Bring r23713 and r23717 from trunk to 1.8 branch:
Clean up warnings, switch library code to use Standard C/POSIX wrapper
macros, remove internal calls to API routines, update checkapi and checkposix
scripts.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
Big-Endian Linux/64 (ostrich)
Merge r23313 from trunk to 1.8 branch:
Bring changes from Coverity branch to the trunk:
r20612:
Changed string functions to versions with string length to fix coverity issues
922, 942 and 943.
r20614:
Use HDsnprintf. --gh
r20675:
Fix for coverity #1714 due to the fix for #810.
Use HDfree() instead of H5MM_xfree().
r20678:
Repaired coverity issue #598 -- failure to check return value from a
call to fstat(), or to tidy up in the event of failure.
r20679:
Use HDstrncpy. --gh
r20681:
Use HDstrncat and HDstrncpy. --gh
Tested on:
Mac OSX/64 10.8.2 (amazon) w/debug, C++ & FORTRAN
(too minor to require h5committest)
Purpose: Implement H5Dscatter and H5Dgather
Description:
Adds 2 new API functions, H5Dscatter and H5Dgather. H5Dscatter retrieves data
from a specified callback function and scatters it into a selection, defined by
a supplied dataspace, within a supplied memory buffer. H5Dgather gathers data
from a selection within a supplied memory buffer and passes it in a contiguous
form to a supplied callback function. Added tests for these functions
Tested: jam, ostrich, koala (h5committest); ummon; ummon (1.8)
This has been developed and tested in the trunk branch and is
now made available in the v1.8 branch.
Tested: Linux (Jam), linux 64 (koala), ppc64 (ostrich), Mac (fred, duck and Owl) passed.
Failed in SunOS (linew). Will fix when the new Sun is available.
HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Added H5Pget_mpio_no_collective_cause() function that retrive reasons why the collective I/O was broken during Read/Write IO access.
Reasons to break collective I/O:
- SET_INDEPENDENT
- DATATYPE_CONVERSION
- DATA_TRANSFORMS
- MPIPOSIX
- NOT_SIMPLE_OR_SCALAR_DATASPACES (NULL Space)
- POINT_SELECTIONS
- NOT_CONTIGUOUS_OR_CHUNKED_DATASET (Compact or External-Storage)
- FILTERS
Merged from HDF5 trunk r22735, r22741 , 22743, 22744, 22763.
Tested:
jam-pp (linux32-LE), koala-pp (linux64-LE), wallaby-pp
Convert configure.in to configure.ac.
Align TESTS usage with autotools convention.
Update all references from configure.in to configure.ac
Tested: h5committest
Bring r22219 from trunk to 1.8 branch: (with release manager's blessing)
Merge "file image" changes from feature branch back to trunk.
Tested on:
h5committested
Bring r21442 and r21529 from trunk to 1.8 branch: Add new API routines
for querying if collective raw data I/O was actually performed collectively.
Tested:
Linux/32 2.6 (jam)
(h5committested on trunk)
Test scripts sometimes need to filter some system-specific messages from the
actual output so that it can match the correct expected output. These filtering
functions, ususally called "STDOUT_FILTER()" and "STDERR_FILTER()" were being
repeated in individual test scripts. This becomes a maintenance problem and
is error prone.
Solution:
Extract the two filter functions code to bin/output_filter.sh and then each
test script sources it in. This allows reuse of coding and is much easier to
maintain and to add new filtering.
Tested:
LLNL Zeus (linux64 cluster) and Dawndev (Blue-Gene cluster), both for serial
mode only.
Bring r20651 & r20652 from trunk to 1.8 branch:
Switch from using 'pthread_create' to 'pthread_self' when trying to
detect the pthread library, so that the Intel C compiler is happier with the
prototype.
Teach the tracing script & routines about the 'unsigned long' and
'unsigned long long' types, so that the H5Pset_fapl_log() API routine gets
tracing information correct.
Tested on:
FreeBSD/32 6.3 (duty)
(h5committested on trunk)
The content of bin/config_para_ibm_sp.sh has been added to
release_docs/INSTALL_parallel long ago. Just got around to remove it.
Tested: no need since nothing refer to config_para_ibm_sp.sh except MANIFEST.
Ran bin/chkmanifest.
Description:
In an AIX 6.1 system, configure --enable-shared could not build a shared
HDF5 library. The problem was because the version of config.guess was too
old to recongnize AIX 6.X and also configure.in had a local fix which did
not recognize AIX 6.X.
Solution:
1. Mike McGreevy updated bin/config.guess to handle AIX 6.X.
2 Albert fixed configure.in to recognize AIX 6.X.
Note that though HDF5 can build shared lib for AIX 6.X systems
but it still could not install the proper library as in AIX 5.X
systems. Also, bin/config.sub should be updated too.
Tested: BP which is the AIX 6.1 system that exposed this problem.
Tested with h5committest on amani, jam, and heiwa, and on linew.
