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Author SHA1 Message Date
Dana Robinson
04b24163f7 Cleans warnings and cruft from ttsafe_attr_vlen.c 2020-08-12 15:21:38 -07:00
Dana Robinson
037bad4f72 Fixes Windows issues due to exposed pthread code 2020-08-12 15:07:15 -07:00
Allen Byrne
cecaed97f7 HDFFV-11127 - force RTLD_LOCAL in dlopen 2020-08-12 16:14:44 -05:00
Elena
752411bfda Fixed several typos in the comments found by Larry during the review. 2020-08-12 15:19:41 -05:00
Dana Robinson
7dcd7830ae Merge pull request #2754 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:testhdf5_ref_valgrind to develop 
* commit '4f0283db788fc1a0db94e7825567210021b3b594':
  Fixes a size mismatch when copying old-style to new-style references
  Fixes memory leads in trefer.c
 2020-08-12 13:54:09 -05:00
Dana Robinson
4f0283db78 Fixes a size mismatch when copying old-style to new-style references 2020-08-12 11:38:04 -07:00
Dana Robinson
ed51c0e302 Fixes memory leads in trefer.c 2020-08-12 09:52:10 -07:00
Quincey Koziol
f2681e36ae Merge remote-tracking branch 'origin/develop' into remove_unneeded_tagging 2020-08-12 11:17:52 -05:00
Quincey Koziol
3f46a380e0 Merge remote-tracking branch 'origin/develop' into namespace_cleanup_01 2020-08-12 11:17:27 -05:00
Elena
69cbfd4f9e Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~epourmal/hdf5_ep into develop 2020-08-12 08:53:45 -05:00
Elena
768f8abb18 The H5DSis_scale function was updated to return "not a dimension scale" (0) 
instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are
not written according to Dimension Scales Specification (HDFFV-10436).
 2020-08-12 08:40:11 -05:00
Dana Robinson
dca1733238 Merge pull request #2752 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor to develop 
* commit '78c6be05a84f854074a4df2e10c15a56444e4015':
  Fixes the splitter VFD test on Windows.
 2020-08-12 08:03:11 -05:00
Dana Robinson
78c6be05a8 Fixes the splitter VFD test on Windows. 2020-08-11 17:46:54 -07:00
Quincey Koziol
4083be1ff2 Merge remote-tracking branch 'origin/develop' into namespace_cleanup_01 2020-08-11 06:36:41 -05:00
Binh-Minh Ribler
1008afc457 Merge pull request #2746 in HDFFV/hdf5 from bmr_HDFFV-10591-2 to develop 
Part of HDFFV-10591 fix.

