Removed duplicate h5p, h5a, and h5d, double precision functions in _F90 and _F03 files
that are already defined in H5_DBLE_InterfaceInclude
Tested: jam (gcc 4.5, intel 12.0)
1) --enable-fortran2003 will enable only F2003 features. It is not a replacement for --enable-fortran. If compiler is not F2003 compliant configure should fail.
2) if --enable-fortran2003 is specified with out --enable-fortran configure fails
3) Configure help indicates that --enable-fortran2003 is in addition to --enable-fortran
Updated the version checks of different compilers.
Tested: jam (gcc 4.1 4.6, intel 10.1 11.1 12.0, pgi)
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)
Switch from H5P_DATASET_ACCESS_DEFAULT to H5P_DEFAULT for calls to
H5Rdereference2().
Tested on:
Mac OS X/32 10.6.8 (amazon) w/debug
(too minor to require h5committest)
Changed the length of the fortran string passed to HD5packFstring in the function nh5pget_external_c. The 3rd
argument should be the fortran length of the string, not the C length of the string (which includes the null).
Tested: jam (intel and gnu), also checked the example h5ex_d_extern.f90 which detected the problem on Amazon c2
machine (reported by Larry).
General shared library improvements for CYGWIN / AIX
Description:
Shared libraries are disabled on both CYGWIN and AIX due
to inability to build them correctly. Part of the problem
in both of these situations is the lack of the libtool
flag -no-undefined, which tells libtool that all needed
symbols are defined at link time (a requirement on these
systems) and that it's okay to build shared libraries.
Another problem are lack of dependencies between wrapper
libraries and core C HDF5 library.
This patch addresses both of these by fixing configure to
add in -no-undefined flag for libtool during linking and
adds automake dependencies in the Makefile.am files.
After testing, both CYGWIN and AIX now generate shared
libraries, but there are still some test failures in each.
(cache_api, dt_arith, and testerror.sh on CYGWIN, and
fortran tests on AIX).
Even though the shared libraries are not quite perfect,
this is a general improvement to what we had before, so
I'm applying the patch anyways. Note that default behavior
of shared libraries on these systems being disabled has
NOT been changed and requires the use of the
--enable-unsupported to attempt to build them.
We will need to address the test failures in each
architecture prior to formally supporting shared
libraries on each.
Tested:
h5committested & CYGWIN tested (on bangan)
(AIX tested by Albert on bp-login2)
Add "silent make" mode configure option.
Description:
Automake 1.11 has a new option available that allows for a
silent make mode. This functionality needs to be explicitly
enabled in configure.in via the use of the automake macro
AM_SILENT_RULES, which is what this commit is adding.
This introduces a new configure option:
--{en|dis}able-silent-rules
This option is on by default, and simplies compile and link
line outputs when building the library. Disabling this option
will print full "verbose" output (i.e., full compile and
linking lines for each target).
Tested:
This was tested on jam & h5committested
r20440 and r20469:
1. The dataspace code has another bug - when the maximal dimension isn't passed in for H5Sset_extent_simple, it
is supposed to be same as the dimension. The current library sets NULL to it. I corrected it and added a
test case to it.
2. I corrected the tests of Fortran and C++ for this problem.
Tested on heiwa, jam, and amani.
Fixed issue HDFFV-5866 (BZ 2156). Changed scripts to run examples to use specific names for compiled executable files instead of a.out, which did not work on Cywin as it produces a.exe by default. Removed issue from known problems section of RELEASE.txt.
Tested with Cygwin 1.7.8 on Windows 7.
This line, and those below, will be ignored--
M release_docs/RELEASE.txt
M hl/c++/examples/run-hlc++-ex.sh.in
M hl/fortran/examples/run-hlfortran-ex.sh.in
M hl/examples/run-hlc-ex.sh.in
M c++/examples/run-c++-ex.sh.in
M fortran/examples/run-fortran-ex.sh.in
M examples/run-c-ex.sh.in
- Revise shared Fortran library disabling scenarios in configure
- Improve configure output summary
Description:
Shared Fortran libraries are not supported on Mac, but were being
disabled by configure in a way that also forced the C libraries
to be static-only. This has been fixed, so now only shared Fortran
is disabled while shared C can remain.
