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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
of the University of Illinois", which is kept in the top-level COPYING file.
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* H5Oflush causes H5Fclose to trigger an assertion failure in metadata cache for parallel. This commit makes sure H5Oflush fails for parallel until this problem is solved in the future.
* Committing clang-format changes
* Changed the use of H5F_get_driver_id to H5F_HAS_FEATURE.
Co-authored-by: songyulu <songyulu@jelly.ad.hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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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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* Committing clang-format changes
* Brings the native VFD H5Fdelete() implementation from Bitbucket
Only brings the 'del' callbacks, not the 'open/close' scheme.
* Formatter changes
* Committing clang-format changes
* Fixes direct VFD callback name
* Removes UNUSED macro from family API call
* Adds barrier and rank 0 check to MPI-I/O VFD delete
* Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"
This reverts commit 909765f759d9d96e84f4b8b1cc14f7d2b3ac8143.
* Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete""
This reverts commit 9b04bef1157853fc79fcb8fcc3e8ba1371091702.
* Adds a second barrier after the delete in MPI-I/O VFD
* Only delete files in the core VFD when the backing store flag is set
* Fixes string issues in multi VFD
Also, h5test.c cleanup code now uses H5Fdelete().
* Formatted source
* Rework fapl checks for MPI-I/O VFD delete callback
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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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 - files not in src or test.
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H5F_get_access_plist (#342)
* Avoid freeing MPI_COMM_WORLD in H5_mpi_comm_free
* Copy MPI Comm and Info to new FAPL in H5F_get_access_plist
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* OESS-98 convert plugin option to FetchContent, add tests
* Fixes for pkcfg files because of plugin option
* OESS-98 fix tools test for plugins
* Keep doxygen comments under 100 chars long - format hint
* Whitespace
* HDFFV-11144 - Reclassify CMake messages
* HDFFV-11099/11100 added help text
* Reworked switch statement to compare string instead
* Fix typo
* Update CDash mode
* Correct name of threadsafe
* Correct option name
* Undo accidental commit
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
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* Add H5Fwait, H5Dwait, and other changes for async vol connector
* Revert temporary testing changes
* Add H5Fwait to header file
* Add H5VLreset_lib_state() routine.
* Correct VOL wrap context when retrieving library state for file open & create.
* Manage the API context's VOL connector state as part of the library state.
* Set the 'VOL connector property valid' flag when restoring the library state.
* Don't push new API context on stack when retrieving "current" one.
* Check for NULL VOL wrap context before decrementing refcount on it, when
freeing the API context state.
* Manage recount of underlying connector for VOL wrap context.
* Add H5TSmutex_acquire() and H5TSmutex_release() routines to acquire and
release the global lock on the HDF5 library.
* Update library with new functions related to library global lock
* Add asynchronous token API
* Add new lightweight FUNC_ENTER / LEAVE macros for helping to structure the
threadsafety (H5TS*) routines.
* Sync w/develop
* Initial event set code framework.
* Elaborate on the H5ES routines, starting to add API routines.
Update the "close ID" callbacks to allow asynchronous request tokens to be
passed in from an asynchronous close API call.
Refactor current asynchronous API routines (H5Fopen/H5Fclose and
H5Dread/H5Dread) to use event sets instead of directly working with request
tokens from the application.
Clean up a few other minor warnings & code style issues.
* Implement H5EScreate, H5ESget_count, and H5ESclose.
It should be possible to write a simple application that creates an event
set and uses it with H5Fopen_async, H5Dread_async, H5Dwrite_async, and
H5Fclose_async, then calls H5ESclose (which waits for all async events to
complete).
* Add source file for event set test.
* Refactor sync & async API routines to call common routine.
Move dataset API read / write routines to src/H5D.c, along with all the other
API routines.
Progress on "fake" async VOL connector, for testing.
* Modify async implementation to wrap async requests in a H5VL_object_t
struct so the VOL layer can find the connector when accessing the
request at a later point.
* Free the requests is H5ESclose. Remove comments implying that request
wait, notify, and cancel callbacks should free the request.
* Fix bug in error handling in H5Fclose.
* Fix bugs in async file routines. Rename H5VL_create_object_generic to
H5VL_create_object.
* Add explicit async version of H5Fcreate.
* Add more _async routines
* Correct typo for return value from H5Awrite changes
* Add H5EStest and H5ESwait routines
* Updated with API tracing info
* Fix NULL pointer dereference in H5ES__wait
* Add H5is_library_terminating() routine, so that VOL connectors can detect
when the library is shutting down.
* Fix typo
* Remove event from event set's linked list
* Move block of code so that vol_obj is valid
* Avoid setting properties in the DXPL when reseting the library state (and in
the test code).
