Commit Graph

10731 Commits

Author SHA1 Message Date
Scot Breitenfeld
f85aafd50d [svn-r15693] Description:
Added test for h5tget_native_type_f
2008-09-24 15:00:54 -05:00
Scot Breitenfeld
457514fab7 [svn-r15692] Description:
Added the optional 'mounted' variable to H5Gget_info_by_idx_f/H5Gget_info_f/H5Gget_info_by_name_f to see that it passes the correct values.
2008-09-24 12:51:57 -05:00
Scot Breitenfeld
3a26bc2d0f [svn-r15691] Cosmetic changes. 2008-09-24 11:28:46 -05:00
Scot Breitenfeld
8866806873 [svn-r15690] Description:
In nH5Sget_select_bounds_c swapped array bounds to account for C and Fortran reversed array notation.
2008-09-24 11:26:32 -05:00
Scot Breitenfeld
acf7dd2c74 [svn-r15689] Description:
Added additional tests for h5sget_select_bounds_f
2008-09-24 11:23:54 -05:00
Scot Breitenfeld
844a56e79b [svn-r15688] Description:
Added additional tests for h5sget_select_hyper_blocklist_f
and 5sget_select_elem_pointlist_f
2008-09-23 16:52:19 -05:00
Scot Breitenfeld
9b4a0aea49 [svn-r15687] Description:
Fixed 
nh5sget_select_hyper_blocklist_c
nh5sget_select_elem_pointlist_

for bug 1319. by transposing arrays for C-FORTRAN convention.
2008-09-23 16:51:07 -05:00
Pedro Vicente Nunes
44e038362b [svn-r15684] New feature (h5diff -c) 2008-09-23 11:26:32 -05:00
Neil Fortner
5bbc0eedff [svn-r15682] Purpose: fix bug 1298
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)
2008-09-22 18:41:31 -05:00
Quincey Koziol
fe6cf16d94 [svn-r15681] Description:
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
2008-09-22 17:42:21 -05:00
Pedro Vicente Nunes
d0859bb174 [svn-r15678] formatted code
tested: windows, linux
2008-09-22 13:40:38 -05:00
Quincey Koziol
071e281a3d [svn-r15676] Description:
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
2008-09-22 12:13:21 -05:00
Scott Wegner
02156246da [svn-r15675] Purpose: Add new source file H5EAdblock.c to Windows.
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
2008-09-22 11:35:25 -05:00
Quincey Koziol
00bd6ae9c2 [svn-r15674] Description:
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
2008-09-22 10:22:03 -05:00
Scot Breitenfeld
0402e02527 [svn-r15673] Description:
Changed the error check string to match the function being called, changed the string H5Sselect_all to H5Sselect_none
2008-09-22 10:03:36 -05:00
Neil Fortner
6d28e06f30 [svn-r15668] Purpose: Add feature requested in bug #1282
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)
2008-09-21 13:35:43 -05:00
HDF Tester
dcd4c0b049 [svn-r15667] Snapshot version 1.9 release 18 2008-09-21 09:08:35 -05:00
Albert Cheng
c857aa12c1 [svn-r15665] Bug fix: (ID 1157)
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.
2008-09-19 18:18:33 -05:00
Pedro Vicente Nunes
205b9019cf [svn-r15664] fix comments
tested: linux
2008-09-19 15:06:17 -05:00
Scott Wegner
8dd19b5db5 [svn-r15661] Purpose: Add szip/zlib link dependencies to Windows earray[dll] 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.
2008-09-19 12:15:22 -05:00
Scott Wegner
ed54f5ab7e [svn-r15660] Purpose: Fix minor Windows issues in new H5EA interface.
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)
2008-09-19 12:13:10 -05:00
Scott Wegner
82f30910c2 [svn-r15659] Purpose: Fix Windows Fortran DLL definitions file
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
2008-09-19 11:06:47 -05:00
Scott Wegner
dab236581c [svn-r15658] Purpose: Replace __func__ usage with FUNC macro
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)
2008-09-19 09:32:24 -05:00
Neil Fortner
c254b0bc27 [svn-r15656] Purpose: fix bug 1286
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
2008-09-18 15:53:30 -05:00
Christian Chilan
67cf35a463 [svn-r15655] Changed the absolute path of the data file to a relative path.
Tested on kagiso, smirom, and linew.
2008-09-18 14:25:42 -05:00
Pedro Vicente Nunes
6eb624a09d [svn-r15653] cleaned warnings
tested: windows, linux
2008-09-18 13:08:04 -05:00
Pedro Vicente Nunes
fffa1adc9a [svn-r15652] Cleaned compiler warnings
Bug fix: do not print print compression ratio when the requested filter is NONE

