Bug fix.
Description:
mpich2 using f95 did not support function 'unlink'.
Removed the unlink call for now. Need a better solution.
Platforms tested:
heping using mpich and mpich2 versions of mpif90.
Misc. update:
bug fix.
Description:
When a parallel test script test fails, make would continue because the
way it was setup inside a for loop. Fixed it by issuing an exit 1 inside
the loop.
There was also a typo error in the newer command comparision that it
must be $${chkname} in order to be valid. Also, the test script itself
was not checked in the newer lists. All fixed.
Platforms tested:
h5committested and also hand tested in heping pp mode.
New feature.
Description:
Added the time command to the make check target to report time usage
of the execute of each test and test scripts. This gives us some idea
how long each test takes and some vague idea it is compute bound or
not.
powerpc-ibm-aix5.x:
Change $RUNPARALLEL default setting to allow it being invoked by the
time command.
Platforms tested:
h5committested.
Feature
Description:
Added H5_CFLAGS, etc. to 1.7 branch.
Now compilation flags can be put in H5_*FLAGS and they'll be used when
building hdf5 but not in h5cc.
Platforms tested:
mir, sleipnir, modi4
Misc. update:
Bug fix
Description:
Disabled C++ shared libraries for Sun Workshop compiler.
Solution:
This bug only seems to happen when using the -xarch=v9 flag to compile in
64-bit mode, but disabling shared libraries entirely for this compiler is
an easier fix (I don't know how to detect 64 bit mode from the command line).
The framework for disabling shared libraries for other C++ compilers is
in place.
Platforms tested:
sol, mir, sleipnir, modi4
Bug fix/feature
Description:
Disabled shared libraries for a number of Fortran compilers that don't
support them.
This allows other compilers to support shared Fortran libraries.
Solution:
Added a conditional, SHARED_FORTRAN_CONDITIONAL, which is true if
Fortran supports shared libraries. It is set in configure.in.
Platforms tested:
mir, sleipnir, colonelk, heping
tidy up.
Description:
MPE option created *.clog file whenever it is executed in MPI.
The cleanup of *.clog files were done in individual Makefile.in.
Often, it is forgotten.
Solution:
Moved the cleaning of *.clog files to CHECK_CLEANFILES in commence.am
so that it is applied whenever check-clean is called.
Platforms tested:
heping pp using MPE.
Bug fixes
Description:
This checkin fixes an occasional error on kelgia on sol during distclean.
It also causes test scripts to depend properly on the programs they're
supposed to be testing.
Solution:
The kelgia bug was due to some files being cleaned by automake and manually.
Removed the manual cleaning in src/Makefile.am.
Test script dependencies now need to be specified manually, since the
makefile can't guess what they test from their name. Currently all test
scripts in a given directory have a single list of dependencies--this was
easy and seems to be sufficient.
These dependencies are listed in the SCRIPT_DEPEND variable in the Makefile.am.
Platforms tested:
heping, mir, modi4, sol
Misc. update:
minor tidy up.
Description:
Changed both test programs and test scripts to use the same suffixes
(.chkexe and .chklog). Changed from .log to .chklog to avoid running
into potential conflicts by other "things" (e.g., config.log).
Tested:
Heping.
Bug fix and improvement.
Description:
The test output were not displayed for parallel tests.
The serial tests output were always displayed whether the test was
actually ran this time or not.
Solution:
Moved the display of test output inside the target where the actual
tests are run.
Platforms tested:
Tested in heping using pp and fortran.
Bug fix and code minor cleanup.
Description:
The attempt to redirect stderr together to the log files were
done in the wrong order such that stderr output goes to where
stdout WAS. Fixed that.
Code minor cleanup--use shell variables to hold the name of the
log file and the test instead of generating them repeatedly. This
makes easier code reading, less crowded and avoid typos.
Only conclude.in is changed. The Makefile.in changes are all
derived from automake.
Platforms tested:
h5committested.
Makefile feature
Description:
'make check-clean' now cleans *.h5 files created by tests as well as
.log and .chkexe files.
