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* 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 1e1dac1dac58fa18f6b7788346d1ba7d3315b0f9.
* 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
---------
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* Updated source file copyright headers to remove "Copyright by the Board of Trustees
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* Update format source to clang 13
* More format changes
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* Added support for vector I/O calls to the VFD layer, and
associated test code. Note that this includes the optimization
to allow shortened sizes and types arrays to allow more space
efficient representations of vectors in which all entries are
of the same size and/or type. See the Selection I/o RFC for
further details.
Tested serial and parallel, debug and production on Charis.
serial and parallel debug only on Jelly.
* ran code formatter
quick serial build and test on jelly
* Add H5FD_read_selection() and H5FD_write_selection(). Currently only
translate to scalar calls. Fix const buf in H5FD_write_vector().
* Format source
* Fix comments
* Add selection I/O to chunk code, used when: not using chunk cache, no
datatype conversion, no I/O filters, no page buffer, not using collective
I/O. Requires global variable H5_use_selection_io_g be set to TRUE.
Implemented selection to vector I/O transaltion at the file driver
layer.
* Fix formatting unrelated to previous change to stop github from
complaining.
* Add full API support for selection I/O. Add tests for this.
* Implement selection I/O for contiguous datasets. Fix bug in selection
I/O translation. Add const qualifiers to some internal selection I/O
routines to maintain const-correctness while avoiding memcpys.
* Added vector read / write support to the MPIO VFD, with associated
test code (see testpar/t_vfd.c).
Note that this implementation does NOT support vector entries of
size greater than 2 GB. This must be repaired before release,
but it should be good enough for correctness testing.
As MPIO requires vector I/O requests to be sorted in increasing
address order, also added a vector sort utility in H5FDint.c This
function is tested in passing by the MPIO vector I/O extension.
In passing, repaired a bug in size / type vector extension management
in H5FD_read/write_vector()
Tested parallel debug and production on charis and Jelly.
* Ran source code formatter
* Add support for independent parallel I/O with selection I/O. Add
HDF5_USE_SELECTION_IO env var to control selection I/O (default off).
* Implement parallel collective support for selection I/O.
* Fix comments and run formatter.
* Update selection IO branch with develop (#1215)
Merged branch 'develop' into selection_io
* Sync with develop (#1262)
Updated the branch with develop changes.
* Implement big I/O support for vector I/O requests in the MPIO file
driver.
* Free arrays in H5FD__mpio_read/write_vector() as soon as they're not
needed, to cut down on memory usage during I/O.
* Address comments from code review. Fix const warnings with
H5S_SEL_ITER_INIT().
* Committing clang-format changes
* Feature/subfiling (#1464)
* Initial checkin of merged sub-filing VFD.
Passes regression tests (debug/shared/paralle) on Jelly.
However, bugs and many compiler warnings remain -- not suitable
for merge to develop.
* Minor mods to src/H5FDsubfile_mpi.c to address errors reported by autogen.sh
* Code formatting run -- no test
* Merged my subfiling code fixes into the new selection_io_branch
* Forgot to add the FindMERCURY.cmake file. This will probably disappear soon
* attempting to make a more reliable subfile file open which doesn't return errors. For some unknown reason, the regular posix open will occasionally fail to create a subfile. Some better error handling for file close has been added.
* added NULL option for H5FD_subfiling_config_t in H5Pset_fapl_subfiling (#1034)
* NULL option automatically stacks IOC VFD for subfiling and returns a valid fapl.
* added doxygen subfiling APIs
* Various fixes which allow the IOR benchmark to run correctly
* Lots of updates including the packaging up of the mercury_util source files to enable easier builds for our Benchmarking
* Interim checkin of selection_io_with_subfiling_vfd branch
Moddified testpar/t_vfd.c to test the subfiling vfd with default configuration.
Must update this code to run with a variety of configurations -- most particularly
multiple IO concentrators, and stripe depth small enough to test the other IO
concentrators.
testpar/t_vfd.c exposed a large number of race condidtions -- symtoms included:
1) Crashes (usually seg faults)
2) Heap corruption
3) Stack corruption
4) Double frees of heap space
5) Hangs
6) Out of order execution of I/O requests / violations of POSIX semantics
7) Swapped write requests
Items 1 - 4 turned out to be primarily caused by file close issues --
specifically, the main I/O concentrator thread and its pool of worker threads
were not being shut down properly on file close. Addressing this issue in
combination with some other minor fixes seems to have addressed these issues.
