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Author SHA1 Message Date
Quincey Koziol
a9ffedfd61 Merge pull request #2819 in HDFFV/hdf5 from coll_chunk_fill_fix to develop 
* 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'
 2020-08-21 16:17:10 -05:00
Quincey Koziol
4c43ff0b8b Simplify default use of MPI_BYTE 2020-08-20 18:24:07 -05:00
Quincey Koziol
fa0d395370 Don't free builtin MPI_BYTE MPI type 2020-08-20 18:22:39 -05:00
Quincey Koziol
d67de87ecd Simplify code to avoid using a boolean to free MPI types 2020-08-20 17:08:24 -05:00
Quincey Koziol
91bd6f9a63 Avoid creating MPI datatypes on ranks with 0 chunks to write' 2020-08-20 14:31:35 -05:00
Larry Knox
6d73a778c6 Merge pull request #2816 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop 
* commit '76d93a78fe583b99efa295cd44359092310172a3':
  Revert "Merge pull request #2796 in HDFFV/hdf5 from small_chunk_io_opt to develop"
 2020-08-20 11:05:41 -05:00
Larry Knox
76d93a78fe Revert "Merge pull request #2796 in HDFFV/hdf5 from small_chunk_io_opt to develop" 
This reverts commit a7a8e6451a, reversing
changes made to 30422a6b55.
 2020-08-20 10:57:29 -05:00
Quincey Koziol
a7a8e6451a Merge pull request #2796 in HDFFV/hdf5 from small_chunk_io_opt to develop 
* commit 'ad9a2ceabe2dd9045111f8b57774948a124607b9':
  Only initialize the contiguous or compact I/O info struct when needed.
 2020-08-19 16:56:20 -05:00
Larry Knox
30422a6b55 Merge pull request #2806 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop 
* commit '98754591b8dcf2be70957d67ec7172c53cbaa827':
  Revert "Merge pull request #2477 in HDFFV/hdf5 from pio_update to develop"
 2020-08-18 13:31:46 -05:00
Larry Knox
98754591b8 Revert "Merge pull request #2477 in HDFFV/hdf5 from pio_update to develop" 
This reverts commit ba80bcaff2, reversing
changes made to 522ef0dd5c.
 2020-08-18 12:51:13 -05:00
Larry Knox
18012b1d98 Merge pull request #2801 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:swmr_test_fail_cmake to develop 
* commit '857e0f4404cb5a754d799110b89f0f16b503b4ce':
  Fixes CMake issue with file locking variable
 2020-08-18 08:20:41 -05:00
Dana Robinson
857e0f4404 Fixes CMake issue with file locking variable 2020-08-18 06:18:23 -07:00
Larry Knox
3f5382bb62 Merge pull request #2795 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr2020:hdf5_bmr2020_addrsani to develop 
* commit '5352b1dbc92313d91d3502dd8352352abe8749a7':
  Fixed typo
  Fix HDFFV-11101
 2020-08-18 08:03:29 -05:00
Larry Knox
ba80bcaff2 Merge pull request #2477 in HDFFV/hdf5 from pio_update to develop 
* commit 'a20bf599b682bfa0a91d571a922973e0c53b524a':
  Don't track file offset position when using pread / pwrite.
 2020-08-18 08:02:55 -05:00
Larry Knox
522ef0dd5c Merge pull request #2734 in HDFFV/hdf5 from ~DYOUNG/werror:cse to develop 
* commit 'fa7f8ad2f3fe509ff69dc574ddad0ae4d329ccca':
  Improve code readability: extract common subexpressions into temporary variables.
 2020-08-18 08:01:27 -05:00
Larry Knox
057cd67021 Merge pull request #2735 in HDFFV/hdf5 from ~DYOUNG/werror:virtual-write-one 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:
 2020-08-18 08:00:54 -05:00
Dana Robinson
f4d03432a4 Removes inappropriate file locking call 2020-08-18 05:53:33 -07:00
Binh-Minh Ribler
5352b1dbc9 Fixed typo 2020-08-17 22:37:26 -05:00
Dana Robinson
e9ee2d9906 Trivial whitespace change to H5Pencdec.c 2020-08-17 16:37:53 -07:00
Quincey Koziol
ad9a2ceabe Only initialize the contiguous or compact I/O info struct when needed. 2020-08-17 18:29:55 -05:00
Dana Robinson
433078bc80 Merge pull request #2794 in HDFFV/hdf5 from ~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
 2020-08-17 18:02:34 -05:00
Binh-Minh Ribler
5bb893a2c2 Fix HDFFV-11101 
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)
 2020-08-17 17:51:15 -05:00
Dana Robinson
f02ced7e74 Moves lock flag to H5F_shared_t and adds test. 2020-08-17 14:25:04 -07:00
Dana Robinson
32a1188bbd Adds fix for H5Fstart_swmr_write lock issue 2020-08-17 10:54:07 -07:00
Dana Robinson
b2d917437d Minor refactoring based on 1.10 normalization work 2020-08-17 09:12:59 -07:00
Dana Robinson
d53c9be189 Merge branch 'develop' into develop_minor 2020-08-17 09:00:42 -07:00
John Mainzer
5d8c5849e5 Merge pull request #2769 in HDFFV/hdf5 from mdc_sl_opt to develop 
* 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.
