2
0
mirror of https://github.com/HDFGroup/hdf5.git synced 2024-12-27 08:01:04 +08:00
Commit Graph

15921 Commits

Author SHA1 Message Date
Dana Robinson
978e83fb5b Merge branch 'develop' into eoc_valgrind_bugfix 2016-11-28 13:01:10 -05:00
Quincey Koziol
1921f7f4ad Merge pull request in HDFFV/hdf5 from ~KOZIOL/hdf5:develop to develop
* commit '2cb2d5a533c2de7503014da3250c3088e1ba089d':
  Remove "collective write list" parameter from H5C__flush_single_entry() as it is only used in a couple of places.  The collective write list has been moved to be internal to the cache data structure instead.
  Eliminate unnecessary data structure for parallel collective metadata cache I/O
2016-11-28 10:30:46 -06:00
Dana Robinson
4ddc4a602f Merge pull request in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_memfix to develop
Fix for tfile.c valgrind issues.

* commit '191cc19ae0a2feb72d2171a0808fdc71a3b862dd':
  Added vlen reclaim functions to a test in tfile.c that leaks memory.
2016-11-28 09:37:23 -06:00
Dana Robinson
4ab127aa9c Merge pull request in HDFFV/hdf5 from ~DEROBINS/hdf5_der:gitignore to develop
Updated .gitignore to be more manageable and future-proof.

* commit '1aa2373b2e1a651bec507dcb14a89b51815a972c':
  Simplified .gitignore by using patterns.
  Added src/H5config.h.in~ to .gitignore.
2016-11-28 07:44:15 -06:00
Quincey Koziol
2cb2d5a533 Remove "collective write list" parameter from H5C__flush_single_entry() as it
is only used in a couple of places.  The collective write list has been moved
to be internal to the cache data structure instead.
2016-11-28 01:26:33 -06:00
Quincey Koziol
460b573a73 Eliminate unnecessary data structure for parallel collective metadata cache I/O 2016-11-27 19:00:12 -06:00
Dana Robinson
1aa2373b2e Simplified .gitignore by using patterns. 2016-11-27 16:05:03 -05:00
Dana Robinson
2c3d02e6e5 Merge branch 'develop' into eoc_valgrind_bugfix 2016-11-26 13:11:08 -05:00
Dana Robinson
a8d1aff235 Tentative fix for valgrind issues related to EoC.
Adds /*out*/ parameters to H5O_close() and H5F_try_close() so
that H5D/G_close() will know when H5O_close() has triggered a
file close and thus the file struct is not reliable.

Also removes the H5F_CLOSING() macro and related which were
formerly used to check if the file was closing.
2016-11-26 10:47:32 -05:00
Dana Robinson
c9bbc2f1cc Added src/H5config.h.in~ to .gitignore. 2016-11-25 21:09:45 -05:00
Quincey Koziol
61e0a035bc Merge pull request in HDFFV/hdf5 from ~KOZIOL/hdf5:develop to develop
* commit 'ea4d18c3d9c3b6c77030abdf2f0509bc68224559':
  Remove unnecessary assert.
  Add a flag for H5C__flush_single_entry() to allow the parallel code to request that images for entries be generated, even when not writing the entry from an MPI rank.
2016-11-25 19:47:25 -06:00
Quincey Koziol
ea4d18c3d9 Remove unnecessary assert. 2016-11-25 17:18:52 -06:00
Quincey Koziol
98e9194d4f Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~koziol/hdf5 into develop 2016-11-25 16:08:34 -06:00
Quincey Koziol
1071d8bf73 Add a flag for H5C__flush_single_entry() to allow the parallel code to request
that images for entries be generated, even when not writing the entry from an
MPI rank.
2016-11-25 16:07:23 -06:00
Dana Robinson
191cc19ae0 Added vlen reclaim functions to a test in tfile.c
that leaks memory.
2016-11-23 16:45:47 -05:00
Dana Robinson
b0321f7e7d Merge pull request in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_memfix to develop
Fixed a few memory issues in the tests.

* commit 'e2863ca880a6983558d3ba3e5219164a57287f04':
  Fixed a few memory problems in test/cache_logging.c and test/h5test.c (which show up in test/vfd.c).
2016-11-23 12:58:12 -06:00
Allen Byrne
4bb51bbbaa Merge pull request in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit 'c2e60909e35d988e86d78b7c8bfc0d2d51c4e75f':
  Add test to memcheck ignore and increase cache test timeout
2016-11-23 09:16:22 -06:00
Dana Robinson
e2863ca880 Fixed a few memory problems in test/cache_logging.c and
test/h5test.c (which show up in test/vfd.c).
2016-11-22 20:55:03 -05:00
Allen Byrne
c2e60909e3 Add test to memcheck ignore and increase cache test timeout 2016-11-22 15:04:34 -06:00
Dana Robinson
fff898558e Merge pull request in HDFFV/hdf5 from ~DEROBINS/hdf5_der:eoc_valgrind_bugfix to develop
Applied the evict-on-close "check for file closing" change that was successful for groups to datasets.