Items 5 & 6 appear to have been caused by issue of I/O requests to the
thread pool in an order that did not maintain POSIX semantics. A rewrite of
the I/O request dispatch code appears to have solved these issues.
Item 7 seems to have been caused by multiple write requests from a given
rank being read by the wrong worker thread. Code to issue "unique" tags for
each write request via the ACK message appears to have cleaned this up.
Note that the code is still in poor condtition. A partial list of known
defects includes:
a) Race condiditon on file close that allows superblock writes to arrive
at the I/O concentrator after it has been shutdown. This defect is
most evident when testpar/t_subfiling_vfd is run with 8 ranks.
b) No error reporting from I/O concentrators -- must design and implement
this. For now, mostly just asserts, which suggests that it should be
run in debug mode.
c) Much commented out and/or un-used code.
d) Code orgnaization
e) Build system with bits of Mercury is awkward -- think of shifting
to pthreads with our own thread pool code.
f) Need to add native support for vector and selection I/O to the subfiling
VFD.
g) Need to review, and posibly rework configuration code.
h) Need to store subfile configuration data in a superblock extension message,
and add code to use this data on file open.
i) Test code is inadequate -- expect more issues as it is extended.
In particular, there is no unit test code for the I/O request dispatch code.
While I think it is correct at present, we need test code to verify this.
Similarly, we need to test with multiple I/O concentrators and much smaller
stripe depth.
My actual code changes were limited to:
src/H5FDioc.c
src/H5FDioc_threads.c
src/H5FDsubfile_int.c
src/H5FDsubfile_mpi.c
src/H5FDsubfiling.c
src/H5FDsubfiling.h
src/H5FDsubfiling_priv.h
testpar/t_subfiling_vfd.c
testpar/t_vfd.c
I'm not sure what is going on with the deletions in src/mercury/src/util.
Tested parallel/debug on Charis and Jelly
* subfiling with selection IO (#1219)
Merged branch 'selection_io' into subfiling branch.
* Subfile name fixes (#1250)
* fixed subfiling naming convention, and added leading zero to rank names.
* Merge branch 'selection_io' into selection_io_with_subfiling_vfd (#1265)
* Added script to join subfiles into a single HDF5 file (#1350)
* Modified H5FD__subfiling_query() to report that the sub-filing VFD supports MPI
This exposed issues with truncate and get EOF in the sub-filing VFD.
I believe I have addressed these issues (get EOF not as fully tested as it should be), howeer,
it exposed race conditions resulting in hangs. As of this writing, I have not been able
to chase these down.
Note that the tests that expose these race conditions are in testpar/t_subfiling_vfd.c, and
are currently skipped. Unskip these tests to reproduce the race conditions.
tested (to the extent possible) debug/parallel on charis and jelly.
* Committing clang-format changes
* fixed H5MM_free
Co-authored-by: mainzer <mainzer#hdfgroup.org>
Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com>
Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org>
Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Move Subfiling VFD components into H5FDsubfiling source directory
* Update Autotools build and add H5_HAVE_SUBFILING_VFD macro to H5pubconf.h
* Tidy up CMake build of subfiling sources
* Merge branch 'develop' into feature/subfiling (#1539)
Merge branch 'develop' into feature/subfiling
* Add VFD interface version field to Subfiling and IOC VFDs
* Merge branch 'develop' into feature/subfiling (#1557)
Merge branch 'develop' into feature/subfiling
* Merge branch 'develop' into feature/subfiling (#1563)
Merge branch 'develop' into feature/subfiling
* Tidy up merge artifacts after rebase on develop
* Fix incorrect variable in mirror VFD utils CMake
* Ensure VFD values are always defined
* Add subfiling to CMake VFD_LIST if built
* Mark MPI I/O driver self-initialization global as static
* Add Subfiling VFD to predefined VFDs for HDF5_DRIVER env. variable
* Initial progress towards separating private vs. public subfiling code
* include libgen.h in t_vfd tests for correct dirname/basename
* Committing clang-format changes
* removed mercury option, included subfiling header path (#1577)
Added subfiling status to configure output, installed h5fuse.sh to build directory for use in future tests.
