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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Jordan Henderson2017-08-111-3/+11
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| * Fix for HDFFV-10217 infinite loop in H5VM_power2up().Vailin Choi2017-07-101-3/+11
| | | | | | | | | | | | The function H5VM_power2up() returns the next power of 2 for n. When n exceeds 2^63, it overflows and becomes 0 causing the infinite looping. The fix ensures that the function checks for n >= 2^63 and returns 0.
* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Jordan Henderson2017-07-051-103/+107
|\ \ | |/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '6428a637752753cc8a9007c0c3c38b9ea9cc97fd': (165 commits) Skip HDFFV-10160 filenotclosed test for split/multi driver Temporary skip this test for split/multi driver. Further investigation to resolve the failure is needed. Please enter the commit message for your changes. Lines starting More minor whitespace cleanup Fixed a minor comment typo in H5R.c * Reverted removal of H5I_REFERENCE to avoid breaking binary compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19() in tmisc.c. Added missing free() call to test_misc19(). Purged the unused H5I_REFERENCE from the library. Added a test for VFD IDs to testhdf5. Revert "Partial removal of NDEBUG ifdefs from the library." Partial removal of NDEBUG ifdefs from the library. Removed compiler flag cleanup since Solaris chokes on it. Fix for HDFFV-10160 Modifications to fix the assertion/abort failure when the application does not close the file. Fixed a bug in autotools Fortran processing where a test for the presence of a C long double type always returned true. Updated the --enable-debug/production handling in configure.ac so that it more reliably indicates that the configure option can no longer be used. Previously, using --enable-debug="", etc. would not trigger an error (even though such usage is unlikely). Added awk processing to remove extraneous whitespace from H5_ flags in configure. Fixed a comment in configure.ac HDFFV-10219 another mode change HDFFV-10219 change subset to use BINARY mode for h5dump HDFFV-10219 default input binary to NATIVE Set default of var to NATIVE HDFFV-10219 - disable h5dump tests until h5import NATIVE is fixed ...
| * Revert "Merge pull request #567 in HDFFV/hdf5 from ↵Dana Robinson2017-06-091-24/+16
| | | | | | | | | | | | | | ~DEROBINS/hdf5_der:develop to develop" This reverts commit 4242753848c44ab3b5d226e66225eac2f64db314, reversing changes made to b0e79fe6dd20ec7aa1b3e5f0f8b370639a4ef5bd.
| * * Made STATIC free lists EXTERN for H5O_layout_t.Dana Robinson2017-06-071-1/+1
| | | | | | | | * Made all non-global instances of H5O_layout_t in H5Pdcpl.c dynamic.
| * Updated H5O_layout_t dynamic work to use the H5FL interface.Dana Robinson2017-06-071-2/+5
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| * Made some H5O_layout_t stack allocations dynamic (quiets warnings).Dana Robinson2017-06-061-16/+21
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| * Fixed many minor warnings.Dana Robinson2017-05-251-97/+103
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| * Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | | | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* | Merge pull request #2 in ~JHENDERSON/hdf5 from HDFFV/hdf5:develop to ↵Jordan Henderson2017-03-101-3/+2
|\ \ | |/ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | feature/parallel_filters * commit '56e5b4ed05fb3bad51c226ec5b567871a45e0bce': (112 commits) updated AM_SILENT_RULES syntax Added a check for AM_SILENT_RULES before enabling it. Fix alignment Fix vds tests Correct result code for strings test Add extension to filename HDFFV-10128 fix string compare and add tests Description: Only format changes: mostly tabs vs. spaces Platforms tested: Linux/64 (jelly) - very minor Lowercase math and set CMake commands Added "flush" and "refresh" to testflushrefresh.sh error output so it's easier to see where errors in the script occur. Misc. small cleanups to sync against incoming page buffering changes. Update CMake formatting Update CMake files and formatting Normalize against incoming page buffering changes. HDFFV-10120 verify nozlib checking with tools tests cmake non-code typo Correct issues from pull request reviews. Corrected version of 4b5e05c084f93c35dae946c2c9e814d565a613b0: Fix some more signed -> unsigned value issues with cache data structures, also misc. style cleanups. All to align w/incoming page_buffering changes. Revert "Fix some more signed -> unsigned value issues with cache data structures, also" Added virtual to list ...
| * Update sanity checks for dataset refresh code.Quincey Koziol2017-01-311-3/+2
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* | Switch working branch from master to developJordan Henderson2017-01-131-4/+0
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* Tentative fix for valgrind issues related to EoC.Dana Robinson2016-11-261-5/+6
| | | | | | | | | 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.
