Code cleanup/minor bug fixes
Description:
Corrected a few typos and changed the order that the printf() format
strings are tested for 'long long's to move 'll' ahead of 'q', since 'll' is
the form for the ANSI C99 standard.
Platforms tested:
h5committested
Misc. update:
Bug Fix
Description:
On "user02", the Fortran compiler is "efc". We weren't testing for
this compiler (and I don't know how it was succeeding before...).
Solution:
Added efc to the list of Fortran compilers we check for.
Platforms tested:
Couldn't test as I don't have access to user02. But this doesn't
affect other platforms.
Misc. update:
Bug Fix
Description:
C++ on Irix 6.5 needs some special libraries (libCio or some such
thing). These were defined using the DEFAULT_LIBS macro. However,
they weren't being placed into the Makefiles since it wasn't
AC_SUBST'ed in configure.in and wasn't declared in commence.in.
Solution:
Added to configure.in and also added and commence.in
Platforms tested:
Modi4 (C++, small change and only Irix specific)
Misc. update:
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:
Feature change.
Description:
--prefix default was /usr/local. This is not approprirate for
development version since it is not likely that one would want
to install a development version in the /usr/local area.
Solution:
Change --prefix default to `pwd`/hdf5, a directory in the build
directory. This eliminates the problem that the builder may not
have permission to install in the default install directory.
It also allows multiple builds in the same host or multiple srcdir
using the same source.
Platforms tested:
h5committested.
Also tested in eirene by trying various configure combination to
verify the new effect.
Misc. update:
Update configuration
Description:
Now that we've split the tree (Yea!), change the main trunk back to debug
on and production off.
Also, change the version # to 1.7.0
update for release
Description:
Set the version information to 1.6.0-pre1 to get ready for
v1.6 release.
Platforms tested:
h5committested.
Misc. update:
Code cleanup
Description:
Make the default for the function stack work like the default for the
API tracing: when debug is enabled, the function stack defaults to on and
when debug is disabled, the function stack defaults to off.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
Purpose: Maintenance
Description: Bumped the version number to 1.5.62 after creating
a tar ball for the fourth round of testing.
Solution: run bin/h5vers -s scipt on arabica
Platforms tested: N/A
Misc. update:
Update
Description:
Changed the --enable-mpe flag to --with-mpe so that we could
specify the directory information for where the MPE stuff is
kept. (with the =DIR option that we have for --with-* flags)
Solution:
7%
Platforms tested:
Copper (where MPE is...small change no requiring h5committest).
Misc. update:
Bug fix.
Description:
the MPI_Get_count test does not work correctly (the macro name
MPI_GET_COUNT_WORKS is not even used in source code.) For some
reason, this test sometimes hangs in AIX.
Solution:
Blocked out the test for now and removed the code later when
things are verified to be correct.
Platforms tested:
h5committested.
ALso tested in Copper (32/64bit parallel, 32 bit serial).
Misc. update:
Purpose: Maintenance for the third round of testing
Description: Increased the version number to 1.5.59 after creating
a tar ball for testing.
Solution:
Platforms tested:
Misc. update:
Purpose: Maintenance for the second round of testing
Description: Used bin/h5vers to change version number to 1.5.55
Solution:
Platforms tested: arabica
Misc. update:
Update
Description:
GPFS should only be checked for if the --enable-gpfs flag is used.
Otherwise, it shouldn't.
Platforms tested:
Linux (Configure only fix so only needed to test it to make sure the
configure does the right thing and that the build won't
break. I need to test it on a machine that has GPFS to make
sure it works there...)
Fix
Description:
The SZLIB stuff was being checked by default. This isn't right as not
everyone will have SZLIB stuff.
Solution:
Made the default "no" instead of "yes"
Platforms tested:
Modi4 (Fortran & Parallel)
Verbena (Fortran & C++)
Arabica (Fortran)
Misc. update:
Purpose: Maintenance
Description: I changed release version to 1.5.54.
Email about tetsing of 1.5.53 will be send after this checkins.
Solution: used bin/h5vers -s to change the version number
Platforms tested: Done on arabica
Misc. update:
Feature
Description:
Added new flag to the H5pubconf.h file --- NO_SHARED_WRITING
(H5_NO_SHARED_WRITING). It's only defined for CodeWarrior and should
never be defined for other platforms unless the "open()" bug that CW
has shows up on other platforms.
Platforms tested:
Verbena. Configure only, so no need for full tests.
Misc. update:
Update
Description:
Added printing of the compiler used in the end message.
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:
Update
Description:
The "--enable-parallel=TYPE" option was revamped but the help string
wasn't modified.
Solution:
Modified it to print out just "--enable-parallel" because we no
longer support the "=TYPE" option.
Platforms tested:
arabica (Fortran)
Modi4 (Parallel & Fortran)
Burrwhite (Fortran & C++)
Misc. update:
Fix
Description:
Previous changes in the configure were overwritten.
Solution:
Updated configure.in with the changes that were lost.
Platforms tested:
Linux & Modi4.
Misc. update:
Purpose: New tool
Description: Pankaj created h5import tool long time ago. I am finally checking
the source code in for the 1.6 release.
Known problems: h5import test will crash if srcdir option
is used; will be fixed before the release.
