Matt L ac169ed3e8 Optimize VDS operations with r-tree (#5843) ...

Optimize VDS operations using R-tree spatial index, adding new API functions and tests for improved performance.

Behavior:
Introduces R-tree spatial index for optimizing VDS operations in H5Dvirtual.c.
Adds H5Pset_dset_use_spatial_tree() and H5Pget_dset_use_spatial_tree() to control R-tree usage.
Default behavior uses R-tree for VDS with more than 1000 mappings.
Implementation:
Adds H5RT.c, H5RTprivate.h, and H5RTpkg.h for R-tree implementation.
Updates H5Pdapl.c and H5Pdcpl.c to include R-tree properties.
Modifies H5Dvirtual.c to integrate R-tree in VDS I/O operations.
Testing:
Adds rtree.c for testing R-tree creation, search, and copy operations.
Tests R-tree integration with VDS in test/dsets.c.
Verifies R-tree behavior with different dataset access property list settings.

2025-10-07 12:13:28 -05:00

..

API

Add predefined datatypes for bfloat16 data (#5402)

2025-09-26 13:33:56 -05:00

testfiles

Fix bugs involving recursive link operations that could be triggered by deleting links to their parent group (#5853)

2025-09-30 12:20:49 -05:00

accum_swmr_reader.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

accum.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

app_ref.c

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2024-10-18 21:13:04 -07:00

atomic_reader.c

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2024-10-18 21:13:04 -07:00

atomic_writer.c

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2024-10-18 21:13:04 -07:00

AtomicWriterReader.txt

spelling fixes (#1561)

2022-03-31 10:42:30 -05:00

big.c

Refactor warning macros (#5432)

2025-05-23 11:46:40 -05:00

bittests.c

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2024-10-18 21:13:04 -07:00

btree2.c

Add new -testexpress option to testframe testing framework (#5286)

2025-01-31 20:11:48 -06:00

cache_api.c

Add new -testexpress option to testframe testing framework (#5286)

2025-01-31 20:11:48 -06:00

cache_common.c

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2024-10-18 21:13:04 -07:00

cache_common.h

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

cache_image.c

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2024-10-18 21:13:04 -07:00

cache_logging.c

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2024-10-18 21:13:04 -07:00

cache_tagging.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

cache.c

Add new -testexpress option to testframe testing framework (#5286)

2025-01-31 20:11:48 -06:00

chunk_info.c

Add H5Dread_chunk2() (#5506)

2025-06-17 11:11:13 -05:00

CMakeLists.txt

Add internal spatial tree (#5800)

2025-10-02 06:49:52 -05:00

CMakePassthroughVOLTests.cmake

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2024-10-18 21:13:04 -07:00

CMakeTests.cmake

Remove 1 hour timeout limit for objcopy test (#5648)

2025-07-07 07:38:11 -05:00

CMakeVFDTests.cmake

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2024-10-18 21:13:04 -07:00

cmpd_dset.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

cmpd_dtransform.c

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2024-10-18 21:13:04 -07:00

cork.c

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2024-10-18 21:13:04 -07:00

cross_read.c

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2024-10-18 21:13:04 -07:00

dangle.c

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2024-10-18 21:13:04 -07:00

del_many_dense_attrs.c

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2024-10-18 21:13:04 -07:00

direct_chunk.c

Add H5Dread_chunk2() (#5506)

2025-06-17 11:11:13 -05:00

dsets.c

Optimize VDS operations with r-tree (#5843)

2025-10-07 12:13:28 -05:00

dt_arith.c

Add predefined datatypes for bfloat16 data (#5402)

2025-09-26 13:33:56 -05:00

dtransform.c

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2024-10-18 21:13:04 -07:00

dtypes.c

Add predefined datatypes for bfloat16 data (#5402)

2025-09-26 13:33:56 -05:00

earray.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

efc.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

enc_dec_plist_cross_platform.c

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2024-10-18 21:13:04 -07:00

enc_dec_plist.c

Change default page buffer size to 64MiB when using ROS3 driver (#5685)

2025-08-06 23:04:10 -05:00

enum.c

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2024-10-18 21:13:04 -07:00

err_compat.c

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2024-10-18 21:13:04 -07:00

error_test.c

Refactor warning macros (#5432)

2025-05-23 11:46:40 -05:00

event_set.c

Integrate API tests with testing framework (#5133)

2024-11-26 07:34:52 -06:00

evict_on_close.c

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2024-10-18 21:13:04 -07:00

extend.c

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2024-10-18 21:13:04 -07:00

external_common.c

Fix minor Windows warnings (#5021)

2024-10-28 05:54:16 -07:00

external_common.h

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2024-10-18 21:13:04 -07:00

external_env.c

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2024-10-18 21:13:04 -07:00

external_fname.h

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2024-10-18 21:13:04 -07:00

external.c

fix for cray compiler failing test (#5347)

