H5Z_FILTER_NONE (#3572)
* Update release script. (#3577)
* fixed function declaration (#3579)
* Fixed GH-3554 (#3584)
Removed the extra condition
* Remove h5dwalk.1 man page. (#3589)
* Removed the use of -commons linking option on Darwin (#3581)
Removed the use of -commons linking option on Darwin as COMMON and EQUIVALENCE is no long used
* Fix docs for H5Pset_dxpl_mpio_collective_opt() (#3594)
* Fix typo: arange->arrange in src/H5Cmpio.c. (#3597)
* Fix docs for H5Acreate2 and H5Acreate_by_name (#3598)
* Use HDoff_t with lseek consistently (#3600)
lseek on Windows uses __int64 for both the offset and return type
instead of off_t like most POSIX systems. This changes ensures we
use HDoff_t (which is typdef'd correctly on Windows) w/ lseek.
* Replaces HDgetenv with getenv (#3599)
* Develop tools move (#3580)
Reorganizes the tools files to support the VOL tests
* Clean up Subfiling VFD header doxygen formatting (#3601)
* Remove `sh` to run bash script. (#3590)
* Correct path name of ddl file to be changed (#3607)
* Fix potential uninitialized variable (#3602)
Moves a union initialization up a bit so it's performed before code
that can jump to the cleanup target, where file descriptors could
be checked without being initialized.
This could only happen in test code and only in an out-of-memory
situation.
Fixes Coverity 1542254
* Remove unnecessary assignment in test generator (#3603)
Fixes what looks like a copy/paste/modify error in the format convert
test file generator, where an array element is assigned one value
and them immediately overwritten by another value.
Fixes Coverity issue 1542285
* Remove useless define TRUE/FALSE statements. (#3604)
* Fix typo behaviour and dependes. (#3605)
* Fix typos (#3609)
* Fixed unused variable in H5CS.c (#3552) (#3612)
* Fixed#3552
* Fix grammar (#3614)
* Cleanup unused statements (#3553) (#3617)
Removed unnecessary assert statements and noise comments.
* Fix Intel oneAPI icc warning (#3619)
* Fix several spelling/grammar issues (#3621)
* Add HPC CDash to README.md (#3623)
* Disable static + thread-safe on Windows w/ CMake (#3622)
The thread-safety feature on Windows requires a hook in DllMain() and
thus is only available when HDF5 is built as a shared library.
This was previously a warning, but has now been elevated to a fatal
error that cannot be overridden with ALLOW_UNSUPPORTED.
Fixes GitHub #3613
* Remove unused member from H5D_shared_t struct. (#3628)
* Remove old EXTERNALPROJECT_ADD in favor of FETCH_CONTENT (#3624)
* Fix grammar (#3635)
* Disambiguate error output messages. (#3634)
* Disambiguate error output messages.
* Address @brtnfld review.
* Fail CMake on Windows when sub-filing VFD is enabled (#3636)
* Improve consistency in past tense usage (#3638)
* Split out test logic to separate file (#3639)
* Drop MPI-2 support (#3643)
* Switch IEEE flags for NAG Fortran (#3644)
Default is -ieee=stop, which causes problems when the H5T
module performs floating-point type introspection.
The new mode is -ieee=full
* Remove 1.10.11 info from README.md (#3646)
* Fixes GH#1027 compilation error (#3654)
* Remove 1.10 badge (#3650)
* Use real URLs and updated names for plugins (#3651)
* synchronize TGZ naming convention/usage
* Update parallel compression feature to support multi-dataset I/O (#3591)
* Add more tests for selection I/O. (#3528)
* Adjust 1.14 files after merging
---------
Malformed hdf5 files may provide more dimensions than the array dim[] in
H5IMget_image_info() is able to hold. Check number of elements first by calling
H5Sget_simple_extent_dims() with NULL for both 'dims' and 'maxdims' arguments.
This will cause the function to return only the number of dimensions.
The fix addresse a stack overflow on write.
This fixes CVE-2018-17439 / HDFFV-10589 / Bug #2226.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.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.
* Removed the: file, func, line args in the _async APIs from the doxygen arguments. Documented H5ESclean.
* format fixes
* fixed DOXYGEN_PREDEFINED
* Fixed the #ifdet logic for doxygen, added missing multi-dataset va_args
* format fixes
* Use H5_DOXYGEN instead of H5_DOXYGEN_FORTRAN
* reordered multidataset declarations
* alt. for H5Aclose_async and H5Acreate_async
* made doxgyen API into seperate blocks
* updated codespell
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes the module directory from the Automake flags as this
generated a large number of "missing include directory" warnings
and is unecessary
* Adds the module path to libhdf5.settings
* 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