Solution:
check-clean is now a separate target in its own right, which cleans less
than mostlyclean (check-clean < mostlyclean < clean < distclean).
Platforms tested:
mir, heping, modi4 (serial and parallel)
Feature: check-clean target
Description:
'make check-clean' cleans up output files from tests.
Solution:
Tests create foo.chkexe and foo.log files. Scripts create foo.chksh and
foo.logsh files. 'make check-clean' will clean these files up so that
the tests can be re-run.
Also suppressed some not-very-useful output of Makefiles when it would
echo commands.
Platforms tested:
mir, sleipnir, modi4
Misc. update:
Configuration feature
Description:
Serial test output is now stored in log files and printed when all tests
in a directory complete, or when a test fails. This should make test output
more readable and useful.
Also made changes to clean up ii_files directories that are created by some
C++ compilers/linkers.
Also fixed a few minor Makefile bugs.
Solution:
When serial tests run, their output is saved in *.log or *.logsh. While
running, tests only print when they begin and when they complete; their
more specific output (from the log file) is printed if the test fails or
when all tests have completed.
Comments welcome.
Platforms tested:
mir, modi4 (parallel and serial), copper, shanti
Bug fixes
Description:
A number of minor changes to Makefiles. Some files will now be cleaned
properly, some comments are more informative, etc.
Platforms tested:
heping, mir, modi4
bug fix
Description:
rwdsetexample and attrexample both modify the same file created by
dsetexample. Need to serialize all three of them.
Platforms tested:
Did 50 times of make check in fortran/examples. It used to fail
at least once. Now it does not fail.
Bug fix
Description:
The ".chksh" file for a test script was being created in the "source"
location rather than the build location. This can cause problems when
multiple builds are running because "slower" machines will see the ".cshsh"
file from faster machines and will not run the test script as they should.
Solution:
Use 'basename' command to strip off the path of the script and create
the ".chksh" file in the build location.
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
bug fix.
Description:
-nt is not a universal option for the test command in all platforms.
The use of it in conclude.am cause some platforms to bark at the
Makefile generated.
Solution:
Created a command script bin/newer which tests if file1 is newer
than file2. Replace the "test file1 -nt file2" by
"newer file1 file2".
Platforms tested:
Tested in sol.
Bug fix
Description:
Fixed error in Fortran examples on modi4.
Solution:
Added another dependency in the Fortran examples.
Platforms tested:
mir, modi4 (serial and parallel)
Bug fix
Description:
Added dependencies to examples Makefiles so that examples can be run in
parallel.
Solution:
The examples directories (for C, C++, and Fortran) all have some dependencies
explicitly spelled out in their Makefiles.am. This is a good short-term
solution, and should prevent errors in the Daily Tests.
Platforms tested:
mir, modi4 (parallel and sequential)
Bug fix
Description:
Fixed bugs that caused tests to be unable to find testhdf5.sh during
daily tests, and another that broke sol and shanti.
Solution:
When tests are run, their path is ./$testname .
When scripts are run, their path has no leading "./". Fixed.
Sol and shanti don't recognize the -e option for test, but they do know
-f. Fixed.
Also modified release notes.
Platforms tested:
mir, shanti, heping
Feature: tests now use parallel make and only run once
Description:
When make is invoked in parallel (using the -j option), several tests will
now be run simultaneously. This should speed up testing on a number of
systems.
When a test passes, it creates a foo.chkexe or foo.chksh file, which prevents
the test from running again unless the test or library changes.
Solution:
Most of the changes live in config/conclude.am. Added *.chkexe and *.chksh
files to the list of files to be cleaned at "make mostlyclean" time.
Parallel tests still run one at a time, but use the same make instructions
as serial tests.
Platforms tested:
mir, eirene, sleipnir, pommier, copper, modi4 (some errors occurred, probably
due to the test being run before updating hdf5. Will re-run tests after
checkin.)
bug fix
Description:
check-s and check-p were set as pre-requistics of test. They
would get executed in parallel if parallel make is used. This
could cause problems since serial tests are used to be executed
before parallel tests. It is not known if it is always okay to
run serial and parallel tests in simultantously.