Solution:
Platforms tested: vebena, arabica, modi4 were tested. h5import tests passed
I also tested on arabica with srcdir option to make sure that
there is a problem when srcdir is used. After that I disabled
h5import tests. Daily tests will build h5import, but will not run
h5import tests.
Misc. update:
Code cleanup
Description:
Re-arranged configure output for external I/O filters to show that zlib
and szlib are used for external I/O filters and display them with the output
for the internal I/O filters.
Solution:
Platforms tested:
FreeBSD 4.8 (sleipnir)
Linux 2.4 (eirene)
IRIX64 6.5 (modi4)
Misc. update:
This is the first check-in message related to szip support at HDF5 1.6 release
Description:
szip compression support is required by NASA ESDIS. The compression algorithm
is a good compression algorithm for scientific data. In HDF5, we add another filter
function to make szip as a default compression package as we did for gzip(or zlib).
Solution:
In the configure.in and configure, I handled szip exactly the same as what zlib was built into
the HDF5.
Currently if you don't specify in the configure command line with:
./configure --with-szlib=/.....
Unless you put your szip library in your path,you will build the same HDF5 library like before.
Also, I only use static szip library to test with HDF5.
Platforms tested:
Since there are changes of configure.in and configure,I didn't use h5committest.
I tested with four platforms.
1) Linux 2.4 (eirene)
2) Solaris 2.7(arabica)
3) windows 2000(VS 6.0)
4) SGI IRIX6.5-64(modi4)
For test 1)-3), only basic C tests were done
For modi4 test, I tested 64-bit C,parallel and fortran.
ALl tests passed, except a warning message from szip library when checksum is used in some order, which doesn't cause any real problems.
Misc. update:
Update
Description:
Added Flexible Parallel HDF5 support to the ending message that
configure spits out.
Reordered a few other of the messages so that they're in alphabetical
order.
Platforms tested:
Linux
Bug fix
Description:
The "system scope" for threads isn't supported on all platforms.
Solution:
Add detection of this feature to the configure script and check for
"H5_HAVE_SYSTEM_SCOPE_THREADS" in the appropriate places.
Platforms tested:
modi4 w/threadsafe
New feature for developers.
Description:
Added "function stack" tracing to library. This allows developers (there
is no public API) to call H5FS_print within the library and get a listing
of the functions traversed to reach that point in the library. Eventually,
I may add support for reporting the parameters to each function also...
Mainly for debugging parallel I/O programs, but I think it will come in
handy in other cases also.
The function stack tracking is controlled with a configure switch:
--enable-funcstack, which defaults to enabled currently. When we branch
for 1.6, we should change the default setting on the branch to be disabled.
Also, added a destructor to the thread-specific keys when thread-safety is
turned on in the library. Otherwise, they were leaking memory and causing
difficult to debug errors in threaded programs (like the test/ttsafe test).
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) w/thread-safety enabled.
Misc. update:
Updated MANIFEST with new files added (src/H5FS.c & src/H5FDprivate.h)
Update release_docs/RELEASE with thread-safety bug fix.
Update
Description:
Updated the configure scripts. Fortran and C++ didn't have proper
checks for Linux LFS support. Also needed to remove the "-g" flag
from the compile line if --enable-production is set. For that, I took
how it's being done in HDF5 Lite...
Platforms tested:
Linux
Bug Fix
Description:
Some compilers were having problems if we included the -I/usr/include
and -L/usr/lib flags which are completely redundant. This could occur
if the user configured with something like:
./configure --with-zlib=/usr/include,/usr/lib
Solution:
Check if the --with-* command is specified with /usr/include and
/usr/lib. If so, then don't place them in the compile macros.
Platforms tested:
Linux, Modi4
Another patch
Description:
libtool will fail if pgcc compiler is used.
Now apply the patch if gcc is NOT used.
Platforms tested:
Tested only on eirene because I am sure it is correct and am trying
to beat the daily test checkout.
a patch
Description:
When intel compilers (icc, ecc) are used in a linux system, the libtool
generated has a wrong setting of '$wl" for linking.
Put in a "ed ..." command script to edit the generated libtool with
the proper setting. The libtool people has fixed this problem.
This can ben taken out when that version of libtool is released.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}? YES.
Other platforms/configurations tested? platinum and titan using
gcc and intel CC.
Misc. update:
Update MANIFEST if you add or remove any file.
Update release_docs/RELEASE for bug fixes, new features, etc.
Update applicable document files too.
Lots of performance improvements & a couple new internal API interfaces.
Description:
Performance Improvements:
- Cached file offset & length sizes in shared file struct, to avoid
constantly looking them up in the FCPL.
- Generic property improvements:
- Added "revision" number to generic property classes to speed
up comparisons.
- Changed method of storing properties from using a hash-table
to the TBBT routines in the library.
- Share the propery names between classes and the lists derived
from them.
- Removed redundant 'def_value' buffer from each property.
- Switching code to use a "copy on write" strategy for
properties in each list, where the properties in each list
are shared with the properties in the class, until a
property's value is changed in a list.
- Fixed error in layout code which was allocating too many buffers.
- Redefined public macros of the form (H5open()/H5check, <variable>)
internally to only be (<variable>), avoiding innumerable useless
calls to H5open() and H5check_version().