This prompted two additional changes:
1. While working on the check that addresses whether or not
shared Fortran libraries are allowed, removed old and no
longer needed check(s) that disable shared Fortran
libraries with HP, Intel 8, PGI, and Absoft compilers.
(Essentially, Mac is the only situation in which Fortran
shared are disabled by configure.)
2. Having two different states of libraries (i.e. shared C
library with static-only Fortran library) was not apparent
in the configure summary, which labeled all libraries as
either shared and/or static. I've added lines to both the
C++ and Fortran output sections to list shared/static-ness
of these libraries specifically.
Additionally, I've made sure that the new --enable-unsupported
configure option correctly overrides configure if it tries to
disable a shared library.
Tested:
jam, fred, & h5committest
Bring changes from Coverity branch to trunk:
r19930:
Fix memory leaks involving VL attributes in h5repack and h5diff. The buffers in
copy_attr and diff_attr were not checked for the presence of a vlen before being
freed, and vlen storage was never reclaimed. Added checks and calls to
H5D_vlen_reclaim().
r19933:
Purpose: Fix memory leak in H5L_move_cb()
Description: H5L_move_cb copied the source link using H5O_msg_copy() but freed
it manually using H5MM_xfree(). Since H5O_link_copy allocates the link using
H5FL_MALLOC, this causes the link to be allocated from the free list but is
never put back on the free list when it is freed. This prevents the link free
list from shutting down properly. Modified H5L_move_cb() and H5L_move_dest_cb()
to free the link properly using H5O_msg_free().
r19973:
Fix resource leaks by freeing string created by HD5f2string
r19974:
Issue #345: Inialize buf variable to null
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(h5committested on Coverity branch)
Bring Coverity revisions from branch back to trunk, and clean up some other
misc. compiler warnings also.
r19500:
Fix coverity items 1446 and 1447. Moved up calls to memset in test_cont in
ohdr.c so the test never tries to close uninitialized locations.
r19501:
Fix coverity items 1398-1445. Various uninitialized variable errors in fheap.c.
r19502:
Fixed coverity issue 579 and some additional warnings in the file as well.
r19503:
Bug fix: This fix addressed the "RESOURCE_LEAK" problems #789 and 790, run 26
r19504:
minor mods to try to keep coverity from flagging false positives.
r19505:
Fixed coverity issues 566 - 571. Declared variables that are passed to functions that use them as arrays to be arrays of size 1.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug, production & parallel
(h5committested on trunk)
Corrected use/name of source folder aliases.
Duplicated FindMPI.cmake so that non-c++ compiler is found first (recommemded commands did not work).
Tested: local linux with mpich
- Add an install rule to copy compiled fortran module files
- Only build the xlatefile utility if testing and tools are enabled
- Don't do MPI HAVE_XXX checks until MPI_FOUND is true
- Install needs H5version.h & H5overflow.h to be copied
- Add debug information flags to debug compile and link lines for win32 Intel compiler
Improve configure's large-file support control.
Description:
Modified configure to now attempt to add defines necessary for
supporting largefiles on all systems, instead of solely on linux. This
is in response to user requests to enable largefile support on Solaris
by default, as well as to give extra control on AIX (instead of just
jamming the necessary flag into the config files).
The old --enable-linux-lfs flag has been removed in favor of the
--enable-largefile flag (enabled by default), which can be used on all
platforms.
On systems where large files cannot be supported in this manner,
configure will report as such.
Tested:
h5committest
AIX (NCSA's blue_print machine)
duty, liberty, and linew.
Autotool Upgrade / Libtool Bug Fix
Description:
Updated autotools referenced in bin/reconfigure as follows:
Autoconf 2.64 --> Autoconf 2.65
Automake 1.11 --> Automake 1.11.1
Libtool 2.2.6a --> Libtool 2.2.6b-mcg
The referenced libtool version is a custom version of 2.2.6b. It
has been tweaked to fix a bug in libtool that occurs
when using PGI 10.0 compilers. A check incorrectly categorizes
the C++ compiler as version 1.0 instead of 10.0, and the link
line is subsequently set up incorrectly and fails to compile.
A patch has been made available and will be included in the next
release of libtool, but in the meantime I've applied the patch to a custom
installation as indicated above. This bin/reconfigure now references
the custom installation, and the resulting configure script will correctly
categorize the PGI 10.0 C++ compiler.