Solution:
Change check-s and check-p as actions of the target test so
that they get executed sequnentially.
Platforms tested:
heping PP.
Added check-s and check-p targets.
Description:
Added check-s and check-p targets to 1.7 branch to match changes to 1.6
branch. Now parallel and serial tests can be run separately.
Platforms tested:
mir, modi4, copper
Output tweak
Description:
Test output in C++ and Fortran directories now puts "C++ API:" or
"Fortran API:" in front of the name of the test being run.
I had overlooked the line of code that caused this to happen.
Solution:
Added HDF_CXX and HDF_FORTRAN variables to C++ and Fortran Makefiles.am.
Platforms tested:
heping (minor change)
Bug fix.
Description:
Data file name is hardcoded to be in current directory which does not
necessarily support MPIO. Changed it to /tmp/sds.h5 for slightly larger
chance of success but the eventual solution is to set it according to
environment variables. Patch it this way for now.
Platforms tested:
mir.
Misc. update:
Description: Removed support for SRB driver
Solution: Removed or modified appropriate files; ran reconfigure
to regenerate Makefile.in and configure files.
Platforms tested: heping and shanti
Misc. update: ran bin/chkmanifest on heping
Configuration feature
Description:
Different Fortran compilers mangle function names in different ways
(upper case, lower case, adding underscores). To link between
Fortran and C functions, we need to know what a given function's
name is under a given compiler.
Solution:
Use autoconf's FC_WRAPPERS check to determine the Fortran
naming scheme and define the FC_FUNC_ macro to name our
functions (in H5f90proto.h). Removed references to
our old FNAME macro, as well as flags that indicated whether
function names were upper or lower case.
Platforms tested:
mir, pommier, modi4, copper, more
Feature
Description:
Added support for conditional compilation of parallel Fortran
examples. No such examples exist currently, but it should be
possible to add them to the Makefile.am with no fuss and have
them compile only when parallel is enabled.
Platforms tested:
eirene, copper, modi4
Misc. update:
Bug fix
Description:
On some machines, $RUNSERIAL variable needs to be used to run
tests. Set $RUNTESTS (which is used for non-parallel tests) to
be $RUNSERIAL in configure.am.
Also, since I was updating all Makefiles.in anyway, I updated
commence.am to point to autotools installs in AFS instead of
those on heping.
Platforms tested:
mir, sleipnir, modi4, copper
Purpose:
"Bug fix"
Description:
Hardcoded Makefiles to use /bin/sh instead of letting configure
detect shell automatically. This is what v1.6 does, and avoids
problems on janus.
Platforms tested:
sleipnir, copper, modi4, mir
Feature - conditional compilation
Description:
SRB file driver and tests are now compiled only when SRB is enabled
(using --with-srb during configure).
Solution:
Added an automake conditional in configure.in, altered Makefiles.am in
src and test directories to depend on that conditional.
This should make a nice example for posterity to add conditionally
compiled sources.
Platforms tested:
heping (only configure change)
Windows fortran examples was checked into a wrong directory.
The correct directory is hdf5/windows/fortran/examples.
The current directory is hdf5/fortran/examples.
Description:
Solution:
Platforms tested:
Misc. update:
Windows fortran examples was checked into a wrong directory.
The correct directory is hdf5/windows/fortran/examples.
The current directory is hdf5/fortran/examples.
Description:
Solution:
Platforms tested:
Misc. update:
ndows fortran examples was checked into a wrong directory.
The correct directory is hdf5/windows/fortran/examples.
The current directory is hdf5/fortran/examples.Description:
Solution:
Platforms tested:
Misc. update:
Windows fortran examples was checked into a wrong directory.
The correct directory is hdf5/windows/fortran/examples.
The current directory is hdf5/fortran/examples.Description:
Solution:
Platforms tested:
Misc. update:
Windows fortran examples was checked into a wrong directory.
