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* Remove superfluous dot from hl doxygen. (#1891)vchoi-hdfgroup2022-07-147-17/+13
| | | Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
* Eliminate unnecessary error output (#1879)Allen Byrne2022-07-142-17/+20
| | | | | | | * Eliminate unnecessary error output * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for a tools compile issue when deprecated symbols are disabled (#1884)Dana Robinson2022-07-132-14/+30
| | | | | | | | | | | | | * Fix for a tools compile issue when deprecated symbols are disabled Introduced in #1811, also uses VOL token instead of addr * Fix for similar compile issues in java when deprecated symbols are disabled. * Committing clang-format changes Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* H5Oflush fails for parallel (#1876)raylu-hdf2022-07-129-1/+142
| | | | | | | | | | * 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>
* Moves -Wstrict-overflow=5 to the developer warnings (#1878)Dana Robinson2022-07-126-8/+18
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* Removes definitions for (U)LLONG_MAX and (S)SIZET_MAX (#1877)Dana Robinson2022-07-115-28/+21
| | | | | | | LLONG_MAX and ULLONG_MAX are defined in limits.h in C99. SIZET_MAX should be SIZE_MAX, which has been around forever. SSIZET_MAX should be SSIZE_MAX, which is defined whereever ssize_t is found. I've kept the definition for SSIZE_MAX (renamed from SSIZET_MAX) for platforms where ssize_T is not present (e.g., Windows).
* Fixes for warnings identified by MSVC (#1874)Dana Robinson2022-07-112-13/+10
| | | | | | | | | * Fixes for warnings identified by MSVC * Committing clang-format changes * Moves the casts in H5Binternal.c to the other side Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop HDFFV-11310 (#1811)Allen Byrne2022-07-1120-568/+2706
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Rework java vl check in read/write. Handle old refs in h5dump * Committing clang-format changes * Java changes allow default VL reads * Fix JNI utility for old refs * HDFFV-11310 - implement vlen read/write for atomic types. * format check fix * Mostly format fixes * More format issues * Two format changes * Use JNI names for sizeof * format change * fix size typo * Change to older method to initialize list * remove unused var * format fix * switch writeVL functions to use datatype instead of java type * Add VL option to generic read/write check * Correct function name typo * Add JIRA issue * Correct note to match change in code. * HDFFV-11318 add VL references as byte arrays * Add release note and format changes * Another format update * Fix unreleased allocations * Fix format * format correction Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Support for UnifyFS with MPI_File_sync (#1801)Houjun Tang2022-07-1110-11/+172
| | | | | | | | | | | | | | | | | | | | | | | | | * Initial implementation for supporting UnifyFS in HDF5 with MPI_File_sync after write * Committing clang-format changes * Fix format * Fix env variable and return value check * Fix flag retrieve * Fix issues with getting/setting the flag * Fix merge conflicts * Update * Committing clang-format changes * Update based on suggestions * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Reduce -Wstrict-overflow= from 5 to 2 (#1872)Dana Robinson2022-07-112-2/+2
| | | | The signal-to-noise ratio of the higher warning level is very low and the noise obscures things we should fix
* Misc clang warning fixes (#1869)Dana Robinson2022-07-1119-904/+741
| | | | | | | | | | | | | | | | | * Minor clang warning fixes in src and test * Fixes clang warnings in high-level library * clang format-nonliteral warning fixes * Committing clang-format changes * Fixed int -> float clang cast warnings in h5diff * Quiets some warnings in flex/bison generated code * Suppress overlong string warning for libinfo on clang Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes for production mode gcc warnings (#1873)Dana Robinson2022-07-118-38/+75
| | | | | | | | | | | | * Fixes for production mode gcc warnings With the strict-overflow changes, this brings the number of warnings in the C library w/ gcc 12 to zero. * Fix typo * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes C++ sign-conversion warnings w/ clang 14 (#1870)Dana Robinson2022-07-1115-59/+108
| | | | | | | * Fixes sign-conversion warnings w/ clang 14 * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adds the mirror and direct VFDs to GitHub actions (#1871)Dana Robinson2022-07-112-6/+54
| | | Both Autotools and CMake
* Adds format attribute to additional functions (#1868)Dana Robinson2022-07-114-9/+9
| | | | | | | | | * Adds format attribute to (s|p)io_perf code * Added gcc format attribute to additional test code * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adds explicit indices to drivernames array in the tools (#1867)Dana Robinson2022-07-111-1/+4
| | | Will help keep the drivernames and driver_idx enum in sync.
* Adds the malloc attribute to appropriate functions (gcc only) (#1866)Dana Robinson2022-07-113-55/+71
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* Updates the patterns in Doxyfile.in to accept H5*develop.h (#1865)Dana Robinson2022-07-111-3/+1
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* Merge pull request #1857 from gheber/fix-doxy-warnings-and-cosmeticsGerd Heber2022-07-094-91/+82
|\ | | | | Fix Doxygen warnings and cosmetics
| * Resolve Allen's comment.Gerd Heber2022-07-081-1/+1
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| * Fix Doxygen warningsGerd Heber2022-07-083-84/+75
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| * Cosmetic changes to RM frontGerd Heber2022-07-081-7/+7
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* | Convert assertion on (possibly corrupt) file contents to normal error check ↵jhendersonHDF2022-07-082-2/+13
| | | | | | | | | | | | | | | | | | (#1861) * Convert assertion on (possibly corrupt) file contents to normal error check * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* | Fix for memory allocation issue identified by fuzzer (#732) (#1860)Dana Robinson2022-07-081-1/+1
| | | | | | | | | | | | | | GitHub issue #732 claims that mallocing a particular buffer can trigger undefined behavior and that callocing the buffer fixes the issue. I did not confirm this, but the fix is trivial and better anyway.
