summaryrefslogtreecommitdiffstats
path: root/configure.ac
Commit message (Collapse)AuthorAgeFilesLines
* Remove Autotools sed hack (#3848)Dana Robinson2023-11-131-6/+0
| | | | | | | | | | configure.ac contains a sed line that cleans up incorrect library flags which was added to paper over some bugs in earlier versions of the Autotools. These issues are not a problem with the current versions of the Autootols. The sed line causes problems on MacOS, so it has been removed. Fixes #3843
* Renamed h5fuse.sh to h5fuse (#3834)Scot Breitenfeld2023-11-071-2/+2
| | | * provide an alternative to mapfile for older bash
* Add an option to disable doxygen warn as error (#3708)Allen Byrne2023-10-191-0/+25
| | | | | | | | | | | | Add for both CMake and the Autotools * HDF5_ENABLE_DOXY_WARNINGS: ON/OFF (Default: ON) * --enable-doxygen-errors: enable/disable (Default: enable) The default will fail compile if the doxygen parsing generates warnings. The option can be disabled if certain versions of doxygen have parsing issues. i.e. 1.9.5, 1.9.8. Fixes #3398
* Add support for AOCC & Flang w/ the Autotools (#3674)Dana Robinson2023-10-151-3/+6
| | | | | | | | | | | | | * Adds a config/clang-fflags options file to support Flang * Corrects missing "-Wl," from linker options in the libtool wrappers when using Flang, the MPI Fortran compiler wrappers, and building the shared library. This would often result in unrecognized options like -soname. * Enable -nomp w/ Flang to avoid linking to the OpenMPI library. CMake can build the parallel, shared library w/ Fortran using AOCC and Flang, so no changes were needed for that build system. Fixes GitHub issues #3439, #1588, #366, #280
* Drop MPI-2 support (#3643)Scot Breitenfeld2023-10-081-0/+14
|
* Removed the use of -commons linking option on Darwin (#3581)Scot Breitenfeld2023-09-251-8/+0
| | | | Removed the use of -commons linking option on Darwin as COMMON and EQUIVALENCE is no long used
* Adds link to h5fuse.sh in testpar for autotools (#3557)Scot Breitenfeld2023-09-221-0/+5
| | | | * Make the h5fuse.sh utility available to parallel subfiling tests so h5fuse testing is not skipped.
* Convert some H5MM calls to standard C equivalents (#2382)Dana Robinson2023-08-251-2/+2
| | | | | | | | | * 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
* Enable szip by default in Autotools (#3412)Dana Robinson2023-08-231-3/+8
| | | | | 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.
* Subfiling VFD source cleanup (#3241)jhendersonHDF2023-07-131-0/+17
| | | | | | | | | | | | | | | | * 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
* Remove checks for setsysinfo, which is unused (#3205)Dana Robinson2023-06-291-1/+1
| | | | * Autotools * CMake
* Revert long double checks (#3133)Dana Robinson2023-06-151-0/+173
| | | | | | | * Revert "Remove long double conversion work-arounds (#3097)" This reverts commit 1e1dac1dac58fa18f6b7788346d1ba7d3315b0f9. * Update comments to reflect newer systems
* Remove unused HD macros (#3120)Dana Robinson2023-06-141-2/+1
| | | | | | | | | * 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
* Remove H5detect and H5make_libsettings (#3104)Dana Robinson2023-06-131-5/+19
| | | | | | | | 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
* Remove long double conversion work-arounds (#3097)Dana Robinson2023-06-121-173/+0
| | | | | | | | | | | | | | | | | | | | | Several options and public symbols that were provided to paper over non-standard long double conversions between signed/unsigned long and long long values were removed from the Autotools and CMake. These were added twenty years ago, when C99 and 64-bit platforms were less common and are no longer needed. Autotools: --enable-dconv-accuracy CMake: HDF5_WANT_DATA_ACCURACY H5pubconf.h symbols: H5_WANT_DATA_ACCURACY H5_LDOUBLE_TO_LONG_SPECIAL H5_LONG_TO_LDOUBLE_SPECIAL H5_LDOUBLE_TO_LLONG_ACCURATE H5_LLONG_TO_LDOUBLE_CORRECT H5_DISABLE_SOME_LDOUBLE_CONV
* Make some changes to configure.ac to suppor MinGW (#3096)Dana Robinson2023-06-121-1/+6
| | | | | | | Adds some H5pubconf.h entries and cpp flags for building on MinGW using the Autotools. Also updates the Windows-related H5pubconf.h comments to be more accurate in CMake.