The correct directory is hdf5/windows/fortran/examples.
The current directory is hdf5/fortran/examples.:wq:
Description:
Solution:
Platforms tested:
Misc. update:
Windows fortran example project files were checked into the wrong directory,
has to remove them.
The correct directory to be checked in is /hdf5/windows/fortran/examples,
The currect directory inside CVS tree is /hdf5/fortran/examples.
Description:
Solution:
Platforms tested:
Misc. update:
Purpose:
Added C++ wrapper for Packet Table API.
Description:
Added macro for high-level C++ library (LIBH5CPP_HL), which changes every
Makefile.in.
Added directories for high-level C++ library (though currently only Packet
Table API is supported).
Added both C++ source and tests.
Platforms tested:
sleipnir, mir, modi4
Misc. update:
Automake version upgrade
Description:
Upgraded automake version from 1.6.2 to 1.9.5.
Changed bin/reconfigure script to use automake 1.9.5.
Changed configure.in and Makefiles to use new FCFLAGS and FC variables
instead of FFLAGS and F9X.
Automake and configure should now do the lion's share of the work
supporting Fortran 9X; macros in acsite.m4 are now mostly unused (will
be cleaned later).
Altered how configure handles pmake; now root-level Makefile.in is
processed by bin/reconfigure to have a .MAKEFLAGS target, since
automake no longer allows us to define unused variables.
Configure now always checks for C++ compiler even if it is not
used, since automake thinks this is the Right Thing To Do and
will break otherwise.
Platforms tested:
Sol, copper, heping, mir, sleipnir, eirene, pommier, kelgia, modi4.
Removed GASS configuration and software packages associated with
it. The following software are no longer configurable.
checking for main in -lcrypto... yes
checking for SSL_get_version in -lssl... yes
checking globus_common.h usability... yes
checking globus_common.h presence... yes
checking for globus_common.h... yes
checking for globus_module_activate in -lglobus_common... yes
checking for main in -lglobus_gass_cache... yes
checking for main in -lglobus_gaa... yes
checking for main in -lglobus_gss... yes
checking for main in -lglobus_gss_assist... yes
checking for main in -lglobus_io... yes
checking for main in -lglobus_gass_transfer_assist... yes
checking for main in -lglobus_gass_transfer... yes
checking for globus_gass_open in -lglobus_gass_file... yes
Platforms tested:
h5committested (but copper was down.) tested in modi4 too.
Purpose:
Bug fix
Description:
modi4 dies during build with strange errors.
The root cause of these is a two-year-old hack in HDF5's libtool
script that only takes effect on IRIX.
Solution:
Edited the libtool hack (by editing ltmain.sh) to correct a bug in
the hack.
Also made sure that compiler-specific DEFAULT_LIBS are used
when linking.
Platforms tested:
sleipnir, copper, modi4, sol
Bug fix
Description:
pmake (on modi4, for instance) complains about undefined variables
if it is run without the -V flag, which turns those errors to warnings.
Solution:
Added test to configure.in to see if $MAKE will allow Makefiles
with undefined variables. If not, sets -V flag in AM_MAKEFLAGS.
Ensured that all custom make targets use AM_MAKEFLAGS.
Also defined all variables that caused errors in top-level Makefile.am.
This means that pmake can be used to build hdf5 *from the top level
only*. To run make from a subdirectory, still need to use -V flag
(or use make or gmake).
Platforms tested:
modi4, heping, copper, sleipnir
Purpose:
Bug fix
Description:
Parallel builds were breaking in tools/lib
Solution:
talign didn't realize it depended on libh5tools.la because its
dependencies listed the full path (../../tools/lib/libh5tools.la).
Changed this, and made similar changes in a couple of other
directories.
This checkin should also add the --foreign flag to every Makefile.in
Platforms tested:
sleipnir (minor change)
New feature
Description:
Add basic code for new B-tree implementation. They don't do much yet,
aren't hooked up to anything yet and the format may change, but I'd like to
start getting them into the daily tests.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/parallel
Too minor to require h5committest
Bug fix
Description:
Found the permanant fix to automake/CVS dependency problem
Solution:
Added AM_MAINTAINER_MODE macro to configure.in.
