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* Update README.mdarchitecture_docsGerd Heber2023-02-281-1/+1
| | | Link purpose, etc. section
* Update purpose_objectives_values.mdGerd Heber2023-02-281-1/+1
| | | Fixed image reference.
* Create purpose_objectives_values.mdGerd Heber2023-02-281-0/+78
| | | First cut of Purpose, Objectives, & Values.
* Create README.mdGerd Heber2023-02-281-0/+90
| | | Outline
* Add a BRANCH.md file and placeholder document in doc/archDana Robinson2023-01-262-0/+9
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* CMake: Find MPI in HDF5 CMake config (#2400)kwryankrattiger2023-01-181-0/+2
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* Port VOL connector Guide to doxygen (#2333)Allen Byrne2023-01-183-2/+4916
| | | | | | | * Port VOL connector Guide to doxygen * Fix spelling * Updated VOL UG ref and added release note
* Include shlwapi.h explicitly on Windows (#2407)Mark Kittisopikul2023-01-172-4/+3
| | | | | | | | * Include shlwapi.h explicitly * Add shlwapi library to LINK_LIB when header is detected Looking for StrStrIA in the shlwapi library is not reliable due to stdcall on mingw32.
* HDFFV-11208 (OESS-320): H5VLquery_optional had an assertion failure with a ↵raylu-hdf2023-01-101-0/+80
| | | | | | | | | | | | | | | committed datatype (#2398) * HDFFV-11208 (OESS-320): H5VLquery_optional had an assertion failure with a committed datatype. Added a test case for the fix that Quincey checked in. * Committing clang-format changes * Fixed a typo in a comment. * Fixed a typo in a comment. * Minor change: changed H5Tcommit to H5Tcommit2. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Pass-through connector testing flexibility (#2399)Quincey Koziol2023-01-092-8/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. * Play nice with existing plugin paths * Use API routine to determine if native connector is terminal. * Committing clang-format changes * Make string size larger, to allow for connectors with longer names. * Be more flexible about testing external pass through connectors, especially if they have registered new optional operations. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Determine if native connector is terminal (#2397)Quincey Koziol2023-01-092-8/+12
| | | | | | | | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. * Play nice with existing plugin paths * Use API routine to determine if native connector is terminal. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Play nice with existing plugin paths (#2394)Quincey Koziol2023-01-065-5/+5
| | | | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. * Play nice with existing plugin paths Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Update FORTRAN VOL connector test for external pass-through testing (#2393)Quincey Koziol2023-01-053-2/+6
| | | | | | | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. * Parse connector name from HDF5_PLUGIN_PATH environment variable better * Correct H5VLquery_optional to use H5VL routine instead of H5I. Also add an error message to the failure return value from not finding a plugin. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Updates README.md (#2387)Dana Robinson2023-01-043-25/+26
| | | | | | | | | | | | | | | | | | | * Updates release schedule for 2023 * Fixes broken build badge * Another build badge tweak * Even more badge tweaking * More branch tweaking * More badge tweaking * More badge tweaks * Even more badge tweaking * Adds badges for other branches
* Correct VOL connector env string parsing issue (#2350)Quincey Koziol2023-01-041-1/+1
| | | | | | | | | | | | * Correct concurrency bugs when running tests, along with a bugfix & small warning cleanup. * Committing clang-format changes * Allow spaces (and tabs) in VOL connector info string from environment variable. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: AWS ParallelCluster user <ec2-user@ip-10-0-0-65.us-east-2.compute.internal> Co-authored-by: Koziol <qkoziol@88665a374c70.ant.amazon.com>
* Adds -Warray-temporaries to the developer warnings (#2385)Dana Robinson2023-01-035-1/+13
| | | | These generate a LOT of noise that we are not going to address anytime soon.