 2020-08-17 08:25:05 -05:00
mainzer
d00bab96fb Minor copy edits to comments -- no code changes. 2020-08-17 08:19:33 -05:00
Larry Knox
0f9c22edc7 Merge pull request #2784 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop 
* 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.
 2020-08-16 20:57:16 -05:00
Dana Robinson
5787404804 Trivialities noticed while normalizing 1.10 2020-08-16 18:10:48 -07:00
Larry Knox
0d14414ddd 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.
 2020-08-16 18:41:13 -05:00
Binh-Minh Ribler
24c23c79d8 Merge pull request #2771 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr:hdf5_bmr_HDFFV-10933 to develop 
Fixed HDFFV-10933

* commit '16349c5fddce8a74644e18d01d7ea8186aaaa255':
  Fixed HDFFV-10933
 2020-08-16 15:34:18 -05:00
Allen Byrne
f02e016372 Merge pull request #2779 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop 
* commit '31673041d8342002d11ced2a7def938438dd912d':
  Fix javadoc warning
 2020-08-16 12:14:32 -05:00
Quincey Koziol
a20bf599b6 Merge remote-tracking branch 'origin/develop' into pio_update 2020-08-16 11:49:15 -05:00
Allen Byrne
31673041d8 Fix javadoc warning 2020-08-16 11:07:59 -05:00
Allen Byrne
c81f01d5dc Merge pull request #2776 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop 
* commit '6a344232f641135e6bc5f89d66a01c68d29bfa00':
  Add testfiles
  TRILABS-277 Use JIRA number as #ifdef
 2020-08-15 19:47:07 -05:00
Allen Byrne
6a344232f6 Add testfiles 2020-08-15 18:10:57 -05:00
mainzer
7b9f61c157 Merge branch 'develop' into mdc_sl_opt 2020-08-15 17:53:29 -05:00
Allen Byrne
57c4aeb0cc TRILABS-277 Use JIRA number as #ifdef 2020-08-15 17:25:22 -05:00
Allen Byrne
94ae09469b Merge pull request #2768 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop 
* commit '2d659de898f23b78bbbb47a1dbd5ffb5d9f953a6':
  HDFFV-9984 fix test logic
  HDFFV-9984 - correct name of ref files
  HDFFV-9984 add missing ref file
  HDFFV-9984 - add missing ref files
  HDFFV-9984 Add options to merge/prune external links during repack
 2020-08-15 16:30:55 -05:00
Allen Byrne
2d659de898 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop) 
* commit '40bf112b56c90b7e90c9ec3d7a35a78d1d12288b':
  Trivialities noticed while merging things to 1.10
 2020-08-15 12:04:56 -05:00
Dana Robinson
40bf112b56 Merge pull request #2773 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor to develop 
* commit 'c5b176594082f6e5a8b6d9140f9db1f13530e087':
  Trivialities noticed while merging things to 1.10
 2020-08-15 10:37:55 -05:00
Dana Robinson
c5b1765940 Trivialities noticed while merging things to 1.10 2020-08-15 07:32:50 -07:00
Allen Byrne
7603d2c8be HDFFV-9984 fix test logic 2020-08-14 16:39:40 -05:00
Allen Byrne
b196ddb4a8 HDFFV-9984 - correct name of ref files 2020-08-14 15:21:56 -05:00
Binh-Minh Ribler
16349c5fdd Fixed HDFFV-10933 
Description:
    Updated the original fix by Kent Y. in commit
        200a77d8c3
    - 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)
 2020-08-14 14:49:42 -05:00
Allen Byrne
a21ae8e56b HDFFV-9984 add missing ref file 2020-08-14 13:45:57 -05:00
Allen Byrne
646872cb8e HDFFV-9984 - add missing ref files 2020-08-14 13:45:31 -05:00
Allen Byrne
500d87fd1f HDFFV-9984 Add options to merge/prune external links during repack 2020-08-14 12:16:58 -05:00
mainzer
12bb6d7665 Tab to space conversions. 
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.
 2020-08-14 12:16:47 -05:00