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* [svn-r15682] Purpose: fix bug 1298Neil Fortner2008-09-229-47/+228
| | | | | | | | | | | Description: The optimized "subset" compound conversion function would improperly copy the "blank" space at the end of compound types. Modified H5T_conv_struct_init to detect when the subset type has extra space at the end, and calculate the size of the data that should be copied into the conversion buffer for each element. Changes to the functions that implement these conversions. Tested: kagiso, linew, smirom (h5committest)
* [svn-r15681] Description:Quincey Koziol2008-09-222-3/+255
| | | | | | | | | | | | | | | | | | | | | | Correct small error in allocating data block elements and add some more tests. Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15678] formatted codePedro Vicente Nunes2008-09-221-4/+8
| | | | tested: windows, linux
* [svn-r15676] Description:Quincey Koziol2008-09-2229-182/+164
| | | | | | | | | | | | | | | | | | | | | | | Centralize all macros for declaring "magic numbers"/signatures for objects in the file into src/H5Fprivate.h, so it's easier to know what values have already been defined, etc. Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15675] Purpose: Add new source file H5EAdblock.c to Windows.Scott Wegner2008-09-224-0/+14
| | | | | | | | Description: New source file H5EAdblock.c was added to the library. This checkin adds the file to our Windows projects, hdf5 and hdf5dll (VS2005 and VS.NET project files) Tested: Build only, VS2005 on WinXP
* [svn-r15674] Description:Quincey Koziol2008-09-2220-178/+1854
| | | | | | | | | | | | | | | | | | | | | | Add base support for extensible array "data blocks" to code, tests and h5debug. Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15673] Description:Scot Breitenfeld2008-09-221-1/+1
| | | | Changed the error check string to match the function being called, changed the string H5Sselect_all to H5Sselect_none
* [svn-r15668] Purpose: Add feature requested in bug #1282Neil Fortner2008-09-2115-60/+328
| | | | | | | | | | Description: Adds capability to h5ls to traverse external links when the -r (recursive) option is given. Changes to the way absolute path names are patched in h5trav.c. Changes to the way recursive traversal starting from a non-root group is handled (which also fixes some preexisting issues). Tests added for these cases. Tested: kagiso, smirom, linew (h5committest)
* [svn-r15667] Snapshot version 1.9 release 18HDF Tester2008-09-218-21/+21
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* [svn-r15665] Bug fix: (ID 1157)Albert Cheng2008-09-191-2/+4
| | | | | | | | | | | | | | | | | | | Description: Program would crash, complaining MPI calls were invoked after MPI_Finalize() has occurred. Previously, H5close() before MPI_Finalize() would remove the crash. Solution: It turned out that two H5 property objects (mpio_pl and acc_tpl) were not closed before MPI_Finalize(). In the at_exit code, HDF5 library attempted to close them by releasing the MPI Communicators in them too. That was the error. Adding code to close them properly before MPI_Finalize() took care things. Tested: Only in kagiso parallel. Did not run h5committest since kagiso would have been the one running parallel test. This part of code would not be compiled at all in non-phdf5 mode.
* [svn-r15664] fix comments Pedro Vicente Nunes2008-09-191-8/+15
| | | | tested: linux
* [svn-r15661] Purpose: Add szip/zlib link dependencies to Windows earray[dll] ↵Scott Wegner2008-09-192-42/+42
| | | | | | | projects Description: earray[dll] builds were failing on Windows because of missing link dependencies to szip and zlib libraries (amongst other reasons). This checkin adds those dependencies.
* [svn-r15660] Purpose: Fix minor Windows issues in new H5EA interface.Scott Wegner2008-09-192-9/+9
| | | | | | | | | | | | | Description: We've run into a few Windows-specific problems with the new H5EA interface. In particular, this checkin makes the following changes: -- Change shutdown defined in earray.c to shutdown_ea, to avoid conflicting with another Windows-specific system call. -- Prefix H5EA_get in H5EAprivate.h with H5_DLL, so the function is properly exported in Windows DLL version. These changes shouldn't break any other platforms. Tested: VS2005 on WinXP h5committest (linew kagiso smirom)
* [svn-r15659] Purpose: Fix Windows Fortran DLL definitions fileScott Wegner2008-09-192-44/+45
| | | | | | | | Description: We recently moved the Windows-specific fortran source code into a separate file for specifying DLL exports. However there were a couple definitions missing in the port from 1.8 to the trunk branch. This checkin correctly includes the .def file into our Windows project, and adds the missing definitions to hdf5_fortrandll.def. Tested: VS2005 on WinXP
* [svn-r15658] Purpose: Replace __func__ usage with FUNC macroScott Wegner2008-09-191-16/+16
| | | | | | | | Description: Some compilers (i.e. Visual Studio on Windows) don't support the C99 keyword __func__. It does, however, have a similar keyword, __FUNCTION__. In H5EApkg.h we define a macro, FUNC, which will pick the right version and use it accordingly. This checkin changes H5EA.c to use FUNC instead of __func__. Tested: h5committest (linew smirom kagiso)
* [svn-r15656] Purpose: fix bug 1286Neil Fortner2008-09-188-53/+685
| | | | | | Description: Added configure test to see if pointer alignment restrictions are enforced (as in dereferencing an unaligned pointer causes an error). Added code in H5Tvlen.c to avoid dereferencing unaligned pointers, conditionally compiled based on the configure test. Added test case in dtypes.c which would previously cause such machines to fail. Tested: kagiso, smirom, linew (h5committest); linew64
* [svn-r15655] Changed the absolute path of the data file to a relative path.Christian Chilan2008-09-181-3/+7
| | | | Tested on kagiso, smirom, and linew.
