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* New references for Dimension Scale APIs (#1139)jhendersonHDF2021-11-0519-425/+826
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Enable usage of new-style references with dimension scale APIs * Add API to check if an object ID represents a native connector object * Modified code to use new function H5DSwith_new_ref to determine if new references should be used with Dimension Scales. The new function return TRUE if non-native connector is used or if H5_DIMENSION_SCALES_WITH_NEW_REF varible is define at configure time (--enable-dimension-scales-with-new-ref). Tested on jelly. ToDo: generate testing file on BE system and enable the test; add flag to CMake; test netCDF-4 with the new references. * Adding new test files generated on BE system (hedgehog) created by 32 and 64-bit library. test_ds chokes on test_ds_le_new_ref.h5 on BE system; test passes for test_ds_be_new_ref-32bit.h5 for the 32-bit library and fails for the 64-bit library, and vice versa. I am checking the files for further investigation; but current implementation of the new references is not portable between LE and BE systems, and 32 and 64-bit systems. * Minor fixes for testing issues * Update test_ds.c Enabled broken test; tests pass now. * Update RELEASE.txt Documented new option to use new references with the HDF5 dimension scales APIs (H5DS*). * Update MANIFEST for new 32-bit new-style references test file for H5DS APIs * Update 'dimension scales w/ new-style refs' feature based on review Co-authored-by: Elena <epourmal@hdfgroup.org>
* OESS-168: Remove clang warnings. (#1105)H. Joe Lee2021-11-041-33/+33
| | | | | | | | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes * OESS-168: Address @soumagne review. * Committing clang-format changes * OESS-168: Address @soumagne review. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix Java VOL tests (#1158)Allen Byrne2021-11-034-316/+15
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* OESS-168: Remove clang warnings. (#1146)H. Joe Lee2021-11-021-3/+3
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* OESS-168: Remove clang warnings. (#1135)H. Joe Lee2021-11-021-1/+1
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* OESS-168: Remove clang warnings. (#1127)H. Joe Lee2021-11-021-6/+6
| | | | | * OESS-168: Remove clang warnings. * OESS-168: Address @lrknox clang-format review.
* Set the plugin path to the library default (#1144)Allen Byrne2021-10-291-0/+2
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* correct error checking string (#1143)Scot Breitenfeld2021-10-291-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Split dir create into separate macro (#1141)Allen Byrne2021-10-288-21/+31
| | | | | * Split dir create into separate macro * Correct VFD settings
* Github #1019 - add Fortran developer flags (#1090)Allen Byrne2021-10-275-10/+11
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* H5repack tests should fail if a corrupted file causes h5repack to (#1138)Larry Knox2021-10-263-6/+28
| | | | | | * H5repack tests should fail if a corrupted file causes h5repack to segfault/core dump. * Add release note for HDFV-10590, CVE-2018-17432.
* Consolidate VFD create list macro (#1132)Allen Byrne2021-10-267-10/+5
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* Removes the "try free" behavior from the skip lists (#1126)Dana Robinson2021-10-223-678/+200
| | | | | | | | | | | | | | * Removes the "try free" behavior from the skip lists This was only used in the ID code when iterating and a callback could delete IDs. It is not used anywhere else in the library and is now pointless overhead. Also quiets the const warnings when returning stored elements. They only need to be const with respect to the skip list code, which should never modify them. The library can do whatever it wants with the elements it stored. * Formatted source
* OESS-168: Remove clang warnings. (#1117)H. Joe Lee2021-10-211-1/+1
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* Fix map open to use correct VOL argument structure (#1116)jhendersonHDF2021-10-211-1/+3
| | | Fix map iterate by setting key memory type ID field
* Add release note for HDFFV-11150 fix. (#1106)Larry Knox2021-10-211-1/+23
| | | | | * Add release note for HDFFV-11150 fix. * Add note about gif tool CVEs.
