Commit Graph

70 Commits

Author SHA1 Message Date
Scot Breitenfeld
915a7ab591
fixed true/false and added missing h5_interm_group example (#5092) 2024-11-13 05:18:14 -08:00
Allen Byrne
d09ea66934
Rename HDF5_ENABLE_Z_LIB_SUPPORT to HDF5_ENABLE_ZLIB_SUPPORT (#5074) 2024-11-05 15:59:28 -06:00
Allen Byrne
ad3ea2633a
Move hl example into HDF5Examples (#5057) 2024-11-04 05:22:27 -08:00
jhendersonHDF
90429f5e7d
Implement support for complex number datatypes (#4630)
* 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.
2024-10-31 13:54:25 -07:00
Allen Byrne
5425a571e0
Convert develop to v2.0.0 (#5006)
Switches previous 1.16/17/18 values to 2.0
2024-10-27 21:51:07 -07:00
Dana Robinson
7f1e49206d
Renamed COPYING to LICENSE (#4978)
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.
2024-10-18 21:13:04 -07:00
Dana Robinson
54f8f12ed9
Update clang-format to 17 (#4931)
Also bump the clang-format GitHub actions to 17
2024-10-04 19:49:35 -07:00
Allen Byrne
b5aecf32e2 Correct test script 2024-10-02 19:53:38 -05:00
Allen Byrne
07756c87f5 Update develop to 1.18 API 2024-10-02 19:53:38 -05:00
Allen Byrne
a8520298e9
Add workflow that reports to CDash (#4864) 2024-09-26 12:06:05 -05:00
Allen Byrne
0737d0dbf7
Correct URLs in documentation (#4823) 2024-09-12 22:46:58 -05:00
Allen Byrne
5e94301e71
Add THREADS check to configuration file (#4746)
* Cleanup threads package checks

* Check first if package was found

* Remove unnecessary dependent checks

* Remove Unused options and fix names of option prefix
2024-09-07 20:45:12 -05:00
Allen Byrne
4ffeb77fdb
Correct the URL paths (#4802) 2024-09-04 07:32:42 -05:00
Allen Byrne
bca2806055
Update URL documentation links to support site (#4781) 2024-08-29 16:27:44 -05:00
Allen Byrne
d7e0ad5200
Change osx refs to macos (#4707) 2024-08-13 14:43:28 -05:00
Allen Byrne
f77b70859f
Rework Dynamic Analysis and sanitize testing (#4681)
* Ignore predetermined failing test and check pointer before use

* Rework Analysis process
2024-08-05 09:53:53 -05:00
Quincey Koziol
9fd88560d5
Refactor threading and other concurrency support (#4469)
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.
2024-07-31 12:34:43 -05:00
Allen Byrne
d309a40325
Fix binary examples process (#4666) 2024-07-30 07:33:46 -05:00
Larry Knox
f54abf7032
Remove outdated line from Copyright header in new files. (#4676) 2024-07-29 12:57:36 -05:00
Allen Byrne
1fafdc9da3
Fix the examples for testing java with binaries (#4660) 2024-07-19 10:07:39 -05:00
Allen Byrne
e71605966a
Update doxygen Learn Basics / example refs. Add Reference sections (#4640) 2024-07-15 22:02:08 -05:00
Allen Byrne
6fa09bdb15
Add h5* compiler wrapper testing for CMake #4605 (#4613)
* Add show option

