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* The version string has a second use for packagingAllen Byrne2020-08-262-2/+4
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* Merge pull request #2839 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-08-251-0/+20
|\ | | | | | | | | * commit '336b30024216b142eb096bf85986786ecf65e993': Add back function for VERIFY_EXTERNAL_CONSOLIDATION
| * Add back function for VERIFY_EXTERNAL_CONSOLIDATIONAllen Byrne2020-08-251-0/+20
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* Merge pull request #2826 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-08-242-1/+5
|\ | | | | | | | | | | | | | | | | * commit 'ec1c324a0d184d2778e9155140367a7d3a307fa1': Revert H5_VERS_SUBRELEASE check Add special case when H5_VERS_SUBRELEASE is 0 Condition if (H5_VERS_SUBRELEASE) is incorrectly false when H5_VERS_SUBRELEASE is 0, a valid value for H5_VERS_SUBRELEASE. Updated to if (${H5_VERS_SUBRELEASE} STREQUAL "") with corresponding reversal of action statements to avoid NOT. Add hypen to subrelease regex Fix S3/HDFS test
| * Revert H5_VERS_SUBRELEASE checkAllen Byrne2020-08-241-5/+1
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| * Add special case when H5_VERS_SUBRELEASE is 0Allen Byrne2020-08-241-3/+7
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| * Condition if (H5_VERS_SUBRELEASE) is incorrectly false whenLarry Knox2020-08-241-3/+3
| | | | | | | | | | | | H5_VERS_SUBRELEASE is 0, a valid value for H5_VERS_SUBRELEASE. Updated to if (${H5_VERS_SUBRELEASE} STREQUAL "") with corresponding reversal of action statements to avoid NOT.
| * Add hypen to subrelease regexAllen Byrne2020-08-231-1/+1
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| * Fix S3/HDFS testAllen Byrne2020-08-231-0/+4
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* Merge pull request #2819 in HDFFV/hdf5 from coll_chunk_fill_fix to developQuincey Koziol2020-08-211-54/+60
|\ | | | | | | | | | | | | | | * commit '4c43ff0b8b015ccfc1f4aeab18f189d629a5beb9': Simplify default use of MPI_BYTE Don't free builtin MPI_BYTE MPI type Simplify code to avoid using a boolean to free MPI types Avoid creating MPI datatypes on ranks with 0 chunks to write'
| * Simplify default use of MPI_BYTEQuincey Koziol2020-08-201-8/+3
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| * Don't free builtin MPI_BYTE MPI typeQuincey Koziol2020-08-201-2/+2
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| * Simplify code to avoid using a boolean to free MPI typesQuincey Koziol2020-08-201-7/+3
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| * Avoid creating MPI datatypes on ranks with 0 chunks to write'Quincey Koziol2020-08-201-53/+68
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* Merge pull request #2816 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-08-201-34/+20
|\ | | | | | | | | * commit '76d93a78fe583b99efa295cd44359092310172a3': Revert "Merge pull request #2796 in HDFFV/hdf5 from small_chunk_io_opt to develop"
| * Revert "Merge pull request #2796 in HDFFV/hdf5 from small_chunk_io_opt to ↵Larry Knox2020-08-201-34/+20
|/ | | | | | | develop" This reverts commit a7a8e6451a37d1bd072c7281b432f1436795daef, reversing changes made to 30422a6b55a135ec406d484a6c66f995057e0a50.
* Merge pull request #2796 in HDFFV/hdf5 from small_chunk_io_opt to developQuincey Koziol2020-08-191-20/+34
|\ | | | | | | | | * commit 'ad9a2ceabe2dd9045111f8b57774948a124607b9': Only initialize the contiguous or compact I/O info struct when needed.
| * Only initialize the contiguous or compact I/O info struct when needed.Quincey Koziol2020-08-171-20/+34
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* | Merge pull request #2806 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-08-184-48/+0
|\ \ | | | | | | | | | | | | * commit '98754591b8dcf2be70957d67ec7172c53cbaa827': Revert "Merge pull request #2477 in HDFFV/hdf5 from pio_update to develop"
| * | Revert "Merge pull request #2477 in HDFFV/hdf5 from pio_update to develop"Larry Knox2020-08-184-48/+0
|/ / | | | | | | | | This reverts commit ba80bcaff24113f438da0f40cb5b5479d4a21cc6, reversing changes made to 522ef0dd5ca1daa2b26c3fe4459ddbb1eaf6ec20.
