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* [svn-r21603] Purpose: Add generic skip list implementationNeil Fortner2011-10-1813-48/+100
| | | | | | | | | | | | | Description: Added new H5SL_TYPE_GENERIC skip list type, which uses void *'s as keys and a client-supplied callback for key comparison. This was added to support the upcoming "merge named datatype" feature for H5Ocopy, but may be used in other places as well. Also added testing. Also fixed a potential bug with the H5SL_TYPE_OBJ implementation, and added testing for that. Tested: jam, koala, heiwa (h5committest), durandal
* [svn-r21601] Converted some C stdlib functions to use the HD prefix in ↵Dana Robinson2011-10-181-19/+19
| | | | | | H5Omtime.c Tested on local linux (minor change)
* [svn-r21587] Snapshot version 1.9 release 95HDF Tester2011-10-162-3/+3
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* [svn-r21561] Description:Quincey Koziol2011-10-143-29/+22
| | | | | | | | | | | | Correct error in loading local heap prefix & data block from the file. Sometimes the local heap's prefix could be loaded before the data block (e.g. using H5Oget_info), but then when the data block was loaded later, the free list information would get lost, causing the heap's size to grow larger than necessary. This is Jira bug #HDFFV-7767 Tested on: Mac OS X/32 10.7.2 (amazon) w/debug (h5committest coming up)
* [svn-r21556] Purpose: Fix bug in H5OcopyNeil Fortner2011-10-1317-290/+266
| | | | | | | | | | | | | Description: H5Ocopy could get confused when copying a named datatype containing an attribute which used that named datatype as its datatype. This happened because H5Ocopy would recurse into the attribute's datatype before the object the attribute was in was fully copied (i.e. before the "post-copy" pass). Modified H5Ocopy to avoid recursing before the post-copy step in this case. Required many changes, including to how non-committed shared messages are copied. Tested: jam, koala, heiwa (h5committest); durandal
* [svn-r21546] Reverts 21497 (deep string copy of log file name). This string ↵Dana Robinson2011-10-131-2/+4
| | | | is copied correctly deep in the H5P code. Tested on local linux (trivial change).
* [svn-r21529] Description:Quincey Koziol2011-10-122-3/+75
| | | | | | | | Update tracing information with new types introduced in "actual I/O mode" query routines. Tested on: bin/reconfigure on jam
* [svn-r21518] - Added definition for HDfseek() to be used later.Dana Robinson2011-10-111-1/+5
| | | | | | - Added comment about requiring _O_BINARY being set on Windows to avoid CR-LF issues. Tested on Windows (minor changes).
* [svn-r21517] - Added checks for clock_gettime() to configure.in.Dana Robinson2011-10-111-0/+3
| | | | | | | | Tested on Linux, FreeBSD, Solaris, MacOSX to ensure they are found correctly and everything builds. No code currently relys on clock_gettime(). - Brought Windows and VMS H5pubconf.h files into sync with the Linux file. Tested on Windows. Ray will test on VMS when this is pushed to the 1.8.x branch.
* [svn-r21510] Change to comments.Dana Robinson2011-10-101-23/+7
| | | | Just checked to make sure it still compiled on Windows.
* [svn-r21508] Revoked svn check-ins 20913 and 20921 (fix for HDFFV-7579) ↵Dana Robinson2011-10-104-178/+2
| | | | pending a careful evaluation of enum conversion behavior.
* [svn-r21504] Updated svn flags as needed on source files from H5A* to H5C*.Dana Robinson2011-10-101-0/+0
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* [svn-r21502] - Removed Windows VFD code. H5Pset_fapl_windows() actually ↵Dana Robinson2011-10-102-1057/+59
| | | | | | | | sets the SEC2 driver, though it will still report H5FD_WINDOWS. - Set svn:eol-style and svn:keyword properties on H5FDwindows.c/h. Tested on 64- and 32-bit Windows 7 (doesn't affect non-Windows platforms).
* [svn-r21501] - Propagated Windows VFD tweaks to SEC2 and log VFDs.Dana Robinson2011-10-102-235/+353
| | | | | | | | | | - Created typedefs and #defines to make POSIX I/O type-safe on Windows and true POSIX platforms. - Added pre-checks and removed post-checks for POSIX I/O sizes. When the number of bytes to be sent exceeds the maximum return value, the operation is split into smaller subsets. - General code tidying and cleanup. Tested on: jam (64-bit linux), jam + threadsafe, jam + parallel, Windows 7 (64- and 32-bit), freedom (64-bt BSD).
* [svn-r21499] Snapshot version 1.9 release 94HDF Tester2011-10-092-3/+3
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* [svn-r21497] Changed H5Pset_fapl_log() to deep copy the log file name ↵Dana Robinson2011-10-091-1/+4
| | | | | | instead of copying the pointer. Tested on jam (simple change).