* Refactor argument tracing to implement new capability for tracing arguments
of non-API routines, with the H5ARG_TRACE macro. This macro is updated
automatically with the bin/trace script that runs as part of the autogen.sh
process. Major changes were in src/H5trace.c and bin/trace, with the other
changes being cleanups to the argument lists, to improve their presentation
in the tracing output.
Also - added the "managed string" routines, which can dynamically allocate
strings, appending printf-formatted output to the string efficiently.
* Release memory for managed strings
* Fix printf() formats.
* More printf() format fixes.
* Add H5Eappend_stack routine and regression tests
* Clean up a few missed merge conflicts and update the error stacks.
* Remove unnecessary fork() operations and ten second sleep().
* Restore commented out attribute out, to better enable tracking down the previous failure
* Allow multiple H5ARG_TRACE macros within a routine to be updated
* Switch to using "new" H5ES_insert (which takes the arguments for the caller routine) for all event set operations. Renames H5ES_insert_new to H5ES_insert and removes the previous H5ES_insert.
* Merge "managed" string routines into "ref-counted" strings, and refactor code to use them.
* Add missing file.
* Add caller's name and arguments to event, for error reporting
* Refactor event set setup for "API common" internal routines
* Checkin async API routines for H5A* and H5G* modules as listed in ID-283.
Fix couple h5dump expected output files due to the changes.
* Add some of the error query routines needed for event sets.
* Refactor to make async setup / teardown and "common" routines cleaner
* (1) Add async APIs to H5L, H5F, and H5D modules
(2) Fix errors in previous checkins of async APIs in H5A and H5G modules
(3) h5dump expected output changes
* Enhance event info, for better error handling
* Change name of temporary vol_obj variable, to help reduce coding errors
* Fix oversight with vol_obj pointer
* Minor code cleanup
* Add missing \'valid\' flag for VOL wrapper context, when restoring the library\'s state
* Run source formatter
* Change H5TSmutex lock and release to include a lock count
* Update error reporting ideas
* Minor updates to improve sanity checking for retrieving / restoring library state
* Updated with feedback from h5py team members
* Refactor internal event set list and event handling, add implementation for H5ESget_err_info
* Change the VOL request subclass callbacks that switch from using "H5ES_status_t" to "H5VL_request_status_t", and also add a H5VL_request_status_t* parameter to the 'cancel' callback in the request subclass. Also more code quality cleanups to add iterator callbacks to internal event set routines.
* Update API tracing for new H5VL_request_status_t typedef
* Finish converting internal event set operations to use list iterator callbacks, instead of directly accessing the list structure
* Add H5VL_REQUEST_GET_ERR_STACK operation to request subclass, for retrieving a copy of the error stack for a failed asynchronous operation
* Remove 'canceled' event status from Java constants
* Be safer about releasing resources when inserting a newly opened/created object or file into an event set
* Remove H5EStest, add H5ES_WAIT_NONE for 0 timeout, and revise parameters to H5ESwait, to make it more "aggregate".
* Remove H5ES_STATUS_CANCELED from Java wrappers also
* (a) Add async APIs for H5O module as listed in jira issue ID-283.
(b) Remove verification of name parameter in async related routines for H55A and H5L modules
because it is checked in H5VL_setup* routine.
(c) Modify h5dump expected output due to the async changes.
* Corrections based on PR feedback.
* Further changes to make based on PR feedback.
* Fix missed merge marker, and reformatted line
* Clean up some warnings
* Correct level of indirection
* Relocate prototype (and doxygen info) for H5Aclose
* Change non-static function declarations to be static
* Ensure that H5TSpublic.h header gets installed (#129)
* Add 'wrapper' versions of async calls, to allow language wrappers and layers on top of HDF5 to pass in their application information.
* Switch H5Aexists\*_async and H5Lexists\*_async to use flag to return status, instead of return value. Make the corresponding changes through most of the v1 and v2 B-tree code. Clean up warnings in H5public.h and cmpd_dtransform.c.
* Add H5Iregister_future routine and tests.
* Correct return value for H5Lexists_async
* Add H5_DLL macro to public H5ES API routines
* Update supported -> flags parameter for introspect_query callback
* Remove my email address. Update passthrough VOL connector ID.
* Fix comment for post_open_api_common
* Remove unused non-blocking VOL connector
* Minor cleanup in async branch in preparation for merge to develop
* Update CMake and the Autotools to use the new pass-through VOL ID
* Fix for SWMR daily test failures (#160)
The H5I_register_using_existing_id() call did not initialize the future
ID callbacks, causing the library to segfault when it tried to
resolve those function pointers.