Ran bin/reconfigure to regenerate configure and makefiles.
Tested:
jam and amani with PGI 10.0 compilers.
h5committest
In order to compile stand-alone Fortran wrappers the following files need to be installed via make install:
(1) From the source: trunk/fortran/src/H5f90i.h
- defines the character type and includes the file H5f90i_gen.h
(2) From the compiled source: trunk/fortran/src/H5f90i_gen.h
- a generated file at hdf5 compile time relating the C types to the Fortran types for interoperability.
Since these C/Fortran types need to match those used in generating h5cc and h5fc commands we include the files H5f90i_gen.h and H5f90i.h in the hdf5/include install directory when Fortran is enabled.
the files are installed with the other fortran files in include and also removed when the installation is cleaned.
Test: jam
Added H5T_CSET_UTF8_F to the list of possible values for cset in the description of h5tset_cset_f and h5tget_cset_f.
Tested: N/A, edited comments only.
Bring revisions from Coverity fixing branch to trunk:
r18184:
Fixed Coverity issue 373. Allocated memory freed in line 762 in case of error.
r18185:
Fixed Coverity issues 357 & 358. Added check for NULL pointer before use.
r18186:
Fix coverity item 65. Added code to h5unjam to correctly handle failures in
read() and write, and also to correctly handle writes that write less than
requested.
r18187:
Fix coverity items 115 and 116. Added code to H5Tenum.c to correctly close
opened datatypes in case of failure.
r18188:
Fixed Coverity issue 46. Check that dataset->shared is not null when freeing
memory after error.
r18190:
Fix coverity item 95. Added code to H5T_create_vlen to correctly close
allocated datatype in case of failure.
r18191:
Fixed Coverity error 59. Checked sfirst for -1 value before use in line 10533.
r18192:
Fix Coverity items 121 and 28
Added Asserts:
121: assert that all dimensions of count have values greater than zero.
28: assert curr_span pointer is not null before dereference.
Note: still need too add checks in hyperslab APIs that fail
when count values are zero, and appropriate tests.
r18194:
Fixed Coverity issues 61 & 62. Checked variable snpoints for value < 0 in line
218.
Tested on:
Mac OS X/32 10.6.2 (amazon) w/debug & production
(already daily tested on coverity branch)
Bring back changes from Coverity session on 1/15/10:
r18111:
Fix Coverity issue #130: make certain that the cache gets freed on error.
r18112:
Fix Coverity issue #43 by making cache testing calls protected by 'pass'
variable.
r18113:
Fix Coverity issue #129 by releasing the cache on error.
r18115:
Coverity #45 fix: patched an error check in H5Screate_simple to prevent future dereferencing of a NULL point.
Added a verification in test/th5s.c.
r18116:
Fix Coverity issue #43 by releasing cache on error.
r18117:
Coverity #362,363 by adding HGOTO_DONE, freeing allocations and associated changes. REsolving coverity results #364-368, 369, 370-372, 377, 379, and 380.
r18118:
Fix Coverity issue #42: assert that cache & test specification pointer are
valid.
r18122:
Coverity #362,363 by adding HGOTO_DONE and freeing allocations. This also takes care of #357,358.
r18123:
Coverity #359-361, 373-376: Added HGOTO_DONE(FAIL) statement after checking allocation for NULL. Verified allocation is freed in done block.
r18128:
Fixed coverity issue #10 -- removed dead code.
Tested on:
Mac OS X/32 10.6.2 (amazon)
The mixed use of RUNTEST (original) and RUNTESTS (new) caused
confusion. E.g., the timings in test/ was still using the old
$RUNTEST. It made more sense to use $RUNTEST which is used
by the dejagnu feature of automake. So, I changed all
$RUNTEST or $RUNTESTS to $RUNEXEC.
config/commence.am & config/conclude.am are the two files
that got changes. Also fixed an error in test/Makefile.am.
The rest are changed by bin/reconfigure.
Tested: h5committested.
Changed the link type definitions to match the changes made in the source.