* [svn-r15653] cleaned warningsPedro Vicente Nunes2008-09-183-74/+22
| | | | tested: windows, linux
* [svn-r15652] Cleaned compiler warnings Pedro Vicente Nunes2008-09-183-26/+64
| | | | | | Bug fix: do not print print compression ratio when the requested filter is NONE Tested: windows, linux
* [svn-r15650] Cleaned compiler warnings Pedro Vicente Nunes2008-09-181-4/+4
| | | | | | Bug fix: change the options block size variable from int to hsize_t, to match the H5Pset_userblock call Tested: windows, linux
* [svn-r15649] Included macros for portability of h5perf code among HDF5 versions.Christian Chilan2008-09-171-13/+35
| | | | Tested on kagiso, abe, and cobalt.
* [svn-r15643] add a failure condition of writing user blockPedro Vicente Nunes2008-09-171-161/+178
| | | | Tested: windows, linux
* [svn-r15639] Purpose: Check for __func__ keyword during configureScott Wegner2008-09-175-16/+90
| | | | | | | | | | Description: In some of the new H5EA* code, many new C99 features are being used. Most of them are portable to all compilers, but the __func__ keyword in particular isn't supported in Visual Studio on Windows. Instead, Windows defines the __FUNCTION__ keyword, which can be used as a direct substitute. We now check for the __func__ keyword during configure and define the feature flag H5_HAVE_C99_FUNC. There was previously a check for __FUNCTION__, and the feature flags H5_HAVE_FUNCTION. In H5EApkg.h, we check for the presents of each of these in order to see which to use. If neither are avaiable, fail. Tested: h5committest (kagiso, smirom, linew)
* [svn-r15637] Bug 710: partial fix.Albert Cheng2008-09-163-148/+150
| | | | | | | | | | | Temporary removed b2 from the --enable-debug=all list so that this option will pass. "configure --help" lists the --enable-debug=all and users tend to use it and end up with compile failures in the b2 debug code. Since this bug will not be fixed soon, this is a temporary fix to let the configure and build work. Tested: h5committest plus "--enable-debu=all" test in kagiso.
* [svn-r15636] formatted codePedro Vicente Nunes2008-09-161-3790/+3850
| | | | tested: windows, linux
* [svn-r15635] add info regarding user block to usagePedro Vicente Nunes2008-09-161-1/+2
| | | | tested: windows, linux
* [svn-r15634] Add a default user block size of 1024 when none is givenPedro Vicente Nunes2008-09-162-5/+11
| | | | Tested: windows, linux
* [svn-r15633] Description:Scot Breitenfeld2008-09-162-1/+205
| | | | Added test routines for h5t_get/set_fields_f.
* [svn-r15630] Description:Scot Breitenfeld2008-09-161-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | In nh5tget_offset_c: (1) The return value type of H5Tget_offset was set to size_t where it should be of type int. (2) Was if offset was equal to 0 it returned the error code of -1 back to Fortran, this was changed to return an error code of -1 when the offset value is < 0. In h5tget_norm_c: (1) was if the return value of H5Tget_norm = 0 it would return an error code to Fortran, but from enum of the return value: typedef enum H5T_norm_t { H5T_NORM_ERROR = -1, /*error */ H5T_NORM_IMPLIED = 0, /*msb of mantissa isn't stored, always 1 */ H5T_NORM_MSBSET = 1, /*msb of mantissa is always 1 */ H5T_NORM_NONE = 2 /*not normalized */ /*H5T_NORM_NONE must be last */ } H5T_norm_t; only when -1 is returned is there an error, changed it to return an error only if the value of H5T_NORM_ERROR = -1.
* [svn-r15628] Description:Quincey Koziol2008-09-16240-4810/+4810
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r15627] This check-in fixes a bug inside parallel HDF5 testsuite.MuQun Yang2008-09-161-2/+22
| | | | | | | | | When enable-debug is turned on, a special macro block H5_HAVE_INSTRUMENTED_LIBRARY inside HDF5 will be executed to check if some collective chunk IO test cases are being run with the correct settings(one link, multiple chunk etc.). However,when complicated derived datatype in some mpi-io packages are not supported, the library has to switch one link IO with/without the optimization to multiple chunk IO with/without the optimization. The current testsuite doesn't know this and generates a false assertion failure message. This check-in fix this problem by providing a second property to avoid the false faiure message. Tested at abe(NCSA linux cluster) and kagiso.