* Added the H5F_CLOSING() check that makes valgrind happy inDana Robinson2016-11-211-1/+1
| | | | the evict-on-close code in H5G_close() to H5D_close().
* - Removed BRANCH.txt and MANIFEST entryDana Robinson2016-09-301-0/+1
| | | | - Fixed a missing line in H5Dint.c
* - Removed non-implemented code from H5Gint.cDana Robinson2016-09-301-8/+0
| | | | | - Removed commented-out debug code from H5Dint.c - Added blank lines to eliminate delta in a fortran file.
* Merge branch 'develop' into evict_on_closeDana Robinson2016-09-141-0/+5
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| * [svn-r30143] Fix for HDFFV-9940.Vailin Choi2016-07-041-0/+5
| | | | | | | | Tested on jam, osx1010test, moohan, platypus, emu, kite, kituo, mayll, ostrich, quail.
* | [svn-r30108] Moved group flush and evict code to H5G_close from H5Gclose.Dana Robinson2016-06-261-1/+1
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* | [svn-r30107] Moved dataset flush and evict code to H5D_close from H5Dclose.Dana Robinson2016-06-251-14/+30
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* [svn-r30075] Description:Quincey Koziol2016-06-141-0/+187
| | | | | | | | | | Bring object/dataset/group/named datatype features from revise_chunks branch to trunk. Also CMake support for h5format_convert and a bunch of misc. cleanups. Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r30068] Description:Quincey Koziol2016-06-131-0/+8
| | | | | | | | Bring metadata cache corking to trunk. Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29969] Description:Quincey Koziol2016-05-291-24/+55
| | | | | | | | | | | Bring r29934 from revise_chunks branch to trunk: (1) Fix for HDFFV-9434: throw an error instead of assertion when v1 btree level hits the 1 byte limit. (2) Modifications to better handle error recovery when conversion by h5format_convert fails. Tested on: MacOSX/64 10.11.5 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29924] Description:Quincey Koziol2016-05-121-0/+120
| | | | | | | | Bring h5format_convert tool from revise_chunks branch to trunk. Tested on: MacoSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29884] VDS correction for get_space_status, with test change.Allen Byrne2016-05-041-32/+40
| | | | | Add new files for repack tests. Add repack tests for VDS files.
* [svn-r29850] Description:Quincey Koziol2016-05-011-12/+99
| | | | | | | | | | Bring H5DOappend(), H5P[s|g]et_object_flush_cb, and H5P[s|g]et_append_flush from revise_chunks branch to trunk. Brings along updated metadata cache entry tagging, and the internal object flush routine. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29635] Description:Quincey Koziol2016-04-051-0/+5
| | | | | | | | | Bring support for earray and v2 B-trees from revise_chunks branch to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29612] Description:Quincey Koziol2016-04-031-21/+26
| | | | | | | | | Bring updated layout and EFL property comparisons and new "latest format" flags from revise_chunks branch. Tested on: MacOSX/64 10.11.4 (amazon) w/serial, parallel & production (h5committest forthcoming)
* [svn-r29607] Description:Quincey Koziol2016-04-021-5/+13
| | | | | | | | | Bring "don't filter partial edge chunks" capability from revise_chunks to trunk. Tested on: MacOSX/64 10.11.4 (amazon) w/debug, production & parallel (h5committest forthcoming)
* [svn-r29421] Fix for HDFFV-9516.Dana Robinson2016-03-151-0/+12
| | | | | | | | Corrects a problem where H5Dget_access_plist() returns a dapl that does not contain all dapl fields. Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1 autotools serial
* [svn-r29202] Fix for unknown message HDFFV-9697.Vailin Choi2016-02-241-2/+8
| | | | Tested on jam, ostrich, platypus, kite, quail, osx1010test, emu, mayll, moohan.
* [svn-r29182] Re-commit of HDFFV-8740 fix, which adds the ability to configureDana Robinson2016-02-221-2/+111
| | | | | | | | | | | | external dataset storage path behavior. This check-in fixes a bug in the original check-in where the external path stored in the file struct was not copied on reopen causing subsequent dataset operations to fail. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 autotools serial w/ fortran and C++ autotools parallel (MPICH 3.1.4) w/ fortran
* [svn-r29084] Revert of:Dana Robinson2016-02-111-111/+2
| | | | | | | | | | | | | | | r29069 and 72 (gheap cleanup) r29041 and 43 (HDFFV-8740 external storage) These cause problems in the daily tests. They will be re-introduced when their respective problems have been addressed. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 autotools serial (check-vfd) w/ Fortran and C++ autotools parallel w/ Fortran CMake serial
* [svn-r29081] - merge in the phdf5_metadata_opt/ branch with the collective ↵Mohamad Chaarawi2016-02-101-5/+5
| | | | | | | | metadata optimizations. - rename H5AC_dxpl_id to H5AC_ind_read_dxpl_id and update all usage in the library tested on bb-8 with parallel and serial.