- ! H5L_LINK_SOFT_F - Soft link
- ! H5L_LINK_EXTERNAL_F - External link
- ! H5L_LINK_ERROR _F - Error
+ ! H5L_TYPE_HARD_F - Hard link
+ ! H5L_TYPE_SOFT_F - Soft link
+ ! H5L_TYPE_EXTERNAL_F - External link
+ ! H5L_TYPE_ERROR _F - Error
Tested: jam (intel)
Changed comments to reflect changes made to the link_type names to match those in C (bug 1720) from,
H5L_LINK_HARD_F, H5L_LINK_SOFT_F,H5L_LINK_EXTERNAL_F,H5L_LINK_ERROR_F
to
H5L_TYPE_HARD_F, H5L_TYPE_SOFT_F,H5L_TYPE_EXTERNAL_F,H5L_TYPE_ERROR_F
MSB January 8, 2010.
Tested: No source changed.
h5cc link-line reordering
Description:
Re-ordered flags in h5cc such that LDFLAGS appears after hdf5 library
include path. This is to ensure third party library locations don't
interfere with locating the correct version of hdf5 library.
Tested:
passed daily tests in 1.8 branch (as verified by Larry just now).
CFLAGS overhaul
Description:
Modified the way configure handles CFLAGS.
(note: all changes also apply to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS).
1. The configure process will now always preserve a user's CFLAGS
environment variable setup. Any additional flags necessary for compilation
added at configure time will be passed into the Makefiles as AM_CFLAGS,
which is an automake construct to be used in addition to CFLAGS.
This will allow a user to have the final say, as CFLAGS will always appear
later in the compile line than AM_CFLAGS. Additionally, setting CFLAGS
during make will no longer completely erase all flags set by configure,
since they're maintained in AM_CFLAGS.
2. Additionally, where possible, flags previously being assigned directly
into CFLAGS (and thus propagating into h5cc) have now been redirected into
H5_CFLAGS, so they're used ONLY for compiling hdf5, and not embedded into
the h5cc wrapper script as well.
*Note that H5_CFLAGS ultimately is assigned into AM_CFLAGS for use in the
Makefiles. Complete description of changes and build process will be
included in a Configure Document that Elena and I are working on.
3. Removed unsupported config files. This includes:
config/dec-osf*
config/hpux11.00
config/irix5.x
config/powerpc-ibm-aix4.x
config/rs6000-ibm-aix5.x
config/unicos*
4. Modified configure summary to display additional values. Specifically,
appropriate AM_* variables are being shown, as well as H5_FCFLAGS and
H5_CXXFLAGS, which were for some reason not already present.
Tested:
- H5committest
- Tested on all THG / NCSA machines, using several combinations of the more
prominent configure options (c++, fortran, szip, threadsafe, parallel,
et cetera). (Thanks to Quincey for rysnc testing setup!)
- With regards to new automated testing, anything *necessary* for
compilation will be caught by the daily tests as it stands now. (i.e.,
if LDFLAGS is not properly set when szip is used, linking will fail).
Additionally, with regards to which flags get into h5cc, if any
*necessary* flags have been improperly removed, then daily tests should
fail during make installcheck. Additional machine-specific desired
behaviors and/or checks may have to be set up separately within the
daily tests, so this is something to work on.
Bring changes from file free space branch back to the trunk. *yay!*
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) 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 (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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Bug 1652 - h5lget_info_by_idx_f missing/broken functionalit
* added returned val_sel, link_type and address that were missing
In the process, fixed the integer type in H5lget_info_f for address and val_sel
* wrote test for val_sel, address, and link_type returned values
* to check address values added h5Oopen_by_addr_f function and test program.
Tested: smirom (pgf90/pgcc, ifort/icc)
linew
jam (gcc/g95)
Bug 1653 - H5_LINK_* values defined in H5f90global.f90 are incorrect
The Fortran EQUIVALENCE constant variables did not match those from the C definitions, fixed.
Missed because there is not a Fortran test function that uses these constants.
Tested: smirom (ifort, g95)
Updating autotools
Description:
Installed new autotools and used them to reconfigure HDF5.
- Automake upgraded to 1.11
- Autoconf upgraded to 2.64
- bin/reconfigure script edited to use new versions (on jam), and
run to generate new configure script and Makefile.in's.
- configure.in script edited to add "_cv_" to all AC_CACHE_VAL strings
(in order to comply with new autoconf standard).
Tested:
Tested on machines jam, smirom, liberty, linew.
Tested w/ features c++, fortran, parallel.
