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* [svn-r21531] Merge of 21501 and 21502 from trunk:Dana Robinson2011-10-127-1582/+734
| | | | | | | | | | | | | | | | | | | | | Note that this differs slightly from the trunk code since the VFL API won't be changed until 1.10. In the 1.8 branch, the term() function is public and this required some #defines for the Windows VFD. 21501: - Propagated Windows VFD tweaks to SEC2 and log VFDs. - 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. 21502: - Removed Windows VFD code. H5Pset_fapl_windows() actually sets the SEC2 driver, though it will still report H5FD_WINDOWS.
* [svn-r21528] Merge of 21517 and 21520 from trunk:Dana Robinson2011-10-125-137/+361
| | | | | | | | | | - Added checks for clock_gettime() to configure.in. Tested on Linux, FreeBSD, Solaris, MacOSX to ensure they are found correctly and everything builds. No code currently reliess on clock_gettime(). - Brought Windows and VMS H5pubconf.h files into sync with the Linux file. Some data sizes were corrected in both VMS and Windows. Tested on Windows. Ray will test on VMS when this is pushed to the 1.8.x branch.
* [svn-r21527] Updated cygwin versionsAllen Byrne2011-10-121-2/+2
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* [svn-r21524] Reverts 20920 (HDFFV-7579 fix) (this is 20913/21 from the trunk)Dana Robinson2011-10-117-306/+8
| | | | | | This change reverts the HDFFV-7579 fix while we more carefully consider enum conversions as a part of the h5compare work. Tested on jam, Windows 7 and linew.
* [svn-r21522] - H5MM_strdup() and H5MM_xstrdup() comments changed to ↵Dana Robinson2011-10-111-25/+22
| | | | | | | | 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 jam (simple change).
* [svn-r21521] Merge of trunk 21497Dana Robinson2011-10-111-1/+4
| | | | | | Changed H5Pset_fapl_log() to deep copy the log file name instead of copying the pointer. Tested on jam (simple change).
* [svn-r21519] Merge of 21518 from trunkDana Robinson2011-10-111-1/+5
| | | | | | | | - Added definition for HDfseek() to be used later. - Added comment about requiring _O_BINARY being set on Windows to avoid CR-LF issues. Tested on Windows (minor changes).
* [svn-r21513] Add HDprefix and change when pio_timer.h is includedAllen Byrne2011-10-113-7/+7
| | | | Tested
* [svn-r21512] Synchronize macros for naming with other librariesAllen Byrne2011-10-111-13/+6
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* [svn-r21503] Edited for language. Did not edit "Known Problems" Mark Evans2011-10-101-56/+59
| | | | or "Platforms Tested" sections.
* [svn-r21500] Snapshot version 1.8 release 8 (snap17)HDF Tester2011-10-107-23/+23
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* [svn-r21494] Add new mach/mach_time.h header check.Allen Byrne2011-10-072-0/+4
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* [svn-r21488] Bug:Albert Cheng2011-10-071-4/+4
| | | | | | | | | | | h5dump was used in test script but was not invoked by RUNSERIAL. THis does not work in batch machines like Blue Gene in LLNL. Solution: Added $RUNSERIAL to invoke $H5DUMP_BIN. Tested: LLNL BlueGene (udawn)
* [svn-r21482] Add option to enable windows stdioAllen Byrne2011-10-061-0/+10
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* [svn-r21479] Merge revision 21101 from trunk to 1.8 branch:Mike McGreevy2011-10-0515-789/+289
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | HDFFV-7639 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-r21470] Updated with the change of Windows platform switched back to ↵Albert Cheng2011-10-041-0/+3
| | | | | | use SEC2 as the default VFD.
* [svn-r21468] Maintenance: Modified command file according new source ↵Elena Pourmal2011-10-041-2/+9
| | | | | | structure created to support F90/F2003 Currently VMS supports F90 only.
* [svn-r21466] Maintenance: To support F2003 features we renamed some files. ↵Elena Pourmal2011-10-041-2/+2
| | | | | | Brought the change to VMS. Platforms tested: VMS server.
* [svn-r21460] Problem:Albert Cheng2011-10-041-1/+1
| | | | | | | | | | Some machines, like LLNL udawn, a blue-gene machine, requires all executables, be launched by some command like mpirun. Solution: Added $RUNSERIAL to launch the executable. Tested: LLNL uDawn.
