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.
New version of the function h5tools_dump_simple_subset, to display subsetting. The new algorithm is:
Introduced an outer loop for cases where dimensionality is greater
than 2D. In each iteration a 2D block is displayed by rows in a inner
loop. The remainning slower dimensions above the first 2 are incremented
one at a time in the outer loop
Note: when blocks are introduced, the display is not correct. This is a bug that requires an improvement of the algorithm.
Fixed#720 h5dump: improve how region references are displayed. h5dump now uses the new API function H5Rget_name to display the name of the dataset referenced instead of its ID. Added a case to the script test file
fix for bugzilla bug #551
several programming errors contributed to this bug
1) the parsing of subsetting was using atoi to convert the parameter to an int,
which caused problems for numbers greater that int. Substitute with atof
2) several index counters were declared as int, use hsize_t instead
3) the numerical format passed for printf was %lu, defined one compatible with
hsize_t instead (unsigned long long)
Fix several bugs
1) the parsing of subsetting was using atoi to convert the parameter to an int, which caused problems for numbers greater that int. Substitute with atof
2) the printing of indices in the subsetting case was not being done. Solution: calculate the element position at the start of the subsetting using the algorythm
Given an index I(z,y,x) its position from the beginning of an array of sizes A(size_z, size_y,size_x) is given by
Position of I(z,y,x) = index_z * size_y * size_x
+ index_y * size_x
+ index_x
And pass that position to the function that dumps data, h5tools_dump_simple_data.
3) several index counters were declared as int, use hsize_t instead
4) modified the test generation program so that it includes test cases for subsetting of 1d, 2d, 3d, and 4d arrays and add these tests to the shell script
Take out separate memory type in the file for SOHM objects and create
aliases for existing memory types for SOHM use.
Tested on:
FreeBSD/32 4.11 (sleipnir)
fixed 2 initializations of char* with HDstrdup and HDcalloc
info->prefix = HDcalloc(1, 1);
fname = HDstrdup(argv[opt_ind]);
some were exposed by compiler warnings
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.
This feature is still in progress; Shared Object Header Messages are not
complete as a feature and are not thoroughly tested. There are still
"TODO" comments in the code (comments with the word "JAMES" in them,
so as not to be confused with other TODO comments).
Hopefully this checkin will reduce the liklihood of conflicts as I finish
implementing this feature.
All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
Add new H5Lget_val_by_idx() routine & tests.
Also includes most of changes for H5Ldelete_by_idx() routine.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
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.
h5dump bug 701. Symptom: The creation of a hardlink pointing to the root group "/" causes h5dump to display it as a link pointing to itself.
Cure: the root group was not being inserted in the table that keeps track of object names and links.
Added a test for this in the test generation program, the creation of a hardlink to the root
the linkval buffer, per Elena and Frank's suggestions while revising
the documentation. Added error checking using this size, as well as a
couple of tests.
Tested on juniper, kagiso, and sol.
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.
Add "use the latest format" support for dataspace object header encode/
decode routines and clean up format a bit for the latest format (new to 1.8.x
releases)
Remove storing 'perm' parameter for array datatypes in memory and the file,
and add test to make certain that if any user applications are attempting to
store them, we get some reports back. (Should be unlikely, since the RefMan
says that the parameter is not implemented and is unsupported).
Carry those changes into the tests, etc.
Clean up a bunch more compiler warnings.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-1.6-compat
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
revised binary flags, added a new file to the test generator program to
be used in the binary tests
usage is now
-o F, --output=F Output raw data into file F
-b F, --binary=F Binary output, of form F (into file -o F).
Recommended usage is with --dataset=P
Form F of binary output is: MEMORY for memory type,
FILE for the disk file type, LE or BE for pre-existing
little or big endian types
example
./h5dump -d integer -b MEMORY -o out.bin tbinary.h5
Code cleanup.
Description:
Removed argc and argv from the function arguments of h5tools_get_fapl() and
h5tools_fopen(). They were used to call MPI_Init() which was no longer
needed.
Tested:
heping (serial and parallel).
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
Clean up compiler warnings/failures in test/links.c, especially when
--disable-production flag used with --enable-group-revision
Modify binary dumping in h5dump to clean up files created [a band-aid
solution to not actually creating the files in the srcdir, but better than
just leaving the files around... :-/ ]
Tested:
FreeBSD 4.11 (sleipnir) (w/ configure flags above)
Too minor to require h5committest
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.