* Adds 'make install' and 'make check-install' to the CI (Autotools only) (#2381)Dana Robinson2023-01-031-0/+14
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* Adds RELEASE.txt notes and updates Doxygen (#2377) (#2379)Dana Robinson2022-12-293-8/+42
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* Adds Doxygen markup for H5FDdriver_query() (#2376)Dana Robinson2022-12-282-4/+23
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* Restore line 264 of main.yml: "thread_safety:" (#2374)Larry Knox2022-12-281-0/+1
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* Purged references to HDF5 1.13.x from the Doxygen documentation (#2365)Dana Robinson2022-12-2710-38/+30
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* Adds missing Doxygen for H5ESpublic.h (#2364)Dana Robinson2022-12-271-16/+77
| | | | | | | * Adds missing Doxygen for H5ESpublic.h * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix for Autotools --disable-deprecated-symbols (#2363)Dana Robinson2022-12-242-11/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Robinson2022-12-247-56/+32
| | | | * Fixes the broken Autotools option * Removes the "build HL tools" option
* Update testh5cc.sh.in for new major version 1.14. (#2349)Larry Knox2022-12-222-9/+59
| | | | | * Update testh5cc.sh.in for new major version 1.14. * iFix sha256sum commands in release script.
* Adds Doxygen VOL flag markup (#2340)Dana Robinson2022-12-211-55/+63
| | | | | | | | | | | * Initial doxygen markup * Committing clang-format changes * Adds Doxygen comments to VOL flags * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Onion VFD header cleanup (#2337)Dana Robinson2022-12-213-112/+85
| | | | | | | | | * Partial work towards cleaning up the onion VFD code * Committing clang-format changes * A few minor tweaks to the onion VFD public header Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* H5F_LIBVER_LATEST changes for move to 1.15 (#2288)Allen Byrne2022-12-2137-43/+132
| | | | | | | | | | | | | | | * 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
* Fix up the H5Pencode2 test for virtual layout. (#2325)vchoi-hdfgroup2022-12-211-91/+87
| | | | | | | | | | * Fix up the H5Pencode2 test for virtual layout. * Committing clang-format changes * Remove VERIFY and use TEST_ERROR. Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix doxygen warnings and remove javadocs (#2324)Allen Byrne2022-12-2016-63/+28
| | | | | * Fix doxygen warnings and remove javadocs * fix typo
* Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info (#2074)Mark Kittisopikul2022-12-194-20/+20
| | | | | | | * Align arg types of H5D_chunk_iter_op_t with H5Dget_chunk_info * Modify chunk_info test to for unsigned / hsize_t types * Fix types in test
* Removed idioms and misc. text clean-up (#2320)Scot Breitenfeld2022-12-171-9/+4
| | | | | * removed idioms and misc. text clean-up, Issue #2135 * removed idioms and misc. text clean-up, Issue #2135
* Disable hl tools by default (#2313)Allen Byrne2022-12-175-6/+48
| | | | | | | | | | | * Disable hl tools by default * identify the tools * Only GIF tools are depecated * Add new option * Update autotools
* Only document Fortran functions (#2319)Scot Breitenfeld2022-12-171-1/+9
| | | | | | | | | * Only document Fortran functions * Only document Fortran functions * Only document Fortran functions * Only document Fortran functions
* moved onion VFD to FAPL group (#2321)Scot Breitenfeld2022-12-171-4/+4
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* Hdffv 11052 (#2315)vchoi-hdfgroup2022-12-161-3/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump. When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value" all the way till the end of the routine. The user-provided corrupted file has an illegal file size causing failure when reading the image during the closing process. At the end of this routine it sets f->shared to NULL and then frees "f". This is done whether there is error or not in "ret_value". Due to the failure in reading the file earlier, the routine then returns error. The error return from H5F__dest() causes the file object "f" not being removed from the ID node table. When the library finally exits, it will try to close the file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f). Fix: a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine. b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before. c) h5debug.c main(): track error return from H5Fclose(). * Committing clang-format changes * Add test and release note info for fix to HDFFV-11052 which is merged via PR#2291. * Committing clang-format changes * Add the test file to Cmake. * Skip test_misc37() for drivers that is not default compatible as it is using a pre-generated file. * 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 duplicated build mode from -Werror GitHub actions (#2314)Dana Robinson2022-12-161-2/+2
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* Converts the YAML build mode arrays to objects in special runs (#2308)Dana Robinson2022-12-161-37/+41
| | | | | | | | | | | | | * Converts the YAML build mode arrays to objects in special runs * Adds a dump of the matrix context for each test This would have made it a LOT easier to debug the build_mode issues... * Disable the mirror VFD in the -Werror checks We can re-enable this after we fix the warnings, but I don't want to conflate code and GitHub changes, so this is a better way to get the CI to pass for now.