2025-03-03 14:11:00 -06:00

farray.c

chore: decapitalize Fixed Array (#5659)

2025-07-15 18:20:13 +02:00

fheap.c

Add new -testexpress option to testframe testing framework (#5286)

2025-01-31 20:11:48 -06:00

file_image.c

Refactor warning macros (#5432)

2025-05-23 11:46:40 -05:00

filenotclosed.c

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fillval.c

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filter_fail.c

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filter_plugin1_dsets.c

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filter_plugin2_dsets.c

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filter_plugin3_dsets.c

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filter_plugin4_groups.c

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filter_plugin.c

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flush1.c

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flush2.c

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flushrefresh.c

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2024-10-18 21:13:04 -07:00

flushrefreshTest.cmake

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2024-10-18 21:13:04 -07:00

freespace.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

gen_bad_compound.c

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gen_bad_offset.c

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gen_bad_ohdr.c

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gen_bogus.c

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gen_bounds.c

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gen_cross.c

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gen_deflate.c

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gen_file_image.c

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gen_filespace.c

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gen_filters.c

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gen_mergemsg.c

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gen_new_array.c

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gen_new_fill.c

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gen_new_group.c

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gen_new_mtime.c

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gen_new_super.c

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gen_noencoder.c

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gen_nullspace.c

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gen_old_array.c

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gen_old_group.c

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gen_old_layout.c

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gen_old_mtime.c

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gen_plist.c

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gen_sizes_lheap.c

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gen_specmetaread.c

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gen_udlinks.c

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2024-10-18 21:13:04 -07:00

genall5.c

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genall5.h

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2024-10-18 21:13:04 -07:00

getname.c

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2024-10-18 21:13:04 -07:00

gheap.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

h5test.c

Re-write ROS3 VFD S3 backend to use AWS' C S3 library (#5548)

2025-05-29 17:51:29 -05:00

h5test.h

Re-write ROS3 VFD S3 backend to use AWS' C S3 library (#5548)

2025-05-29 17:51:29 -05:00

H5srcdir_str.h.in

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2024-10-18 21:13:04 -07:00

H5srcdir.h

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2024-10-18 21:13:04 -07:00

hdfs.c

Add new multithreaded concurrency configuration (#5015)

2024-12-19 01:35:21 -08:00

hyperslab.c

Add new multithreaded concurrency configuration (#5015)

2024-12-19 01:35:21 -08:00

istore.c

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2024-10-18 21:13:04 -07:00

lheap.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

links_env.c

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2024-10-18 21:13:04 -07:00

links.c

Fix bugs involving recursive link operations that could be triggered by deleting links to their parent group (#5853)

2025-09-30 12:20:49 -05:00

mdset.c

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2024-10-18 21:13:04 -07:00

mf.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

mirror_vfd.c

Fix codespell issues (#5256)

2025-01-21 17:36:27 -06:00

mount.c

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2024-10-18 21:13:04 -07:00

mtime.c

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2024-10-18 21:13:04 -07:00

ntypes.c

Add predefined datatypes for bfloat16 data (#5402)

2025-09-26 13:33:56 -05:00

null_vfd_plugin.c

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null_vfd_plugin.h

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null_vol_connector.c

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null_vol_connector.h

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2024-10-18 21:13:04 -07:00

objcopy_ref.c

Refactor warning macros (#5432)

2025-05-23 11:46:40 -05:00

objcopy.c

Refactor warning macros (#5432)

2025-05-23 11:46:40 -05:00

ohdr.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

onion.c

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2024-10-18 21:13:04 -07:00

page_buffer.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00

POSIX_Order_Write_Test_Report.docx

Moved remaining SWMR-related test files to develop.

2017-01-26 14:34:12 -05:00

POSIX_Order_Write_Test_Report.pdf

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2017-01-26 14:34:12 -05:00

reserved.c

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2024-10-18 21:13:04 -07:00

ros3.c

Add documentation and s3proxy testing for ROS3 VFD (#5560)

2025-06-19 16:22:49 -05:00

rtree.c

Optimize VDS operations with r-tree (#5843)

2025-10-07 12:13:28 -05:00

s3comms.c

Add documentation and s3proxy testing for ROS3 VFD (#5560)

2025-06-19 16:22:49 -05:00

select_io_dset.c

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2024-10-18 21:13:04 -07:00

set_extent.c

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2024-10-18 21:13:04 -07:00

ShellTests.cmake

Add check for PERL_FOUND around actual test (#5130)

2024-11-19 16:18:17 -06:00

space_overflow.c

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stab.c

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2024-10-18 21:13:04 -07:00

swmr_addrem_writer.c

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swmr_common.c

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2024-10-18 21:13:04 -07:00

swmr_common.h

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2024-10-18 21:13:04 -07:00

swmr_generator.c

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2024-10-18 21:13:04 -07:00

SWMR_POSIX_Order_UG.txt

Fixed Spelling Errors (#1166)