1. changed the -F flag option names to "BE and "LE" for big and little endian
2. added a more verbose usage message for these options
3. add a new test
4. add a make clean instruction to *.bin
new feature
Description:
added support for h5dump to dump binary data using the file type format
added one test to the test script that tests this
Solution:
Platforms tested:
mir
shanti
copper
Misc. update:
Code cleanup
Description:
Trim trailing whitespace in Makefile.am and C/C++ source files to make
diffing changes easier.
Platforms tested:
None necessary, whitespace only change
new feature. h5dump output of binary data
Description:
a new switch -b FILE_NAME that dumps the contents of memory data to file FILE_NAME in binary form
new program binread.c that reads the contents of this file and outputs it to stdout
added a test for the h5dump shell script that does a run of -b
the binread.c program reads the data used in this run, usage is ./binread FILE_NAME
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
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)
Anti-feature
Description:
Revert changes to H5G_stat_t struct, to make it compatible with the 1.6.x
branch again. The information that was added to the H5G_stat_t struct will
be reported through other API routines.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/C++
Linux 2.4/64 (mir) w/C++ & Fortran
Solaris 2.9 (shanti)
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 fixes
Description:
h5dump/h5ls were not displaying long doubles correctly
Solution:
1) the print datatype functions were incorrectly testing for the valid return value from H5Tequal,
(TRUE), causing the display of an incorrect name of a dataype in error cases from H5Tequal
2) h5tools_print_str did not have a case for native long double
3) added a file generator for a long double dataset
4) added one script test for the long double data (commented , some sytems don't have a native long double match, and the output differs)
5) added a vms file and h5dump script test
Platforms tested:
linux 32, 64
solaris
AIX
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
Solution: Support VAX float and double types with new byte order. There're some
details not yet included,
1. the alignment detection for VAX order in H5detect.c.
2. support for special values in library conversion functions.
3. the infinity for VAX in H5T_init_inf.
4. support for VAX types in printing hexadecimal format.
Platforms tested: h5committest and fuss.
Code cleanup
Description:
Check in some of the code cleanups from working on the external link
support. (This doesn't include any of the external link features)
Platforms tested:
FreeBSD 4.11 (sleipnir)
Mac OSX.4 (amazon)
Linux 2.4
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
Configure feature
Description:
Added 'make trace' target.
Solution:
Added tracing to 1.7. This was done automatically in 1.6, but left out
of 1.7 until now (oops!).
Tracing in 1.7 only happens manually, when the user types 'make trace.'
Tracing automatically requires more framework than it's worth.
I also fixed a couple of tracing bugs and ran trace.
Platforms tested:
mir, sleipnir, modi4
Misc. update:
Bug fix
Description:
Before this checkin, 'gmake check-s' would fail if there was a file in
the current directory named 'check-s'.
This is fixed under gmake (not sure how to fix for other makes).
Solution:
check, progs, install, etc. are what gmake calls "phony" targets,
which means that no file should be created. These targets can be
specified by a line of the form
.PHONY: check progs install ...
Automake adds this line for targets it knows about, but HDF5 has a
lot of custom rules. This checkin adds a .PHONY line for those rules.
I believe that only gmake recognizes the .PHONY line (at least, pmake
doesn't seem to), but a partial solution is better than none.
This error should occur very rarely anyway (the user has to manually
create files with names like 'build-check-s' or '_test').
Platforms tested:
mir, sleipnir, modi4
Bug fix/feature
Description:
Added support for -shlib in h5fc and h5c++.
Made check-install use -shlib when only shared libraries have been installed.
Solution:
h5fc and h5c++ didn't recognize -shlib. Stole code from h5cc to link against
shared libraries.
When static libraries are disabled, the examples Makefiles will automatically
use the -shlib option to link against shared libraries. Thus,
--disable-static and make check-install should work together.
Platforms tested:
heping(disable-static, enable-static, fortran, c++), modi4 (disable-static, fortran, c++, parallel, enable-static)
Bug fix
Description:
Failed parallel tests now cause make to exit with an error.
Solution:
Edited config/conclude.am to throw an error if parallel test programs fail.
Platforms tested:
heping, modi4
Bug fix
Description:
Changed configure.in to use an environment variable TR to set the path
to the tr utility.