* [svn-r15626] This check-in fixes a bug inside parallel HDF5 testsuite.MuQun Yang2008-09-162-2/+32
| | | | | | | | | When enable-debug is turned on, a special macro block H5_HAVE_INSTRUMENTED_LIBRARY inside HDF5 will be executed to check if some collective chunk IO test cases are being run with the correct settings(one link, multiple chunk etc.). However,when complicated derived datatype in some mpi-io packages are not supported, the library has to switch one link IO with/without the optimization to multiple chunk IO with/without the optimization. The current testsuite doesn't know this and generates a false assertion failure message. This check-in fix this problem by providing a second property to avoid the false faiure message. Tested at abe(NCSA linux cluster) and kagiso.
* [svn-r15622] Purpose: Add new source files to Windows projectsScott Wegner2008-09-154-0/+42
| | | | | | | | Description: This checkin adds the following source files to our Windows projects: -- H5EAiblock.c -- H5EAstat.c -- H5EAdbg.c
* [svn-r15619] Snapshot version 1.9 release 17HDF Tester2008-09-148-57/+59
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* [svn-r15618] Description:Quincey Koziol2008-09-111-57/+197
| | | | | | | | | | | | | | | | | | | | | | Add additional test and make a few cleanups in extensible array unit test. Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15617] Description:Quincey Koziol2008-09-1111-166/+429
| | | | | | | | | | | | | | | | | | | | | | | | Clean up how v2 B-tree (and extensible array) classes are determined in h5debug. Add support for extensible array headers and index blocks to h5debug Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15614] Description:Quincey Koziol2008-09-1116-159/+1238
| | | | | | | | | | | | | | | | | | | | | | More extensible array features: add support for setting/getting elements in the array's index block. Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15612] Description:Quincey Koziol2008-09-114-12/+11
| | | | | | | | | | | | | | | | | | | | | Minor formatting cleanups Tested on: Mac OS X/32 10.5.4 (amazon) in debug mode Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) 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, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15609] Description:Quincey Koziol2008-09-1056-2304/+2559
| | | | | | | | Omnibus compiler warning cleanup & some reformatting also. Tested on: Mac OS X/32 10.5.4 (amazon) Too minor to require h5committest
* [svn-r15604] The MPI compiler(mvapich2-0.9.8p2patched-intel-ofed-1.2) at ↵MuQun Yang2008-09-081-1/+3
| | | | | | | | | NCSA's linux cluster(Abe) fails to handle collective IO calls with very complicate MPI derived datatype. All the values of input parameters from HDF5 are correct before passing to MPI-IO collective calls. Sometimes the following errors happen: rank 0 in job 77 honest1.ncsa.uiuc.edu_60945 caused collective abort of all ranks exit status of rank 0: killed by signal 9 Up to this point, we decide to turn off the use of advanced MPI derived datatype features inside HDF5 so that complicated selection tests are ensured to be handled by HDF5. This check-in reflects this.
* [svn-r15601] Description:Scot Breitenfeld2008-09-081-0/+1
| | | | Added windows fortran DLL function file, hdf5_fortrandll.def
* [svn-r15598] Description:Scot Breitenfeld2008-09-0816-3022/+861
| | | | Moved all the windows DLL function declarations to one file (hdf5_fortrandll.def).
* [svn-r15595] Snapshot version 1.9 release 16HDF Tester2008-09-078-21/+21
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* [svn-r15591] Description:Scot Breitenfeld2008-09-031-7/+7
| | | | Changed the detection of double back which was failing on 32 bit machines.
* [svn-r15590] Description:Scot Breitenfeld2008-09-031-1/+1
| | | | Changed blank spacing in Fortran output so the output aligns correctly
* [svn-r15588] Purpose: Add new h5repack tests to WindowsScott Wegner2008-09-031-1/+5
| | | | | | | | Description: New h5repack tests were added in revision 15551 and 15557, and also the syntax of one test was changed. This was causing errors on Windows. This checkin should fix those errors. Tested: VS2005 on WinXP
* [svn-r15586] Description:Scot Breitenfeld2008-09-032-45/+61
| | | | | Changed the test for intrinsic Fortran function SIZEOF by using AC_TRY_RUN instead of AC_TRY_COMPILE.
* [svn-r15585] Purpose: Use H5test_kind_SIZEOF.f90 rather than H5test_kind.f90 ↵Scott Wegner2008-09-031-17/+17
| | | | | | | in Windows Description: A new version of H5test_kind is safer for platforms that support sizeof. We have replaced H5test_kind.f90 with it on Windows
* [svn-r15584] Purpose: Add new extensible array source code and test project ↵Scott Wegner2008-09-0313-4/+1196
| | | | | | | | | for Windows Description: In revision 15549, new source code was added for the extensible array interface. This checkin adds the source code to Windows, along with the new test project, earray. Note: The new H5EA interface causes compilation errors on Windows, and will need to be fixed in the source.
* [svn-r15582] Added script to build h5perf_serial in standalone mode.Christian Chilan2008-09-022-0/+29
| | | | Tested on kagiso, smirom, and linew.
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