Tested w/ compilers gcc, pgcc, icc.
Further testing via Daily Tests should catch any other outliers. Upon
passing DT's, I'll propogate the new tools into 1.8, hdf4, et cetera.
Added filename argument to file_space routine to avoid conflicts of the files when running fortranlib_test_1_8.f90 and fortranlib_test.f90 at the same time (i.e. when running the tests in parallel).
tested: smirom (ifort, pgf90, g95, gfortran), linew
If the AR command has embedded shell separators such as the case of
"AR = ar -X 64", $AR ends up as a blank.
Solution:
Put quotes around the command substitution string to protect against embedded
separators. Applied the same to both AR and RANLIB assignments.
Tested:
At Up (AIX 5.3) only because that was where I discovered the error
when AR is ar -X 64
H5D_CHUNK_CACHE_NSLOTS_DEFAULT_F
H5D_CHUNK_CACHE_NBYTES_DEFAULT_F
H5D_CHUNK_CACHE_W0_DEFAULT_F
to
H5D_CHUNK_CACHE_NSLOTS_DFLT_F
H5D_CHUNK_CACHE_NBYTES_DFLT_F
H5D_CHUNK_CACHE_W0_DFLT_F
to get under the 31 limit for variable names
H5D_CHUNK_CACHE_NSLOTS_DEFAULT_F
H5D_CHUNK_CACHE_NBYTES_DEFAULT_F
H5D_CHUNK_CACHE_W0_DEFAULT_F
to
H5D_CHUNK_CACHE_NSLOTS_DFLT_F
H5D_CHUNK_CACHE_NBYTES_DFLT_F
H5D_CHUNK_CACHE_W0_DFLT_F
to get under the 31 limit for variable names
- Updated bin/reconfigure to use latest version of automake (1.10.2).
Re-generated Makefile.in's by running bin/reconfigure.
- Added libtool version numbers to c++, fortran, hl, hl c++, and hl fortran
libraries.
Tested:
jam, liberty, smirom
Fixed warnings from absoft's compiler for !DEC$ statements.
Solution: There should not be a space after !DEC$ statements, removed the spaces.
Platforms tested:
Jam with gcc and f95
Bug Fix
Description:
Fixing BZ #1381. The --includedir=DIR configure option, which is used
to specify the installation location of C header files, did not work
correctly as the path was hard-coded in config/commence.am. I'm presuming
this is because an older version of automake didn't know where to put
c header files. In any case, removing this line now defaults the includedir
to the same directory that it is currently hard-coded to, and also fixes
the configure flag to allow customization of this value.
Tested:
jam, liberty
the way h5ls prints types, it starts searching for NATIVE types first. One solution would be h5ls not to detect these native types, using for example the same print datatype function that h5dump does, that would make the output look the same on all platforms ("32-bit little-endian integer" would be printed instead). Drawback, this "native" information would not be available. Other solution is to have not one but 2 expected outputs and make the shell script detect the endianess and compare with one output or other
tested: h5committest
*Fixed cd_nelements in nh5pget_filter_c - cd_nelments not pased in or returned correctly. Since
cd_nelmts has IN/OUT attributes, fixed the input and
returned value of cd_nelmnts to satisfy this specification.
*Fixed 'name' returned in nH5Pget_external_c - if the size of the fortran buffer is larger then
the returned string from the function then we need to give HD5packFstring the
fortran buffer size so that it fills the remaining unused characters with blanks. Found
with the gfortran compiler.
Platforms tested: smirom, liberty
Description:
- Remove need to set LD_LIBRARY_PATH when using shared szip library.
- Libtool 2.2.6a is now used to generate libraries.
- 'make check install' dependency bug is fixed, and should no longer
break the build.
- removed hard coding of shell in config/commence.am, as this causes
problems on Solaris with the new version of libtool.
- RELEASE.txt with appropriate changes.
Tested:
- kagiso, smirom, linew (merged from 1.8, pretty quick tests)
Description:
Visual Studio compiler was complaining because variables were declared mid-function, when they should be declared at the top. This checkin simply moves the declarations to the top.