Solution:
There are two kind of tr on Solaris with slightly different syntax.
HDF5's configure relies on the "standard" tr. Traditionally, HDF5ers
have needed to make sure that the "right" tr was found before the
wrong one in their path; now they can use an environment variable.
Platforms tested:
mir, shanti, sol
Misc. update:
Forgot to update release notes. Off to do that now.
Makefile bug fix
Description:
Previously, automake didn't output rules to build perform/mpi-perf or
the test/gen_* programs.
Now these can be built by typing 'make mpi-perf' (or 'make foo') or by
configuring with --enable-build-all.
Solution:
Automake doesn't like having rules for programs it doesn't build. Tricked
it by having these programs built "sometimes"--whenever the user enables
--build-all. This should be used mostly for testing and to ensure that
these helper programs compile.
***IMPORTANT***
These programs do *not* currently compile. When --enable-build-all is used
(not the default), gen_new_fill fails because it uses an old API. This is
an existing "bug" that has simply been exposed by this checkin.
Platforms tested:
sleipnir, modi4, sol
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
Code cleanup
Description:
Changed some scale+offset filter symbols from H5_SO_... -> H5Z_SO_...
to indicate that they are in the H5Z package.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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:
Code cleanup (sorta)
Description:
Adjust H5G_stat_t to prepare for eventual "external link" information.
This also puts the information for regular objects and soft links into more
obviously separate places.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
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.
Code cleanup & speedup
Description:
Refactor h5dump & related code to be considerably cleaner & faster for
files with large #'s of objects.
Platforms tested:
FreeBS 4.11 (sleipnir)
Linux 2.4
Code cleanup
Description:
Clean up code somewhat:
- Move from HDmemset() -> H5G_ent_reset() to clear out group entry info
- Simplify H5G_unlink() call
- Use portability macros instead of direct system calls in more places
- Improve readbility by neatening whitespace, etc.
- Move some macros into source code module instead of header files
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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:
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 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
H5Pset_scaleoffset API is changed due to addition of the floating-point filter
Description:
Only add a parameter, nothing should change for the tool.
Solution:
Platforms tested:
Linux 2.4
Misc. update:
Bug fix/code cleanup
Description:
Add tests to determine that very long (64K+) object names are working.
Fixed a couple of bugs in h5dump where they weren't...
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
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
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)
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.
Description: On SGI Altix(cobalt) Linux, wrong values were printed out for enum data type
members. No apparent reason was discovered.
Solution: use another pointer to the buffer containing the member value. It seems fix the
problem.
Platforms tested: cobalt - simple change, where the bug was discovered.
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:
Arabica exhibited strange errors when linker found wrong versions of
header files. This happened because include directories were
given to linker in the wrong order.
Solution:
Move include directories from AM_CFLAGS variable to INCLUDES
variable to put them before CPPFLAGS variable. Trust me, it works.
This bug may also have contributed to strange errors on other platforms
(kelgia?).
Platforms tested:
copper, sleipnir, arabica.
(h5dump broke while building on arabica, but this happened in
a clean checkout, too).
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, new test file
Description:
h5dump was not properly displaying array indices > 3D
Solution:
added the same algorythm and data structure that h5diff uses to calculate the array index
from a element number position
Platforms tested:
linux
solaris
Misc. update:
Description: The byte order for all 1-byte integer types was fixed as little-endian
even on a big-endian machine. This's corrected in h5detect.c. When types are only
1 byte long, a native int is used substitute the type to detect byte order. Some tools
like h5dump and h5repack are also corrected in this case.
Platforms tested: fuss, copper, sol.(There're some failures from the recent configure
change).
Misc. update: Information in the RELEASE.txt.
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
Remove feature
Description:
Retire threaded, balanced binary tree code from HDF5 use. Requiescat in
pace...
Also, regenerate dependencies files.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require full h5committesting (the code is already
disconnected from everything except its tests)
Bug fix.
Description:
When building h5dumpgentest.c with Visual C++ 6.0, I got the following warning message:
h5dumpgentest.c(4528) : warning C4013: 'h5tools_can_encode' undefined; assuming extern returning int
Solution:
Add the header file h5tools.h into h5dumpgentest.c.
Platforms tested:
Heping (Linux)
Visual C++ 6.0 on Windows XP/2000.
.NET on Windows XP.
(Tested with SZIP-with-encoder and SZIP-without-encoder).