- Reuse already zeroed buffers in H5F_contig_fill instead of
constantly re-zeroing them.
- Don't write fill values if writing entire dataset.
- Use gettimeofday() system call instead of time() system when
checking the modification time of a dataset.
- Added reference counted string API and use it for tracking the
names of objects opening in a file (for the ID->name code).
- Removed redundant H5P_get() calls in B-tree routines.
- Redefine H5T datatype macros internally to the library, to avoid
calling H5check redundantly.
- Keep dataspace information for dataset locally instead of reading
from disk each time. Added new module to track open objects
in a file, to allow this (which will be useful eventually for
some FPH5 metadata caching issues).
- Remove H5AC_find macro which was inlining metadata cache lookups,
and call function instead.
- Remove redundant memset() calls from H5G_namei() routine.
- Remove redundant checking of object type when locating objects
in metadata cache and rely on the address only.
- Create default dataset object to use when default dataset creation
property list is used to create datasets, bypassing querying
for all the property list values.
- Use default I/O vector size when performing raw data with the
default dataset transfer property list, instead of querying for
I/O vector size.
- Remove H5P_DEFAULT internally to the library, replacing it with
more specific default property list based on the type of
property list needed.
- Remove redundant memset() calls in object header message (H5O*)
routines.
- Remove redunant memset() calls in data I/O routines.
- Split free-list allocation routines into malloc() and calloc()-
like routines, instead of one combined routine.
- Remove lots of indirection in H5O*() routines.
- Simplify metadata cache entry comparison routine (used when
flushing entire cache out).
- Only enable metadata cache statistics when H5AC_DEBUG is turned
on, instead of always tracking them.
- Simplify address comparison macro (H5F_addr_eq).
- Remove redundant metadata cache entry protections during dataset
creation by protecting the object header once and making all
the modifications necessary for the dataset creation before
unprotecting it.
- Reduce # of "number of element in extent" computations performed
by computing and storing the value during dataspace creation.
- Simplify checking for group location's file information, when file
has not been involving in file-mounting operations.
- Use binary encoding for modification time, instead of ASCII.
- Hoist H5HL_peek calls (to get information in a local heap)
out of loops in many group routine.
- Use static variable for iterators of selections, instead of
dynamically allocation them each time.
- Lookup & insert new entries in one step, avoiding traversing
group's B-tree twice.
- Fixed memory leak in H5Gget_objname_idx() routine (tangential to
performance improvements, but fixed along the way).
- Use free-list for reference counted strings.
- Don't bother copying object names into cached group entries,
since they are re-created when an object is opened.
The benchmark I used to measure these results created several thousand
small (2K) datasets in a file and wrote out the data for them. This is
Elena's "regular.c" benchmark.
These changes resulted in approximately ~4.3x speedup of the
development branch when compared to the previous code in the
development branch and ~1.4x speedup compared to the release
branch.
Additionally, these changes reduce the total memory used (code and
data) by the development branch by ~800KB, bringing the development
branch back into the same ballpark as the release branch.
I'll send out a more detailed description of the benchmark results
as a followup note.
New internal API routines:
Added "reference counted strings" API for tracking strings that get
used by multiple owners without duplicating the strings.
Added "ternary search tree" API for text->object mappings.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Other platforms/configurations tested?
FreeBSD 4.7 (sleipnir) serial & parallel
Solaris 2.6 (baldric) serial
new feature
Description:
Added MPICH/MPE instrumentation support.
All source code are bracketed by the macro H5_HAVE_MPE.
Use "--enable-mpe" to configure it in.
Currently only worked in Eirene because the MPE library is
not installed in all machines yet.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}? Yep.
Other platforms/configurations tested?
--enable-mpe feature tested in Eirene.
Cleanup
Description:
Removed the option (--enable-parallel=mpich). It did not work.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}? All passed.
New feature.
Description:
Add in '--enable-filters=filter1,filter2' flag to configure script. This
can also be used as '--enable-filters=all' or just '--enable-filters' to
enable all the internal I/O filters in the library.
This flag can also be set to '--disable-filters' to disable all the internal
I/O filters. Individual filters can not be disabled due to the limitations
of autoconf.
Additionally, added "H5_HAVE_FILTER_<foo>" macros to H5pubconf.h header
file, so the presence of each filter can be detected.
This is in preparation for Kent's shuffling filter to be imported shortly.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Tested FreeBSD 4.7 (sleipnir) also
Update
Description:
Added new files to the MANIFEST and added a new configure switch for
enabling building of the Flexible parallel HDF5 module.
Platforms tested:
Modi4 Eirene Arabica
fix/feature
Description:
v1.4's configure had enable-trace default as on. That is not right for
production code as it increase the object code and uses up compute time.
Changed --enable-trace default to depend on --enable-debug. If debug is
on, trace is on. Otherwise it is off.
Also added the printing of CFLAGS, CPPFLAGS, and LDFLAGS in the summary.
Platforms tested:
eirene, arabica (pp).
Small Coding Change
Description:
Zeroed out the MPI_Status structure in one of our tests to determine
if MPI_Get_count() works on the machine or not. This is similar to
what we do in the library code to the status...