* commit 'f863d4f970c2f54298a69f95bb6a15e710e1ed75':
  Addition to HDFFV-10591
 2020-08-10 21:56:57 -05:00
Jordan Henderson
af390794f4 Merge pull request #2655 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop 
* commit '7c3d4402d730789173e413b48951fede5f6932f3':
  Fix issue in H5VL_wrap_register where datatype VOL objects are casted to H5T_t *
 2020-08-10 17:36:07 -05:00
Quincey Koziol
c48d1b0ff4 Merge remote-tracking branch 'origin/develop' into remove_unneeded_tagging 2020-08-10 13:15:13 -05:00
Quincey Koziol
98c184e130 Merge remote-tracking branch 'origin/develop' into namespace_cleanup_01 2020-08-10 13:14:02 -05:00
Quincey Koziol
79a2e34f88 Correct typos w/HGOTO_DONE & HGOTO_ERROR 2020-08-10 12:58:20 -05:00
Dana Robinson
c0ff30d239 Merge pull request #2748 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:flock_windows_fix to develop 
* commit '0ed65346033e7fbc71634d4911f9761e2ec145b2':
  Fixes flock Windows failure
 2020-08-10 11:03:35 -05:00
Binh-Minh Ribler
f863d4f970 Addition to HDFFV-10591 
Description
    Added missing parameter description and improved format.
Platforms tested:
    Linux/64 (jelly)
 2020-08-09 18:13:42 -05:00
Quincey Koziol
e1a7a1acbe Remove redundant calls to set the metadata cache tag 2020-08-08 08:44:34 -05:00
Dana Robinson
0d69520c70 Merge pull request #2741 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor to develop 
* commit 'a975a8d0eb3244d1a08afc80133a12279d1f90e5':
  Removes unsuffixed float warnings
 2020-08-07 16:29:30 -05:00
Dana Robinson
0ed6534603 Fixes flock Windows failure 2020-08-07 12:40:04 -07:00
Dana Robinson
a975a8d0eb Removes unsuffixed float warnings 
These warnings can only be addressed with gnu extensions.
 2020-08-07 11:50:22 -07:00
Quincey Koziol
5f6eec0b20 Move H5T_vlen_reclaim to package scope 2020-08-07 11:08:19 -05:00
Quincey Koziol
a2340cec3b Merge remote-tracking branch 'origin/develop' into namespace_cleanup_01 2020-08-07 10:06:34 -05:00
Dana Robinson
51ab52ad42 Merge pull request #2740 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:code_tidy to develop 
* commit '5ce2a178043d9749d30076a2e62249d9998c40ec':
  Removes staff email addresses from the repository Removes redundant C library headers from hl library
 2020-08-07 00:23:53 -05:00
Dana Robinson
5ce2a17804 Removes staff email addresses from the repository 
Removes redundant C library headers from hl library
 2020-08-06 17:58:07 -07:00
Dana Robinson
72363de1c0 Merge pull request #2730 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:file_locking_squash_2 to develop 
* commit '47ad0ac7237b464e939fe54dd129a151944d9706':
  Renames BEST-EFFORT to BEST_EFFORT for file locking env var
  Updated the file locking Fortran property list wrappers and added a test.
  Fixed missing parens in VFDs
  Minor change to header comments in file locking C++ changes.
  Squash merge of file locking fixes
 2020-08-06 18:31:41 -05:00
Quincey Koziol
8fe3cece3c Switch H5VM inline routines back to single underscope and put a comment in their header about this naming 2020-08-06 17:46:40 -05:00
Dana Robinson
47ad0ac723 Renames BEST-EFFORT to BEST_EFFORT for file locking env var 2020-08-06 15:09:59 -07:00
Dana Robinson
7391f5f26c Merge branch 'develop' into file_locking_squash_2 2020-08-06 15:08:28 -07:00
Quincey Koziol
07e4ef9da4 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.
 2020-08-06 15:56:04 -05:00
Jerome Soumagne
302dfeb11b Merge pull request #2715 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:fix_vlen_ref to develop 
* commit 'ef6db167a86e6c065d46963dbd75cd325fe83813':
  H5R: fix encoding of references that are part of compound types
 2020-08-06 14:22:29 -05:00
Dana Robinson
ee274b97f8 Merge pull request #2738 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor to develop 
* commit '91ca481ff152e7a6b0326fcdb59e506141d2d32a':
  Reverts H5FDsplitter.c changes so they don't conflict with Quincey's big cleanup patch
  Fixes -Wnull-dereference warnings around the cache logging calls
  Fixes -Wnull-dereference warning in hl/src/H5DS.c
  Adds -Wnull-dereference to the warnings we ignore in flex/bison generated code (that we have no control over).
  Fixes warnings in the splitter VFD and tests
 2020-08-06 14:11:16 -05:00
Dana Robinson
91ca481ff1 Reverts H5FDsplitter.c changes so they don't conflict with Quincey's 
big cleanup patch
 2020-08-06 08:41:27 -07:00
Dana Robinson
bd6f3bcdab Fixes -Wnull-dereference warnings around the cache logging calls 2020-08-05 23:14:40 -07:00
Dana Robinson
b1c78579da Fixes -Wnull-dereference warning in hl/src/H5DS.c 2020-08-05 22:56:15 -07:00
Dana Robinson
e327843f7a Adds -Wnull-dereference to the warnings we ignore in flex/bison 
generated code (that we have no control over).
 2020-08-05 22:51:34 -07:00
Dana Robinson
8e7f3e38a7 Fixes warnings in the splitter VFD and tests 2020-08-05 22:13:38 -07:00
Dana Robinson
482ade4657 Merge pull request #2737 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor to develop 
* commit '65e92e1d56dd2e04ebe7b7713fee9e9e38cd8849':
  Warning fixes in tools and h5test.c
 2020-08-05 21:35:41 -05:00
Dana Robinson
65e92e1d56 Warning fixes in tools and h5test.c 2020-08-05 17:15:57 -07:00
mainzer
33f35183cb 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.

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.
 2020-08-05 15:39:49 -05:00
Jordan Henderson
7c3d4402d7 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop) 
* commit 'f59bb712dec221a076728b6c582818bcf814d71a': (55 commits)
  Fixes indenting in tools test scripts
  Minor normalizations with 1.12 branch
  Fixed bad parens in H5trace.c
  Minor normalizations with hdf5_1_10
  Mingw copy disabled
  Warnings reduction in tools
  Correct reference file
  Correct h5diff filenames
  Fixed typos in error messages.
  Updated the Java tests to deal with H5Sset_extent_none changes
  Fixed additional typos in tselect.c comments.
  Fixes typo in tselect.c
  Updates H5Sset_extent_none() to set H5S_NULL
  Only one line needed to compare
  Revert err file
  Minor normalization with 1.10 branch
  Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)
  revert error-stack enable
  Minor normalization with 1.10.
  Add release notes for tools
  ...
 2020-08-04 20:43:37 -05:00
David Young
7b48e3409a 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:

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
 2020-08-04 16:39:57 -05:00
David Young
fa7f8ad2f3 Improve code readability: extract common subexpressions into temporary 
variables.
 2020-08-04 16:28:04 -05:00
Dana Robinson
f59bb712de Merge pull request #2733 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor to develop 
* commit 'be02566f49f953bc80c5b5018871138e201ea633':
  Fixes indenting in tools test scripts
 2020-08-04 12:12:45 -05:00
Dana Robinson
be02566f49 Fixes indenting in tools test scripts 2020-08-04 09:14:36 -07:00
Dana Robinson
b2c90cc84e Updated the file locking Fortran property list wrappers and added 
a test.
 2020-08-03 18:43:19 -07:00