Misc. update:
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 (#264)
Description:
h5dump did not print attribute data in ASCII format when
-r is used.
Solution:
Added the ability to print in ASCII for Attributes Data also.
Added a test for printing Attributes with -r option.
Platforms tested:
H5committested.
Also in heping.
Misc. update:
Update MANIFEST.
Refactor code
Description:
Refactor common code for determining the native type for using in the
tools into separate routine.
Also, reduce diffs between the two branches and bring back some fixes from
the development branch to the release branch.
Platforms tested:
FreeBSD 4.10 (sleipnir)
too minor to require h5committest
Purpose: change feature
Description: Back up support bitfield and time datatypes in H5Tget_native_type.Leave it to future support. Let it return "not supported" error message for
now.
Platforms tested: h5committest and fuss.
Misc. update: RELEASE.txt
Code cleanup
Description:
Tweak recent "forward compatibility" changes to the H5E* API (which allowed
for the old H5E API functions to remain unchanged) by allowing for the error
stack callback function (H5E_auto_t) to also remain unchanged from the 1.6
branch. This required changing the H5E{get|set}_auto routines to have the
old style H5E_auto_t type (which didn't have a stack ID parameter) and the new
H5E{get|set}_auto_stack routines to have a newer "H5E_auto_stack_t" type (which
has a stack ID parameter). This should make the H5E API changes as forwardly
compatible as possible.
One side-affect of this change was that it was impossible to determine if
the current auto error callback was the old style (H5E_auto_t) or the new style
(H5E_auto_stack_t) of callback, so a new API function (H5Eauto_is_stack) was
adde to query this.
Platforms tested:
FreeBSD 4.10 (sleipnir)
IRIX64 6.5 (modi4)
h5committest
Description: Restore 6 old error API functions back to the library to be backward
compatible with v1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear, H5Eset_auto,
H5Eget_auto. These functions do not have error stack as parameter.
Solution: Internally, these functions use default error stack.
Platforms tested: h5committest and fuss.
Misc. update: RELEASE.txt
h5dump new tests
Description:
added new tests for the print of array indices (nested objects, several ranks)
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
h5dump new tests
Description:
added more tests for the escape/not escape feature for string data (with vlen, with
compound, with char data)
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
h5dump new tests
Description:
added new tests for the -p option, superblock, file contents, fill values, array indices.
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
change features
Description:
for the file contents dump and for hardlinks, one arrow "->" is printed, followed
by the first found name for that object
options for not printing specific types of objects were postponed
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Description:
the original code that showed a name for HARDLINK was reassigning that name to a name
made in the dump traversal (made by concatenation by nested objects)
Solution:
removed this reassigmnet
now the name showed after HARDLINK is always the first name found for that object
(this object is printed once interely; subsequent printings show the word HARDLINK
and the first name )
Platforms tested:
linux
AIX
solaris
Misc. update:
Code cleanup
Description:
Clean up almost all warnings from Windows builds.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
Purpose:
HDF5 now supports SZIP with no encoder.
Description:
SZIP can be configured to have both encoder and decoder or just to have the decoder. HDF5 can now query the configuration of any filter, and will throw errors if users try to write using a filter with encoding disabled.
Solution:
Added H5Zget_filter_info function, changed API for H5Pget_filter and H5P_get_filter_by_id. See SZIP RFC.
Platforms tested:
Copper (fortran, C++, parallel), Sleipnir (C++), Arabica (fortran, C++), Verbena (fortran, C++)
Misc. update:
bug fix
Description:
the indentation was not made properly for nested objects when printing array indices
Solution:
added the indentation to h5tools_simple_prefix function
Platforms tested:
linux
AIX
solaris
Misc. update:
Code cleanup & small bug fix
Description:
Regenerate dependency files
Add htri_t as separate type from hbool_t for code tracing purposes.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
too minor to require h5committest
h5dump new feature, bug fix
Description:
added the dump of unmamed types to the file contents
fixed a bug in the type array, it was printing invalid characters with the array indices option on
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
dumper new features
Description:
1) added options for not printing : datasets, groups, datatypes, links
2) added a section for the user block
3) in the traversal routine, added the printing of an arrow for soft links and t
he word HARDLINK for hardlinks
the print of the file contents is made during traversal , instead of at the e
nd of it (this is helpful
for very large files, where the wait time can be very long)
4) changed the description of the fill value properties
5) added a colon after the printing of the array indices
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
Code cleanup
Description:
Reduce compiler warnings on SGI IRIX
Platforms tested:
FreeBSD 4.10 (sleipnir)
SGI IRIX6 (Cheryl's machine)
Too minor to require full h5committest
h5dump output change, new tests
Description:
the storage layout output format the storage layout output format had some changes
same for the user defined filter
add an option (-y) for not printing the array indices (default is print indices )
the option for escaping non printable characters covers all characters (default is not escape)
(this might be not very portable, the test files are tstring.ddl and tstringe.ddl )
add tests for the new options
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Description: After I added H5S_NULL dataspace to dumper test, the output violate
XML schema for attribute data.
