Complete overhaul of the concurrency-related aspects of the library (threading, atomics, locking, etc.), adding private routines in the H5TS package to allow internal algorithms to use all of these capabilities.
Adds many new features & components in the H5TS package that are equivalent to common concurrency data structures and capabilities: "regular" and recursive mutices, condition variables, semaphores, thread barriers, 'once' support, thread pools, atomic variables, thread-local keys, and spawning & joining internal threads.
Now supports C11, pthreads, and Windows threading for all H5TS capabilities, except the recursive readers/writers lock, which is not supported on Windows (because Windows threads don't provide a callback on thread-local variable deletion).
The "global" API lock is switched to use a recursive mutex from the H5TS package, instead of its own variant.
API context code (H5CX package) and error stacks (H5E package) now use the common thread-local info, instead of their own variants.
Subfiling code is switched from using Mercury threading features to the new internal H5TS features.
Removes the mercury threading code.
Adds a configure option (--enable-threads / HDF5_ENABLE_THREADS), enabled by default, to control whether threading is enabled within the library.
* Always use DECIMAL_DIG instead of LDBL_DIG. This was controlled by
an ifdef that is always true in C99 or greater
It's confusing to use float.h C constants as variable names in
configure.ac and the PAC_FC_LDBL_DIG macro.
* Directly compare MY_FLT128_DIG and MY_LDBL_DIG
* Make uniform across CMake and Autotools
* Don't export quadmath.h variables to H5pubconf.h
* off_t --> HDoff_t in test
* off_t --> HDoff_t in h5ls, h5dump, & h5repack
* Minor off_t tweak to configure.ac
* off_t --> HDoff_t fixes in src
This changes the type of the offset parameter in H5Pget_external()
to HDoff_t to match H5Pset_external(), along with other minor tweaks.
* off_t --> HDoff_t in C++ wrappers
* Fix off_t usage in Java wrapper
Move without other changes:
src/libhdf5.settings.in -> src/libhdf5.settings.autotools.in
config/cmake/libhdf5.settings.cmake.in -> src/libhdf5.settings.cmake.in
* Revert "Remove Autotools sed hack (#3848)"
This reverts commit 8b3ffdef30.
* Fix libtool sed cleanup on MacOS
Convert sed -i line to sed > libtool.bak && mv libtool.bak libtool
to avoid non-portable -i option.
* Clean up random number generator code
Depending on the platform, we use a mix of random, rand, and rand_r
to generate pseudo-random numbers, along with a messy set of ifdefs
in H5private.h. We are not a cryptographic library, only use random
numbers in our test code, and have no need for anything more than the
C standard's (s)rand(). There's no point dithering about using rand()
vs random() when we're also doing bad things like using mod to
restrict the range, which introduces bias.
Also removes CMake/configure checks for rand_r and random
* Remove random/rand_r checks from build system
* Fix missed HDrandom after GitHub merge
Run configure checks with and without CFLAGS/CMAKE_C_FLAGS since some
compilers work in one case while not working in the other case
Sync CMake configure checks with Autotools
Add configure option to enable or disable extension features in general
Add configure option to enable or disable _Float16 support
Add new config options to various settings files
* 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
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
* 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
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
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
* 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
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.
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
* Switch warnings as errors to default OFF
* Enable mac docs
* Add doxygen action uses step
* Use html div around snippet
* Allow preset name to be an argument to cmake-ctest.yml
* 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>
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
Add for both CMake and the Autotools
* HDF5_ENABLE_DOXY_WARNINGS: ON/OFF (Default: ON)
* --enable-doxygen-errors: enable/disable (Default: enable)
The default will fail compile if the doxygen parsing generates warnings.
The option can be disabled if certain versions of doxygen have parsing
issues. i.e. 1.9.5, 1.9.8.
Fixes#3398
* 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
* 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
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.
* 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
* 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
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
Several options and public symbols that were provided to paper
over non-standard long double conversions between signed/unsigned
long and long long values were removed from the Autotools and
CMake. These were added twenty years ago, when C99 and 64-bit
platforms were less common and are no longer needed.
Autotools:
--enable-dconv-accuracy
CMake:
HDF5_WANT_DATA_ACCURACY
H5pubconf.h symbols:
H5_WANT_DATA_ACCURACY
H5_LDOUBLE_TO_LONG_SPECIAL
H5_LONG_TO_LDOUBLE_SPECIAL
H5_LDOUBLE_TO_LLONG_ACCURATE
H5_LLONG_TO_LDOUBLE_CORRECT
H5_DISABLE_SOME_LDOUBLE_CONV
