When using the '-s' (h5ls) or '-r' (h5dump) option to display 1-byte integer datasets and attributes as ASCII characters, a closing double-quote character for data values was dropped in some cases.
For objects with multiple hard links, use hash table to map between
object tokens and pathnames during traversal to avoid linear scan over
all previous objects for each hard link seen
Use separate hash table for h5trav "table" interface to map between
object tokens and an index into the table of visited objects. This
facilitates quick lookups of objects when adding hard link name aliases
for h5repack processing
Build-tree exports can't diverge from install-tree exports — the export(EXPORT ...) reads directly from the install export sets. No manual list to keep in sync.
Removed 3 global variables (HDF5_STATIC_LIBRARIES_TO_EXPORT, HDF5_JAVA_LIBRARIES_TO_EXPORT, HDF5_UTILS_TO_EXPORT) and their ~21 set_global_variable calls across tool/utility files.
Fixed the static-only build bug in the PR where the base export set was guarded by BUILD_SHARED_LIBS, breaking tools export.
Removed redundant utils in export files — the PR was dumping tools into all three build-tree export files (java, static, shared). Now they correctly appear only in the base export.
Adds predefined datatypes for FP6 data in E2M3 and E3M2 formats
Does not add support for any native FP6 types; datatype conversions are performed in software
Adds predefined datatypes for FP8 data in E4M3 and E5M2 formats
Does not add support for any native FP8 types; datatype conversions are performed in software
Adds predefined datatypes for little- and big-endian bfloat16 data
Does not add support for any native bfloat16 types; datatype conversions are performed in software
Also adds missing float16 predefined types to fortran
Adds workflow to build ROS3 VFD and optionally build aws-c-s3 library
from source or use package managers
Adds testing of ROS3 VFD with s3proxy and docker
Adds new H5Pset_fapl_ros3_endpoint()/H5Pget_fapl_ros3_endpoint() API
functions to set/get an alternative endpoint URL to use when opening
files with the ROS3 VFD
Cleans up warnings in tools and tests related to ROS3 VFD structure size
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Refactor warning macros
Replaces the scheme in H5warnings.h with a more compiler-agnostic
one that relocates ifdef complexity to the warnings header file
and uses better naming.
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Added infrastructure support for multithreaded concurrency by adding an optional way to switch to using a non-recursive R/W lock for the global API lock. This is enabled with a new 'concurrency' configuration flag for the autotools & CMake builds, which is disabled by default.
When the 'concurrency' build option is chosen, the global API lock will use the R/W lock and all API calls currently will acquire a write lock, ensuring exclusive access by one thread. Over time, the API routines that are converted to support multithreaded concurrency will switch to acquiring a read lock instead.
Reentering the library from application callbacks is managed by the 'disable locking for this thread' (DLFTT) threadsafety protocol. This is internally handled within the H5_API_LOCK / H5_API_UNLOCK macros in H5private.h (as before), which invoke the 'dlftt' routines in H5TSint.c.
To support this change, the threadsafety configuration macros for the library have been updated:
- --enable-threadsafe now defines the H5_HAVE_THREADSAFE macro
- --enable-concurrency defines the H5_HAVE_CONCURRENCY macro
The new H5_HAVE_THREADSAFE_API macro is set if either H5_HAVE_THREADSAFE or H5_HAVE_CONCURRENCY is enabled.
New Github actions are added to include the concurrency configuration in the CI for the develop branch.
To support the new non-recursive R/W locking for API routines, some other changes are necessary:
Added macro wrappers around all callback invocations that could call an
application function, and therefore re-enter the library:
H5_BEFORE_USER_CB* / H5_AFTER_USER_CB*
Added H5_user_cb_prepare / H5_user_cb_restore routines that save the
state of the library when callback leaves the library. Includes error
stack and threadsafe reentry state currently.
There's also some small cleanups to various places in the library:
Moved the H5E_mpi_error_str / H5E_mpi_error_str_len globals to be local for
pushing MPI errors, so that multiple threads can't interfere with each
other.
Added H5TS_rwlock_trywrlock() routine to R/W lock interface.
Emulate R/W locks on MacOS because its implementation of
pthread_rwlock_wrlock() does not conform to the POSIX standard.
Don't acquire the global API lock in H5close, since it's acquired in H5_term_library, which is necessary because H5_term_library is invoked via other code paths that don't hold the global API lock.
Don't call H5Eget_auto2 API routine within H5_term_library.
Switched 'return NULL' in H5allocate_memory to HGOTO_DONE(NULL).
Switched H5Pget_file_space_strategy / H5Pset_file_space_strategy to use
internal routines instead of API routines.