* Correct java exception declarations (#1121)Allen Byrne2021-10-201-16/+19
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* Fixed HL_test_packet, incorrect length assignment (#1100)Allen Byrne2021-10-202-3/+7
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* Move test utilities to utils/test folder (#1109)Allen Byrne2021-10-2032-333/+340
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Move test utilities to utils/test folder * Fix makefile assignment * Add new dir * add new folder * Correct copied makefile * Fix dir typo * Add missing include dir * Remove unnecessary lib link * Correct dependent dirs * Fix conditional checks * Disable test if not built * fix path to executable * Use fixture for swmr_vfd check * Add release note * Correct shell tests and c++ flag warning * Update autotools c++ warning * Fix typo
* OESS-168: Remove clang warnings. (#1075)H. Joe Lee2021-10-201-12/+12
| | | | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes * OESS-168: Fix CI failure. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1072)H. Joe Lee2021-10-151-13/+13
| | | | | | | | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes * Address review by @jehndersonHDF. * Address review by @jehndersonHDF. * OESS-168: Fix CI failure. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1077)H. Joe Lee2021-10-081-1/+1
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* OESS-168: Remove clang warnings. (#1076)H. Joe Lee2021-10-082-10/+10
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* Add missing dataset reference text (#1081)Allen Byrne2021-10-071-4/+4
| | | | | * Add missing dataset reference text * Only print name if not printing data
* OESS-168: Remove clang warnings. (#1074)H. Joe Lee2021-10-061-2/+2
| | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1071)H. Joe Lee2021-10-061-3/+3
| | | | | * OESS-168: Remove clang warnings. * Address review by @jehndersonHDF.
* To reduce maintenance effort, delete the `noerror-` variants of the compiler ↵David Young2021-10-0616-356/+75
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | flags files (#1033) * Avoid maintenance headaches: delete the `noerror-` variants of the compiler flags files, since they essentially duplicate the `error-` files modulo the replacement of `-Werror=` with `-W` and any changes in comments. (I verified the duplication with a script.) For autoconf, reinstate the use of the `demote_errors` shell function to derive the `noerror-` content from the `error-` content. `demote_errors` replaces `-Werror=` with `-W` when `WARNINGS_AS_ERRORS` is `no`. Slightly reorder `configure.ac` so that the setting of `WARNINGS_AS_ERRORS` takes effect before the `error-` files are sourced. * Take a stab at updating the CMake files to match the changes I made to the autoconf files to remove `noerror-` files. I'm not much of a CMake user so these changes are quite rough. Looks like the duplication can be reduced with the introduction of a new macro. * Delete `noerror-` files from the MANIFEST. * Reduce duplication in the CMake files: perform the HDF5_ENABLE_WARNINGS_AS_ERRORS test once in the ADD_H5_FLAGS macro. * Add a release note.
* Add tools/src/h5perf/Makefile.in (#1066)Larry Knox2021-10-041-0/+1
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* Fix ASAN issue in h5dump error path (#1051)Allen Byrne2021-10-032-3/+1
| | | | | * Fix ASAN issue in h5dump error path * Rework error allocation free.
* ASAN fix for test_ld - free sub-allocation of fields (#1052)Allen Byrne2021-10-011-34/+36
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* Fix bug with cross platform compatibility of references within vlens. (#1064)Neil Fortner2021-10-012-2/+11
| | | No testing yet.
* OESS-168: Remove clang warnings. (#1057)H. Joe Lee2021-09-301-56/+56
| | | | | | | * OESS-168: Remove clang warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* OESS-168: Remove clang warnings. (#1056)H. Joe Lee2021-09-301-20/+20
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* Move HDstrcmp operations inside casting block for PGI compilers (#1063)jhendersonHDF2021-09-301-6/+6
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* Fix Mirror, HDFS and ROS3 case statements for VFD value in H5trace (#1062)jhendersonHDF2021-09-301-6/+6
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* Update compact dataset I/O routines to handle driver-level memory copy (#1054)jhendersonHDF2021-09-305-13/+187
| | | | | | | | | | * Update compact dataset I/O routines to handle driver-level memory copy * Combine compact I/O read/write struct into single I/O struct Rename CTL memory copy flag and H5Fquery routine to get file driver structure * Add RELEASE.txt entry for new "ctl" memory copy operation
* VFD plugins (#602)jhendersonHDF2021-09-29169-2283/+6120
| | | | | | | | | | | | | | | | | * Implement support for loading of Virtual File Drivers as plugins Fix plugin caching for VOL connector and VFD plugins Fix plugin iteration to skip paths that can't be opened * Enable dynamic loading of VFDs with HDF5_DRIVER environment variable * Temporarily disable error reporting during H5F_open double file open * Default to using HDstat in h5_get_file_size for unknown VFDs * Use macros for some environment variables that HDF5 interprets * Update "null" and "ctl testing" VFDs
* OESS-168: Remove clang warnings. (#1050)H. Joe Lee2021-09-291-1/+1
| | | This patch will remove clang double-promotion warning.
