Embed the content of libhdf5.settings into the hdf5 executables so that an
"orphaned" executables can display (via the Unix strings command, for example)
the library settings used to build the executables.
This is a prototype implementation. Much improvement is needed.
configure.in:
Added the --disable-embedded-libinfo option to disable this feature.
configure:
src/H5config.h.in:
Generated by autotools like automake.
src/H5detect.c:
Implement insert_libhdf5_settings() to insert the contents of
libhdf5.settings into the library as an extern string variable so that it
is included in all HDF5 executable. Much improvement is needed.
fortran/src/Makefile.in:
Auto-generated by bin/reconfigure. (i.e., I did make any changes to cause
its direct regeneration).
Tested:
Jam serial, using default and --disable-embedded-libinfo, configure options.
Bug Fix
Description:
Removing the code from configure which strips the '-g' flag from CFLAGS
when in production mode. The current default CFLAGS in production mode
does not include '-g', as intended, but we should allow users to
override this and enable '-g' by setting the CFLAGS environment variable
if desired. Note that this applies to FCFLAGS and CXXFLAGS as well.
Tested:
kagiso, linew, 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
Bring r16305 back from revise_chunks branch:
Add detection of C99 "designated initializers" to configure script and
use new H5_HAVE_C99_DESIGNATED_INITIALIZER macro to conditionally compile
default layout variables in src/H5Pdcpl.c
Also, minor code cleanups, etc.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(Other platforms tested on branch)
Bug Fix
Description:
Resolved issues with broken sanity checks that were failing when the 'b2'
debugging package was enabled (v2 b-tree debugging):
- Fixed outdated assertions that would not compile. They now compile
and function correctly.
- Removed too far outdated assertions that would require too much
unnecessary refactoring of code in order to satisfy their
initial purpose.
- Re-enabled b2 debugging package when "--enable-debug=all" is
specified on the configure line.
Tested:
jam, smirom, linew
Description: Adding the SZIP path to LD_LIBRARY_PATH within configure was
inadvertently blowing away anything already in LD_LIBRARY_PATH. This
fixes that, which solves, among other things, the problem where
configure failed to learn how to print 'long long' on cobalt.
Tested: full make check install: kagiso, smirom
configure / make / h5ls test only : cobalt, linew
th user's definition of H5_USE_16_API. The H5_USE_16_API_DEFAULT is defined through
configure with the flag --with-default-api-version=v16.
Tested with h5committest.
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)
Fix various problems with a the core & sec2 VFDs.
Improve the h5_get_file_size() routine to handle files created with
VFDs that use multiple files.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (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
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
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)
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.
Moved AM_CONDITIONAL([FORTRAN_HAVE_SIZEOF]....) outside of Fortran conditional loop so that the value gets registered regardless of whether Fortran is enabled.
Added a test program to determine if -r8 or the default of REAL is DOUBLE PRECISION. Sets the variable FORTRAN_DEFAULT_REALisDBLE_F to true if default REAL is DOUBLE PRECISION.
Description: While '-Wl,-rpath' information was being removed from compile
lines when using --disable-sharedlib-rpath, some information
was still hidden in another variable tht never got reset and
thus snuck into the executables. This fix should take care of
that issue.
Tested: kagiso, smirom
bug fix.
Description:
Removed a few debug print statments that was left in by mistake.
Removed initialization for macro system INSTRUMENT to match how it
behaves before.
Tested platforms:
h5committested (kagiso, smirom and linew). It failed in fortran
test in smirom but I believed that was not caused by my changes
in configure.in.
Description: The macro H5_HAVE_WINDOW_PATH is now defined to 1 only when
MinGW is in use. This is needed to fix the "links" test, and
the external link feature in the library.
Tested: kagiso
Description: The configure option --disable-sharedlib-rpath will disable
embedding of the '-Wl,-rpath' information into executables
when shared libraries are produced.
Tested: kagiso
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.
Description: Typo in the configure.in script. CC_VERSION should be set using
CC_NOFLAGS, but is currently using CC_NOFLAG, which does not exist.
