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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.
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TFLOPS machine has retired long ago. Removed all code specific for its
support.
Test:
h5committested.
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PathScale was mistaken as the Gcc compiler such that gcc flags were added
to it but PathScale did not honor many of them. (e.g. -Wvariadic-macros,
-Wold-style-definition, -Winit-self, -Wvariadic-macros, -Wmissing-include-dirs,
-Winit-self, -Wc++-compat)
Solution:
Added a pre-condition to detect pathScale compiler before Gcc is
accepted.
Tested:
Sandia Glory where PathScale compiler is available.
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gfortran is more likely installed with gcc now.
Tested:
jam and amani which covers both linux and linux64.
No h5committest because this is gnu compiler specific, usually
applicable to Linux.
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Updated with new warning flags from gcc 4.4
Tested:
FreeBSD/64 6.3 (liberty) w/gcc 4.4.0
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For gcc v4.3 and v4.4, with production mode,
if -O3 is used, H5Tinit.c would fail to compile. Actually bad H5Tinit.c is
produced.
If -O (same as -O1) is used, H5Tinit.c compiled okay but test/dt_arith
would fail with:
Testing hard normalized long double -> signed char conversions time: comm
and terminated abnormally
When -O0 (no optimizatio) is used, H5Tinit.c compilete okay and all tests
passed.
Solution:
Changed the config/gnu-flags to use -O0 for gcc v4.3 and 4.4 for production
flags for now so that build and tests would work. Still need to investigate
if the error is due to Gcc optimization bug or our code errors.
Tested:
In liberty with gcc43 and gcc44. Also, tested in jam and smirom with
older versions of gcc.
There are no gcc 43 or 44 compilers installed in other THG machines that
I know.
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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
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by rev 16489.
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replacing all instances with long long.
Tested:
h5comittest
fedora 10 x64
Vista 32, VS2005, IVF101
XP32, Cygwin
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Changed 'THG' to 'The HDF Group' in various HDF5 source files,
most of which are <subdirectory>/COPYING.
-- Closes Bugzilla entry 1403.
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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)
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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
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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.
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