* added check for stdatomic.h (#1578)
* added check for stdatomic.h with subfiling
* added H5_HAVE_SUBFILING_VFD for cmake
* fix old-style-definition warning (#1582)
* fix old-style-definition warning
* added test for enable parallel with subfiling VFD (#1586)
Fails if subfiling VFD is not used with parallel support.
* Subfiling/IOC VFD fixes and tidying (#1619)
* Rename CMake option for Subfiling VFD to be consistent with other VFDs
* Miscellaneous Subfiling fixes
Add error message for unset MPI communicator
Support dynamic loading of subfiling VFD with default configuration
* Temporary fix for subfile name issue
* Added subfile checks (#1634)
* added subfile checks
* Feature/subfiling (#1655)
* Subfiling/IOC VFD cleanup
Fix misuse of MPI_COMM_WORLD in IOC VFD
Propagate Subfiling FAPL MPI settings down to IOC FAPL in default
configuration case
Cleanup IOC VFD debugging code
Change sprintf to snprintf in a few places
* Major work on separating Subfiling and IOC VFDs from each other
* Re-write async_completion func to not overuse stack
* Replace usage of MPI_COMM_WORLD with file's actual MPI communicator
* Refactor H5FDsubfile_mpi.c
* Remove empty file H5FDsubfile_mpi.c
* Separate IOC VFD errors to its own error stack
* Committing clang-format changes
* Remove H5TRACE macros from H5FDioc.c
* Integrate H5FDioc_threads.c with IOC error stack
* Fix for subfile name generation
Use number of I/O concentrators from existing subfiling configuration file, if one exists
* Add temporary barrier in "Get EOF" operation to prevent races on EOF
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for retrieval of machine Host ID
* Default to MPI_COMM_WORLD if no MPI params set
* added libs rt and pthreads (#1673)
* added libs rt and pthreads
* Feature/subfiling (#1689)
* More tidying of IOC VFD and subfiling debug code
* Remove old unused log file code
* Clear FID from active file map on failure
* Fix bug in generation of subfile names when truncating file
* Change subfile names to start from 1 instead of 0
* Use long long for user-specified stripe size from environment variable
* Skip 0-sized I/Os in low-level IOC I/O routines
* Don't update EOF on read
* Convert printed warning about data size mismatch to assertion
* Don't add base file address to I/O addresses twice
Base address should already be applied as part of H5FDwrite/read_vector calls
* Account for 0-sized I/O vector entries in subfile write/read functions
* Rewrite init_indep_io for clarity
* Correction for IOC wraparound calculations
* Some corrections to iovec calculations
* Remove temporary barrier on EOF retrieval
* Complete work request queue entry on error instead of skipping over
* Account for stripe size wraparound for sf_col_offset calculation
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Re-write and fix bugs in I/O vector filling routines (#1703)
* Rewrite I/O vector filling routines for clarity
* Fix bug with iovec_fill_last when last I/O size is 0
* added subfiling_dir line read (#1714)
* added subfiling_dir line read and use it
* shellcheck fixes
* I/O request dispatch logic update (#1731)
Short-circuit I/O request dispatch when head of I/O queue is an
in-progress get EOF or truncate operation. This prevents an issue where
a write operation can be dispatched alongside a get EOF/truncate
operation, whereas all I/O requests are supposed to be ineligible for
dispatch until the get EOF/truncate is completed
* h5fuse.sh.in clean-up (#1757)
* Added command-line options
* Committing clang-format changes
* Align with changes from develop
* Mimic MPI I/O VFD for EOF handling
* Initialize context_id field for work request objects
* Use logfile for some debugging information
* Use atomic store to set IOC ready flag
* Use separate communicator for sending file EOF data
Minor IOC cleanup
* Use H5_subfile_fid_to_context to get context ID for file in Subfiling
VFD
* IOVEC calculation fixes
* Updates for debugging code
* Minor fixes for threaded code
* Committing clang-format changes
* Use separate MPI communicator for barrier operations
* Committing clang-format changes
* Rewrite EOF routine to use nonblocking MPI communication
* Committing clang-format changes
* Always dispatch I/O work requests in IOC main loop
* Return distinct MPI communicator to library when requested
* Minor warning cleanup
* Committing clang-format changes
* Generate h5fuse.sh from h5fuse.sh.in in CMake
* Send truncate messages to correct IOC rank
* Committing clang-format changes
* Miscellaneous cleanup
Post some MPI receives before sends