Tested: kagiso (configure issue)
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)
The development branch was changed to default enable-production for the
v1.8 release but had not switched back to default development mode.
Solution:
Changed it back to --disable-production (aka development) as the default.
Also ran bin/reconfigure to update configure.
Tested:
Smirom only. No h5committest since the change is trivial and if it works
at smirom, it should work everywhere else.
Description:
Previously, we created a patch for Cygwin to skip checking for the timezone variable. We made this change in both the trunk and hdf5_1_8 branch. However, in the branch version, we seemed to have used wrong quotes in our check ('uname' rather than `uname`). This corrects the typo
Tested:
Cygwin on WinXP
Description:
This is the same patch that Mike McGreevy helped me with on the 1.8 branch. The latest cygwin DLL has trouble with the global timezone variable. Now in configure, we target CYGWIN with a case statement, and avoid the problem.
Tested:
Cygwin on WinXP
Tested: kagiso only. Not need for h5committest since it is a configure simple
change. If it works correct in kagiso, it should work the same for all other
machines.
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
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.
Remove --enable-hdfv1_6 configure flag, now that all dependencies on it
have been removed and new --with-default-api-version=[v16|v18] and
--disable-deprecated-symbols flags have taken its place.
Update types in bin/trace so that bin/reconfigure runs cleanly.
Run bin/reconfigure to regenerate configure script, along with
other associated files, etc.
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
First real use of API versioning code, H5E routines switched to use
new API versioning scheme.
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)
1. In H5Dwrite and H5Dread, let the data buffer point to a fake address if the application passes
in an empty buffer. This is mainly for MPIO programs that some processes may not have any
data to write or read but still participate the I/O. This solution solves some MPI's problem
like the ChaMPIon on tungsten which doesn't support empty buffer.
2. The ChaMPIon on tungsten doesn't support complex derived MPI data type correctly and collective
I/O when some processes don't have any data to write or read correctly. Detect the compiler
"cmpicc" in the system-specific config file and set the variables for these two cases to false.
The PHDF5 library already has set up a way to switch collective chunked I/O to independent
under these two cases.
3. A bug fix - During the work of the optimization for compound data I/O, the case for switching
collective chunked I/O to independent I/O was leftout. Fixed it by adding I/O caching to it in
H5D_multi_chunk_collective_io in H5Dmpio.c.
Tested on tungsten, cobalt, and kagiso for parallel; on linew and smirom for serial.
Description: Configure will now detect the presence of the 'siglongjmp' function. If present,
the macro H5_HAVE_SIGLONGJMP will be defined in src/H5pubconf.h.
Tested: kagiso, smirom, linew
Remove stray reference to "group revision" configure flag
Remove Windows-specific EOL characters from src/H5FDwindows.c
Add some missing types to bin/trace
Re-run bin/reconfigure script to regenerate information after changes above.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (linux)
Solaris/32 2.10 (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: When the compiler has the __offsetof__ extension, the
H5_HAVE_OFFSETOF macro will be defined. When the compiler
does not have the extension, the macro will remain undefined.
Tested: kagiso
Hook "default VFD" configure macros into library.
Also, make "default VFD" default to sec2 instead of nothing.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Mac OS X/32 10.4.9 (amazon)
Description: this flag will define the macro H5_DEFAULT_VFD in src/pubconf.h
and set it to be either H5FD_SEC2 or H5FD_STDIO, depending on the
value set with the configuration flag (either sec2 or stdio).
Tested: kagiso, smirom, linew
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).
Change back to clearing memory buffers by default, but give users option
to disable this, for performance reasons (--disable-clear-file-buffers).
Also, add configure option (--enable-using-memchecker) to conveniently
control making the library "play nice" with memory checking tools like valgrind
and purify.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (kagiso)
Change --enable-debug default to no if producton is enabled.
Platform tested:
kagiso just doing configure with various combinations of option and varified the
output.
check if fseeko is available. Using it instead of fseek can support
big files because the offset is of type off_t not long int. Also
added the test for STDIO in big.c.
Switch the default setting for configure from --enable-production/--disable-debug
to --disable-production/--enable-debug.