* [svn-r21458] Problem:Albert Cheng2011-10-041-0/+10
| | | | | | | | | | | Function TOOLTEST_OUTPUT does not filter the extra system messages sent to stdout or stderr, thus causing output mismatched with expected output. Solution: Added STDOUT_FILTER and STDERR_FILTER to filter them out. Tested: Tested LLNL uDawn (Blue-Gene cluster), for serial mode only.
* [svn-r21444] Snapshot version 1.8 release 8 (snap16)HDF Tester2011-10-039-28/+28
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* [svn-r21439] Issue 7701 - H5LTdtype_to_text had memory corruption while ↵Raymond Lu2011-09-303-171/+391
| | | | | | | | being querried about the size of the buffer needed. The problem happened when the internal buffer is reallocated, the new address got lost. I revised the code to pass the new address as the return value of functions. I also added two new test cases. This commit only includes hl/test/test_lite.c, hl/src/H5LT.c, hl/src/H5LTprivate.h. All others are property changes of the merge from the trunk. Tested on jam, linew, and koala.
* [svn-r21438] Added listing of all cmake options availableAllen Byrne2011-09-301-0/+47
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* [svn-r21430] Add F2003 IF-ENDIF protection blocks around _F03 file processingAllen Byrne2011-09-282-27/+51
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* [svn-r21426] Add 2003 fortran to settings textAllen Byrne2011-09-271-0/+1
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* [svn-r21423] Add 2003 fortran to cmake build/configureAllen Byrne2011-09-276-1/+53
| | | | Tested: local linux
* [svn-r21421] Merged the Fortran 2003 changes from the trunk into the 1.8 ↵Scot Breitenfeld2011-09-27224-24540/+61907
| | | | | | | | | | | branch, used: svn merge -r 20506:21414 https://svn.hdfgroup.uiuc.edu/hdf5/trunk/fortran Tested: jam (gnu, intel, pgi compilers) Also merged effected non-Fortran files: svn merge -r21247:r21248 https://svn.hdfgroup.uiuc.edu/hdf5/trunk/src/libhdf5.settings.in
* [svn-r21418] Change windows default driver to SEC2Allen Byrne2011-09-264-5/+14
| | | | Add option to allow -fPIC
* [svn-r21416] Snapshot version 1.8 release 8 (snap15)HDF Tester2011-09-267-23/+23
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* [svn-r21414] Description:Jonathan Kim2011-09-231-2/+8
| | | | | | | | | | | Skip parallel diff test "-c non_comparables1.h5 non_comparables2.h5" due to hanging issue occurring on koala (linux64-LE) intermittently. Plan to put back when resolved. The test was related to J7693. Merged from HDF5 trunk r21413. Tested: jam (linux32-LE), koala (linux64-LE)
* [svn-r21404] Purpose:Jonathan Kim2011-09-2129-40/+313
| | | | | | | | | | | | | | | | | | | | | | HDFFV-7693 - h5diff produces different behavior between versions: 1.8.3 and 1.8.6 Description: There were two issues on this. One was not displaying all the comparable objects if non-comparable object/attribute exist and compared before comparables ones. This issue occurred after 1.8.4 release. This is the issue from user. The other issue was not displaying all the comparable attributes, if non-comparable object/attribute exist and compared ahead. This issue were exist even before 1.8.4 release. So it's possible some attribute comparison may have not displayed correctly in the past, if non-comparable data were exist in common object. Fixed h5diff to display all the comparable object and attribute regardless of non-comparables. Merged from HDF5 trunk r21396 and r21397. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam, Windows)
* [svn-r21402] Update MANIFEST for a new file from previous checkin (HDFFV-5932)Jonathan Kim2011-09-201-0/+1
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* [svn-r21400] Purpose:Jonathan Kim2011-09-205-164/+337
| | | | | | | | | | | | | HDFFV-5932 - h5repack breaks files with dimension scales Description: - Fixed h5repack to update values of references(object and region) of attributes in h5repack for 1) references, 2) ARRAY of references, 3) VLEN of references, and 4) COMPOUND of references. - Merged from HDF5 trunk 21393, 21382, 21386, 21389. (support Peter) Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)
* [svn-r21399] Snapshot version 1.8 release 8 (snap14)HDF Tester2011-09-197-23/+23
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* [svn-r21394] Updated tuning of fraction of tests skipped in t_shapesame.c as ↵John Mainzer2011-09-141-2/+2
| | | | | | | | a function of express test level to reflect results of testing with Ray. Tested parallel on jam -- no further testing as the change was very minor.
* [svn-r21380] John Mainzer2011-09-131-2804/+3033
| | | | | | | | | | | Ported shape same test express test mods from trunk to 1.8 branch. This was mostly a matter of copying testpar/t_shapesame.c from trunk to the 1.8 branch, as the root versions of the files were almost identical. Tested parallel on Jam only, as changes have been well tested on the trunk.