* [svn-r29057] added dxpl type checking when debug mode is enabled ↵Mohamad Chaarawi2016-02-071-20/+33
| | | | | | (H5_DEBUG_BUILD) tested on bb-8 with Serial and Parallel, debug and production builds.
* [svn-r29041] Patch from Steffen Kiess that allows a relative path to be ↵Dana Robinson2016-02-041-2/+111
| | | | | | | | | | | specified for external dataset files set via H5Pset_external(). Resolves HDFFV-8740 Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 autotools serial
* [svn-r28950] - remove META_FLUSH_COLLECTIVELY property for delayed sanity ↵Mohamad Chaarawi2016-01-211-4/+4
| | | | | | | | | | checks from metadata dxpls - remove H5AC_ind_dxpl_id and use only H5AC_dxpl_id everywhere instead. - remove flush_me_collectively flag from cache entries - add a collective sanity check (MPI_Barrier) for every HDF5 API routine that could possibly touch the file. This is trigerred when the environment variable H5_COLL_API_SANITY_CHECK is set to a non 0 digit. tested on BB-8 with serial and parallel.
* [svn-r28723] Description:Quincey Koziol2015-12-221-0/+5
| | | | | | | | | Bring over rest of performance improvements for extending chunked datasets and normalize against revise_chunks branch. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel) (h5committest forthcoming)
* [svn-r28646] Minor normalization with revise_chunks.Dana Robinson2015-12-141-7/+5
| | | | | | | | | Also purged obsolete /*ARGSUSED*/ from the library. Tested on: Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial only (these changes have been in revise_chunks for a long time)
* [svn-r28606] Description:Quincey Koziol2015-12-131-43/+36
| | | | | | | | | | Revisions to normalize revise chunks vs. trunk, plus push dataset metadata changes into the cache immediately (instead of holding them within the dataset data structures). Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest not required on this branch)
* [svn-r28452] Description:Quincey Koziol2015-11-231-2/+2
| | | | | | | | Normalization changes against revise_chunks branch. Tested on: MacOSX/64 10.11.1 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r27946] Brought VDS branch in sync with trunk (up to r27945).Dana Robinson2015-10-041-37/+11
|\ | | | | | | | | | | | | | | Tested on Ubuntu 15.04 (Linux 3.19 x86_64), gcc 4.9.2, MPICH 3.1.4 and CMake 3.3.2. - Autotools serial w/ Fortran, C++ - Autotools parallel w/ Fortran - CMake serial w/ Fortran, C++
| * [svn-r27939] Remove H5D__iterate and use H5S_select_iterate directlyJerome Soumagne2015-10-021-37/+11
| | | | | | | | | | Add internal library callback to H5S_select_iterate to avoid having to pass hid_t objects internally
* | [svn-r27835] Description:Quincey Koziol2015-09-211-82/+206
|\ \ | |/ | | | | | | | | | | | | Sync w/trunk. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest not required on this branch)
| * [svn-r27811] Description:Quincey Koziol2015-09-161-42/+128
| | | | | | | | | | | | | | | | | | | | | | Refactor property list code to "deep copy" properties in the correct way, retraining the rest of the library to copy & release things correctly. This cleans up another batch of memory leaks, etc. within the library. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/32 2.6.x (jam) w/serial & parallel (h5committest forthcoming)
| * [svn-r27768] Description:Quincey Koziol2015-09-141-40/+73
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* | [svn-r27630] Description:Quincey Koziol2015-08-311-47/+56
|\ \ | |/ | | | | | | | | | | | | Bring in changes from the trunk, through r27628. Tested on: MacOSX/64 10.10.5 (amazon) w/serial (h5committest not required on this branch)
| * [svn-r27618] Description:Quincey Koziol2015-08-291-2/+4
| | | | | | | | | | | | | | | | | | | | Align w/vds branch: Remove extraneous sieve buffer flush in chunk flush callback, and move error check out of the middle of retrieving properties for dataset. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest forthcoming)
| * [svn-r27615] Description:Quincey Koziol2015-08-291-40/+47
| | | | | | | | | | | | | | | | | | Protect dataset that's closing from being flushed again, if it's the last one holding a file open. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest forthcoming)
| * [svn-r27612] Description:Quincey Koziol2015-08-291-3/+67
| | | | | | | | | | | | | | | | | | Align w/vds branch: Whitespace cleanup, move common code for opening a dataset into a new routine, misc. style cleanups. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel (h5committest upcoming)
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