Platform Tested:
In kagiso with fortran and C++. No commit test because changes
happened in configure and it is straight forward.
The static szip libraries are working as intended, but when shared szip
libraries are present and intended for use they cannot be opened. A check
has been implemented to test if shared szip libraries are functional on
current platform. If they are not, and the user is trying to use them,
szip is now disbaled and the user is informed.
This issue occurs on kagiso, and the resolution was tested on kagiso.
platform, since configure already uses rm, but it will prevent a bug in the
(bizarre) case that a system has rm somewhere other than /bin.
Tested on smirom and kagiso.
Description:
The lone colon test left behind the a.out file. Added a /bin/rm to clean it up.
Platform tested:
Kagiso only since it is a trivial change.
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.
Auto-detect the support for the posix_memalign routine and disable
the direct I/O VFD if posix_memalign is not supported. This should allow
direct I/O to be auto-detected and disabled on FreeBSD. (Direct I/O itself
works fine, but doesn't have the alignment requirements on FreeBSD that it
has on Linux, so the code would have to be re-worked to not use posix_memalign
and we don't need to support that right now).
Tested on:
FreeBSD/32 6.1 (duty)
Linux/32 2.4 (kagiso)
Maintenance for the HPUX 11.23 platform.
Problem:
C++ shared libraries are not supported for the 64bit mode (+DD64 compiler flag)
Solution:
Disable shared C++ library when +DD64 flag is detected.
Platforms tested:
sirius (HPUX 11.23 at UMKC) and kagiso
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.
It seems that the latest version of libtool is linking against shared versions
of the szip libraries in Fortran, rather than the static versions. ifort
doesn't support shared libraries at all.
To solve the problem, we avoid shared libraries entirely unless we're
building shared Fortran libraries ourselves.
If libtool always behaves like this now, it may cause similar problems on
other machines. If you notice that a machine is breaking when it links against
a shared library, let me know.
Tested on kagiso; nothing new is broken. If Albert has time this afternoon
I'll ask him to test on tg-login3 as well.
option --enable-direct-vfd/--disable-direct-vfd to enable/disable Direct I/O support. The default
is enabled. There's a small test in test/vfd.c. Another way to test it is to set environment
variable HDF5_DRIVER to "direct" and run "make check" in the test/ directory. There'll be some
further improvement in the following checkin including allowing user to provide memory boundary
value, file block size, and copying buffer size.
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
Use a slightly less efficient method of computing the log2() on SGI IRIX64,
in order to avoid a compiler bug when optimizations are turned on.
Tested on:
SGI IRIX64 6.5 (atlantia)
Removed free space manager from "enable-debug=all" list of flags, it's
not really designed for "user level" debugging.
Tested on:
FreeBSD 4.11 (sleipnir)
Refactored object deletion code for fractal heap to fix scaling problems.
Passing all previous tests again now.
Tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (chicago)
Mac OS X (amazon)
it uses the API function H5Gcopy to copy groups and datasets from file
to file, read from a command line
note: the test script is not finished yet
tested on heping, copper, shanti
1) Added trace file support to the metadata cache. This allows capture
of all metadata cache calls in trace files for purposes of optimization
and debuging.
2) Added an expunge entry function. This allows an entry to be deleteded
from the cache without writing it to disk even if it is dirty.
3) Added a function call to resize pinned entries.
4) Added code to deal with entries that are dirty on load. This is
needed in support of a bug fix which can alter object headers on
load to repair files.
5) Added progress reporting code to the "MDC API smoke check" test in
cache_api.c. To enable the progress reporting, set report_progress
to TRUE in mdc_api_call_smoke_check().
Tested with h5committest, and a parallel test on phoenix (dual athelon
linux box).
Description: Mac OS 10.4 on PowerPC chip has some errors to convert (unsigned)
long long to long double. When the bit sequences are 0x003ff..., 0x007fff...,
0x00ffff..., 0x01ffff..., 0x7fffff..., the converted values are twice as big
as they should be.
Solution: Detect the error in configure and disable the compiler conversion
and test case.
Platforms tested: h5committest, Mac OS 10.4, and fuss.