Now automake will never try to regenerate Makefiles, Makefiles.in,
configure, H5config.h, etc. when they are out of date, nor will it
print any warnings.
Developers should be very very careful to use reconfigure script,
and can add --enable-maintainer-mode flag to configure on heping
to regenerate these files correctly.
Platforms tested:
heping sleipnir copper
Bug fix
Description:
Configuration files' timestamps were incorrect.
Solution:
Update Makefiles.in. Also added correct paths to autotools on heping,
so heping build should be able to re-generate configuration files even
if they are still broken.
Platforms tested:
sleipnir
Bug fix
Description:
Dependencies between configure files (aclocal, configure.in, configure,
Makefiles.am and .in) are still causing Makefiles to try to run autotools
during build.
Solution:
Committed all Makefiles.in to update their timestamps.
As a temporary measure, forcibly prevented automake from running
autotools during build by redefining the variables it uses.
Platforms tested:
sleipnir (No changes to Makefile content)
Bug fix
Description:
Different compilers use different flags to include Fortran module files
Solution:
Changed boilerplate to use configure variable rather than hardcoded -M flag.
Platforms tested:
sleipnir, sol, copper
Configuration feature
Description:
HDF5 now uses automake to generate Makefiles
Solution:
Makefile.in files are now generated from Makefile.am files.
To reconfigure (after chaning a Makefile.am or configure.in):
/bin/sh bin/reconfigure.sh
Platforms tested:
Many
Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
Bug fix.
Description:
The Example dimension size is incorrect. Changed it to 3.
Platforms tested:
Tested in TG-NCSA which detected the error.
Misc. update:
Purpose: Maintenance
Description: h5dwrite/read_f and h5awrite_read_f functions were overloaded
with dims argument being of type INTEGER and INTEGER(HSIZE_T).
We promised to remove overloading in 1.4 release. It was
removed from documentation but not from the source code.
Solution: Finish code cleanup.
Platforms tested: Solaris 2.7 32 and 64 bit, and copper with --enable-
parallel. Windows are broken, so Kent and Xuan
will test it with their changes later.
Misc. update:
Bug fix.
Description:
"make check" failed because the macro "$<" is not known to those
makes.
Solution:
Replace that macro with a string name in the form of a more basic
macro of "$@".
Platforms tested:
h5committested (copper used make.)
Misc. update:
Improvement
Description:
If the library is built in parallel mode, then name the "h5cc" and
"h5fc" programs "h5pcc" and "h5pfc" resp. This saves the user from
worrying about mixing serial and parallel builds of the library and
having to specify the pathnames and so-forth.
Platforms tested:
Linux (w/ parallel & Fortran)
Modi4 (w/ parallel & Fortran)
Sol (Serial & Fortran & C++)
Misc. update:
Updated release/docs/RELEASE
Updated the copyright notice--mostly by rearranging
some text to make them consistent.
Solution:
Platforms tested:
"h5committested"--sol is down, so, no SUn test.
Misc. update:
No longer needed. make check-install or make check does the
checking now.
Platforms tested:
no h5committest since I am removing a script command that is not
needed any more.
Misc. update:
no need to update doucment since it was an internal command
that was never documented.
Update
Description:
Revamped the configuration system. The configurations for the Fortran
and C++ libraries are no longer separate from the "main"
configuration system. This involved removing the "configure*" and
"aclocal.m4" files from the fortran/ and c++/ subdirectories. Also
merging settings in the config/ subdirectories into the main config/
subdirectory.
Fortran header files had to be modified a little for Linux. It was
checking if it was a Linux machine by some #defines, however with the
-std=c99 switch, these defines weren't there. I added a check for
some other ones which should be there whether the -std=c99 switch is
used or not.