* Added selective async APIs (#150)
* Added selective async APIs
Description:
Added the following APIs:
H5Ropen_attr_async
H5Ropen_object_async
H5Ropen_region_async
H5Mcreate_async
H5Mopen_async
H5Mput_async
H5Mget_async
H5Mclose_async
H5Tcommit_async
H5Topen_async
H5Tcopy_async
H5Tclose_async
- Updated an expected output file to include a new internal function
in the error stack for the failure case.
* Updated async APIs per reviews, including removing async version of
H5Tcopy.
* Removed statements that were added by mistake in the previous commit.
* Fix compile issues in H5M and warnings elsewhere
* Reformat code
* Brings VOL_LIST changes from develop. (#163)
Co-authored-by: Houjun Tang <htang4@lbl.gov>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: vchoi-hdfgroup <55293060+vchoi-hdfgroup@users.noreply.github.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <derobins@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
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dataset read" tests into one test. The second test is dependent on the
file created by the first test, and will not pass when run by itself.
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Add test for HDFFV-10501 fix
Add release note for HDFFV-10501 fix
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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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in parallel,
with an alignment threshold set to be larger than the chunk size but smaller
than the size of the small data aggregator.
Tested: koala, ostrich (h5committest); jelly, ummon
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coll md functions.
- ifdef some code that don't need to be built in parallel
- more minor enhancements
tested on bb-8 with parallel and serial
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Tested on: jam w/ parallel and fortran
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MPI_COMM_SELF is destroyed.
- add tests for above.
- this is a fix for HDFFV-883.
tested h5committest
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read/write bug.
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Remove all traces of MPI-POSIX VFD and GPFS detection/code.
Remove remaining traces of stream VFD.
Remove testpar/t_posix_compliant test (it's not actually verifying anything).
Clean up H5D__mpio_opt_possible() further.
Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).
A few other small code cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
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Check in Mohamad's changes to support collective I/O on point selections,
along with some other minor cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
(h5committest forthcoming)
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Stop aliasing property to indicate internal collective metadata operations
with property to perform collective raw data operations from the application.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/paralllel
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HDFFV-8146 - Remove "multi-chunk IO without optimization" sub-feature from MPI I/O optimization for chunked dataset feature
Description:
The “multi-chunk IO without optimization” feature is removed and made the related xfer property (H5FD_MPIO_CHUNK_MULTI_IO) go directly to “multi-chunk-io” feature.
Also update/fix/cleanup testings (chunk collective IO and actual chunk opt mode) accordingly.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE), Windows (32-LE cmake), cmake (jam)
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Add encode/decode API routines for property lists: H5Pencode/H5Pdecode.
Tested on:
FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode
FreeBSD/64 8.2 (freedom) w/gcc4.6, w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (koala) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (ostrich) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (ember) w/Intel compilers, w/parallel, C++ & FORTRAN,
in production mode
Mac OS X/32 10.7.3 (amazon) in debug mode
Mac OS X/32 10.7.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.7.3 (amazon) w/parallel, in debug mode
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HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Added H5Pget_mpio_no_collective_cause() function that retrive reasons why the collective I/O was broken during Read/Write IO access.
Reasons to break collective I/O:
- SET_INDEPENDENT
- DATATYPE_CONVERSION
- DATA_TRANSFORMS
- MPIPOSIX
- NOT_SIMPLE_OR_SCALAR_DATASPACES (NULL Space)
- POINT_SELECTIONS
- NOT_CONTIGUOUS_OR_CHUNKED_DATASET (Compact or External-Storage)
- FILTERS
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
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Merge "file image" changes from feature branch back to trunk.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug
(h5committest upcoming)
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opened with the MPI-IO VFD
Add test cases for these two routines
Jira issue HDFFV-7961
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Check in "actual I/O mode" feature to trunk. Will merge back to 1.8 branch
after it bakes over the weekend.
Tested on:
FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode
FreeBSD/64 8.2 (freedom) w/gcc4.6, w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (koala) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (ember) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.8 (amazon) in debug mode
Mac OS X/32 10.6.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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The shape same tests ran too long. Break them into smaller subtests
so that they can finish sub-test in a shorter time. Easier to tell
which one sub-test is taking too much time and/or errors occur in
one fo the sub-tests.
This one breaks the contig_hyperslab_dr_pio_test() into 4 smaller
sub-tests.
Tested: h5committest
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John Mainzer fixed the bug and added a test which wrote file and flush a few
time; close the file then open it by serial and read simple structure. I
changed the test to two parallel running parts of ..._writer and ..._reader
and have the reader verify the file after every flush by the writer.
Tested: parallel in Jam and Amani.
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the failure
of the H5Ocache.c code to update its image of the on disk representation
of the object header on a call to the clear callback.
This wasn't an issue as long as all flushes of the object header were
made from the same process, but if an object header is modified, and
then flushed on one process and cleared on the rest, the changes were
not be reflected in the images of the on disk representation on all
processes where the object header was cleared rather than flushed.