Free some duplicated MPI communicator/Info objects
Remove unnecessary extra MPI_Barrier
* Warning cleanup
* Fix for leaked MPI communicator
* Retrieve file EOF on single rank and bcast it
* Fixes for a few failure paths
* Cleanup of IOC file opens
* Committing clang-format changes
* Use plan MPI_Send for send of EOF messages
* Always check MPI thread support level during Subfiling init
* Committing clang-format changes
* Handle a hang on failure when IOCs can't open subfiles
* Committing clang-format changes
* Refactor file open status consensus check
* Committing clang-format changes
* Fix for MPI_Comm_free being called after MPI_Finalize
* Fix VFD test by setting MPI params before setting subfiling on FAPL
* Update Subfiling VFD error handling and error stack usage
* Improvements for Subfiling logfiles
* Remove prototypes for currently unused routines
* Disable I/O queue stat collecting by default
* Remove unused serialization mutex variable
* Update VFD testing to take subfiling VFD into account
* Fix usage of global subfiling application layout object
* Minor fixes for failure pathways
* Keep track of the number of failures in an IOC I/O queue
* Make sure not to exceed MPI_TAG_UB value for data communication messages
* Committing clang-format changes
* Update for rename of some H5FD 'ctl' opcodes
* Always include Subfiling's public header files in hdf5.h
* Remove old unused code and comments
* Implement support for per-file I/O queues
Allows the subfiling VFD to have multiple HDF5 files open simultaneously
* Use simple MPI_Iprobe over unnecessary MPI_Improbe
* Committing clang-format changes
* Update HDF5 testing to query driver for H5FD_FEAT_DEFAULT_VFD_COMPATIBLE
flag
* Fix a few bugs related to file multi-opens
* Avoid calling MPI routines if subfiling gets reinitialized
* Fix issue when files are closed in a random order
* Update HDF5 testing to query VFD for "using MPI" feature flag
* Register atexit handler in subfiling VFD to call MPI_Finalize after HDF5
closes
* Fail for collective I/O requests until support is implemented
* Correct VOL test function prototypes
* Minor cleanup of old code and comments
* Update mercury dependency
* Cleanup of subfiling configuration structure
* Committing clang-format changes
* Build system updates for Subfiling VFD
* Fix possible hang on failure in t_vfd tests caused by mismatched
MPI_Barrier calls
* Copy subfiling IOC fapl in "fapl get" method
* Mirror subfiling superblock writes to stub file for legacy POSIX-y HDF5
applications
* Allow collective I/O for MPI_BYTE types and rank 0 bcast strategy
* Committing clang-format changes
* Use different scheme for subfiling write message MPI tag calculations
* Committing clang-format changes
* Avoid performing fstat calls on all MPI ranks
* Add MPI_Barrier before finalizing IOC threads
* Use try_lock in I/O queue dispatch to minimize contention from worker threads
* Use simple Waitall for nonblocking I/O waits
* Add configurable IOC main thread delay and try_lock option to I/O queue dispatch
* Fix bug that could cause serialization of non-overlapping I/O requests
* Temporarily treat collective subfiling vector I/O calls as independent
* Removed unused mercury bits
* Add stubs for subfiling and IOC file delete callback
* Update VFD testing for Subfiling VFD
* Work around HDF5 metadata cache bug for Subfiling VFD when MPI Comm size
= 1
* Committing clang-format changes
Co-authored-by: mainzer <mainzer#hdfgroup.org>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: jrmainzer <72230804+jrmainzer@users.noreply.github.com>
Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org>
Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
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* Straightforward conversion of sprintf to the safer snprintf
* Trickier conversion of sprintf to safer snprintf
This involved minor changes to private function signatures to take the size of the buffer.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* h5test.h testing macros get enclosed in do..while loops
* Adds missed macro in hl C++ code
* Fixes macro in Windows code
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* fixed missed closing of a dataset
* fixed missed closing of a dataset
* fixed typo in error return
* Committing clang-format changes
* minor edits
* code format
* Committing clang-format changes
* code format
* minor edit
* switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging
* Committing clang-format changes
* changed size_i in printf to reflect the I/O.