Platforms tested:
Verbena (Fortran & C++)
Sol (Fortran & C++)
Copper (Fortran & C++)
Modi4 (Parallel, Fortran, & C++)
Misc. update:
Code cleanup
Description:
h5pset_preserve_f function changed from an INTEGER to a LOGICAL parameter,
change it here too.
Platforms tested:
h5committested
Code Cleanup
Description:
Warning messages were being produced by the "make" program because
the "docdir" was being specified twice as a target in the generated
Makefiles. This is because the "EXAMPLESDIR" was also defined as
"docdir".
Solution:
Made "EXAMPLESDIR" unique for C, Fortran, and C++ in the commence.in
file and removed EXAMPLESDIR from the Makefile.ins
Platforms tested:
Dangermouse (only affects make system, not code).
Misc. update:
Update
Description:
Updated so that the example programs are built with the new h5fc
script after it's installed. (So you need to cd into the examples/
directory and type "make check" or similar. This is how it is in the
C part).
Platforms tested:
Modi4 (Parallel & Fortran)
Burrwhite (Fortran & C++)
Baldric (Fortran), but make check didn't work because of "libucb.so"
error that I can't fix...)
Misc. update:
Purpose:
Code clean up.
Description:
Many F90 compilers were not happy about character*(*) declarations.
Solution:
Used F90 character(len=*) declarations.
Platforms tested:
Solaris 2.7 and Linux 2.4
Purpose:
Feature Add
Description:
Added "install-example" and "install-all" to the Makefile system.
The behaviour of the "make install*" options:
make install - Installs binaries, libraries, include
files, and example programs.
make install-examples - Installs only the example programs.
The directories are:
${prefix}/doc/hdf5/examples/{c,c++,fortran}
make install-all - Install the binaries, libraries, include
files, example programs, and
documentation. The whole kit-n'-caboodle.
make uninstall-examples - Get rid of those example files (but not
the ${prefix}/doc/hdf5/examples/...
directories)
There's a new bin/ program which helps create directories which are
deeply nested called "mkdirs". It's a simple shell script.
Platforms tested:
Linux
Purpose:
Codemaintenance
Description:
read/write APIs have been changed.
Solution:
Made necessary changes to the source code.
Platforms tested:
Linux, Solaris 2.7, O2K, T3E
Bug fix
Description:
The /bin/csh shell was causing problems if you were using a different
shell than csh (like bash). It couldn't find the compiler.
Solution:
Changed to the more standard /bin/sh
Platforms tested:
Linux
Bug Fix
Description:
We were not propagating the FFLAGS macro. I.e., we were
overwriting it after it was set in the commence.in includes.
Solution:
Include it with a ``@FFLAGS@'' where we'd normally overwrite it
so that it isn't.
Platforms tested:
T3E
Bug fix
Description:
The setting does not work for the --srcdir option as source file names
are hard set in the action lines.
Solution:
Changed the dependence targets to the form of *.lo and the action lines
would use the *.lo files. This way, *.lo files are created when
-srcdir option is used or not. Also added that they all depend on
the C hdf5 library.
Platforms tested:
IRIX64 -64 with --srcdir
Bug Fix
Description:
Wasn't picking up the header files from the proper source and
build directories. There were some funky things happening in
there.
Solution:
Put the correct path in.
Platforms tested:
Modi4
*sigh*
Description:
Wasn't picking up a header file which is in the source directory.
Solution:
Changed some flags so that it does this now.
Platforms tested:
Modi4
Bug Fix 37
Description:
Okay...this is really it now. Sorry for all the other "fixes".
This will take care of the top_builddir macro for the Fortran
interface.
Solution:
Hardcoded the path to the build directory.
Platforms tested:
Modi4.
Purpose:
Updated source code to use new APIs to write/read references
Description and Solution:
Write/read subrotine has extra parameter - size of the reference array.
I modified the source to reflect this change.
Platforms tested:
Solaris 2.6
Adding the Fortran interface to the HDF5 library
Description:
Fortran is now a subdirectory of the HDF5 library tree.
Platforms tested:
Solaris and IRIX (O2K)