Solution: changed.
Platforms tested: RH8(fuss), minor change, only dumper is involved.
h5dump new feature
Description:
add processing of tab characters (in the context of the new option process CR/LF)
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Code cleanup
Description:
Add more files that should be removed to the clean & distclean targets.
Platforms tested:
FreeBSD 4.10 (sleipnir)
Too minor to require h5committest
h5dump update
Description:
updated the h5dump test files generator , so that it coincides with the 1.6 branch
Solution:
Platforms tested:
linux (small)
Misc. update:
Description:
added the code for print strings with new line and display the path of references (new source files h5tools_ref.c and .h )
added a test suite in testh5dump.sh.in for
( note : to create testh5dump.sh , one must redo ./configure; this detects the availability of filters
and generates testh5dump.sh accordingly)
1) storage layout
2) fill value
3) print reference with path
4) print strings with new lines
5) filters
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Bug fix
Description:
Correct path to new testh5dump.sh, now that it's generated.
Platforms tested:
FreeBSD 4.10 (sleipnir) w & w/o srcdir
Too minor to require h5committest
Update shell scripts
Description:
Switch to generating the testh5dump.sh script at configure time, so we can
determine which filters are available to test.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too small to require h5committest
h5dump new version
Description:
added the changes already made for 1.6
support for dumping of
1) filters
2) storage layout
3) fill value
4) comments
5) superblock
6) file contents
7) array indices
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Bug fixes
Description:
Updated dependencies
Fixed error with C++ compiler builds of main library
Added H5Pset_data_transform to MPE info
Platforms tested:
FreeBSD 4.9 (sleipnir)
Code cleanup
Description:
Clean up lots of warnings based on those reported from the SGI compilers
as well as gcc.
Platforms tested:
SGI O3900, IRIX64 6.5 (Cheryl's SGI machine)
FreeBSD 4.9 (sleipnir) w/ & w/o parallel
h5committest
small bug fix
Description:
a dataset creation property list was not closed
Solution:
closed it, calling H5Pclose(dcpl);
Platforms tested:
linux (small fix)
Misc. update:
Bug fix
Description:
Fix h5tools routines to not try to call MPI_Init() unless an MPI-based
VFD is actually used.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
Linux 2.4 (verbena) w/parallel
New Feature. (Contributed by Robb)
Description:
Allow h5ls to specify a VFL with the '--vfl=' command line flag.
Add MPI-I/O & MPI-POSIX VFL drivers to list of drivers available for
h5ls and h5dump.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
h5committested
Description: h5dump and h5ls failed an assertion check when a dataset's
datatype is enumerate type and there are special characters in the names
of these values.
Platforms tested: h5committest
Bug fix
Description:
Variable length strings and sequences with NULL pointers were not handled
by library, causing problems access the data. This also affected fill values
for variable-length datatypes.
Solution:
Address the issues in the library by detecting NULL sequences/strings
and avoid trying to convert them.
Patched up dumper to display NULL sequences/strings.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
Code cleanup
Description:
Change field member count and indices for compound and enumerated types from
'int' to 'unsigned' to better reflect actual use.
Cleaned up a few other minor compiler warnings, etc.
Platforms tested:
FreeBSD 4.9 (sleipnir)
Linux 2.4 (verbena)
too minor to require h5committest
Bug fixes and code cleanup
Description:
Changes to h5dump code:
- Dump shared datatypes for any class of datatype, not just compound
datatypes.
- Cleaned up formatting to greatly reduce the amount of trailing
whitespace emitted in output. Also removed some spurious blank
lines from named datatype output.
Added code to generate named datatype attribute test file.
