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* Persist dataset access properties when using H5Fstart_swmr_write (#1862)Neil Fortner2022-07-194-31/+122
| | | | | | | | | | | | | * Fix HDFFV-11308 - dataset access properties disappear when using H5Fstart_swmr_write. * Committing clang-format changes * Add test for H5Fstart_swmr_write() persisting DAPL settings. Fix bugs in the library exposed by this test. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix some hard-coded MPI I/O VFD checks (#1898)jhendersonHDF2022-07-182-4/+16
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* H5Oflush fails for parallel (#1876)raylu-hdf2022-07-124-0/+20
| | | | | | | | | | * 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>
* 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>
* 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>
* Misc clang warning fixes (#1869)Dana Robinson2022-07-113-4/+15
| | | | | | | | | | | | | | | | | * 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 Robinson2022-07-115-15/+28
| | | | | | | | | | | | * 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>
* Adds the malloc attribute to appropriate functions (gcc only) (#1866)Dana Robinson2022-07-113-55/+71
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* Convert assertion on (possibly corrupt) file contents to normal error check ↵jhendersonHDF2022-07-081-1/+3
| | | | | | | | | (#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.
* 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
* Fix invalid comment about character encoding in H5Fint.c (#1845)jhendersonHDF2022-07-011-2/+5
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* Removes workaround for platforms that lack C99 stuct initializers (#1842)Dana Robinson2022-07-011-133/+0
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* Fix for gcc-12 warning about string truncation in H5Opline.c (#1835)Dana Robinson2022-06-301-6/+10
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* Fixes a few minor parallel warnings (#1832)Dana Robinson2022-06-291-1/+16
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* Quiets const warnings (#1831)Dana Robinson2022-06-2914-40/+50
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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
* Set a constant in H5SM to UINT_MAX instead of -1U (#1822)Dana Robinson2022-06-231-1/+1
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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 McBride2022-06-225-24/+25
| | | | | | | | | | | * 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 McBride2022-06-2215-55/+56
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Fix bugs in parallel selection I/O (#1803)Neil Fortner2022-06-091-40/+44
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* Add a workaround for buggy PGI C Compiler version 19.10, which quits (#1705)David Young2022-05-081-4/+15
| | | | with the unhelpful and misleading error message `PGC-S-0053-Illegal use of void type` when I put a `static` qualifier on my tables.
* Re-promote some GNU warnings to errors (#1508)David Young2022-05-061-8/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Promote some GCC warnings back to errors and deal with build breakage. I tested configuring and building with GCC 8.3.0 with `.../configure --prefix=$HOME/wrk/install/manydsets --enable-build-mode=production --enable-symbols=-gdwarf-4 --enable-warnings-as-errors --enable-java --enable-hl --enable-fortran --enable-cxx --enable-mirror-vfd --enable-ros3-vfd --enable-direct-vfd` and with the same options but `--enable-build-mode=debug`. * Promote -Wrestrict to -Werror=restrict to help catch overlapping arguments to strcpy, memcpy, et cetera, at compile time. * NFCI: sort lines. * Committing clang-format changes * NFCI: remove whitespace at EOL. * Re-use temporary variable `shared`. * Remove merge oopsie. * Mention that no op codes are understood per review comment. * Change this back to the develop branch's way, since this change isn't integral to the PR. * Committing clang-format changes * NFCI: reduce differences with `develop` branch in the hope that that also kicks off CI. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Fix a few Clang sanitizer warnings (#1727)jhendersonHDF2022-05-052-12/+23
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* Fix some const cast and stack/static object size warnings (#1700)jhendersonHDF2022-05-0110-61/+94
| | | | | | | | | * Fix various warnings * Move HDfree_const to H5private.h for wider use * Print output from all ranks in parallel tests on allocation failure * Move const pointer freeing macro to h5test.h for now
* Fix SWMR/refresh bug hidden by library free lists (#1702)jhendersonHDF2022-04-301-4/+10