* commit '88b6f2e24cafcfaffe7d99ab6c5afc2290ce93b4':
  Added the H5F_CLOSING() check that makes valgrind happy in the evict-on-close code in H5G_close() to H5D_close().
2016-11-22 08:54:47 -06:00
Dana Robinson
72ecaf0940 Merge branch 'develop' into eoc_valgrind_bugfix 2016-11-21 17:48:03 -05:00
Dana Robinson
88b6f2e24c Added the H5F_CLOSING() check that makes valgrind happy in
the evict-on-close code in H5G_close() to H5D_close().
2016-11-21 17:45:46 -05:00
Dana Robinson
a44d7b8754 Merge pull request in HDFFV/hdf5 from ~DEROBINS/hdf5_der:eoc_valgrind_bugfix to develop
Two minor evict-on-close changes:

* Fix for a valgrind-reported issue where invoking EoC behavior when the file is closing leads to garbage file data being passed to downstream calls. The solution is to ignore EoC when the file is closing anyway.

* Added brackets so an infinite loop that arises when evicting tagged entries (due to pinned entries preventing progress) raises an error instead.

* commit '4e7b19f8260a7adb0e3b3df30e2d8289fccdcca6':
  Two minor cache changes:
2016-11-21 12:28:48 -06:00
Quincey Koziol
cbd05409c5 Merge pull request in HDFFV/hdf5 from ~KOZIOL/hdf5:develop_merge_revise_chunks_09 to develop
* commit '3b0c2b24da5689990c4bc0fcd3afecdf063086c8':
  Bring over support for retrying metadata cache entry loads, along with all the supporting metadata cache callback changes, etc.
2016-11-20 15:33:13 -06:00
Dana Robinson
4e7b19f826 Two minor cache changes:
* Evict-on-close behavior is now skipped when the file is closing.
  This fixes a potential issue discovered by Valgind on Windows
  where potentially garbage data would be availble for manipulation.

* Added brackets to some code in the tagged entry evict iterators
  so that the flag that determines if progress was made only gets
  set if things are actually evicted. This prevents an infinite
  loop (and emits an error) when pinned entries prevent eviction
  and thus progress.
2016-11-20 11:57:46 -05:00
Quincey Koziol
3b0c2b24da Bring over support for retrying metadata cache entry loads, along with all the
supporting metadata cache callback changes, etc.
2016-11-20 04:24:57 -08:00
Quincey Koziol
f6ad126673 Merge pull request in HDFFV/hdf5 from ~KOZIOL/hdf5:develop_merge_revise_chunks_08 to develop
* commit 'eba0ff43c968ef9a0b09edf19c1e337cfcae0816':
  Remove 'clear' callback from metadata cache client interface, using the new 'entry cleaned' notify action innstead.
2016-11-17 21:03:43 -06:00
Quincey Koziol
eba0ff43c9 Remove 'clear' callback from metadata cache client interface, using the
new 'entry cleaned' notify action innstead.
2016-11-17 17:48:21 -08:00
Quincey Koziol
248a93cde8 Merge pull request in HDFFV/hdf5 from ~KOZIOL/hdf5:develop_merge_revise_chunks_07 to develop
* commit 'be27e1ad79dfa0507f589b29d938b7e1020a5b2d':
  Remove explicit support within the metadata cache for tracked compressed entries, they are now completely handled in the clients.
2016-11-17 16:25:28 -06:00
Quincey Koziol
be27e1ad79 Remove explicit support within the metadata cache for tracked compressed
entries, they are now completely handled in the clients.
2016-11-17 12:58:04 -08:00
Allen Byrne
fe849d26cd Merge pull request in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit '45d817af9ca4db92db0eba81e4c330380c26a41e':
  Repair comment chars to C style
2016-11-17 13:34:50 -06:00
Allen Byrne
45d817af9c Repair comment chars to C style 2016-11-17 09:28:18 -06:00
Binh-Minh Ribler
e10c0e7894 Merge pull request in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr_cpp:develop to develop
Removed the obsolete macros H5_NO_NAMESPACE and H5_NO_STD from the examples.