* OESS-168: Remove clang warnings (#1049)H. Joe Lee2021-09-291-1/+1
| | | This patch will remove clang double-promotion warning.
* OESS-168: Remove clang warnings. (#1047)H. Joe Lee2021-09-291-1/+1
| | | | | This patch will remove clang warnings on Mac: 'float' to 'double' [-Wdouble-promotion]
* OESS-168: Remove clang warnings. (#1046)H. Joe Lee2021-09-291-9/+9
| | | | | | | This patch will remove clang warnings on Mac: ``` warning: implicit conversion increases floating-point precision: 'float' to 'double' [-Wdouble-promotion] ```
* Update version to 1.13.0-7 after snapshot release 1.13.0-6. (#1048)Larry Knox2021-09-296-7/+7
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* Update Platforms Tested in RELEASE.txt. (#1045)hdf5-1_13_0-rc6Larry Knox2021-09-286-149/+103
| | | | | | * Update Platforms Tested in RELEASE.txt. Remove Tested Configuration Features Summary for updated replacement. * Set version to 1.13.0-6 for rc6 snapshot.
* Develop cmake install dir (#1041)Allen Byrne2021-09-284-9/+18
| | | | | | | * Corrected path searched by CMake find_package command * Correct path for depend libs * Adjust examples script for install path
* Develop libaec up (#1037)Allen Byrne2021-09-281-1/+7
| | | | | * Upgrade libaec to 1.0.6 * correct include file name
* MS clang needs EHsc flag (#1035)Allen Byrne2021-09-241-2/+2
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* VFD ctl feature (#981)jhendersonHDF2021-09-2320-160/+1082
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Added "ctl" callback to the VFD interface, and the associated H5FDctl() and H5FD_ctl() calls. Modified the MPIO VFD accordingly -- specifically: Added ctl() call with op-code support to expose rank, size, and communicator. Modified H5FD_mpi_get_rank(), H5FD_mpi_get_size(), and H5FD_mpi_get_comm() to use the new ctl() callback. In passing removed the const qualifier from the file parameter of these functions, as the file parameter of the ctl callback is not const. Deleted the old H5FD__mpio_mpi_rank(), H5FD__mpio_mpi_size(), and H5FD__mpio_communicator() calls from the MPIO VFD. Deleted H5FD_class_mpi_t from H5FDprivate.h, and modified the MPIO VFD accordingly. Note that all VFDs now use H5FD_class_t, with no special class for VFDs that that support MPI. Some minor touch ups to the Neil's selection I/O mods in passing. Tested serial and parallel, debug and production on charis and jelly. * Reserve a range of VFD "ctl" opcodes for library and experimental usage * Add "ctl" callbacks to passthrough VFDs * Add RELEASE.txt entry for "ctl" callback * Use H5FDopen with H5F_ACC_RDWR flag instead of H5F_ACC_TRUNC in vfd test * Remove handling of passthrough "ctl" flag from multi VFD * Move logic for testing H5FD_CTL__TEST_OPCODE into a testing VFD Revise description of "ctl" callback in RELEASE.txt Remove unused H5FD_CTL__NUM_OPCODES definition Fix some warnings in multi VFD Co-authored-by: mainzer <mainzer#hdfgroup.org>
* Need to match clang and versions not just "Clang" (#1029)Allen Byrne2021-09-224-20/+12
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* HDFFV-11266 - add option to build HL tools (#1018)Allen Byrne2021-09-167-5/+47
| | | | | | | * HDFFV-11266 - add option to build HL tools * Correct if syntax * Correct name of conditional
* Disable fortran warning (#1014)Allen Byrne2021-09-162-7/+8
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