* | Merge pull request #2801 in HDFFV/hdf5 from ↵Larry Knox2020-08-181-1/+1
|\ \ | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:swmr_test_fail_cmake to develop * commit '857e0f4404cb5a754d799110b89f0f16b503b4ce': Fixes CMake issue with file locking variable
| * | Fixes CMake issue with file locking variableDana Robinson2020-08-181-1/+1
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* | Merge pull request #2795 in HDFFV/hdf5 from ↵Larry Knox2020-08-183-1/+8
|\ \ | | | | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_bmr2020:hdf5_bmr2020_addrsani to develop * commit '5352b1dbc92313d91d3502dd8352352abe8749a7': Fixed typo Fix HDFFV-11101
| * | Fixed typoBinh-Minh Ribler2020-08-181-1/+1
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| * | Fix HDFFV-11101Binh-Minh Ribler2020-08-172-0/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description Added initialization to local structs in the src function H5MF_settle_raw_data_fsm() and the test function test_bt2_hdr_fd() to prevent the following error in two different occurrences: MemorySanitizer: use-of-uninitialized-value Platforms tested: Linux/64 (jelly) Linux/64 (platypus)
* | | Merge pull request #2477 in HDFFV/hdf5 from pio_update to developLarry Knox2020-08-184-0/+48
|\ \ \ | | | | | | | | | | | | | | | | * commit 'a20bf599b682bfa0a91d571a922973e0c53b524a': Don't track file offset position when using pread / pwrite.
| * \ \ Merge remote-tracking branch 'origin/develop' into pio_updateQuincey Koziol2020-08-161009-34390/+36775
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| * \ \ \ Merge remote-tracking branch 'origin/develop' into pio_updateQuincey Koziol2020-04-1969-2036/+13145
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| * \ \ \ \ Merge remote-tracking branch 'origin/develop' into pio_updateQuincey Koziol2020-04-0970-1511/+1907
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| * \ \ \ \ \ Merge remote-tracking branch 'origin/develop' into pio_updateQuincey Koziol2020-04-042-2/+2
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| * \ \ \ \ \ \ Merge remote-tracking branch 'origin/develop' into pio_updateQuincey Koziol2020-04-0322-565/+790
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| * | | | | | | | Don't track file offset position when using pread / pwrite.Quincey Koziol2020-03-294-32/+80
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* | | | | | | | | Merge pull request #2734 in HDFFV/hdf5 from ~DYOUNG/werror:cse to developLarry Knox2020-08-181-96/+106
|\ \ \ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'fa7f8ad2f3fe509ff69dc574ddad0ae4d329ccca': Improve code readability: extract common subexpressions into temporary variables.
| * | | | | | | | | Improve code readability: extract common subexpressions into temporaryDavid Young2020-08-041-96/+106
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | variables.
* | | | | | | | | | Merge pull request #2735 in HDFFV/hdf5 from ~DYOUNG/werror:virtual-write-one ↵Larry Knox2020-08-181-1/+1
|\ \ \ \ \ \ \ \ \ \ | |_|_|_|_|_|_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '7b48e3409a8c3ba1e83c929656e84196a6dc2e6d': Fix a bug in H5D__virtual_write_one to stop an assertion from failing deep in H5Dwrite---project the *clipped* virtual selection instead of the virtual selection:
| * | | | | | | | | Fix a bug in H5D__virtual_write_one to stop an assertion from failingDavid Young2020-08-041-1/+1
| |/ / / / / / / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | deep in H5Dwrite---project the *clipped* virtual selection instead of the virtual selection: assertion "((src_space)->select.num_elem) == ((dst_space)->select.num_elem)" failed: file "../../../vchoi_fork/src/H5Sselect.c", line 2617, function "H5S_select_project_intersection" with this backtrace: at /home/dyoung/plain-nbsd/src/lib/libc/gen/raise.c:48 at /home/dyoung/plain-nbsd/src/lib/libc/stdlib/abort.c:74 file=0xae9e3e80 "../../../vchoi_fork/src/H5Sselect.c", line=2617, function=0xae9e4ca0 <__func__.15686> "H5S_select_project_intersection", failedexpr=0xae9e0e54 "((src_space)->select.num_elem) == ((dst_space)->select.num_elem)") at /home/dyoung/plain-nbsd/src/lib/libc/gen/assert.c:72 dst_space=0xae26f0dc, src_intersect_space=0xae0b577c, new_space_ptr=0xbfb85fac, share_selection=true) at ../../../vchoi_fork/src/H5Sselect.c:2749 type_info=type_info@entry=0xbfb86084, file_space=file_space@entry=0xae0b577c, source_dset=0xae24741c, io_info=<optimized out>) at ../../../vchoi_fork/src/H5Dvirtual.c:2784 type_info=0xbfb86084, nelmts=256, file_space=0xae0b577c, mem_space=0xae26ec8c, fm=0xadf0401c) at ../../../vchoi_fork/src/H5Dvirtual.c:2873 mem_type_id=216172782113783837, mem_space=0xae26ec8c, file_space=0xae0b577c, buf=0xae203808) at ../../../vchoi_fork/src/H5Dio.c:780 mem_type_id=216172782113783837, mem_space_id=288230376151711754, file_space_id=288230376151711755, dxpl_id=792633534417207304, buf=0xae203808, req=0x0) at ../../../vchoi_fork/src/H5VLnative_dataset.c:206 mem_type_id=216172782113783837, mem_space_id=288230376151711754, file_space_id=288230376151711755, dxpl_id=792633534417207304, buf=0xae203808, req=0x0, cls=<optimized out>) at ../../../vchoi_fork/src/H5VLcallback.c:2152 mem_type_id=216172782113783837, mem_space_id=288230376151711754, file_space_id=288230376151711755, dxpl_id=792633534417207304, buf=0xae203808, req=0x0) at ../../../vchoi_fork/src/H5VLcallback.c:2186 mem_type_id=216172782113783837, mem_space_id=288230376151711754, file_space_id=288230376151711755, dxpl_id=792633534417207304, buf=0xae203808) at ../../../vchoi_fork/src/H5Dio.c:313