* | Updated vfd swmr and reference rfcs (#1854)Gerd Heber2022-07-072-2/+4
|/ | | | | * Add PDFs * Update RFC table
* Suppress the "obsolete" category of Autoconf warnings (#1853)Dana Robinson2022-07-061-1/+4
| | | | | Very new versions of Autoconf complain about our Java macros. Since they work well enough and there is no obvious upgrade path, we're suppressing the category for now.
* Updates messages in cache sanity checks (#1851)Dana Robinson2022-07-061-23/+23
| | | | Previous messages were numbered, which was a maintenance burden, and non-specific
* Minor tweaks to the test_swmr.sh script (#1852)Dana Robinson2022-07-061-10/+7
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* Update Doxyfile.in (#1849)Gerd Heber2022-07-061-0/+1
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* Fix invalid comment about character encoding in H5Fint.c (#1845)jhendersonHDF2022-07-011-2/+5
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* Fixes a bug in h5perf that causes file open failures (#1846)Dana Robinson2022-07-012-2/+2
| | | | | | When the filename was flipped from being a static array to being dynamically allocated, the sizeof(filename) call wasn't updated. This always returns the size of the pointer, truncating the filename.
* Add doxygen for high level modules. (#1839)vchoi-hdfgroup2022-07-0114-10/+4480
| | | | | | | | | | | | * Add doxygen for high level modules. * Committing clang-format changes * Correct spelling based on spelling check. * Committing clang-format changes Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes workaround for platforms that lack C99 stuct initializers (#1842)Dana Robinson2022-07-015-185/+0
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* Adds a -Werror debug Autotools test and updates build modes (#1833)Dana Robinson2022-06-303-4/+64
| | | | | | | | | | * Adds a -Werror debug Autotools test and updates build modes * Un-excludes the workflow files * Strip out -Werror from CFLAGS when running configure tests This causes spurious test failures when the configuration test programs raise warnings.
* Minor configure comment tweaks from autoupdate (#1838)Dana Robinson2022-06-301-2/+2
| | | | The autoupdate script identified some cruft that was unchanged in the comments
* Fix for gcc-12 warning about string truncation in H5Opline.c (#1835)Dana Robinson2022-06-301-6/+10
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* Updates the MinGW configure.ac check for the Winsock library (#1837)Dana Robinson2022-06-301-1/+2
| | | | | | | Ubuntu 22.04 complains about AC_HAVE_LIBRARY being deprecated. This updates the macro to AC_CHECK_LIB, where the specified function is GetUserName(). This change only affects MinGW
* Set Autotools build mode correctly in GitHub workflows (#1834)Dana Robinson2022-06-302-30/+54
| | | | | * Sets build mode correctly w/ Autotools * Updates GitHub gcc and installs OpenMPI
* Fixes a few minor parallel warnings (#1832)Dana Robinson2022-06-294-14/+37
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* remove superfluous initialization, fixes issue with Cray compiler (Crusher) ↵Scot Breitenfeld2022-06-291-1/+0
| | | | (#1828)
* Quiets const warnings (#1831)Dana Robinson2022-06-2915-40/+52
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* Documents Windows badness in H5Pget_external() (#1821)Dana Robinson2022-06-242-1/+13
| | | | | * Documents Windows badness in H5Pget_external() * Added a cast for off_t
* Converts testhdf5 macros to h5test macros in chunk_info.c (#1820)Dana Robinson2022-06-231-30/+66
| | | | The two macro schemes were not designed to work together. Also quiets some MSVC warnings about comparing pointers and integers.
* Set a constant in H5SM to UINT_MAX instead of -1U (#1822)Dana Robinson2022-06-231-1/+1
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* Work-around for MSVC issue with flex-generated code (#1823)Dana Robinson2022-06-234-479/+595
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* Quiets size warning in large library setting string (#1818)Dana Robinson2022-06-221-28/+39
| | | | | | | | | | * Quiets size warning in large library setting string If the size of this string is a problem, people can build with the embedded library info disabled. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* sprintf to snprintf (#1815)Sean McBride2022-06-2243-331/+376
| | | | | | | | | | | * 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>
* Adds notes about off_t sizes on Windows (#1817)Dana Robinson2022-06-221-1/+9
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* Converts __int64 to LONGLONG in LARGE_INTEGER union members on Windows (#1816)Dana Robinson2022-06-224-4/+4
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* Various warning fixes (#1812)Sean McBride2022-06-2237-304/+143
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fixed -Wreserved-id-macro warnings from header include guards * Removed all __int64 and LL suffix stuff now that C99 is minimum requirement * Rename `H5FD_CTL__` to `H5FD_CTL_` to fix -Wreserved-id-macro warnings Double underscore is reserved in C++ and this public header should be C++ compatible. * Never define __STDC_FORMAT_MACROS anymore Defining it causes a -Wreserved-id-macro. Happily, according to the C++11 standard: "The macros defined by <stdint> are provided unconditionally. In particular, the symbols __STDC_LIMIT_MACROS and __STDC_CONSTANT_MACROS (mentioned in C99 footnotes 219, 220, and 222) play no role in C++." https://cplusplus.github.io/LWG/issue984 So looks like it's not necessary to define it with reasonably new toolchains. * Fixed some -Wunused-macros warnings, removed dead code * Fixed all -Wdouble-promotion warnings in C++ files * Fixed remaining -Wsuggest-destructor-override warnings * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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