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* Overhaul CMake LFS support (#4122)Dana Robinson2024-03-125-129/+71
| | | | | | | | | | | | | | | | | | | | | | | | 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
* Initialize selection type in chunk struct (#4087)Glenn Song2024-03-121-0/+4
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* Use AC_SYS_LARGEFILE on Autotools (#4119)Dana Robinson2024-03-122-73/+3
| | | | | 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.
* Remove old cmake check (#4117)Allen Byrne2024-03-121-6/+2
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* Handle IBM long double issues in dsets.c test_floattypes test (#4116)jhendersonHDF2024-03-121-26/+19
| | | * Handle IBM long double issues in dsets.c test_floattypes test
* Implement ID creation optimization for container datatype conversions (#4113)jhendersonHDF2024-03-125-305/+494
| | | | | | | | | | | | | 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
* Adjust aocc workflow to fit the autotools/cmake pattern of other callable ↵Allen Byrne2024-03-127-91/+213
| | | | workflows. (#4115)
* Fix up dsets test for some platforms with different long double format (#4114)jhendersonHDF2024-03-111-13/+30
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* long double tests has problems setting precision with offset (#4102)Allen Byrne2024-03-111-2/+4
| | | | | * long double tests has problems setting precision with offset * Disable long double until more development fixes issues
* Add Doxygen for HDFS VFD (#4106)Dana Robinson2024-03-111-62/+59
| | | | | | | * Add Doxygen for HDFS VFD * Fix Doxygen warning * Update H5FDhdfs.h
* Change compression tests reference files to use masking for compression ↵Allen Byrne2024-03-1016-43/+287
| | | | | ratios (#4083) Rework TEST_FILTER tests to handle slightly different compression ratios
* Remove lint comments (#4107)Dana Robinson2024-03-1012-77/+51
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* Move common variables out of cache test blocks (#4108)Dana Robinson2024-03-101-180/+187
| | | Fixes a stack size warning w/ XCode
* Convert H5B__assert to use error checks (#4109)Dana Robinson2024-03-102-60/+70
| | | | | 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.
* Clean up a few things in H5T.c (#4105)Dana Robinson2024-03-101-31/+23
| | | | * remove (size_t) noise casts * replace (hid_t)FAIL with H5I_INVALID_HID
* Minimize use of abort() (#4110)Dana Robinson2024-03-106-40/+34
| | | The abort() call is used at several places where it probably shouldn't.
* Refactor datatype conversion code to use pointers rather than IDs (#4104)jhendersonHDF2024-03-1026-1711/+2110
| | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Change how stats are printed in H5Z (#4097)Dana Robinson2024-03-101-7/+14
| | | | | | | | 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.
* Remove printf debugging from H5Smpio.c (#4098)Dana Robinson2024-03-103-82/+14
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* Remove H5DEBUG() calls from H5Dmpio.c (#4103)Dana Robinson2024-03-101-3/+2
| | | Just use stdout when a stream is needed.
* Remove a few H5O printf debugging statements (#4096)Dana Robinson2024-03-101-15/+0
| | | | 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.
* msvc: don't declare `HAVE_TIMEZONE` for older MSVC (#3956)Ben Boeckel2024-03-091-1/+3
| | | It was introduced in MSVC 15 (Visual Studio 2017).
* Remove leading / from relative path. (#4101)H. Joe Lee2024-03-091-2/+2
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* Correct missing change of source path for S3 build (#4100)Allen Byrne2024-03-091-0/+7
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* Clean up off_t usage (#4095)Dana Robinson2024-03-0926-63/+70
| | | | * Add comments to C++ and Fortran API calls that use off_t * Remove noise casts for small integers
* Fix the last C++ stack size warning (#4099)Dana Robinson2024-03-091-1/+4
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* Remove H5B debug checks (#4089)Dana Robinson2024-03-097-88/+23
| | | | | | | | | | | | | | | | | | 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
* Expand check for variable-length or reference types when clearing datatype ↵jhendersonHDF2024-03-092-60/+225
| | | | | | 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
* Fixed -Wdeprecated-copy-dtor warnings by implementing a copy assignment ↵Sean McBride2024-03-094-0/+30
| | | | | | | 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]
* virtual creates must use the same datatype as the main file (#4092)Allen Byrne2024-03-083-3/+3
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* Update long double test with correct values (#4060)Allen Byrne2024-03-081-0/+301
| | | Update long double test with correct values
* Merge HDF4 release workflow changes to hdf5 (#4093)Allen Byrne2024-03-084-114/+75
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* Add subfiling for h5dump filedriver option help message (#3878)H. Joe Lee2024-03-089-28/+32
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* Remove printf debugging in H5I package (#4088)Dana Robinson2024-03-083-21/+2
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* Remove extra whitespaces from nvhpc-cmake action. (#4091)H. Joe Lee2024-03-081-1/+1
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* fixes compilation failures due to H5E additions (#4090)Scot Breitenfeld2024-03-082-5/+5
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* update macOS support statement (#4084)Scot Breitenfeld2024-03-081-0/+6
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* Fixed asserts due to H5Pset_est_link_info() values (#4081)Dana Robinson2024-03-083-1/+139
| | | | | | | | | | | | | | | | | | | | | | | * 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
* Remove printf debugging in H5HL code (#4086)Dana Robinson2024-03-084-39/+5
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* Use H5T_STD_I32LE to create datatype in vds examples (#4070)Allen Byrne2024-03-078-15/+15
| | | Fixes issues when VDS examples are tested on BE systems
* Fix bin/trace script w/ out params (#4074)Dana Robinson2024-03-0758-323/+366
| | | | | | | | | | | | | 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
* addressed compilation errors with gfortran 4.8 (#4082)Scot Breitenfeld2024-03-071-20/+20
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* New option for building with static CRT in Windows (#4062)Allen Byrne2024-03-074-43/+17
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* Close and reopen file during dset vlen IO API tests (#4050)mattjala2024-03-071-16/+186
| | | | | - 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
* Increased H5FD_ROS3_MAX_SECRET_TOK_LEN to 4096 to accommodate long AWS ↵Michael Aivazis2024-03-073-79/+90
| | | | | 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
* Add support for the new MSVC preprocessor (#4078)Dana Robinson2024-03-072-3/+24
| | | | | | | | | | | | 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
* Don't load toolchain file in CMake workflows (#4077)jhendersonHDF2024-03-072-9/+0
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* Added new H5E with tests. (#4049)Scot Breitenfeld2024-03-0726-336/+1354
| | | | | | | | | | | 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
* fix path for S3 build path in CI (#4076)Allen Byrne2024-03-061-1/+1
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* Fix uninitialized bytes in selection I/O test (#4073)Dana Robinson2024-03-061-1/+4
| | | | | 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.
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