* Committing clang-format changes
* Fixed seg fault with xlf on BE with -qintsize=8
* fixed error function string
* spelling corrections via codespell, added new spell check github actions
* Committing clang-format changes
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* Committing clang-format changes
* misc
* misc
* misc
* misc
* misc
* misc
* Committing clang-format changes
* misc
* work around for https://github.com/codespell-project/codespell/issues/2137
* misc
* added missing file
* misc
* misc.
* misc
* switch to using Codespell with GitHub Actions
* misc.
* misc.
* fixed more sp errors
* Fix new typos found by codespell.
* fixed proceed with precede
* fixed variable in fortran test
* fixed minnum
* updated spelling list
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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* Implement support for loading of Virtual File Drivers as plugins
Fix plugin caching for VOL connector and VFD plugins
Fix plugin iteration to skip paths that can't be opened
* Enable dynamic loading of VFDs with HDF5_DRIVER environment variable
* Temporarily disable error reporting during H5F_open double file open
* Default to using HDstat in h5_get_file_size for unknown VFDs
* Use macros for some environment variables that HDF5 interprets
* Update "null" and "ctl testing" VFDs
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* Update clang config to put H5E_BEGIN_TRY / H5E_END_TRY on separate lines, empty C++ methods on separate lines, understand that ALL_MEMBERS / UNIQUE_MEMBERS are foreach macros, and properly skip the 'config' directory in the find command without emiting a warning
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Fixed all clang-tidy bugprone-suspicious-string-compare warnings
This change was generated entirely by clang-tidy itself.
* Reformat code with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - src and test directories.
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application to be skipped. (#134)
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Adds missing HD prefixes to API calls in src and test.
Adds some extra processing to bin/checkposix to keep the noise
levels down when running the script (not comprehensive).
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reapplication to my new warnings branch, `warnings-again`. These
changes are included:
commit 915551b7bf64e777dd2007386ec77b1d117770da
Merge: 63858c2 a8892bb
Author: David Young <dyoung@hdfgroup.org>
Date: Mon Nov 25 17:39:49 2019 -0600
Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment
commit a8892bb42d6f6e4fbc30fae0eb2b957f81c938b9
Merge: 5c911d8 f907b51
Author: David Young <dyoung@hdfgroup.org>
Date: Mon Nov 25 17:33:54 2019 -0600
Merge pull request #2055 in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop
* commit 'f907b511d06612dafc7814a7c30f2f3d2b76d52b':
Oops, remove more C99 designated initializers for VS 2010 compatibility.
commit 63858c22e168acaec0af8ced6641f26102cc6bb0
Merge: 20ae787 5c911d8
Author: David Young <dyoung@hdfgroup.org>
Date: Mon Nov 25 17:04:42 2019 -0600
Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment
commit 5c911d8baf3ee7fe654269088eebdf07f59a8192
Merge: b8a5671 62208b0
Author: David Young <dyoung@hdfgroup.org>
Date: Mon Nov 25 16:58:27 2019 -0600
Merge pull request #2030 in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop
* commit '62208b056a09c01855fbac7f75146be58ad6bfe5': (44 commits)
Add an #include to get a function declaration.
Don't use C99 designated initializers, they're not compatible with Visual Studio 2010.
Quiet some more maybe-uninitialized warnings---each is a false positive, *sigh*. This is more code that may not compile with VS2010, *sigh sigh*.
Always warn on maybe-uninitialized. -Wincompatible-pointer-types was not available until GCC 5, so enable it only if that's the GCC version we're using.
Only promote maybe-uninitialized warnings to errors on GCC 8. Even on GCC 8, there may be false positives at low optimization levels? I need to check.
Only use -Werror=cast-function-type with GCC 8 and later.
Put all of the -W options back into the order I found them in so that it's easier to compare old and new config/gnu-flags.