* Merge pull request #2304 from gheber/developGerd Heber2022-12-151-1/+1
|\ | | | | Update hdf5_header.html
| * Update hdf5_header.htmlGerd Heber2022-12-151-1/+1
|/ | | Use less awkward language.
* Hdffv 11052 (#2303)vchoi-hdfgroup2022-12-154-0/+59
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump. When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value" all the way till the end of the routine. The user-provided corrupted file has an illegal file size causing failure when reading the image during the closing process. At the end of this routine it sets f->shared to NULL and then frees "f". This is done whether there is error or not in "ret_value". Due to the failure in reading the file earlier, the routine then returns error. The error return from H5F__dest() causes the file object "f" not being removed from the ID node table. When the library finally exits, it will try to close the file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f). Fix: a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine. b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before. c) h5debug.c main(): track error return from H5Fclose(). * Committing clang-format changes * Add test and release note info for fix to HDFFV-11052 which is merged via PR#2291. * Committing clang-format changes * Add the test file to Cmake. Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixes broken CI matrix actions involving -Werror and API versions (#2302)Dana Robinson2022-12-151-7/+7
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* Adds 'unused' hints for MDS io_info parameters (#2301)Dana Robinson2022-12-143-18/+17
| | | | | | | | | | | | | | | * Adds 'unused' hints for MDS io_info parameters * Committing clang-format changes * Fix issue with formatter * Committing clang-format changes * Final fix for formatter * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* added doc. warning for H5Literate_async return value (#2295)Scot Breitenfeld2022-12-141-0/+5
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* Update windows worker compilers (#2286)Allen Byrne2022-12-144-20/+23
| | | | | | | * Update windows worker compilers * Update bin and test issues * Update script and revert java test
* Updated H5ES documenation (#2293)Scot Breitenfeld2022-12-131-5/+5
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* Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC)… (#2291)vchoi-hdfgroup2022-12-133-26/+38
| | | | | | | | | | | | | | | | | | | | | | * Fix for HDFFV-11052: h5debug fails on a corrupted file (h5_nrefs_POC) producing a core dump. When h5debug closes the corrupted file, the library calls H5F__dest() which performs all the closing operations for the file "f" (H5F_t *) but just keeping note of errors in "ret_value" all the way till the end of the routine. The user-provided corrupted file has an illegal file size causing failure when reading the image during the closing process. At the end of this routine it sets f->shared to NULL and then frees "f". This is done whether there is error or not in "ret_value". Due to the failure in reading the file earlier, the routine then returns error. The error return from H5F__dest() causes the file object "f" not being removed from the ID node table. When the library finally exits, it will try to close the file objects in the table. This causes assert failure when H5F_ID_EXISTS(f) or H5F_NREFS(f). Fix: a) H5F_dest(): free the f only when there is no error in "ret_value" at the end of the routine. b) H5VL__native_file_close(): if f->shared is NULL, free "f"; otherwise, perform closing on "f" as before. c) h5debug.c main(): track error return from H5Fclose(). * 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>
* added doc. warning for H5Oflush in parallel (#2289)Scot Breitenfeld2022-12-101-0/+3
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* fixed unclosed objects in test (#2290)Scot Breitenfeld2022-12-101-6/+10
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* Check for size==0 for all datatypes read from disk, not just compound (#2287)Neil Fortner2022-12-081-9/+5
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