* | | | | | | | | Merge pull request #2794 in HDFFV/hdf5 from ↵Dana Robinson2020-08-175-12/+127
|\ \ \ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:h5f_start_swmr_write_locks_dev2 to develop * commit 'f02ced7e7443563581930a6c2d58d1628608bbdd': Moves lock flag to H5F_shared_t and adds test. Adds fix for H5Fstart_swmr_write lock issue
| * | | | | | | | | Moves lock flag to H5F_shared_t and adds test.Dana Robinson2020-08-175-15/+118
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| * | | | | | | | | Adds fix for H5Fstart_swmr_write lock issueDana Robinson2020-08-172-4/+16
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* | | | | | | | | Merge pull request #2769 in HDFFV/hdf5 from mdc_sl_opt to developJohn Mainzer2020-08-1715-1837/+3630
|\ \ \ \ \ \ \ \ \ | |_|_|_|_|_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'd00bab96fb4da12a18b5de528c96469978c4c927': Minor copy edits to comments -- no code changes. Tab to space conversions. When flushing, the metadata cache attempts to flush entries in increasing address order. To facilitate this, the metadata cache needs a list of of dirty entries in increasing address order. This is implemented via a skip list of all dirty entries in the cache.
| * | | | | | | | Minor copy edits to comments -- no code changes.inactive/mdc_sl_optmainzer2020-08-173-3/+3
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| * | | | | | | | Merge branch 'develop' into mdc_sl_optmainzer2020-08-15364-10247/+6767
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| * | | | | | | | | Tab to space conversions.mainzer2020-08-147-465/+463
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Re-applied tab to space conversions accidentally reverted in the commit of the metadata cache skip list optimization, and performed some additional tab to space conversions in passing. Tested parallel / debug on Jelly.
| * | | | | | | | | Merge branch 'develop' into mdc_sl_optmainzer2020-08-13196-3757/+5236
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| * | | | | | | | | | When flushing, the metadata cache attempts to flush entries in increasingmainzer2020-08-0515-1857/+3651
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | address order. To facilitate this, the metadata cache needs a list of of dirty entries in increasing address order. This is implemented via a skip list of all dirty entries in the cache. To date this skip list has been maintained at all times. However, profiling indicates that we can avoid significant overhead by constructing the skip list of dirty entries just before a flush, taking it down afterwareds, and not maintaining it during normal operation. This commit implements this optimization for both serial and parallel. Tested serial and parallel, debug and production on charis and jelly.
* | | | | | | | | | | Merge pull request #2784 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-08-172-10/+10
|\ \ \ \ \ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '0d14414ddd860f24f1386771ed3ba8d2f5e2710d': 1. HDFFV-10830 part 2, move AC_CHECK_HEADERS([szlib.h] after AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress] to avoid compiling H5Z.c with szlib.h after its path is removed from AM_CPPFLAGS. 2. Remove unnecessary links to ${HDF5_TOOLS_LIB_TARGET} in utils/mirror_vfd/CMakeLists.txt that prevent building HDF5 with tools disabled.
| * | | | | | | | | | | 1. HDFFV-10830 part 2, move AC_CHECK_HEADERS([szlib.h] afterLarry Knox2020-08-162-10/+10
|/ / / / / / / / / / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress] to avoid compiling H5Z.c with szlib.h after its path is removed from AM_CPPFLAGS. 2. Remove unnecessary links to ${HDF5_TOOLS_LIB_TARGET} in utils/mirror_vfd/CMakeLists.txt that prevent building HDF5 with tools disabled.
* | | | | | | | | | | Merge pull request #2771 in HDFFV/hdf5 from ↵Binh-Minh Ribler2020-08-165-14/+199
|\ \ \ \ \ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_bmr:hdf5_bmr_HDFFV-10933 to develop Fixed HDFFV-10933 * commit '16349c5fddce8a74644e18d01d7ea8186aaaa255': Fixed HDFFV-10933
| * | | | | | | | | | | Fixed HDFFV-10933Binh-Minh Ribler2020-08-145-14/+199
| | |_|/ / / / / / / / | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: Updated the original fix by Kent Y. in commit 200a77d8c3e51663c375aafffff607ae9b438f4e - used internal functions instead of public API - moved some code into the subroutine for a cleaner look. - added test to dsets.c Platforms tested: Linux/64 (jelly)
* | | | | | | | | | | Merge pull request #2779 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-08-161-0/+4
|\ \ \ \ \ \ \ \ \ \ \ | |_|_|_|_|_|_|_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '31673041d8342002d11ced2a7def938438dd912d': Fix javadoc warning
generated by cgit v0.12 at 2024-12-26 19:15:27 (GMT)