* remove non-static libs and correct names of static libs

* Fixup the pkg-config libs and comp builds

* Fix commands and add fortran pkg-config test scripts

* Add help usage option
2024-07-15 10:16:16 -05:00
Allen Byrne
033f2a8cb5
Add python testing for examples (#4628) 2024-07-12 21:28:38 -07:00
Allen Byrne
dca6370691
Move C++ and Fortran and examples to HDF5Examples folder (#4552) 2024-06-08 06:46:09 -05:00
bmribler
7f83faf9d9
Add Python examples (#4546)
These examples are referred to from the replacement page of https://portal.hdfgroup.org/display/HDF5/Other+Examples.
2024-06-07 17:03:05 -07:00
jhendersonHDF
b823c1609d
Remove an unnecessary check for parallel and thread-safety from examples (#4543) 2024-06-03 15:10:19 -05:00
Allen Byrne
69a4e7d68f
Correct examples tests to just run under dynamic analysis (#4505) 2024-05-21 07:48:47 -07:00
Allen Byrne
f17ca5689e
Update for blosc2 in plugins and prefix hdf5 cmake varnames (#4468) 2024-05-10 13:01:28 -05:00
Allen Byrne
9148f7c563
Prepend MPI_TEST_ to parallel example test names (#4306) 2024-04-02 13:01:02 -05:00
Allen Byrne
1dfaef2586
replace deprecated CMAKE_COMPILER_IS_GNU** (#4272) 2024-03-28 09:20:57 -07:00
H. Joe Lee
c4d2891bac
Match generators with real cmake -G output on Windows (#4252) 2024-03-26 15:08:12 -07:00
Allen Byrne
42f9d2426f
Correct reference copy for 16 API (#4244) 2024-03-26 09:04:36 -07:00
H. Joe Lee
cb3169fc5a
Match minimum CMake version to 3.18 (#4215) 2024-03-25 09:51:01 -07:00
bmribler
81c811b721
Fix links md files (#4239) 2024-03-25 10:54:31 -05:00
Scot Breitenfeld
6837fe5bc8
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
2024-03-25 07:42:03 -05:00
Scot Breitenfeld
c1a56f432e
Revert "Addressed Fortran issues with promoted integers and reals via compil…" (#4220)
This reverts commit 06c42ff038.
2024-03-23 07:16:43 -07:00
bmribler
62a905ae4a
Fix URLs (#4210)
Also removed Copyright.html context because it's no longer valid.
2024-03-22 12:06:09 -05:00
Scot Breitenfeld
06c42ff038
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
2024-03-22 11:52:58 -05:00
Allen Byrne
8f3e544193
Filter plugins updates for registration URL (#4180)
* Update filter plugin URL to new location

* Adjust test array size
2024-03-19 15:11:15 -05:00
jhendersonHDF
a56675e12a
Fix some minor warnings (#4165) 2024-03-16 19:43:47 -07:00
Allen Byrne
50a6522322
Change compression tests reference files to use masking for compression ratios (#4083)
Rework TEST_FILTER tests to handle slightly different compression ratios
2024-03-10 16:43:37 -07:00
Dana Robinson
0ea1d7280b
Clean up off_t usage (#4095)
* Add comments to C++ and Fortran API calls that use off_t
* Remove noise casts for small integers
2024-03-09 09:06:10 -08:00
Allen Byrne
114d2d0211
virtual creates must use the same datatype as the main file (#4092) 2024-03-08 15:50:31 -08:00
Allen Byrne
871a49feca
Use H5T_STD_I32LE to create datatype in vds examples (#4070)
Fixes issues when VDS examples are tested on BE systems
2024-03-07 13:05:28 -08:00
Allen Byrne
42c7e1d073
Ignore UserPresets and Use only C compiler for sanitizers (#4066)
* Remove user presets file

* Only use C compiler for sanitzers
2024-03-05 09:05:38 -08:00
Allen Byrne
7ce8c6f81a
Add options to allow tools type selection and naming (#4046) 2024-03-04 06:53:52 -08:00
Allen Byrne
662ee679e0
Remove limitations on preset generators (#4051) 2024-02-29 16:12:03 -06:00
Allen Byrne
3fd1e90df6
Update and Add general INSTALL (#4016) 2024-02-23 08:02:18 -06:00
Christoph Niethammer
f1e8f42b5a
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>
2024-02-21 14:04:38 -06:00
Allen Byrne
bdddf43f1a
Correct String FIND for runTest and grepTest (#4022) 2024-02-15 17:49:32 -06:00