Fix
Description:
Better check for versions of Linux. We didn't support kernels with
major version numbers >2 and minor version numbers <4...
Solution:
Fixed to check just that.
Platforms tested:
Linux 2.2 && 2.4
Update, Bug Fix, and Feature Add
Description:
- Updated how AC_{ENABLE,WITH} help messages were being generated.
Autoconf now gives you an AC_HELP_STRING macro to use to create
them.
- Fixed the problem with Linux LFS on RedHat 7.3 machines. It wasn't
finding getdents64(), so we can't rely on that being present
anymore...
- Added GPFS detection and setting.
- Updated how compression is specified. It's no longer necessary to
test for HAVE_ZLIB_H, HAVE_LIBZ, and HAVE_COMPRESS2. The one macro
{H5_}HAVE_COMPRESSION takes care of all of these.
Solution:
Changed the check for Linux LFS from looking for getdents() to
looking at the version number of the kernel (using the uname -r
command). You can still override with the --enable-linux-lfs switch
if you really believe that your <2.4 kernel has LFS support.
Platforms tested:
Linux (2.2 and 2.4)
New feature
Description:
Changed parallel I/O tests to use test script instead of just running
testphdf5 executable. This allows the MPI-posix driver to be tested easily.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/parallel and IRIX64 6.5 (modi4) w/parallel
New feature
Description:
Add support in for "dmalloc" debugging malloc library to configure script
and library headers.
Platforms tested:
IRIX64 6.5 (modi4) and FreeBSD 4.6 (sleipnir)
Porting to AIX 5.x
Description:
These have been tested out in v1.4. Folding them in here.
aclocal.m4:
Snow's names were not included in the special hack.
Added its names in.
Removed the trailing * in pacific.llnl.gov too.
configure.in:
fortran/configure.in:
Added a case to group all AIX 5.* versions as aix5.x. This allows
them to share one common config/*aix5.x file.
configure:
fortran/configure:
Derived from configure.in (done in eirene).
config/powerpc-ibm-aix4.x:
Added a comment explaining why not to cache sizeof size_t and off_t
fortran/config/powerpc-ibm-aix4.x:
Turned of cache of sizeof size_t and off_t because they are depedent
on compiler options.
config/powerpc-ibm-aix5.x:
fortran/config/powerpc-ibm-aix5.x:
New config file for AIX 5.X
Platforms tests:
LLNL Blue, Frost, Snow, both serial and parallel.
Update
Description:
Updated the h5vers script to automatically update the configure.in
files so that they reflect the correct version in the AC_INIT line.
Platforms tested:
Linux
Update
Description:
Updated the way we used the AC_INIT macros so that it's current to
the new standard way and not deprecated anymore.
Also, added a test for some functions during parallel Fortran
configure. This required the creation of an H5config_fortran.h file
so that we can test for these...
Platforms tested:
Elena is going to test the changes to the fortran after she checks in
her other code. I will test on SDSC machines after getting her code.
The other changes were tested on Linux.
Feature Fix
Description:
Modified the AC_OUTPUT macro to coincide with the now-standard way of
doing things. I.e., you put all of the files you want to generate
into the AC_CONFIG_FILES macro and invode AC_OUTPUT with no
parameters.
Platforms tested:
Linux
Bug fix
Description:
Zlib-compression was reported according to if a Z-library (e.g., libz.a)
has been found. It actually needs the presence of a valid zlib.h header
file and the compress2() routine.
Solution:
Changed the IF_YES_NO to be more general by accepting multiple arguments
and changed the Zlib-compression depends on zlib.h header and the
compress2() routine.
Platforms tested:
Eirene.
Autotools Update
Description:
I've updated autoconf, automake, and libtool to the latest/greatest
versions; 2.53, 1.6, and 1.4.2 resp.
Many changes come with the new versions:
- ltconfig is no longer used
- acconfig.h is no longer used (#define values are declared with
the macro)
- regeneration of all of the aclocal.m4, configure, and
H5config.h.in files.
- new config.{guess,sub} files
- new ltmain.sh file
Platforms tested:
AIX (blue), and Linux
Code Motion
Description:
Removal of HDF4 from the configure/Makefiles. This is a precursor to
the actual physical removal of the HDF4 tools from the HDF5 tree.
Platforms tested:
Arabica, Dangermouse
Bug Fix
Description:
Didn't need to test that the Pablo library had a function in it only
that it was there.
Solution:
Removed that check. Just checked if we can actually find the physical
library and include files where the user tells us they're hiding.
Platforms tested:
Linux
Bug Fix
Description:
Fixed wrong test for the HAVE_PABLO flag. Was testing if it was not a
null string when I should have been testing if it was equal to "yes".
Solution:
Changed test so that it checks if it's equal to "yes" instead of
non-null...
Platforms tested:
Linux
Bug Fix
Description:
Some -I paths weren't included in the h5cc script. That would cause
the compiler to fail if it was trying to find gass header files or
the like.
Solution:
Added the CPPFLAGS macro to the h5cc.in file so that it'll be there
when it's generated. This will also include some -D options which we
compiled the library with, like the LFS flags on Linux.
Also changed the configure* files so that it will "chmod" the created
h5cc file to 755 (executable) since that wasn't happening all the
time...