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* Be a bit safer with signed arithmetic, thus quieting some signed-overflow ↵David Young2022-04-303-22/+25
| | | | | | | | | | | | | | | | | | | | | | | warnings from GCC (#1706) * Avoid a signed overflow: check the range of `entry_ptr->age` before increasing it instead of increasing it and then checking the range. This quiets a GCC warning. * Avoid the potential for signed overflow by rewriting expressions `MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`. This change quiets some GCC warnings. * Change some local variables that cannot take sensible negative values from signed to unsigned. This quiets GCC warnings about potential signed overflow. * In a handful of instances, check the range of a signed integer before increasing/decreasing it, just in case the increase/decrease overflows. This quiets a handful of GCC signed-overflow warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Address some warnings from casting away of const (#1684)jhendersonHDF2022-04-2616-121/+97
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* Minor things noticed while bringing VFD SWMR in line with develop (#1691)Dana Robinson2022-04-254-13/+12
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* Warnings fixes (#1680)jhendersonHDF2022-04-2510-28/+33
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* Replace H5detect's build-time detection of C99 integer properties with a (#1400)David Young2022-04-224-718/+398
| | | | | | | * Replace H5detect's build-time detection of C99 integer properties with a table-driven routine, `H5T__init_native_int()`, that is run at library initialization time.
* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)David Young2022-04-161-74/+20
| | | | | | | | | | | | | | | | | * Do not conditionally compile code that uses a pointer dereference and assignment to copy a potentially unaligned variable to aligned automatic storage, or vice versa. Instead, always use naked `memcpy(3)`s. Disassembling the generated code reveals that the `memcpy(3)`s optimize (`-O3`) to a single `mov` instruction for x86_64, which is not strict about alignment. This change reduces the size of code and scripts by 143 lines, eases our way to cross-compilation, and avoids invoking undefined behavior. * Committing clang-format changes * Per discussion, use HD and add comments. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1376)H. Joe Lee2022-04-152-3/+3
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* Retrieve MPI-IO hints used by MPI library after file open (#1636)Wei-keng Liao2022-04-151-0/+49
| | | | | | H5Pget_fapl_mpio() should return an MPI info object containing all the MPI-IO hints used by the MPI library underneath, after the file is opened. Some hints, such as cb_nodes (number of I/O aggregators), are useful for HDF5 applications and I/O libraries built on top of HDF5.
* Fixes a typo in H5.c (#1639)Dana Robinson2022-04-141-1/+1
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* Fix these Doxygen warnings #1581 (#1589)Allen Byrne2022-04-133-11/+10
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* Removes unused definitions from module headers (#1624)Dana Robinson2022-04-1138-115/+76
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* Removes the STATIC flavor of FUNC_ENTER macros (#1622)Dana Robinson2022-04-08221-2213/+2188
| | | | | * Removes the STATIC flavor of FUNC_ENTER macros
* Minor things discovered while preparing 1.12.2 (#1620)Dana Robinson2022-04-081-2/+2
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* Fix for unexported global variable on Windows (#1568)Dana Robinson2022-04-011-2/+5
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* spelling fixes (#1561)Scot Breitenfeld2022-03-314-4/+4
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* Add H5_CHECK_MPI_VERSION macro to check for at least MPI version of ↵jhendersonHDF2022-03-306-18/+27
| | | | | | | | | (version, subversion) (#1556) * Fix MPI version check for MPI_Aint_diff usage * Add H5_CHECK_MPI_VERSION macro Adds new H5_CHECK_MPI_VERSION macro to check for MPI library version/subversion pair of at least the specified pair
* Add missing H5FL_TRACK debug parameters to free list array routines (#1555)jhendersonHDF2022-03-301-6/+12
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* Minor comment corrections (#1544)Allen Byrne2022-03-303-15/+13
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* Removes unused H5HP (private heap) package (#1548)Dana Robinson2022-03-304-984/+0
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* Removes unused memory pool (H5MP) package (#1547)Dana Robinson2022-03-307-861/+1
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