2021-12-07 08:27:29 -06:00

swmr_reader.c

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2024-10-18 21:13:04 -07:00

swmr_remove_reader.c

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2024-10-18 21:13:04 -07:00

swmr_remove_writer.c

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2024-10-18 21:13:04 -07:00

swmr_sparse_reader.c

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2024-10-18 21:13:04 -07:00

swmr_sparse_writer.c

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2024-10-18 21:13:04 -07:00

swmr_start_write.c

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2024-10-18 21:13:04 -07:00

SWMR_UseCase_UG.txt

Fixed Spelling Errors (#1166)

2021-12-07 08:27:29 -06:00

swmr_writer.c

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2024-10-18 21:13:04 -07:00

swmr.c

Fix codespell issues (#5256)

2025-01-21 17:36:27 -06:00

tarray.c

Remove const from testing parameters in testframe framework (#5214)

2025-01-08 13:33:00 -06:00

tattr.c

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2025-01-08 13:33:00 -06:00

tcheck_version.c

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2024-10-18 21:13:04 -07:00

tchecksum.c

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2025-01-08 13:33:00 -06:00

tconfig.c

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2025-01-08 13:33:00 -06:00

tcoords.c

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2025-01-08 13:33:00 -06:00

test_flush_refresh.sh.in

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2024-10-18 21:13:04 -07:00

test_swmr.pwsh.in

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test_swmr.sh.in

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test_use_cases.sh.in

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test_vds_swmr.pwsh.in

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test_vds_swmr.sh.in

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2024-10-18 21:13:04 -07:00

testframe.c

Move TestAlarmOn()/TestAlarmOff() back into PerformTests() (#5307)

2025-02-10 15:23:54 -06:00

testframe.h

Add new -testexpress option to testframe testing framework (#5286)

2025-01-31 20:11:48 -06:00

testhdf5.c

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testhdf5.h

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testmeta.c

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tfile.c

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2025-01-08 13:33:00 -06:00

tgenprop.c

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th5_system.c

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2025-01-08 13:33:00 -06:00

th5o.c

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2025-01-08 13:33:00 -06:00

th5s.c

Fix segfault in H5S__get_select_hyper_blocklist() (#5353)

2025-03-18 11:06:36 -05:00

tid.c

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2025-01-08 13:33:00 -06:00

timer.c

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titerate.c

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2025-01-08 13:33:00 -06:00

tmeta.c

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2025-01-08 13:33:00 -06:00

tmisc.c

Fix codespell issues (#5256)

2025-01-21 17:36:27 -06:00

trefer_deprec.c

Remove const from testing parameters in testframe framework (#5214)

2025-01-08 13:33:00 -06:00

trefer_shutdown.c

Rename HD(f)printf() to (f)printf() (#3194)

2023-06-28 08:31:32 -07:00

trefer.c

Separate test file generation from testing in external link reference test (#5760)

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trefstr.c

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tselect.c

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tskiplist.c

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tsohm.c

Add new -testexpress option to testframe testing framework (#5286)

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ttime.c

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ttsafe_acreate.c

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ttsafe_atomic.c

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ttsafe_attr_vlen.c

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ttsafe_cancel.c

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ttsafe_dcreate.c

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ttsafe_develop.c

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ttsafe_error_stacks.c

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ttsafe_error.c

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ttsafe_rec_rwlock.c

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ttsafe_rwlock.c

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ttsafe_semaphore.c

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ttsafe_thread_id.c

Fix codespell issues (#5256)

2025-01-21 17:36:27 -06:00

ttsafe_thread_pool.c

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2025-01-08 13:33:00 -06:00

ttsafe.c

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ttsafe.h

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2025-01-08 13:33:00 -06:00

tunicode.c

Skip unicode tests for specific VFDs (#5823)

2025-09-15 11:42:54 -05:00

tvlstr.c

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tvltypes.c

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twriteorder.c

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unlink.c

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unregister.c

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2024-10-24 10:09:22 -07:00

use_append_chunk_mirror.c

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use_append_chunk.c

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use_append_mchunks.c

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use_common.c

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use_disable_mdc_flushes.c

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use.h

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds_env.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds_swmr_gen.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds_swmr_reader.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds_swmr_writer.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds_swmr.h

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vds.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vfd_plugin.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vfd.c

Re-write ROS3 VFD S3 backend to use AWS' C S3 library (#5548)

2025-05-29 17:51:29 -05:00

vol_plugin.c

Renamed COPYING to LICENSE (#4978)

2024-10-18 21:13:04 -07:00

vol.c

Refactor allocation of API context (#4942)

2024-10-24 10:09:22 -07:00