Platforms tested:
Linux
Purpose:
Bug Fix
Description:
On some systems, doing the shell command:
if test -z $DEBUG_PKG; then
doesn't work if $DEBUG_PKG is null..
Solution:
Changed to "if test "X$DEBUG_PKG" = "X"; then" which will do the same
thing but without the error...
Platforms tested:
Linux
Bug Fix
Description:
When printing out the summary information after the configuration,
the Compilation Mode and Debugging information would be incorrect.
The library is set to compile to "Production" mode for a release.
Yet, the default compilation mode before that was "Development". If
the user doesn't specify "--enable-production" on the command line,
the configure defaults to "Production" mode, but the summary still
reported "Development" mode.
Solution:
Modified script so that after we've determined which compilation mode
we're in, we reset the "enable_production" variable to the correct
setting. So, we no longer have a "default". The summary part then
reads the new value and uses that to determine which mode we're in.
The debugging summary information was reworked so that it would
output the correct summary information. Slight hacking of the summary
script to check the values a bit more closely...
Platforms tested:
Linux (eirene)
New feature check
Description:
Added check to determine if malloc(0) returns a valid pointer for a
particular architecture.
Platforms tested:
FreeBSD 4.5 (sleipnir) where malloc(0) works
Cray SV1 (killeen) where malloc(0) doesn't work
Bug fix.
Description:
FreeBSD would fail the threadsafe feature if static-exec is not on.
Solution:
Force enable-static-exec on if enable-threadsafe is on.
Also moved the chunk of FreeBSD specific code for Pthread setup
from configure.in to config/freebsd.
Also changed enable-threadsafe to check on linking pthread program.
That takes care of platforms (e.g. freebsd) that has pthread
support builtin the default C library. Now one can just use
"enable-threadsafe" if the compiler has pthread support by default.
Platforms tested:
eirene, Sleipnir
Removing the DPSS (gridstorage) driver source code.
Description:
The DPSS (using Grid-Storage) driver is retired.
Removed the configure option with-gridstorage from configure.in.
Cvs remove the following files
./src/H5FDdpss.c
./src/H5FDdpss.h
./test/dpss_read.c
./test/dpss_write.c
Regenerated Dependencies files (some had to be hand-edited since
'make depend' did not cover them.)
Removed reference to DPSS Virtual file driver from H5F.c.
Platforms tested:
modi4 (Parallel; -with-gass=...), eirene, arabica (fortran, cxx).
Purpose:
Feature Fix
Description:
The new feature (allowing the user to specify =DIR for a --with-xxx
option instead of requiring =INC,LIB for them) needed a better
explanation.
Solution:
Created a phoney --with-fnord option whose only purpose is to supply
a --help message.
Platforms tested:
Linux
Purpose:
Feature Add
Description:
Added the feature which will accept a directory for all of the
features which now accept an =INC,LIB directive. The old way of doing
things (=INC,LIB) is still valid, but we prefer the user uses the
=DIR method from now on. It saves typing.
Platforms tested:
Linux
Bug fix
Description:
GASS nor gridstorage worked any more because SSL library testing
was moved after them.
Solution:
Moved SSL library to be tested before GASS or Gridstorage options
are tested. Also make the testing of SSL libraries default to
no testing, so that it won't get activated unnecessarily.
Platforms tested:
IRIX64 -64, serial and parallel. (GASS driver needs globus
software which is available in modi4 only.)
'Bug fix'
Description:
When testing the validity of zlib, the compress() function is
used. HDF5 actually requires a newer version of zlib which
contains compress2(). Compress2 is tested in later part of
the configure. This caused redundent tests and confusion too.
Solution:
Changed zlib test to look for compress2() instead.
Older version of HDF4 libraries (e.g. 4.1r2) would fail this
test correctly. This eliminated the possibility of using an
older version of HDF4 without using zlib compression in HDF5.
But since we need newer version of hdp (with loops detection),
the older version hdf4 is not old any more.
Remark: the compress2 test is not removed. After this change
proven working correctly for all platforms, the extra compress2
test can be removed and source code must be updated too.
Platforms tested:
modi4: tested with hdf4.1r2 and failed as expected. Tested with
newer hdf4 libraries and succeeded as expected.
Purpose:
Final Fantasy...er...fix
Description:
I fixed the problem with the summary printing newlines when we didn't
want it to when using "ksh".
Solution:
There's a flag '\c' which should be used at the end of the line if
you can't use the '-n' flag.
Platforms tested:
linux and modi4.
Purpose:
Bug Fix
Description:
Some platforms don't handle echo -n correctly.
Solution:
Copied some code from the configure which determines which flag to
give echo.
Platforms tested:
Linux
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:
New Feature
Description:
Added final output for the configure script which shows a summary of
options people chose while configuring.
Platforms tested:
Linux
Portability Bug Fixes
Description:
FreeBSD wants the -pthread flag on both the compile and link lines. Also,
the cipher library is required for certain threading features and needs to
be linked in.
Solution:
Add the -pthread to the compile line and the cipher library to the list of
libraries.
Platforms tested:
FreeBSD 4.4 (hawkwind)
New feature
Description:
Added perform programs to test the HDF5 library performance. Programs
are installed in directory perform/.