* [svn-r21496] - H5MM_strdup() and H5MM_xstrdup() comments changed to ↵Dana Robinson2011-10-091-28/+25
| | | | | | | | correctly reflect how they respond to an input NULL string. - H5MM_xstrdup() now reports memory allocation errors via the HDF5 error stack (was previously an assert). Tested on local Windows via ctest (trivial change).
* [svn-r21476] The first part fix for bug HDFFV-7640: does not need to do ↵Vailin Choi2011-10-056-22/+34
| | | | | | H5O_move_msgs_forward() when writing attributes. h5committested. Tests are checked into the performance suite.
* [svn-r21443] Snapshot version 1.9 release 93HDF Tester2011-10-022-3/+3
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* [svn-r21442] Description:Quincey Koziol2011-10-016-15/+228
| | | | | | | | | | | | | | | | | | | | | | Check in "actual I/O mode" feature to trunk. Will merge back to 1.8 branch after it bakes over the weekend. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (koala) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-ia64 2.6 (ember) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode Mac OS X/32 10.6.8 (amazon) in debug mode Mac OS X/32 10.6.8 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r21415] Snapshot version 1.9 release 92HDF Tester2011-09-252-3/+3
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* [svn-r21374] Snapshot version 1.9 release 91HDF Tester2011-09-112-3/+3
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* [svn-r21366] JIRA HDFFV-2748 replace use of _WIN32 in source. Created new ↵Allen Byrne2011-09-0612-1580/+1574
| | | | | | defines H5_HAVE_WIN32_API and H5_HAVE_VISUAL_STUDIO defines to use. These can be properly set during configurration. Tested: windows and local linux - reviewed internally
* [svn-r21360] Snapshot version 1.9 release 90HDF Tester2011-09-042-3/+3
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* [svn-r21353] HDFFV-4018: static function for windows and pthreadsAllen Byrne2011-09-011-0/+6
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* [svn-r21352] Missed stat structure change to use h5_stat_t. Should have been ↵Allen Byrne2011-09-011-1/+1
| | | | part of HDFFV-7687 review and commit. File already used HD prefix on stat function.
* [svn-r21329] Snapshot version 1.9 release 89HDF Tester2011-08-282-3/+3
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* [svn-r21302] Fixed the bin/trace Perl script so that it ignores a final ... ↵Dana Robinson2011-08-231-1/+2
| | | | parameter, which it can't process. This allows the correct H5TRACE8 trace function to be added to H5Epush2. Tested on jam (simple change).
* [svn-r21256] Add libinfo and test to cmake - JIRA 1243Allen Byrne2011-08-181-0/+1
| | | | Tested: local linux
* [svn-r21249] Description: Part II of F2003 branch merge into the trunk.Scot Breitenfeld2011-08-181-0/+3
| | | | | | Ran bin/reconfigure to update the Makefile.in in directories not part of the fortran directory check=in. Updates Makefile.in due to changes made in configure.in for the Fortran 2003 additions. Tested on all platforms run under daily tests.
* [svn-r21248] Mereged the F2003 branch into the trunk.Scot Breitenfeld2011-08-181-0/+1
| | | | | | | | | Items merged: fortran directory, src/libhdf5.settings.in configure.in configure MANIFEST Tested: (all platforms used by daily tests, both with --enable-fortran and --enable-fortran2003)
* [svn-r21228] Added #ifdefs around #include unistd.h and created windows ↵Allen Byrne2011-08-152-347/+370
| | | | | | getlogin() function for building HDF5 parallel on windows. Reviewed and tested locally and tested by user.
* [svn-r21225] Snapshot version 1.9 release 88HDF Tester2011-08-142-3/+3
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* [svn-r21209] Added descriptive comment to H5G_stab_valid comment block. ↵Dana Robinson2011-08-101-0/+6
| | | | Tested locally just to ensure no errors were introduced.
* [svn-r21205] Issue 2763 - adding OAPL_ID as a new parameter to ↵Raymond Lu2011-08-101-0/+3
| | | | | | | | H5Rdereference. I added a check of OAPL_ID against -1 because CMAKE on 64-bit Windows slipped through the function call in the trefer.c test. Tested on jam and CMAKE on 64-bit Windows.