* Add cross-compile defaults to Autotools (#3095)Dana Robinson2023-06-101-8/+14
| | | | | Most instances of AC_RUN_IFELSE do not have an action set for cross-compiling, even though there is an obvious 'reasonable' value.
* Removes old header/library checks (#3078)Dana Robinson2023-06-071-2/+2
| | | | | | | | | | | | | In both CMake and the Autotools, remove checks for: * lstat * srandom In CMake, remove checks for: * string.h * strings.h * stdlib.h We assume these exist. Configure will always check for them (we don't add any special code to do this), but there's no reason to duplicate that nonsense in CMake.
* Remove most unused options which are defaulted #2998 (#3019)Allen Byrne2023-05-261-1/+1
| | | | | * Remove most unused options which are defaulted #2998 * Fix property list references
* Bump Autoconf version to 2.71 (#2944)Dana Robinson2023-05-121-1/+1
| | | Required for building with Intel's oneAPI
* chore(configure.ac): fix output message for enabling tools (#2684) (#2854)H. Joe Lee2023-04-291-1/+1
| | | Close #2684.
* Fix improper include of build directory (#2422, #2621) (#2667)jhendersonHDF2023-04-111-4/+2
|
* Fix new codespell issues (#2521)Mark Kittisopikul2023-03-081-1/+1
| | | | | * Fix new codespell issues * Have codespell ignore ./config/sanitizer/sanitizers.cmake
* Fix for Autotools --disable-deprecated-symbols (#2363)Dana Robinson2022-12-241-4/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | * Fix for Autotools --disable-deprecated-symbols When we added v116 as a valid option, we left the default as v114 so using --disable-deprecated-symbols leads configure to complain that you can't set a default API that was deprecated. The GitHub action didn't catch this because it explicitly specifies v116 This only affects develop w/ the Autotools when --disable-deprecated-symbols is requested. * Added v116 & default to the --with-default-api-version help string The Autotools --with-default-api-version help string was missing v116. This has been added, as well as a "default" target so the CI can catch version problems when we forget to update the defaults upon creating a new major version. The GitHub CI also now uses "default" as the target for the deprecated symbols build. * Fixes the 1.14 API GitHub CI threadsafe/build_mode This action still had the bug we fixed where we set the build mode and threadsafety using an array of size one instead of an object.
* HL GIF tools changes (#2360)Dana Robinson2022-12-241-32/+21
| | | | * Fixes the broken Autotools option * Removes the "build HL tools" option
* H5F_LIBVER_LATEST changes for move to 1.15 (#2288)Allen Byrne2022-12-211-2/+7
| | | | | | | | | | | | | | | * H5F_LIBVER_LATEST changes for move to 1.15 * Add new default api check * Format fixes * Fix default configure * fix lib version tests * Fix another version variable * Add 1.14 doc link
* Disable hl tools by default (#2313)Allen Byrne2022-12-171-0/+17
| | | | | | | | | | | * Disable hl tools by default * identify the tools * Only GIF tools are depecated * Add new option * Update autotools
* Simplify & fix check for szlib encoder (#2263)Ryan Schmidt2022-11-171-4/+1
| | | | | | | | | | Return the result rather than setting the exit code. "return" is a language keyword whereas "exit" is a function for which the <stdlib.h> header has to be included which it wasn't in this test, therefore the test would previously fail to identify that the encoder was enabled if "-Werror=implicit-function-declaration" was used, which it is by default with clang from Xcode 12 and later. Fixes #2262
* moved quad precision checks (#2252)Scot Breitenfeld2022-11-121-25/+25
| | | | | * Only check quad sizes if fortran is enabled * fixed if struct
* removed uninterpretable line (#2249)Scot Breitenfeld2022-11-111-1/+1
|
* Removes MPE instrumentation support. (#2245)Dana Robinson2022-11-091-64/+0
| | | | | | | | | | | * Removes MPE instrumentation support. The Autotools will no longer accept --with-mpe= and the logging commands have been removed from the FUNC_ENTER macros. CMake has never supported instrumenting for MPE. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes dmalloc support (#2239)Dana Robinson2022-11-091-77/+0
| | | | | | | | | | This has not been used to debug the library in a very long time. Most developers use valgrind, -fsanitize=address, or some other memory checker instead of this library. This removes: * dmalloc.h include from H5private.h * --with-dmalloc= Autotools configure option * HDF5_ENABLE_USING_DMALLOC CMake option
* Removes the memory allocation sanity checks feature (#2218)Dana Robinson2022-11-031-46/+0
| | | | | | | | | | | | | | | * Removes the memory allocation sanity checks feature * Committing clang-format changes * Removes zero size checks for H5MM_(c|m)alloc() * Explicitly return NULL when size == 0 in H5allocate_memory() * Committing clang-format changes * Format fix Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update copyright headers (#2184)Larry Knox2022-11-011-1/+0
| | | | | * 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.