Switched H5Oopen_by_addr & H5Ovisit1 to use internal routines instead of
API routines.
Fixed a few places in src/H5Odeprec.c where a major
error ID was passed as a minor ID.
* Implement support for complex number datatypes
Adds the new datatype class H5T_COMPLEX
Adds the new API function H5Tcomplex_create which creates a complex
number datatype from an ID of a base floating-point datatype
Adds the new feature check macros H5_HAVE_COMPLEX_NUMBERS and
H5_HAVE_C99_COMPLEX_NUMBERS
Adds the new datatype size macros H5_SIZEOF_FLOAT_COMPLEX,
H5_SIZEOF_DOUBLE_COMPLEX and H5_SIZEOF_LONG_DOUBLE_COMPLEX
Adds the new datatype ID macros H5T_NATIVE_FLOAT_COMPLEX,
H5T_NATIVE_DOUBLE_COMPLEX, H5T_NATIVE_LDOUBLE_COMPLEX,
H5T_CPLX_IEEE_F16LE, H5T_CPLX_IEEE_F16BE,
H5T_CPLX_IEEE_F32LE, H5T_CPLX_IEEE_F32BE,
H5T_CPLX_IEEE_F64LE and H5T_CPLX_IEEE_F64BE
Adds hard and soft datatype conversion paths between complex number
datatypes and all the integer and floating-point datatypes, as well as
between other complex number datatypes
Adds a special conversion path between complex number datatypes and
array or compound datatypes where the in-memory layout of data is the
same between the datatypes and data can be converted directly
Adds support for complex number datatypes to the h5dump, h5ls and
h5diff/ph5diff tools. Allows h5dump '-m' option to change floating-point
printing format for float complex and double complex datatypes, as well
as long double complex if it has the same size as double complex
Adds minimal support to the h5watch and h5import tools
Adds support for the predefined complex number datatypes and
H5Tcomplex_create function to the Java wrappers. Also adds initial,
untested support to the JNI for future use with HDFView
Adds support for just the H5T_COMPLEX datatype class to the Fortran
wrappers
Adds support for the predefined complex number datatypes and
H5Tcomplex_create function to the high level library H5LT interface
for use with the H5LTtext_to_dtype and H5LTdtype_to_text functions
Changes some usages of "complex" in the library since it conflicts with
the "complex" keyword from the complex.h header. Also changes various
usages of the word "complex" throughout the library to distinguish
compound datatypes from complex datatypes.
* Cast away a signed/unsigned issue in H5HFhuge.c
* Use our platform-independent POSIX types in external_common.c
and h5test.c
* Replace a memset() call with a (const) array initializer in h5test.c
* Fix an unused done: target in h5diff
This is where most people will expect to find license information. The
COPYING_LBNL_HDF5 file has also been renamed to LICENSE_LBNL_HDF5.
The licenses are unchanged.
Cleanup and prepare for thread-safety changes.
Big ideas:
* Wrap H5VL_class_t with H5VL_connector_t, so use of the class can be refcounted within the H5VL package, instead of relying on storing an ID within the H5VL_t struct and incrementing & decrementing the ID's refcount.
* Register H5VL_connector_t* for VOL connector IDs, instead of the H5VL_class_t*
* Stop other packages from rummaging around inside H5VL_connector_t and H5VL_object_t data structures, so that the H5VL package can change implementation details without coupled changes throughout the library
Small things:
* Simplified the coding for creating links
* Moved some routines into more logical locations
* 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
* Fixes and cleanup for ph5diff
Fixes concurrency issues in ph5diff that can cause interleaved
output
Fixes an issue where output can sometimes be dropped if it ended
up in ph5diff's output overflow file
Fixes an issue where MPI_Init is called after HDF5 has been
initialized, preventing the library from setting up an MPI
attribute to perform cleanup on MPI_Finalize
Fixes an issue in config/cmake/runTest.cmake where the CMake
logic would try to access an invalid list index if the number
of lines in a test's output and reference files don't match
* Add release note
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
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 tools library no longer checks for whether MPI is initialized when attempting to use a parallel VFD, such as the MPI I/O VFD or Subfiling VFD. This requires that parallel VFDs check for this situation and initialize MPI on their own if need be, but also allows parallel VFDs to be used with non-parallel HDF5 tools, such as h5dump.
* 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
tbeu
jhendersonHDF
Scot Breitenfeld
H. Joe Lee
efferre79
Allen Byrne
Aleksandar Jelenak
Dana Robinsonandgithub-actions
Matt L
Quincey Koziol
Sean McBrideandgithub-actions