* [svn-r21185] Snapshot version 1.9 release 87HDF Tester2011-08-072-3/+3
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* [svn-r21171] Commit HDFFV-5929 winthreads define fixAllen Byrne2011-08-042-20/+11
| | | | | | Change reference of generated executables in src and fortran/src to use $<TARGETFILE:xxx> format. Tested: local linux
* [svn-r21158] Snapshot version 1.9 release 86HDF Tester2011-07-312-3/+3
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* [svn-r21152] Description:Quincey Koziol2011-07-284-0/+45
| | | | | | | | | | | | | | | | | | | | Further patches for Jira 7638, to ensure that H5D/Aget_type will be attached to the correct top file. (This change to the library should reverted when Jira 7638 is finally finished) Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (koala) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Mac OS X/32 10.6.8 (amazon) in debug mode Mac OS X/32 10.6.8 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r21149] Snapshot version 1.9 release 85HDF Tester2011-07-245-30/+34
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* [svn-r21137] Description:Quincey Koziol2011-07-211-2/+2
| | | | | | | | Tiny change to reduce code coupling w/H5F package. Tested on: FreeBSD/64 8.2 (freedom) w/debug (too minor to require h5committest)
* [svn-r21135] Description:Quincey Koziol2011-07-218-120/+438
| | | | | | | | | | | | | | | | More code cleanups to reduce coupling with the H5F package. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (koala) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Mac OS X/32 10.6.8 (amazon) in debug mode
* [svn-r21133] Description:Quincey Koziol2011-07-2017-192/+631
| | | | | | | | | | | | | | | | | More code cleanups to reduce coupling between packages that use the H5F internal routines, but really aren't part of the H5F "package". Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (koala) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Mac OS X/32 10.6.8 (amazon) in debug mode
* [svn-r21126] Description:Quincey Koziol2011-07-1917-166/+507
| | | | | | | | | | | | | Clean up some compiler warnings, but mainly an interim checkin on the path of reducing code coupling in the library by removing most of the places which were accessing H5F package definitions. Tested on: Mac OS X/32 10.6.8 (amazon) w/debug FreeBSD/32 8.2 (loyalty) w/debug FreeBSD/64 8.2 (freedom) w/debug Linux/64 2.6 (heiwa) w/debug Linux/64 2.6 (ember) w/parallel
* [svn-r21124] Issue 2763 - adding OAPL_ID as a new parameter to ↵Raymond Lu2011-07-191-0/+6
| | | | | | | | | H5Rdereference. A followup commit for r21117. I made 2 changes: 1. Quincey changed H5P_DATASET_ACCESS_DEFAULT to H5P_DEFAULT for the tests that call H5Rdereference. Inside H5R_dereference, I assigned H5P_DATASET_ACCESS_DEFAULT to OAPL_ID if it is H5P_DEFAULT. 2. I added the test for invalid OAPL_ID in trefer.c. Tested on jam, koala, heiwa.
* [svn-r21120] Description:Quincey Koziol2011-07-181-4/+13
| | | | | | | | | | | Check in ugly version of fix for Jira #7638. I'm going to leave the issue open in Jira and when the library has been refactored to use shared file pointers (instead of top file pointers) for file operations, I'll uncomment the check in src/H5Oshared.c Tested on: Mac OS X/32 10.6.8 (amazon) w/debug (too small for h5committest)
* [svn-r21117] Issue 2763 - I added a new parameter of object access property ↵Raymond Lu2011-07-186-16/+94
| | | | | | list to the function H5Rdereference. It's called H5Rdereference2 now. H5Rdereference function has been deprecated to H5Rdereference1. I also added some test cases in trefer.c. Tested on jam, heiwa, and koala.
* [svn-r21101] HDFFV-7639Mike McGreevy2011-07-142-349/+135
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: Remove H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS and H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS #defines from source. Description: Two advanced parallel functionalities, special collective IO and complex derived datatypes, are not supported by older implementations of mpi, and thus our code limits the use of these features with #ifdefs and has checks in configure to set them (or not). Unfortunately, configure can't actually run a parallel check to see if these features are working (nor not) so it resorts to looking in the config files where they are explicity enabled or disabled based on versions of mpi, sytems being built on, or for no documented reason at all (i.e. just set to on or off as some 'default'). Overriding these settings is easy if need be, provided it is known that it needs to be done to get improved performance, and oftentimes it is not. Most new MPI implementations successfully handle the functionality requested when these #defines are set, and many of the "turn these features off" cases in the config files are for old (> 5 years) versions of MPI and retired systems (such as NCSA's tungsten). Therefore, the decision has been made to remove the support for these old versions of MPI and systems that cannot handle these behaviors. The #ifdefs and supporting setup in the config/ files and configure script has been removed, and the code executed when these options were not set removed from the source. In passing, this commit also cleans up some whitespace issues in both t_mpi.c and H5Dmpio.c. Furthermore, in t_mpi.c, the special collective IO test was not getting regularly run due to it being written to work only with four processes (we regularly test with six, previously with three), and thus it failed when actually run due to an out of bounds data buffer assignment. It has been modified to run at any number of processes greater than four, and the memory problem has been fixed so the test passes. Tested: jam, h5committest, ember
* [svn-r21080] Remove redundant EXPORTS symbol since CMake automatically ↵Allen Byrne2011-07-081-1/+0
| | | | creates it.
* [svn-r21063] Description:Quincey Koziol2011-07-011-202/+202
| | | | | | | | | | | | | | | Tweak make_vers script so that it indents preprocessor commands inside #ifdefs, is more forgiving and informative about the input file's prefix, and is better parameterized with the global variables at the beginning of the script. When major versions are branched from the trunk, the $max_idx value should be the only value that needs to be changed in the version of the script on the trunk. Changes to H5version.h file are just indention. Tested on: Mac OS X/32 10.6.8 (amazon) (too minor to require h5committest)
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