Tested:
Simple edit, VS2005 only
We check for all the available reals in Fortran and if 16 byte real is available in Fortran and not in C then we disable the 16 byte real in Fortran. Also added the test for 12 byte real in Fortran so that it can match the 12 byte float in C if available. Note: if KIND=10 and KIND=16 are both avaiable as when using g95, then it may be the case on some systems that the size of KIND=10 and KIND=16 are both 16 bytes, so the program will print twice in H5fort_type_defines.h
#define H5_FORTRAN_HAS_REAL_16
which should not cause any errors.
Removed refences to "double" so that we don't distinguish between writeDoubleToFiles and writeFloatToFiles such that we match the definitions of c_float_4, c_float_8, and c_float_16 in H5f90i_gen.h
Changed the datatype test programs such that we don't distinguish between writeDoubleToFiles and writeFloatToFiles so that we only define c_float_4, c_float_8, and c_float_16 in H5f90i_gen.h
Added the definition of real_4_f, real_8_f, real_16_f depending on if they are available, also in H5f90i_gen.h
The custom rules for installing h5cc, h5fc, and the fortran modules in fortran
and in hl/fortran don't use $(DESTDIR). Added it to all those rules.
Tested: kagiso both serial and parallel with fortran and cxx enabled.
Tested by:
make install
make DESTDIR=/tmp/acheng install
diff -r /tmp/acheng/.../hdf5 hdf5
Description:
We recently moved the Windows-specific fortran source code into a separate file for specifying DLL exports. However there were a couple definitions missing in the port from 1.8 to the trunk branch. This checkin correctly includes the .def file into our Windows project, and adds the missing definitions to hdf5_fortrandll.def.
Tested:
VS2005 on WinXP
In nh5tget_offset_c:
(1) The return value type of H5Tget_offset was set to size_t where
it should be of type int.
(2) Was if offset was equal to 0 it returned the error code of -1 back to
Fortran, this was changed to return an error code of -1 when the
offset value is < 0.
In h5tget_norm_c:
(1) was if the return value of H5Tget_norm = 0 it would return an error
code to Fortran, but from enum of the return value:
typedef enum H5T_norm_t {
H5T_NORM_ERROR = -1, /*error */
H5T_NORM_IMPLIED = 0, /*msb of mantissa isn't stored, always 1 */
H5T_NORM_MSBSET = 1, /*msb of mantissa is always 1 */
H5T_NORM_NONE = 2 /*not normalized */
/*H5T_NORM_NONE must be last */
} H5T_norm_t;
only when -1 is returned is there an error, changed it to return an error
only if the value of H5T_NORM_ERROR = -1.
Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $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...
Compiles either H5test_kind.f90 or H5test_kind_SIZEOF.f90 depending on the availability of intrinsic Fortran function SIZEOF (indicated by the status of FORTRAN_HAVE_SIZEOF).
Was not returning the correct fortran types when -i8 and -r8 flag was specified, fixed. This code is now depreciated and only used when SIZEOF function is not available, H5test_kind_SIZEOF.f90 should be used instead.
H5test_kind_SIZEOF.f90 is the preferred portable program used for Fortran type detection. It uses the intrinsic Fortran function SIZEOF. This program should be used instead of H5test_kind.f90 if the SIZEOF function is available. Most of the newer Fortran compilers support SIZEOF.
Put the DOUBLE PRECISION interfaces in a separate module and added a USE statement for the module. The interfaces are included/excluded depending on
the state of FORTRAN_DEFAULT_REALisDBLE_F which detects if the default REAL is DOUBLE PRECISION. This allows the library to be compiled with -r8 Fortran flag without the user needing to change the source code.
Put the DOUBLE PRECISION interfaces in a separate module. The interfaces are included/excluded depending on
the state of FORTRAN_DEFAULT_REALisDBLE_F which detects if the default REAL is DOUBLE PRECISION. This allows the library to be compiled with -r8 Fortran flag without the user needing to change the source code.
Added missing comma, i.e.
WRITE(*, "("" subroutine i"" i2.2,""()"")") j
should be
WRITE(*, "("" subroutine i"", i2.2,""()"")") j
etc...
as noted in bug 1251 and NAG compiler.
Checked the write fix using Sun f95, g95, pgf90, gfortran, ifort, absoft and all gave the correct write output.
Description:
As part of our Windows cleanup, we try to remove windows-specific tweaks in the source code. There are many instances where Windows code is introduces via ifdef's. We re-evaluate whether they are still required, and found that many of them are not. Others we change to "feature"-specific code, rather than Windows-specific.