Tested: windows, linux
2008-09-18 11:06:28 -05:00
Pedro Vicente Nunes
c3b40626a0 [svn-r15650] Cleaned compiler warnings
Bug fix: change the options block size variable from int to hsize_t, to match the H5Pset_userblock call

Tested: windows, linux
2008-09-18 09:44:21 -05:00
Christian Chilan
6066112389 [svn-r15649] Included macros for portability of h5perf code among HDF5 versions.
Tested on kagiso, abe, and cobalt.
2008-09-17 16:24:45 -05:00
Pedro Vicente Nunes
efb5075937 [svn-r15643] add a failure condition of writing user block
Tested: windows, linux
2008-09-17 11:14:35 -05:00
Scott Wegner
036aa878b0 [svn-r15639] Purpose: Check for __func__ keyword during configure
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)
2008-09-17 09:04:35 -05:00
Albert Cheng
95149cc095 [svn-r15637] Bug 710: partial fix.
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.
2008-09-16 15:58:53 -05:00
Pedro Vicente Nunes
80693ba5de [svn-r15636] formatted code
tested: windows, linux
2008-09-16 15:37:45 -05:00
Pedro Vicente Nunes
2cd16f4c74 [svn-r15635] add info regarding user block to usage
tested: windows, linux
2008-09-16 14:49:43 -05:00
Pedro Vicente Nunes
54e35b67cf [svn-r15634] Add a default user block size of 1024 when none is given
Tested: windows, linux
2008-09-16 14:42:51 -05:00
Scot Breitenfeld
60534aa268 [svn-r15633] Description:
Added test routines for h5t_get/set_fields_f.
2008-09-16 12:31:33 -05:00
Scot Breitenfeld
3f9b3bcb47 [svn-r15630] Description:
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.
2008-09-16 12:00:11 -05:00
Quincey Koziol
bdd7d59902 [svn-r15628] Description:
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...
2008-09-16 10:52:51 -05:00
MuQun Yang
8bc0d5ed90 [svn-r15627] This check-in fixes a bug inside parallel HDF5 testsuite.
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.
2008-09-16 10:03:45 -05:00
MuQun Yang
e7ff2aafa5 [svn-r15626] This check-in fixes a bug inside parallel HDF5 testsuite.
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.
2008-09-16 10:03:21 -05:00
Scott Wegner
876844988a [svn-r15622] Purpose: Add new source files to Windows projects
Description:
This checkin adds the following source files to our Windows projects:
 -- H5EAiblock.c
 -- H5EAstat.c
 -- H5EAdbg.c
2008-09-15 10:09:10 -05:00
HDF Tester
63042260d9 [svn-r15619] Snapshot version 1.9 release 17 2008-09-14 05:39:04 -05:00
Quincey Koziol
93f29787ed [svn-r15618] Description:
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
2008-09-11 16:04:30 -05:00
Quincey Koziol
5fb061e46e [svn-r15617] Description:
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
2008-09-11 15:16:05 -05:00
Quincey Koziol
f1d22675ff [svn-r15614] Description:
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
2008-09-11 09:03:23 -05:00
Quincey Koziol
37ebc24cf8 [svn-r15612] Description:
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
2008-09-11 07:30:35 -05:00
Quincey Koziol
c465e18a68 [svn-r15609] Description:
Omnibus compiler warning cleanup & some reformatting also.

Tested on:
    Mac OS X/32 10.5.4 (amazon)
    Too minor to require h5committest
2008-09-10 14:10:41 -05:00
MuQun Yang
068620ea81 [svn-r15604] The MPI compiler(mvapich2-0.9.8p2patched-intel-ofed-1.2) at 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.
2008-09-08 17:50:47 -05:00
Scot Breitenfeld
0423d629ce [svn-r15601] Description:
Added windows fortran DLL function file, hdf5_fortrandll.def
2008-09-08 10:48:41 -05:00
Scot Breitenfeld
077b644606 [svn-r15598] Description:
Moved all the windows DLL function declarations to one file (hdf5_fortrandll.def).
2008-09-08 10:02:44 -05:00