If one of these processes did the next flush, the changes were lost in
the on disk representation.
Fixed this by causing all dirty messages and to be written to the copy
of the on disk image maintained by the object header code on both flush
and clear.
Also added associated test code in t_mdset.c.
Also checking in some cache debug code developed while chasing this bug.
Commit tested and tested (parallel) on phoenix.
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Bring "shape same" changes from LBL branch to trunk. These changes
allow shapes that are the same, but projected into dataspaces with different
ranks to be detected correctly, and also contains code to project a dataspace
into greater/lesser number of dimensions, so the I/O can proceed in a faster
way.
These changes also contain several bug fixes and _lots_ of code
cleanups to the MPI datatype creation code.
Many other misc. code cleanup are included as well...
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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that are multiples of the number of processors.
Tested on jam and abe.
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that are multiples of the number of processors.
Tested on jam and abe.
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Clean up a few remaining API compatibility issues in the H5E API for
parallel configurations
Tested on:
FreeBSD/64 6.2 (liberty) w/parallel
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1. In H5Dwrite and H5Dread, let the data buffer point to a fake address if the application passes
in an empty buffer. This is mainly for MPIO programs that some processes may not have any
data to write or read but still participate the I/O. This solution solves some MPI's problem
like the ChaMPIon on tungsten which doesn't support empty buffer.
2. The ChaMPIon on tungsten doesn't support complex derived MPI data type correctly and collective
I/O when some processes don't have any data to write or read correctly. Detect the compiler
"cmpicc" in the system-specific config file and set the variables for these two cases to false.
The PHDF5 library already has set up a way to switch collective chunked I/O to independent
under these two cases.
3. A bug fix - During the work of the optimization for compound data I/O, the case for switching
collective chunked I/O to independent I/O was leftout. Fixed it by adding I/O caching to it in
H5D_multi_chunk_collective_io in H5Dmpio.c.
Tested on tungsten, cobalt, and kagiso for parallel; on linew and smirom for serial.
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copyright notice.
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
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independent IO with file setview.
To activite this test,
add the command option -i.
For example, at IBM AIX, type "poe testphdf5 -i" will test the library with independent IO with file setview. It simply replaces all the collective IO tests with independent IO with file setview.
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Adding parallel tests for optional collective chunk APIs
Description:
Three new APIs
"H5Pset_dxpl_mpio_chunk_opt_ratio
H5Pset_dxpl_mpio_chunk_opt_num
H5Pset_dxpl_mpio_chunk_opt"
for optional optimization choices from users
have been added to the libraries.
This check-in adds six tests to verify the funcationality and correctedness
of these APIs.
These tests need to be verified with 3 or more processors and with MPI-IO driver only.
Solution:
Using H5Pinsert, H5Pget, H5Pset to verify that the library indeed goes into the branch we hope for.
Using H5_HAVE_INSTRUMENT macro to isolate these changes so that it won't affect or be misused by the application.
Platforms tested:
h5committest(shanti still refused to be connected)
Parallel tests on heping somehow are skipped. Manually testing at heping. Have checked
1,2,3,4,5 processes.
Misc. update:
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Add tests for optional APIs to support collective chunk IO
Description:
In order to test whether library picks up the user's options,
The number of chunks need to be varied for different processes,
Selection of the number of processes selected in one chunk also
need to be varied.
Solution:
Create two cases,
1. Each chunk only selected by one unique process, this case
library should use independent for collective call.
2. One-third of the processes occupies the top half of the whole domain,
The rest of the processes occupies the lower half of the domain.
The total number of chunk is a fixed number 8.
Platforms tested:
Linux 2.4 with mpich 1.2.6(only)
Since I only checked in the code that handles the selection, haven't added any new tests yet. So it won't affect any platforms.
Misc. update:
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change the array size of collective chunking features of parallel tests.
Description:
Previously array size for collective optimization tests
including
cchunk1,
cchunk2,
cchunk3,
cchunk4,
ccontw,
ccontr,
cschunkw,
cschunkr,
ccchunkw,
ccchunkr
are fixed,
They are only valid for some good number of processors(1,2,3,4,6,8,12,16,24,32,48 etc).
Recently there are more requests for parallel tests to be valid on some odd number of processes such as 5,7,11,13 etc.
Solution:
I change the array size to be dynamic rather than static. Now the fastest change array size is a function of mpi_size. dim2 = constant *mpi_size. After some tunings, theoretically the above tests should be valid for any number of processors. However, other parallel tests still need to be tuned.
To verify the correctness of these tests, using mpirun -np 5 ./testphdf5 -b cchunk1 at heping.
Platforms tested:
h5committest(shanti is refused to be connected)
at heping, 5 and 7 processes are used to verify the correctness.
Misc. update:
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