Platforms tested:
eirene
Purpose:
Bug Fix
Description:
The new way of determining directory information for HDF4 and ZLIB
bombed on me.
Solution:
For some reason, the way I was linking together all of the
"CHECK_LIBRARY" macros wasn't working. I separated them.
Platforms tested:
Kelgia.
Feature shift
Description:
Take out the v1.2.x compatibility stubs and put in the hooks for v1.4.x
compatibility when needed.
Platforms tested:
FreeBSD 4.3 (hawkwind)
Purpose:
Bug Fix
Description:
The way we were generating Dependencies and .depend files was broken.
If the $srcdir or other macros began with a ".", then it would match
anything and cause problems since it would then overwrite the
beginning of the header file's path.
Solution:
Wrote a Perl script which can handle this type of weirdness better.
It's only used when the environment is a GNU one with a GCC
compiler...
Platforms tested:
Linux
Purpose:
Cleanup
Description:
The SSL library was being tested for even if we didn't need it. This
was causing some libraries to be included in our library which
weren't needed (i.e., libcrypto).
Solution:
Only check for the SSL library if either GASS or Grid Storage is
specified.
Platforms tested:
Linux
Bug fix.
Description:
On some systems (linux when not using gcc) the 'dev_t' is not actually
a scalar variable. This causes the code which compares dev_t's in
the file drivers to not compile.
Solution:
Detect this and set the DEV_T_IS_SCALAR flag so we can code around it
in the file drivers.
Platforms tested:
FreeBSD 4.3 (hawkwind), Linux 2.4.2 (chiba city cluster at Argonne)
Purpose:
Bug Fix
Description:
The HP-UX 11 platform needs the NSL library.
Solution:
Check for the HPUX 11 platform and then do the check for the NSL
library.
Platforms tested:
Kelgia
Bug fix... (sorta)
Description:
Added --enable-linux-lfs configure flag to have better control over whether
the enable large file support on Linux machines. Also removed the
-malign-double flag for gcc since it can potentially cause errors which
are difficult to detect.
Platforms tested:
Linix 2.2 & 2.4 (eirene and dangermouse)
Purpose:
Bug Fix
Description:
Changed the README file's name to README.txt to coincide with the
file's actual name change. Also removed check for the nsl library
unless we're dealing with a SunOS system as this can conflict with
libraries on other strange platforms.
Platforms tested:
Eirene.
Code cleanup
Description:
Several system functions don't have prototypes on Linux machines with our
current compile flags.
Solution:
Add _POSIX_SOURCE and _BSD_SOURCE macros to the compile line when compiling
on Linux machines, to pick up missing prototypes.
Platforms tested:
Linux (eirene), FreeBSD 4.3 (hawkwind)
bug fix
Description:
The last reported problem that the parallel example program
in examples could not be compiled, could not be duplicated
again. I guessed maybe Rushad mistook the compile warning
messages as error messages. Just a guess.
Furthermore, the changed examples/Makefile.in and configure.in,
did not work for the parallel case. The examples/ph5example.c
was never included for compiling.
Solution:
Removed the fix in configure.in, put ph5exmple directly back
in the examples/Makefile.in but put it in a variable for
easier future maintenance. Also, easier to identify the
parallel examples too.
Platforms tested:
Eirene, both serial and parallel modes.
Test Addition
Description:
I added a small test to determine if the MPI library has a working
version of the MPI_Get_count() function. If it does, then I define
the macro:
MPI_GET_COUNT_WORKS
This should (hopefully) take care of the kludges in H5FDmpio.c...
NOTE: This isn't implemented in the H5FDmpio.c file since I don't
know the code in there and don't know which solution will work. Also,
the test program I put into the configure script needs to be checked
on a platform which does have a working MPI_Get_count()
function...I.e., this is just a first stab.
Platforms tested:
Linux
Purpose:
Adding new feature
Description:
Added gif2h5 and h52gif conversion utilities
Solution:
The utilites follow the framework built for the gif2hdf and hdf2gif
utilities for hdf4. The main files modified were those that read the
H5 file and those that write H5 file. In the future, if you wish to
continue with the framework and extend it to .png or some other fileformat
the main files to edit will be the gif reader and writer.
One point to note with h52gif. You have to specify the exact location of
the image and the palette that it links to. You can choose not to specify
a palette (uniform grayscale chosen in this case) but you must specify
image location. In the future, someone could edit the readhdf.c source
to enable the reader to parse the hdf file and select all images with
corresponding palettes.
Platforms tested:
modi4 , eirene , hawkwind , arabica , Ren (NT 4.0) , Personal box (win2k)
Bug Fix
Description:
A parallel example was added to the examples/ subdirectory. This was
being built whether --enable-parallel was defined or not. This was
causing some havoc with certain setups.
Solution:
Added logic to make it so that the parallel examples are made only if
--enable-parallel is specified.
Platforms tested:
Linux
Bug Fix
Description:
Small fix. The "off_t" typedef's size wasn't being set correctly.
Solution:
The tests for 64-bit files (getdents64() in particular) needed to
occur before checking for the sizeof off_t.