Tested:
VS2005 on WinXP
VS.NET on WinXP
h5committest (kagisopp, smirom, linew)
Changed the error output formatting so that the
test status writes to standard out looks correct when using the
sun compiler (it did not correctly tab the output).
Uninstall target had non-existant file to remove; error_handler module triggered
a race condition for parallel make with Intel and PGI compilers, therefore we
removed the module and created a subroutine instead.
Platforms tested: kagiso with GNU, Intel and PGI compilers.
Added code to remove module files when make clean
Description:
The module files were not being removed when make clean
and caused compiling errors. fixed.
Made reporting of the test status global by handling the output
via a module. Cleaned-up output to the terminal.
Description:
Put writing the test status as a call to a subroutine
instead of on a per account basis.
Added the dependency of compiling in the correct order
in the Makefiles for use of the Module.
Description:
The fortran Makefile.am used HDF_FORTRAN to indicate it is part of the
Fortran API source so that conclude.am will give fortran api prefix in the
test output. The symbox HDF_FORTRAN is also used in configure for a different
purpose (indicated --enable-fortran). They conflicted.
Similar problem for the symbol HDF_CXX.
Solution:
Changed all the involved Makefile.am to use "FORTRAN_API" instead. It is
a more appropriate name. Same for CXX_API.
Along the way, discovered that the Makefile.am of hl/fortran/test and
hl/cxx/test did not have those symbols at all. Added them in.
Platform tested:
Kagiso only. It is a trivia change.
Cleaned up unused code (i.e. commented out) and removed extraneous output to standard out.
Tested:
N/A - No critical executable source lines were modified, only comments and write statements.
Fixed validation failure when compiled with -i8 and the g95 compiler
Description:
Fixed "off by one error" when converting C character buffer
into fortran character buffer in h5aget_name_by_idx_c
Improvement.
Description:
src/libhdf5.settings was the initial configure summary and is installed.
Then configure is changed to dump a summary of the configure settings to
the output and also append it to src/libhdf5.settings. That created
two different output formats and duplicated information. This is the
initial attempt to clean up this confusion and unify the output format.
It is decided to use the src/libhdf5.settings template as the unified means.
This requires more macros symbols be defined. The following symbols are
all related to generating the src/libhdf5.settings file.
AC_SUBST(EXTERNAL_FILTERS)
AC_SUBST(MPE) MPE=no
AC_SUBST(STATIC_EXEC) STATIC_EXEC=no
AC_SUBST(HDF_FORTRAN) HDF_FORTRAN=no
AC_SUBST(FC) HDF_FORTRAN=no
AC_SUBST(HDF_CXX) HDF_CXX=no
AC_SUBST(CXX) HDF_CXX=no
AC_SUBST(HDF5_HL) HDF5_HL=yes
AC_SUBST(GPFS) GPFS=no
AC_SUBST(LINUX_LFS) LINUX_LFS=no
AC_SUBST(INSTRUMENT) INSTRUMENT=no
AC_SUBST(CODESTACK) CODESTACK=no
AC_SUBST(HAVE_DMALLOC) HAVE_DMALLOC=no
AC_SUBST(DIRECT_VFD) DIRECT_VFD=no
AC_SUBST(THREADSAFE) THREADSAFE=no
AC_SUBST(STATIC_SHARED)
AC_SUBST(enable_shared)
AC_SUBST(enable_static)
AC_SUBST(UNAME_INFO) UNAME_INFO=`uname -a`
The src/libhdf5.settings.in has CONDITIONAL's added to it too. The
untrue conditions turned into a "#" and these lines are cleaned by the
post processing script.
Platform tested:
h5committest on kagiso, smirom and linew.
Changed the interface for the get_name_by_idx_f routine
Description:
Changed the 'size' which is the correct size of the returned
buffer to be an optional parameter.
Description:
There were a number of small tweaks we needed to make to add the new fortran_1_8 code on Windows. We create new project files, add new source to them, add the test to our test suite, and fix a few typos in the Windows-specific source code.