Add new source files to CMakeLists.txt.
Mention the -Werror= flags in libhdf5.settings.in.
free -> HDfree
Promote decleration-after-statement warnings to errors.
Quiet decleration-after-statement warnings.
Move a statement under some declarations since some vintages of Visual Studio don't like declarations after statements.
Document H5D__chunk_mem_xfree_wrapper().
Undo accidental test deletion.
Oops, delete a debug printf that snuck in here.
Undo my changes to the HD macros, hadn't really intended those to be on this branch....
Make errors of some more warnings. Move disabled warnings to DEVELOPER_WARNING_CFLAGS. Put just one warning option on a line, and sort some of the options.
Cast to the parameter type, H5VL_token_t *, instead of to unsigned char *.
Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char to structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc.
...
commit 20ae7877e33931b95e8c3502b027d6c3fe94a11f
Merge: 46f8c61 edd5297
Author: David Young <dyoung@hdfgroup.org>
Date: Fri Nov 22 15:34:09 2019 -0600
Merge remote-tracking branch 'origin/add-werror-and-squash-some' into fprintf-experiment
commit 46f8c613d5117a8be5bc8385a072daa0b4262f06
Author: David Young <dyoung@hdfgroup.org>
Date: Fri Nov 22 15:29:00 2019 -0600
GCC really wants us to use `ll` to format `long long`, so try to make that work
before any other format modifier. Seems like we're not compiling the autoconf
test program with -Werror=format ? Probably should.
commit eee35b8ef3759c391327cd48a9b3c56b6f8abc99
Author: David Young <dyoung@hdfgroup.org>
Date: Fri Nov 22 15:28:05 2019 -0600
It's hard to know just how wide an HDoff_t will be, and I don't think POSIX or
C standards provide a PRI macro for it, so cast to intmax_t and format using
PRIdMAX.
commit 86eab12df7a89b546a38e99f8178dd2adbcb3433
Author: David Young <dyoung@hdfgroup.org>
Date: Fri Nov 22 15:26:25 2019 -0600
URemove some casts.se the right format string for the argument. Here and there
stop casting a printf argument.
commit f722f7cbecbaa99449941484b014426f62f1bed5
Merge: 58e3743 6d5ec83
Author: David Young <dyoung@hdfgroup.org>
Date: Fri Nov 22 14:44:16 2019 -0600
Merge branch 'add-werror-and-squash-some' into fprintf-experiment
commit 58e3743b7faa9836606ee91798fe80dfc0040da7
Author: David Young <dyoung@hdfgroup.org>
Date: Wed Nov 20 21:07:21 2019 -0600
Remove custom HDfprintf implementation, using the standard library's,
instead. Take a swipe at repairing fprintf format strings, mainly
replacing "%Hu" with "%" PRIuHSIZE, "%a" with "%" PRIuHADDR, "%Zu" with
"%zu".
Here and there remove an awkward cast of a printf argument to `long
long` and use PRI[doux]8, PRI[doux]32, or PRI[doux]64, instead.
Change occurrences of "%t" to "%s" and perform a suitable change of
argument, `cond` -> `cond ? "TRUE" : "FALSE"`.
Some occurrences of %Hu, %a, and %t remain, they just weren't flagged by
the compiler because of #ifdef'age.
commit d4366909293fa970c23512ac80e5d865d76cddbf
Author: David Young <dyoung@hdfgroup.org>
Date: Wed Nov 20 20:54:32 2019 -0600
Promote format-string warnigns to errors.
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a do-while wrapper.
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the Autotools and CMake.
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of top file pointers.
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Description:
Applied the typo fixes from user's report.
The previous pull request couldn't be merged because it was too old,
and it was too complicated for me to resolve conflicts.
Platform tested:
Linux/64 (jelly) - very minor
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merge_func_enter_vol
Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
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Code changes to provide versioning support when adding to the enumerated defines for H5F_libver_t.
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hdf5_1_10
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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and correspondingly remove 'const' from some internal routines. Also rename
some H5MF* routines to reflect their static/package usage.
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Tested: ummon
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in r30264.
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where a block could
be unaligned, causing an assertion failure.
Tested: koala, ostrich, jelly (h5committest), ummon
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