Platforms tested:
Linux
Better Mouse Trap^W^WBug Fix
Description:
Instead of having the large file support stuff be in the
config/gnu-flags directory, I added it to the configure.in file so
that it first checks for the syscall ``getdents64()''. If it finds
it, then it removes the ``-malign-double'' flag if the GCC compiler
is 2.95.x since this flag doesn't play well with the LFS stuff.
Solution:
Added test for getdents64(), if found it removes the -malign-double
flag if the compiler is 2.95.x. This is done in the configure.in
file. The gnu-flags file is returned to normal. A new field is added
to the H5config.h.in file because of the getdents64 check.
Platforms tested:
Linux
Portability changes
Description:
Very quick port to Compaq (nee DEC) Alpha OSF5.
Solution:
Added a new "dec-osf5.x" configuration file and changed configure.in
to look for it.
The local test machine is now passing all the tests, except I can't get
the "-L<path>" stuff to work, so tools which depend on the HDF4 library
around tested.
Platforms tested:
Compaq Alpha 5.1 (compaq.ncsa.uiuc.edu)
Bug Fix
Description:
Forgot to propagate the '-c' flag if the install-sh script is being
used. This caused some machines *cough*T3E*cough* to move instead of
copy the files...
Solution:
Added -c flag back in with the install-sh script.
Platforms tested:
Gondolin
Bug Fix
Description:
We shouldn't create Makefiles in the testpar/ directory unless we're
building this as parallel.
Solution:
Put flag in there specifying that we're doing this in Parallel and we
should build the Makefile in testpar/.
Code cleanup
Description:
ssize_t is not defined on certain (non-UNIX) platforms.
Solution:
Added steps to configure to generate SIZEOF_SSIZE_T macro and then used
the new macro to define ssize_t for platforms which don't have it.
Platforms tested:
FreeBSD 4.3 (hawkwind)
Improvement
Description:
Changed the default value of $NPROCS from 2 to 3. This is the
value libSAF uses since 3 processes have a much bigger chance
catching parallel errors than just 2 processes.
Platforms tested:
Modi4 (IRIX64) both serial and parallel modes.
Bug Fix
Description:
On the Nersc machines, the install-sh script wasn't being found in
the proper place.
Solution:
Corrected the "fix" I put in there awhile ago. Essentially, if the
INSTALL macro is the program "install-sh" with anything around it,
then we assume they want our install-sh program and force the
Makefiles to find it in the hdf5/bin directory.
Platforms tested:
Nersc.
Bug Fix
Description:
Removed generation of the Makefile in the
doc/html/Tutor/examples/java directory since they ahve their own
Makefile which is actually distributed with the documents.
Platforms tested:
Linux
Fixlet
Description:
FIxed the hack for the INSTALL macro. It was checking the "whole"
path to the install-sh script instead of if it was just a relative
path with install-sh at the end.
Solution:
Changed the test to match any relative path with install-sh at the
end. This assumes that the install-sh is the one we supply to them
(an assumption it was making before, really).
Platforms tested:
Gondolin, Linux
Fix
Description:
On machines which use the bin/install-sh script, it wasn't picking up
the install-sh script unless it was one directory depth away from it
(ie, it thought that it was in ../bin/install-sh, which isn't good
if, like with the documentation, it's in a deeper directory).
Solution:
Hacked it up so that, if it does use the broken relative-path schema,
then it will change it to use the $(top_srcdir) macro instead.
Platforms tested:
Linux
[is this a bug fix? feature? ...]
Description:
Changed the default settings for enable-production and enable-debug
to no and yes respective, for this development branch.
Platforms tested:
Modi4 parallel and eirene.
Code cleaning
Description:
Moved all gcc compiler flags into the config/gnu-flags file and re-added
the warning flags removed during the beta testing.
Platforms tested:
FreeBSD 4.2 (hawkwind)
Feature Fix
Description:
When user specifies the --disable-hsizet flag, we still warn them
about this when they use gcc 2.91.66.
Solution:
I moved the check above the place where it checks what version gcc
compiler it is. If they did specify the flag and it is a 2.91.66
compiler, then it won't print the message out.
Platforms tested:
Linux
Suppress warnings for release.
Description:
Took out the -Wconversion -Wredundant-decls warning flags for gcc until
after the tree is split.
Platforms tested:
Linux 2.2.16 (eirene)
Warning Reduction
Description:
Removed the -Wpointer-arith flag which complains about addintion with
void * pointers. This is a known gcc 2.95.2 annoyance.
There's still some issues with many str* warnings...not 7000, though.
Platforms tested:
Linux
Name change
Description:
Changed the names of the testh5toh4 and testh4toh5 scripts to the
"canonical" form -- testh4toh5.sh and testh5toh4.sh.
Platforms tested:
Linux
New configure feature.
Description:
The H5private.h header file was re-defining the strdup function on several
platforms, generating a warning.
Solution:
Detect if the system defines a strdup function and don't re-define it, if
so.
Platforms tested:
FreeBSD 4.2 (hawkwind), IRIX64-64 (modi4)
Bug fix
Description:
The zlib.h header check was skipped if it thought it had
found -lz already. That resulted in H5_HAVE_ZLIB_H not defined
which caused compression feature not compiled even though everything
else said it was in.
The --with-hdf4 was default to yes but configure had no clue where to
find them. A plain waste of time and affected ZLIB's searching later.