Tested:
VS2005 on WinXP
* test passing integer constant to subroutine
Description:
! -- CHECK PASSING AN INTEGER CONSTANT IN DIFFERENT FORMS --
! 1) call by passing an integer with the _hsize_t declaration
! 2) call by passing an integer with the INT(,hsize_t) declaration
! 3) call by passing a variable with the attribute hsize_t
This check-in should address Fortran failures on liberty and smirom.
Platforms tested: kagiso with Intel, smirom with g95 -fPIC, liberty with gfortran42
Description: Applying update to autotools that was applied to 1.8 a couple
of weeks ago to the trunk.
Updated bin/reconfigure script to reflect the new versions of
libtool and automake in the /home1/packages/ directory.
Rearranged configure.in script. When using libtool 2.2.2, the
libtool script doesn't generate until later in the configuration
process, so I had to move a test that parsed through the libtool
script to a point after where it was actually being generated.
Ran libtoolize on the project, and ran bin/reconfigure to
regenerate configure and Makefile.in's throughout.
Tested: kagiso, smirom, linew (h5committest)
Currently only one test (dense attributes) is failing. It looks like C library problem and we
have a similar bug report in Bugzilla: when dense storage is used, attributes are not written
to the file; somehow similar C test doesn't expose the problem while Fortran test does.
Platforms tested: linew, kagiso with g95 and PGI
Platforms tested: kagiso with PGI compilers, linew, smirom with GCC and g95 compilers;
some tests and function calls are commented out with !EP string; we will be
working on it.
Platforms tested: kagiso with g95 and Intel compilers; more testing will be done after checking in a fresh
copy from the trunk. New code itself was tested with all Fortran compilers available at THG
Correct the prototype for H5Sselect_elements() to take an 'hsize_t *' for
the coordinates, instead of 'hsize_t **'.
Tested on:
Mac OS X/32 10.5.1 (amazon)
Add work-around to allow reading files that were produced with a buggy
earlier version of the library, which could create objects with the wrong
object header message count. There is now a configure flag
"--enable-strict-format-checks" which triggers a failure on reading a file
with this sort of corruption (when enabled) and allows the object to be read
(when disabled). The default value for the "strict-format-checks" flag is
yes when the "debug" flag is enabled and no when the "debug" flag is disabled.
Note that if strict format checks are disabled (allowing objects with
this particular kind of corruption to be read) and the file is opened with
write access, the library will re-write the object header for the corrupt
object with the correct # of object header messages.
This closes bugzilla bug #1010.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Skip one of the tests in flush2.c since it looks like VMS system
flsuhes the file anyway (like on Winodws with DLLs)
Renamed files family*.h5 that are used in backward compatibility
testing to have only one '.' in a file name, otherwise VMS system
becomes confused and test fails.
Cleaned up the only test (Fortran multi-file test) that is failing on
VMS (C counterpart passesa).
Added new script to facilitate the build process on VMS
Updated MANIFEST
PLatforms tested: VMS server, kagiso and linew (minor changes)
Removed the stream-vfd from the basic library code.
(The stream-vfd source files are not removed yet but the MANIFEST has been
updated to NOT release those stream-vfd source files.)
Platforms tested:
Kagiso and smirom.
Then test the release tar ball in kagiso.
Change H5O[gs]et_comment to H5O[gs]et_comment_by_name and re-add simpler
forms of H5O[gs]et_comment.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Change H5Oget_info -> H5Oget_info_by_name and re-add H5Oget_info in a
simpler form for querying a particular object, to align with other new API
routines.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Change existing H5Gget_info -> H5Gget_info_by_name and add new version
of H5Gget_info, with simpler parameters, to better match new API routines.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Change H5Adelete2 -> H5Adelete_by_name and un-deprecate H5Adelete1 back
to H5Adelete, for better consistency with new other API routiens.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Changed H5Acreate2 -> H5Acreate_by_name, to be more consistent with
other new API routines.
Re-added simpler form of H5Acreate2, which creates attributes directly
on an object.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Change H5Aopen -> H5Aopen_by_name, in order to be more consistent with
other new API routines.
Re-add H5Aopen as a simpler routine, to open attributes on a particular
object. (Much like the old H5Aopen_name routine).
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Make H5Tarray_create() and H5Tget_array_dims() versioned, and drop the
"perm" parameter from the '2' versions.
Shift internal library usage to '2' versions.
Add simple regression tests for '1' versions.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