Added tests for dumping named datatypes in attributes for both DDL and
XML output.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
Code cleanup
Description:
Remove various "fixtype" routines which duplicate (and actually pre-date)
the functionality in H5Tget_native_type in favor of having the tools call
H5Tget_native_type(). This provides the same functionality (actually better
functionality, since the old "fixtype" routines didn't handle alignment of
compound fields correctly) and reduces the amount of code to maintain.
Add additional tests to dump out a "complex" compound datatype which
exercises more code in the library for aligning compound fields correctly.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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:
Bug fix
Description:
Object references were not getting written out correctly to the file, with
recent changes to their memory structure.
Solution:
Convert the object references correctly.
Platforms tested:
h5committested
Code cleanup
Description:
Remove recent changes which duplicated code from config/conclude.in, now
that the output of XML schema XID's is portable.
Platforms tested:
h5committested
Code cleanups & bug fixes
Description:
Lots of changes to chase 'objno' and 'fileno' changes in H5G_stat_t struct,
including changing the output of object IDs from "<number>:<number>" to just
"<number>".
Same change to XML schema XIDs from "xid_<number>-<number>" to just
"xid_<number>"
Cleaned up a number of memory leaks
Use the H5_PRINTF_HADDR_FMT macro for printing 'haddr_t's
Platforms tested:
h5committested
bug fix
Description:
1. function rindex is not recognized by windows. Using strrchr instead.
Thereafer strings.h is not necessary.
2. Variable p_type is defined as "hid_t" type at one function; but it is never used.
At the end of that function, H5Tclose(p_type) is assigned. It may cause problems.
So erase two lines.
Solution:
See above
Platforms tested:
windows 2000, linux 2.4, sol 2.7, AIX 5.1.
Misc. update:
Bug Fix
Description:
pmake failed during make of h5dump because of some undefined
variables.
Solution:
Defined the variables.
Platforms tested:
Modi4 (small change and only Irix specific)
Misc. update:
This is an omibus update to the h5dump program.
1. Fixes bug 888
2. updates XML output to 1.6
Description:
Solution:
Platforms tested:
verbena, arabica, copper (64)
Misc. update:
MANIFEST updated
Need to do release notes.
Bug Fix
Description:
The SUBDIRS macro is now defined as "" in the config/commence.in
file. We shouldn't have definitions of this macro before the
inclusion of config/commence.in.
Solution:
Placed all definitions of SUBDIRS after config/commence.in inclusion.
Platforms tested:
Modi4 (Small fix yet again).
Misc. update:
Cleanup
Description:
h5dumpgentest is already included in TEST_PROGS. Removed its old
entry in PROGS.
Platforms tested:
Only in Copper since this is trivial.
Misc. update:
added writing more attributes to one test file
Description:
added the writing of 3D attributes to one test file of h5ls
Solution:
Platforms tested:
Windows 2000 (octopus)
Linux 2.4 (rockaway)
SunOS 5.7 (arabica)
IRIX 6.5 (modi4)
Misc. update:
Bug fix
Description:
This would sometimes coredump in machines like PSC Alpha cluster
or linux icc if -g is not used.
Solution:
The real problem was because char string arrays were declared
without including space for the null terminator. E.g.,
char s[5][2]={ "s1", "s2", ...}
is not correct. Increased the size and also need to change
the H5S... definitions too.
Platforms tested:
"h5committested"--the h5dumpgentest passed without problem though
it failed in Fortran but that is a current known problem.
Tested in verbena using icc and also in PSC's cluster.
Misc. update:
Can't find this error in the v1.5 know problem list.
Bug fix
Description:
A few groups were left open after they were used.
Solution:
Closed them. :-)
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committested
Feature Add
Description:
It's now possible to print out characters as actual characters
instead of their decimal equivalent numbers. It's the same thing that
h5ls does. The flag to do this is "--string" or "-r".
Platforms tested:
Verbena (Fortran & C++)
Arabica (Fortran)
Modi4 (Fortran & Parallel)
Misc. update:
Bug fix
Description:
"$@" was used to represent all argument provided. This has the
unfortunate effect as one argument of "" when actually no argument
was given. Some machines throw the "" away but some like Tflops
and Alpha Q, retains them as a single argument of "". This caused
the no filename given test to fail.
Solution:
Replaced "$@" with a plain $@.
Platforms tested:
h5committested
Misc. update:
