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
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
Put H5Acreate() under API versioning, with all internal usage shifted
to H5Acreate2().
Add regression tests for H5Acreate1().
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
Remove all plain calls to H5Gopen() from source, replacing them with
either H5Gopen2().
Add test for H5Gopen1().
Reformatted several pieces of code, to clean them up.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
Mac OS X/32 10.4.10 (amazon)
Description:
In h5unjam.c, there was a call to "open", rather than "HDopen". This isn't a problem on most platforms, as the are equivalent. However, on Windows, we use the HDopen macro to unconditionally set the O_BINARY flag. This is needed to safely seek within a file.
Tested:
VS2005 on WinXP
h5committest (kagiso linew smirom)
Pursue calls to H5Gcreate() relentlessly and ruthlessly exterminate
them, leaving only a few tame specimens in text files and comments. ;-)
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
Add --enable-deprecated-symbols configure option, to allow users to
remove deprecated public API symbols at configure time.
Add bin/make_vers script to bin/reconfigure actions.
Run bin/reconfigure to regenerate autotool components.
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (kagiso)
2) Removing configuration of c++/src/H5cxx_pubconf.h file.
Reasoning: the additional pubconf file caused compilation complications, this is cleaner.
Tested: kagiso, smirom
Description: added new configuration to generate a pubconf file
in the c++/src directory, H5cxx_pubconf.h. When C++
compiler recognizes 'offsetof', the macro
H5_CXX_HAVE_OFFSETOF is defined in the new
pubconf file.
tested: kagiso, smirom
Description: a new configure flag has been created that will now set a macro
in the test/Makefile. The flag is with-default-vfd=. When set to
a virtual file driver (e.g. "--with-default-vfd=sec2"), the macro
DEFAULT_VFD will hold this value.
Tested: kagiso, smirom, linew
file size from MPI_File_get_size. Bypass this problem by replacing it with
stat. Add an option --disable-mpi-size in configure to indicate this function
doesn't work properly. Add a test in testpar/t_mpi.c, too. If it returns wrong
file size, print out a warning.
Tested on kagiso (parallel) because already tested the same change to v1.6 on
several platforms (kagiso, cobalt, copper, and sol).
Rename new error handling API routines from H5E<foo>_stack() to
H5E<foo>2().
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Description: Multiple copies of Copyright appeared in Makefile.in. This was
due to automake copying the copyright right in the included files such as
config/commence.am.
Solution: Automake treats double hashes as comments and does not copy them
to Makefile.in. Changed all the copyright notices in config/*.am to use
double hashes for the Copyright right notice.
Tested: kagiso via bin/reconfigure.
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
It seems that while Cygwin supports the time command, it has trouble with
the syntax
srcdir="../../hdf5/test" time ./testhdf5
and complains.
The solution is to test the above case in configure and not to use the time
command if it fails; Cygwin is fine with
srcdir="../../hdf5/test" ./testhdf5
Tested on Cygwin and kagiso. This feature shouldn't be a major compatibility
problem since every platform but Cygwin is already fine with the current
syntax.
The version of libtool used by HDF5 isn't directly affected by the reconfigure
script; instead, libtoolize --force must be used by hand. Libtool was the
source of the problem, so rolling its version back to 1.5.14 should solve the
issue (at least temporarily).
Reconfigure should still work on both heping and kagiso.
Tested on heping, kagiso, and tg-login3.
Should disable linking against shared libraries in Fortran for compilers that
don't support shared libraries.
Should also fix problem when the wrong Fortran file extension was specified.
If these changes don't solve the Daily Test issues, I'll look at backing out
the autotool version change until I have time to fix them.
Tested on heping, kagiso, juniper.
and quote its arguments. Also checks for the 'socket' library on
Solaris.
If this patch passes the Daily Tests and makes the user happy, I'll
port it back to the 1.6 branch.
Tested on mir and sol.
File format is not stable, don't keep files produced!
Description:
First stage of checkins modifying the format of groups to support creation
order. Implement "dense" storage for links in groups.
Try to clarify some of the symbols for the H5L API.
Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest
file format options (including "dense" link storage in groups)
Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation
order tracking in groups (although no index on creation order yet).
Remove --enable-group-revision configure flag, as file format issues are
now handled in a backwardly/forwardly compatible way.
Clean up lots of compiler warnings and other minor formatting issues.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-v1.6 compa
Mac OSX/32 10.4.8 (amazon)
AIX 5.3 (copper) w/parallel & FORTRAN
Since these examples need to follow filesystem paths, the Makefiles need
to create directories in the examples directory; added this to the
Makefile.am.
Tested on Windows, mir, juniper
Users can create external links using H5L_create_external(). These links
point to an object in another HDF5 file. Users can alter the behavior of
external links or create new kinds of links by registering callbacks
using the H5L interface.
Added tests, tools support, etc.
Also a number of other, minor changes have been made (some restructuring of
the H5L interface, for instance).
Additional documentation and examples are forthcoming.
"make check-vfd" will now run all tests in the test directory with different
file drivers (at least, all of those tests that use the testing framework's
FAPL). Tests that fail will be skipped.
This is not a perfect fix, but is better than nothing.
Along with this change, check-vfd should be added to the Daily Tests.
Configuration feature
Description:
'make install' now tests both static and shared libraries if both are installed.
Solution:
Previously, shared libraries were only tested when static libraries were not installed.
Also cleaned up line in commence.am that was including HL library in all Makefiles.
Platforms tested:
mir (Makefile change only)
Bug fix - bugzilla #552
Description:
On Cray X1, trying to use : as an argument confused the system.
Solution:
Added a test in configure to see if : as an argument is bad.
If so, skipped the test.
Platforms tested:
mir, Cray X1 (change to configure only)
Bug fix.
Description:
The ${TR}, though avoid the error, is inconvenient. It is needed
because configure.in use the char range in the style of 'a-z'.
The other style of '[a-z]' is more commonly accepted by all tr
but autoconf tends to strip away [], making the syntax rather
clumsy.
Solution:
Learned from autoconf that it avoids the use of character range
by just spell all the letters out. Changed our tr commands to
use those variables defined by autoconf. Also removed the
definition of ${TR} since it will cause inconsistancy when
autoconf also use plain 'tr' in its generated code.
The Makefile.in are changed because the elimination of ${TR} from
configure triggered its removal from all Makefil.in. That is okay
because ${TR} is not used at all in Makefile.
Platforms tested:
h5committested. (sol failed to connected). also tested in shanti
using both /usr/ucb/tr and /bin/tr (the bad one before.)
Misc. update:
Updated both INSTALL and RELEASE files.
Several bug fixes
Description:
Added config file for Cray X1 (previous file was misnamed)
Simplified some code in hyperslab.c test that seemed to have been
confusing compiler on Cray X1.
Fixed typo in config/commence.am
Cleaned up hl/src/Makefile.am
Solution:
All four fixes should be straightforward. The failure on Cray was
very difficult to debug, but involved arithmetic errors.
This change seems to fix it.
Platforms tested:
heping, copper, sol, some Cray X1 (more testing when system comes back up)
new feature
Description:
1) separated the HL library into "public" and "private" header files, with the same caracteristics as the basic library
2) added the public headers to hdf5.h (with a conditional include macro, defined in configure.in)
3) added the path to HL in all Makefile.am 's , because of the inclusion in hdf5.h
Solution:
Platforms tested:
linux 32, 64
AIX
solaris
with fortran and c++
(one packet table example fails)
Misc. update:
Bug fix
Description:
Previous checkin did a bad thing; 'make clean' failed in example directories.
Solution:
Fixed commence.am so that examples no longer break, and fixed a mistake
in conclude.am.
Platforms tested:
heping (minor makefile change)
Misc. update:
Bug fix
Description:
make check-clean didn't clean results of example tests
Solution:
Fixed Makefiles so that check-clean recurses into example directories.
Also a little Makefile cleanup.
Platforms tested:
mir, modi4, heping, copper
Bug fix
Description:
Fortran type generation was broken in two ways. Fixed both.
Solution:
Firstly, there were a couple of path problems. Fixed a typo and
specified the full path of a file.
Secondly, the dependencies weren't right when building with HDF5-specific
commands (make lib, make check-s, etc.). Tweaked dependencies
to fix the problem.
Platforms tested:
mir, modi4, sleipnir
