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Author SHA1 Message Date
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
Dana Robinson
bd685b0e80 Fixed missing parens in VFDs 2020-08-03 15:47:46 -07:00
Dana Robinson
6e71992502 Minor change to header comments in file locking C++ changes. 2020-08-03 09:35:17 -07:00
Dana Robinson
bc1bed2c55 Squash merge of file locking fixes 2020-08-03 09:11:27 -07:00
Dana Robinson
33c0016eb6 Merge pull request #2727 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor to develop 
* commit 'b9de162eae800a9459f0f1f07d2b043f73f8a907':
  Minor normalizations with 1.12 branch
  Fixed bad parens in H5trace.c
 2020-08-02 18:22:54 -05:00
Dana Robinson
b9de162eae Minor normalizations with 1.12 branch 2020-08-01 10:26:22 -07:00
Dana Robinson
4486905131 Merge branch 'develop' into develop_minor 2020-08-01 10:26:11 -07:00
Dana Robinson
66ce984dee Merge pull request #2723 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor to develop 
* commit '08dca47475f41e93348cf0c2ea708e787c232014':
  Minor normalizations with hdf5_1_10
 2020-08-01 11:36:59 -05:00
Dana Robinson
64ffb37ff6 Fixed bad parens in H5trace.c 2020-07-31 12:23:57 -07:00
Dana Robinson
08dca47475 Minor normalizations with hdf5_1_10 2020-07-31 11:40:29 -07:00
Allen Byrne
5007f82225 Merge pull request #2722 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop 
* commit 'fc57490e02835ddfce644135e93e893f77b379d3':
  Mingw copy disabled
 2020-07-31 13:26:17 -05:00
David Young
651facc144 Use PRIu32 and "zu" formats. Delete some casts from size_t. 2020-07-31 10:34:27 -05:00
Allen Byrne
fc57490e02 Mingw copy disabled 2020-07-31 07:50:11 -05:00
Dana Robinson
50f404c887 Merge pull request #2720 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor to develop 
* commit 'c8ba30d965f0342e5725a11cb562dfb22c8a8d24':
  Minor normalization with 1.10 branch
 2020-07-30 20:16:17 -05:00
David Young
0bb87534a6 Merge remote-tracking branch 'hdffv/develop' into rebased-fprintf-experiment 2020-07-30 18:15:09 -05:00
David Young
3e91eeb270 I'm taking a guess that this code intended to point the 2-digit wide 
hexadecimal octet values, not 2 character-wide pointers to the bytes.  The %02p
format, which is a GNU-ism, disagreed with GCC 8.3.0 and the option flags we
use.
 2020-07-30 18:01:29 -05:00
David Young
ea21b3f89f %08p is not portable, it's a GNU-ism. Use %8p, instead. Squashes a GCC error. 2020-07-30 17:54:04 -05:00
David Young
ddd5e4a6c3 Add format string macros PRI[doxX]HID for hid_t and use PRIdHID. 2020-07-30 17:53:18 -05:00
David Young
36befb6bfe Use HDva_copy() and introduce a bunch of compatbility format-string constants 
for uppercase hexadecimal strings, `PRIX...`.  Should fix the VS2010 errors
that Allen mentioned:

H5system.obj : error LNK2019: unresolved external symbol va_copy referenced in  function HDvasprintf                                                            [C:\autotest\hdf5trunk-StdShar-code-vs10\build\ctest\hdfbld\src\hdf5-shared.vcxproj]                                                                            2                                                                               ..\..\..\hdfsrc\test\h5test.c(2103): error C2146: syntax error : missing ')'    before identifier 'PRIX64'                                                      [C:\autotest\hdf5trunk-StdShar-code-vs10\build\ctest\hdfbld\test\hdf5_test-static.vcxproj]
 2020-07-30 17:32:03 -05:00
Dana Robinson
c8ba30d965 Merge branch 'develop' into develop_minor 2020-07-30 15:23:54 -07:00
Allen Byrne
88aa0d5c76 Merge pull request #2718 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop 
* commit 'ff4a9d0ec2e85cf15f769006e92e756a79869ab8':
  Warnings reduction in tools
 2020-07-30 11:46:39 -05:00
Allen Byrne
ff4a9d0ec2 Warnings reduction in tools 2020-07-30 11:26:14 -05:00
Allen Byrne
2ece66e999 Merge pull request #2716 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop 
* commit '6a1cf090c6a2f970084c714a2f75a31d68a0a6a8':
  Correct reference file
  Correct h5diff filenames
 2020-07-29 15:40:05 -05:00
Allen Byrne
6a1cf090c6 Correct reference file 2020-07-29 12:56:03 -05:00
Allen Byrne
1f7fa50137 Correct h5diff filenames 2020-07-29 08:24:30 -05:00
Binh-Minh Ribler
cf4e78b3c9 Merge pull request #2711 in HDFFV/hdf5 from bmr-HDFFV-11120 to develop 
Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)

* commit '707e30c6be1954c0027374124207e46caae68cbc':
  Fixed typos in error messages.
  Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)
 2020-07-28 19:08:19 -05:00
Jerome Soumagne
ef6db167a8 H5R: fix encoding of references that are part of compound types 
Add corresponding test and some debug information
 2020-07-28 16:36:19 -05:00
Binh-Minh Ribler
707e30c6be Fixed typos in error messages. 2020-07-28 12:20:13 -05:00
Dana Robinson
b201a78b33 Merge pull request #2714 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:h5s_set_extent_none to develop 
* commit 'e4603ff8a171e82de6373ba6eddcf59d5eeab5aa':
  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
 2020-07-28 11:29:04 -05:00
Dana Robinson
e4603ff8a1 Updated the Java tests to deal with H5Sset_extent_none changes 2020-07-28 08:28:38 -07:00
Allen Byrne
10e59f6ba4 Merge pull request #2697 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop 
* commit '5857bb817019b8513f796c9564de3f1845f9a44a':
  Only one line needed to compare
  Revert err file
  revert error-stack enable
  Add release notes for tools
  add test file ext
  Correct file name in test
  Tools refactor
 2020-07-28 07:13:18 -05:00
Dana Robinson
c78326eb92 Fixed additional typos in tselect.c comments. 2020-07-27 17:40:25 -07:00
Dana Robinson
dbba42c306 Fixes typo in tselect.c 2020-07-27 17:38:41 -07:00
Dana Robinson
91f5320ff0 Updates H5Sset_extent_none() to set H5S_NULL 
The API call used to set the internal H5S_NO_CLASS value which
produced errors when such a dataspace was passed to many other API
calls.

Fixes HDFFV-11027
 2020-07-27 17:32:01 -07:00
Allen Byrne
5857bb8170 Only one line needed to compare 2020-07-27 16:15:50 -05:00
Allen Byrne
799f2891c2 Revert err file 2020-07-27 15:47:10 -05:00
Dana Robinson
6e740457cc Minor normalization with 1.10 branch 2020-07-27 11:09:05 -07:00