* commit '51ea7245dfdbda8311961ea4755c8d9c8ce99d76':
  Description:         Removed H5_NO_NAMESPACE from the examples.  They were missed from the         previous cleanup.     Platforms tested:         Linux/32 2.6 (jam)         Linux/64 (platypus)
2016-11-15 10:29:28 -06:00
Binh-Minh Ribler
51ea7245df Description:
Removed H5_NO_NAMESPACE from the examples.  They were missed from the
        previous cleanup.
    Platforms tested:
        Linux/32 2.6 (jam)
        Linux/64 (platypus)
2016-11-14 16:04:27 -06:00
Quincey Koziol
4c708cc78d Merge pull request in HDFFV/hdf5 from ~KOZIOL/hdf5:develop_merge_revise_chunks_06 to develop
* commit 'd4591ff54d9319346f49a3bc67431f0fa26a8d65':
  Bring over new 'notify' metadata cache client callback actions for when an entry is cleaned / dirtied or its [flush dependency] child entry is cleaned / dirtied.
2016-11-12 19:44:57 -06:00
Quincey Koziol
d4591ff54d Bring over new 'notify' metadata cache client callback actions for when an
entry is cleaned / dirtied or its [flush dependency] child entry is cleaned /
dirtied.
2016-11-12 14:01:30 -08:00
Quincey Koziol
d183e9a1a2 Merge pull request in HDFFV/hdf5 from ~KOZIOL/hdf5:develop_merge_revise_chunks_05 to develop
* commit '1c6924f18bd8fdad63c4f191c00605092c17fa6e':
  Refactor H5O code to clean up message allocation, align cache deserialize code with revise_chunks changes, and remove unused "message locking" code.
2016-11-12 13:01:58 -06:00
Quincey Koziol
99f123098e Merge pull request in HDFFV/hdf5 from ~KOZIOL/hdf5:develop_merge_revise_chunks_04 to develop
* commit '80ac4343cdf0640b114b846db87c091c6e7c66a6':
  Align w/minor cleanups in revise_chunks branch.
2016-11-12 13:01:32 -06:00
Quincey Koziol
1c6924f18b Refactor H5O code to clean up message allocation, align cache deserialize code
with revise_chunks changes, and remove unused "message locking" code.
2016-11-12 01:05:47 -08:00
Quincey Koziol
80ac4343cd Align w/minor cleanups in revise_chunks branch. 2016-11-11 23:14:58 -08:00
Quincey Koziol
70938cbf28 Merge pull request in HDFFV/hdf5 from ~KOZIOL/hdf5:develop to develop
* commit '31ffc1e72687b4d27602a044565bde6b1e9d803f':
  Clean up cache code to eliminate dead-ends and unify code.
2016-11-11 17:13:03 -06:00
Dana Robinson
0c542a5b12 Merge pull request in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop to develop
Moved Win32 variables in log VFD to top of function like in revise_chunks.

* commit 'be0dfa3e22bcd1454215e2a348756bf21e749044':
  Moved Win32 variables to top of function in H5FDlog.c.
2016-11-11 16:26:48 -06:00
derobins
be0dfa3e22 Moved Win32 variables to top of function in H5FDlog.c. 2016-11-11 14:16:24 -05:00
Dana Robinson
dd4f4e6f76 Merge pull request in HDFFV/hdf5 from ~DEROBINS/hdf5_der:restore_script_dev to develop
Added autogen "undo" script to bin/

* commit '57a8bb60811b6d788d586836674ab8ea779131d3':
  Adds a script to undo the action of autogen.sh. Useful when git complains about Makefile.in clobbers, etc.
2016-11-10 15:03:36 -06:00
Quincey Koziol
31ffc1e726 Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~koziol/hdf5 into develop_merge_revise_chunks_03 2016-11-10 12:50:11 -08:00
Quincey Koziol
492eae3995 Clean up cache code to eliminate dead-ends and unify code. 2016-11-10 12:49:22 -08:00
Allen Byrne
09f70066db Merge pull request in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop
* commit 'e40faaa8fbc8490af626dd9da3ff741284327e65':
  Update installdir format for windows
  Correct name of list
  Factor out path
  On windows there could be a conflict when two processes try to read the same file
2016-11-10 12:22:56 -06:00
Allen Byrne
e40faaa8fb Update installdir format for windows 2016-11-10 12:22:11 -06:00
Allen Byrne
17ea6aac20 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'ea55d4192e14411e3c67facac57bb547b6fc3402':
  Added subdir-objects to AM_INIT_AUTOMAKE. Quiets automake warnings about forward-compatibility after tools split.
2016-11-10 09:24:58 -06:00
Dana Robinson
ea55d4192e Merge pull request in HDFFV/hdf5 from ~DEROBINS/hdf5_der:subdir-objects to develop
Adds subdir-objects to AM_INIT_AUTOMAKE to quiet forward-compatibility warnings from automake after the tools directory rework.

* commit 'a203f2369af79f4b2b838ab457d81749456c2a4b':
  Added subdir-objects to AM_INIT_AUTOMAKE. Quiets automake warnings about forward-compatibility after tools split.
2016-11-10 09:05:57 -06:00