* [svn-r21379] The tools used "%hhd" to print signed char. But VMS doesn't ↵Raymond Lu2011-09-133-3/+19
| | | | | | know it. So I used H5_VMS to have a different way ("%hd") to print it. Tested on jam and VMS.
* [svn-r21376] JIRA-HDFFV-2748: Relplace WIN32 macros in source. New ↵Allen Byrne2011-09-1227-3319/+3367
| | | | | | | | H5_HAVE_WIN32_API and H5_HAVE_VISUAL_STUDIO defines only need to be set on windows. Autotools configure is not affected. Trunk passed for a week and cmake branch has been in place > 3 weeks. Tested: local linux
* [svn-r21375] Snapshot version 1.8 release 8 (snap13)HDF Tester2011-09-127-23/+23
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* [svn-r21368] Purpose:Jonathan Kim2011-09-0610-35/+728
| | | | | | | | | | | HDFFV-7712 - h5diff: segfault over combinations of complex container types (compound, array, vlen) Description: - Fixed segfault over dataset with container types (array,lven) with multiple nested compound types. (ex: compound->array->compound, compound->vlen->compound) - Merged from HDF5 trunk r21358. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
* [svn-r21365] Related files to files from HDF5-33 review - all changes ran ↵Allen Byrne2011-09-063-57/+77
| | | | | | | | correctly in trunk. Changes have been tested in cmake branch. #ifdef around include <unistd.h> and <time.h> Tested: local linux
* [svn-r21364] Related files to files from HDF5-33 review - all changes ran ↵Allen Byrne2011-09-063-792/+797
| | | | | | | | | | correctly in trunk. Changes have been tested in cmake branch. t_cache.c - define needed for windows t_posix_compliant.c - #ifdef around include <unistd.h> t_shapesame.c - HD prefix needed for stat function Tested: local linux
* [svn-r21363] files from HDF5-33 review - all changes ran correctly in trunk. ↵Allen Byrne2011-09-066-1374/+1380
| | | | | | Changes have been tested in cmake branch. Tested: local linux
* [svn-r21361] Snapshot version 1.8 release 8 (snap12)HDF Tester2011-09-057-23/+23
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* [svn-r21356] Issue 7674 - CLANG compiler complained about the line (about 800):Raymond Lu2011-09-022-10/+57
| | | | | | | | | | tempint = (tempint >> packed_data_offset) & packed_data_mask; The right shift may cause undefined behavior if PACKED_DATA_OFFSET is 32-bit or more. For every kind of native integers, I changed the code to make it zero if PACKED_DATA_OFFSET is greater than or equal to the size of integer. Tested on jam and on MacOS with CLANG compiler.
* [svn-r21355] Purpose:Jonathan Kim2011-09-021-6/+3
| | | | | | | | | | | | | | HDFFV-2511 - GMQS: h5repack: some tests failed in -q32 AIX Description: - Need to be Merged from HDF5 trunk r21283 also, which was missed from previous checkin. - Previously Merged from HDF5 trunk r21265 - Added macro to handle failure in H5Dread/write when memory allocation failed inside the library. Add graceful error message when lack of memory error occurs from HDF5 lib. (XCAO) Tested: jam (linux32-LE), koala (linux64-LE)
* [svn-r21349] Need PATH active by default during install for daily binary ↵Allen Byrne2011-09-011-1/+1
| | | | testing needs
* [svn-r21346] Need PATH active by default during install for daily binary ↵Allen Byrne2011-09-011-2/+2
| | | | testing needs
* [svn-r21344] Purpose:Jonathan Kim2011-08-312-11/+39
| | | | | | | | | | | | HDFFV-2511 - GMQS: h5repack: some tests failed in -q32 AIX Description: - Merged from HDF5 trunk r21265 - Added macro to handle failure in H5Dread/write when memory allocation failed inside the library (XCAO) Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r21343] Issue 7674 - clang compiler with -fcatch-undefined-behavior ↵Raymond Lu2011-08-311-6/+12
| | | | | | | | | -ftrapv discovered several problems in the test suite. One of them is in the INIT_INTEGER macro definition in dt_arith.c. It complained about line 150 where it tried to subtract 1 from the negative minimal value of "int", causing it to overflow (or underflow). So I revised the code to avoid it. Tested on jam and Mac OS Lion with CLANG compiler. But I tested the same change for the trunk with h5committest.
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