-This line, and those below, will be ignored--
M hdf5_1_8/test/Makefile.in
A hdf5_1_8/m4
AM hdf5_1_8/m4/ltsugar.m4
AM hdf5_1_8/m4/libtool.m4
AM hdf5_1_8/m4/ltversion.m4
AM hdf5_1_8/m4/lt~obsolete.m4
AM hdf5_1_8/m4/ltoptions.m4
M hdf5_1_8/configure
M hdf5_1_8/Makefile.in
M hdf5_1_8/testpar/Makefile.in
M hdf5_1_8/configure.in
M hdf5_1_8/src/Makefile.in
M hdf5_1_8/tools/Makefile.in
M hdf5_1_8/tools/misc/Makefile.in
M hdf5_1_8/tools/h5dump/Makefile.in
M hdf5_1_8/tools/h5repack/Makefile.in
M hdf5_1_8/tools/h5jam/Makefile.in
M hdf5_1_8/tools/h5diff/Makefile.in
M hdf5_1_8/tools/lib/Makefile.in
M hdf5_1_8/tools/h5copy/Makefile.in
M hdf5_1_8/tools/h5import/Makefile.in
M hdf5_1_8/tools/h5stat/Makefile.in
M hdf5_1_8/tools/h5ls/Makefile.in
M hdf5_1_8/hl/test/Makefile.in
M hdf5_1_8/hl/tools/Makefile.in
M hdf5_1_8/hl/tools/gif2h5/Makefile.in
M hdf5_1_8/hl/Makefile.in
M hdf5_1_8/hl/src/Makefile.in
M hdf5_1_8/hl/c++/test/Makefile.in
M hdf5_1_8/hl/c++/Makefile.in
M hdf5_1_8/hl/c++/src/Makefile.in
M hdf5_1_8/hl/c++/examples/Makefile.in
M hdf5_1_8/hl/fortran/test/Makefile.in
M hdf5_1_8/hl/fortran/Makefile.in
M hdf5_1_8/hl/fortran/src/Makefile.in
M hdf5_1_8/hl/fortran/examples/Makefile.in
M hdf5_1_8/hl/examples/Makefile.in
M hdf5_1_8/config/commence.am
M hdf5_1_8/MANIFEST
M hdf5_1_8/c++/test/Makefile.in
M hdf5_1_8/c++/Makefile.in
M hdf5_1_8/c++/src/Makefile.in
M hdf5_1_8/c++/examples/Makefile.in
M hdf5_1_8/bin/ltmain.sh
M hdf5_1_8/bin/reconfigure
M hdf5_1_8/perform/Makefile.in
M hdf5_1_8/fortran/test/Makefile.in
M hdf5_1_8/fortran/testpar/Makefile.in
M hdf5_1_8/fortran/Makefile.in
M hdf5_1_8/fortran/src/Makefile.in
M hdf5_1_8/fortran/examples/Makefile.in
M hdf5_1_8/aclocal.m4
M hdf5_1_8/examples/Makefile.in
Cleaned up the code a bit by:
1. It used to that -xxx options must be at the beginning such that
"buildhdf5 --disable-shared -config" was an error. Now -xxx options
can appear anywhere in the command options.
2. Eliminate the need of variables $CONFIG_CXX, $CONFIG_FORTRAN,
$CONFIG_PARALLEL by appending their values to $CONFIG_OP directly.
3. Also append $WITH_SZLIB to $CONFIG_OP when it is defined, not later.
4. Call CONFIG directly instead of setting up $CONFIGURE.
5. Removed the last TIMESTAMP since "trap 0" will call QUIT which calls
TIMESTAMP already. This eliminated the extra timestamp when it finishes
normal.
tested:
Tested by hand since h5committest does not really test this command.
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
Updating autotools
Description:
Bring revisions 17345 and 17357 from trunk to 1.8, specifically:
- 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).
- bin/install-sh script replaced with new version as provided
by automake.
Tested:
- All issues on trunk were resolved, so only tested on jam and linew. Any
other outliers should be caught by daily tests.
Merge these trunk revisions which occurred during the 1.8.3 release code
freeze back to the 1.8 branch:
From Quincey: 16845 16847 16849 16851 16858 16869 16897
From Ray: 16859 16880
From Allen: 16863
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/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 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
- Updated bin/reconfigure to use latest version of automake (1.10.2).
Regenerated 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
Bring r16306 back from trunk:
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 revise_chunks branch)
The Tail command in jam (a newer linux) does not accept the +2l option.
It ended up wiping most of the release_doc/RELEASE.txt file contents.
Replaced the "tail +2l" by "sed -e 1d".
Tested:
Tested in Jam to verify it functions properly again.
was not updated automatically and therefore
was always outdated. Modified h5vers script to update
the version for the VMS configuration file as we do for
the similar windows file.
Platforms tested:
kagiso with bin/h5vers
Description:
1) configure now sets LD_LIBRARY_PATH before checking for presence of
SZIP encoder, so user does not need to set this. The path is then
saved and sent to Makefiles, and used when "make check-install" is
invoked, so user doesn't need to set this manually.
2) Upgraded libtool to version 2.2.6a
3) Rearranged tools build order as h5dump depends on existence of h5diff
and h5import. Since h5dump is a sister directory as opposed to a parent
of either, it doesn't know about the build rules of these tools, so
setting any sort of explicit dependency confuses automake as it won't
know how to build the tools. Instead, setting CONFIG = ordered forces
an in-order traversal of each tools subdirectory. (without it will also
traverse in order by default, but this should prevent gmake's -j option
from jumping ahead as well). 'make check install' should now be able to
be invoked after 'configure' without causing a dependency failure.
4) Removed H5_HAVE_LARGE_HSIZET macro from vms/src/h5pubconf.h, as this macro
has now been out of the code for some time. (vms pubconf needs to be
updated manually, which is why it was still hanging around).
Tested: kagiso, smirom, liberty
Note: h5diff looks to be causing failures in h5copy and h5dump tools tests,
though these were present before any of my changes. My changes only
affect build order and configuration setup, and shouldn't prevent
fixes for these failures coming in after this checkin. Other than these,
tests pass fine.
