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* Merge remote-tracking branch 'hdffv/develop' into rebased-fprintf-experimentDavid Young2020-09-03366-12087/+10698
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| * Merge pull request #2866 in HDFFV/hdf5 from ↵Quincey Koziol2020-09-028-232/+26
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | fix_nil_collective_metadata_write to develop * commit '45021f1826f3710a3008430ddf7216bffb7068f7': Update buffer count Revert PR 405 (https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5/pull-requests/405/overview) and reimplement with correct and simpler code. Revert " Checkin of fix for CGNS bug" Revert "Removed commeted out code from H5C_dump_coll_write_list()"
| | * Update buffer countQuincey Koziol2020-08-281-1/+8
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| | * Merge remote-tracking branch 'origin/develop' into ↵Quincey Koziol2020-08-2827-181/+201
| | |\ | | | | | | | | | | | | fix_nil_collective_metadata_write
| | * | Revert PR 405 ↵Quincey Koziol2020-08-271-37/+18
| | | | | | | | | | | | | | | | | | | | | | | | (https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5/pull-requests/405/overview) and reimplement with correct and simpler code.
| | * | Revert " Checkin of fix for CGNS bug"Quincey Koziol2020-08-278-207/+8
| | | | | | | | | | | | | | | | This reverts commit 94c34773ceae5b30c4afb227d0385ebf4ab6ce28.
| | * | Revert "Removed commeted out code from H5C_dump_coll_write_list()"Quincey Koziol2020-08-271-0/+5
| | | | | | | | | | | | | | | | This reverts commit eb75dc1bb02e13902d73a36caafe763eea585d02.
| * | | Merge pull request #2843 in HDFFV/hdf5 from vol_dataset_io_dxpl_fix to developQuincey Koziol2020-09-022-15/+13
| |\ \ \ | | |_|/ | |/| | | | | | | | | | * commit '4b69577e10ed58bf6536599092390f02a49ff3f9': Bug fix to allow pass-through VOL connectors to set DXPL properties (like requesting collective operations) on dataset I/O
| | * | Bug fix to allow pass-through VOL connectors to set DXPL properties (like ↵Quincey Koziol2020-08-252-15/+13
| | |/ | | | | | | | | | requesting collective operations) on dataset I/O
| * | Merge branch 'develop' into develop_minorDana Robinson2020-08-277-155/+216
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| | * 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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| | * 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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| | * | 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 #2795 in HDFFV/hdf5 from ↵Larry Knox2020-08-181-0/+4
| | |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_bmr2020:hdf5_bmr2020_addrsani to develop * commit '5352b1dbc92313d91d3502dd8352352abe8749a7': Fixed typo Fix HDFFV-11101
| | | * | Fix HDFFV-11101Binh-Minh Ribler2020-08-171-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Koziol2020-08-16413-15591/+13247
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| | | * \ \ \ Merge remote-tracking branch 'origin/develop' into pio_updateQuincey Koziol2020-04-1915-28/+4085
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| | | * \ \ \ \ Merge remote-tracking branch 'origin/develop' into pio_updateQuincey Koziol2020-04-094-117/+113
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| | | * \ \ \ \ \ Merge remote-tracking branch 'origin/develop' into pio_updateQuincey Koziol2020-04-032-41/+92
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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
| | * | | | | | | | Moves lock flag to H5F_shared_t and adds test.Dana Robinson2020-08-174-7/+36
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| | * | | | | | | | Adds fix for H5Fstart_swmr_write lock issueDana Robinson2020-08-172-4/+16
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| * | | | | | | | | Trivial whitespace change to H5Pencdec.cDana Robinson2020-08-171-4/+4
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| * | | | | | | | | Minor refactoring based on 1.10 normalization workDana Robinson2020-08-1724-175/+195
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| * | | | | | | | | Merge branch 'develop' into develop_minorDana Robinson2020-08-1710-787/+2306
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| | * | | | | | | | Merge pull request #2769 in HDFFV/hdf5 from mdc_sl_opt to developJohn Mainzer2020-08-1710-787/+2306
| | |\ \ \ \ \ \ \ \ | | | |_|_|_|_|_|_|/ | | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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_optmainzer2020-08-15343-9882/+6640
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| | | * | | | | | | | Tab to space conversions.mainzer2020-08-146-461/+459
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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_optmainzer2020-08-1338-492/+967
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| | | * | | | | | | | | When flushing, the metadata cache attempts to flush entries in increasingmainzer2020-08-0510-811/+2331
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
| * | | | | | | | | | | Trivialities noticed while normalizing 1.10Dana Robinson2020-08-172-2/+2
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| * | | | | | | | | | Merge pull request #2771 in HDFFV/hdf5 from ↵Binh-Minh Ribler2020-08-163-14/+91
| |\ \ \ \ \ \ \ \ \ \ | | |_|_|_|_|_|_|_|_|/ | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_bmr:hdf5_bmr_HDFFV-10933 to develop Fixed HDFFV-10933 * commit '16349c5fddce8a74644e18d01d7ea8186aaaa255': Fixed HDFFV-10933
| | * | | | | | | | | Fixed HDFFV-10933Binh-Minh Ribler2020-08-143-14/+91
| | | |_|/ / / / / / | | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
| * | | | | | | | | Trivialities noticed while merging things to 1.10Dana Robinson2020-08-155-28/+28
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| * | | | | | | | Fixes naming issues in H5VM inline functionsDana Robinson2020-08-141-10/+10
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| * | | | | | | | Merge remote-tracking branch 'origin/develop' into remove_unneeded_taggingQuincey Koziol2020-08-14343-9850/+6607
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| | * \ \ \ \ \ \ \ Merge pull request #2739 in HDFFV/hdf5 from namespace_cleanup_01 to developQuincey Koziol2020-08-14342-9847/+6604
| | |\ \ \ \ \ \ \ \ | | | |_|/ / / / / / | | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '3f46a380e084d83a84783383bdfbbd9a443e9f27': Correct typos w/HGOTO_DONE & HGOTO_ERROR Move H5T_vlen_reclaim to package scope Switch H5VM inline routines back to single underscope and put a comment in their header about this naming Clean up private / package / static namespace issues (function naming, which header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
| | | * | | | | | | Merge remote-tracking branch 'origin/develop' into namespace_cleanup_01Quincey Koziol2020-08-113-24/+32
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| | | * | | | | | | | Correct typos w/HGOTO_DONE & HGOTO_ERRORQuincey Koziol2020-08-107-50/+47
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