* Update develop branch version to 1.13.4-1 (#2189)Larry Knox2022-10-261-1/+1
| | | | | | * Updated version to 1.13.4-1 after creating hdf5_1_13_3 branch for 1.13.3 release. Added new version to exceptions in lines 74-5 of src/H5.c
* Removed the file, func, line args in the _async APIs fpr doxygen (#2179)Scot Breitenfeld2022-10-251-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | * Removed the: file, func, line args in the _async APIs from the doxygen arguments. Documented H5ESclean. * format fixes * fixed DOXYGEN_PREDEFINED * Fixed the #ifdet logic for doxygen, added missing multi-dataset va_args * format fixes * Use H5_DOXYGEN instead of H5_DOXYGEN_FORTRAN * reordered multidataset declarations * alt. for H5Aclose_async and H5Acreate_async * made doxgyen API into seperate blocks * updated codespell * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Restructure ref manual presentation (#2123)Allen Byrne2022-09-271-2/+4
|
* Use case-insensitive comparison for headers fix #2100 (#2101)Frank Berghaus2022-09-211-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Use case-inseneitive comparison for headers HTTP headers should be case-insensitive. Use case-insensitive string comparisons when working with HTTP header responses to ensure compatibility. * Revert "Use case-inseneitive comparison for headers" This reverts commit a02f591723506b62b7208449be6eef7122120398 * Ignore case when searching HTTP header responses Looking up the Content-Length in the header returned by S3 storage endpoints should ignore case. To guarantee portability implement a function for case-insensitive string search, because it is non-standard. * Add an _ after H5 for the strcasestr implementation It is a private function and should sport that underscore. * Remove author comment from the doc comment * Use search function defined by system if available Check whether the system provides a function implementing case insensitive string searches. Only use the custom implementation if the system does not provide the functionality. * Add tests for case-insensitive search Basic tests: - Search for empty string - Search with exact match - Search with case-insensitive match - search with no match * Enforce clang-format style Some variable definitions in the th5_system tests did not conform to clang-format's expectations. Updated the offending lines. * Correct comment describing test case * Added some spaces to please clang-format * Ignore discarding const Ask the compiler to ignore discarding the const when retunring a match from H5_strcasestr Co-authored-by: Frank Berghaus <frank.berghaus@mpcdf.mpg.de>
* Subfiling VFD updates (#2106)jhendersonHDF2022-09-161-5/+27
|
* develop Merge doxygen from 1.12 branch (#2095)Allen Byrne2022-09-141-2/+4
|
* Corrects more Fortran warnings (#2059)Dana Robinson2022-08-231-0/+1
| | | | | | | | | * Moves -Wunused-dummy-arguments to the developer warnings since this generates a lot of spurious, unfixable noise due to things like callback wrappers * Changes the return cast in h5fget_fileno_c, fixes a comment, and comment on potential badness * Initializes a variable in tH5L_F03.F90 to quiet a 'maybe uninitialized' warning
* Removes ST from the list of debug packages (Autotools only) (#2045)Dana Robinson2022-08-221-2/+2
| | | | | | | | | | * Removes ST from the list of debug packages The ST package (ternary search trees) was removed from the library a while ago * Replaced B2 package I did some crude timing with and without the B2 debug code enabled and it doesn't seem to make much of a difference.
* Update version to 1.13.3-1 after creating hdf5_1_13_2 branch for 1.13.2 (#2004)Larry Knox2022-08-121-1/+1
| | | | release. Added new version to exceptions in line 75 of src/H5.c.
* Revert "Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for ↵Larry Knox2022-08-121-1/+1
| | | | | | | | release" This reverts commit c58558e872d529da6eda327183ca2d14cfa91b95. H5TEST-tcheck_version-release failed.
* Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for releaseLarry Knox2022-08-121-1/+1
| | | | of HDF5 1.13.2.
* Implement improved CMake fortran module folder from GH#1411 (#1922)Allen Byrne2022-07-261-0/+7
| | | | | | | | | * Implement improved CMake fortran module folder from GH#1411 * Update docs * Fix whitespace * Fix name case
* Subfiling VFD (#1883)jhendersonHDF2022-07-221-0/+67
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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>
* Removes workaround for platforms that lack C99 stuct initializers (#1842)Dana Robinson2022-07-011-15/+0
|
* Adds a -Werror debug Autotools test and updates build modes (#1833)Dana Robinson2022-06-301-0/+10
| | | | | | | | | | * 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
generated by cgit v0.12 at 2024-07-02 17:46:57 (GMT)