Solution:
Basically restored what it was before--checking the optional switch
of with-hdf4 first, then with-zlib. (with-hdf4 now defaults to no.)
Added a big chunk of comments explaining why these two options must
be checked in this order.
Changes applied to configure.in. Then ran autoconf to generate
configure.
Platforms tested:
eirene (default and with-hdf4), modi4-64-parallel (with-hdf4),
arabica (with-hdf4) and, gondoline. That is right, even tested
it out with gondoline (with-hdf4 too.) All except modi4 configured,
compiled and tested correctly. Modi4 died in the compiling of
src/H5Zdeflate.c but that was not due to the configure changes.
Prepare for 1.4.0beta1 release
README:
src/H5public.h:
Updated with 1.4.0beta1 version information.
configure.in:
Changed default setting to --enable-production --disable-debug.
configure:
Derived from configure.in via autoconf.
Platforms tested:
Eirene (linux) running just the configure command and compared
difference with previous configure output to verify expected
difference.
Bug fix
Description:
The last modification put an extra comma in the AC_CHECK_HEADERS
that would generate an bad configure file.
Solution:
Removed the comma.
Platforms tested:
Ran autoconf and verified it by comparing the same with
the current working configure file which has been tested.
Purpose:
Bugfix
Description:
Under SunOS 5.5 the symbol FIONBIO wasn't known when compiling
with the Stream VFD configured.
Solution:
This symbol is defined in the system header file <sys/filio.h>.
Here we check whether this header is available.
Platforms tested:
SunOS 5.5 (hatteras), SunOS 5.6 (thor.sistec.kp.dlr.de)
Bug Fix
Description:
Some platforms, when building static libraries, complain that
libc doesn't have dlopen and friends.
Solution:
libtool supports workarounds for this. The one used here may not
work, but it's an attempt to correct it. If it doesn't work, then
there's something going on which I'm not privvy to...
Platforms tested:
(untested as of yet)
* 2000-11-15 Robb Matzke <matzke@llnl.gov> (CC_VERSION)
The compiler is always expanded to a
full path name if possible. This feature enhancement was
requested by Mark Miller, LLNL.
Command-line name change
Description:
Changed --with-stream-vfd to --enable-strea-vfd to be more
consistent with what people expect from the --with-FOO and
--enable-FOO arguments.
Backward compatibility additions
Description:
Added "--enable-hdf5v1_2" flag to enable HDF5 v1.2 compatibility API
functions (H5Tget_member_dims & H5Tinsert_array) being built in the
library.
Platforms tested:
FreeBSD 4.1.1 (hawkwind)
Purpose:
Bugfix
Description:
Rename the [H5_]HAVE_STRUCT_SOCKLEN_T into [H5_]HAVE_SOCKLEN_T.
Solution:
As pointed out by Bill the socklen_t type isn't a structure if
is it defined by the system headers.
So we should better take out the _STRUCT_ from the defines.
Platforms tested:
Purpose:
Bugfix
Description:
Detect whether the 'struct socklen_t' type is defined in the
system include header files.
Solution:
Added an AC_TRY_COMPILE test for 'struct socklen_t' to the configure
script. This test is only executed if the Stream VFD is configured.
Also added detection of <sys/types.h> and <sys/socket.h> system
header files.
Platforms tested:
Solaris 2.6 and 2.7
IRIX64
Linux
Windows NT (command line configure with gcc and cl)
Buglet
Description:
Wasn't picking up specified directories for the run-time linking
stuff that libtools does.
Solution:
There was some confusion about how the regex stuff works with
scripts. It's not `.*' for any character by `*'...Fixed.
Platforms tested:
Arabica
Bug Fix...AGAIN!
Description:
The logic to create the DYNAMIC_DIRS macro was accepting such
things as -lnoop_stubs which would cause libtools to barf.
Solution:
I'm pretty sure I fixed this once before. The change was lost. I
now test to make sure that the flag I'm adding has a "-L" prefix
on it...
Purpose:
Detect whether the system has the netinet/tcp.h header file.
Description:
The Stream VFD uses setsockopt(2) to set TCP_NODELAY on an opened
socket. This constant is defined normally in netinet/tcp.h
except for GNU cc under Windows where this header doesn't exist.
Platforms tested:
Windows NT, GNU cc
Buglet Fix...kinda
Description:
The --enable-c++ flag is in there, but configure can't handle the
++ on the end.
Solution:
Changed it to --enable-cxx instead. N.B. This feature isn't
really needed yet since C++ isn't integrated with the library
proper.
Platforms tested:
Linux
Bug Fix
Description:
Broke on Arabica trying to export the SEARCH macro.
Solution:
Assigned to the SEARCH macro and then exported it.
Platforms tested:
Arabica.
Bug Fix
Description:
When running configure on subdirectories (like fortran/), looking
up how make implements SEARCHes failed.
Solution:
Exporting the SEARCH macro so that subdirectories don't have to
look for it.
Platforms tested:
Modi4.
Bug Fix
Description:
zlib was not being retrieved from the place specified by the user
even if the user used the --with-zlib flag.
Solution:
Removed the automatic inclusion of /usr/ncsa/* into the macros
and use the user-defined place to try to pickup the zlib. I'm
relying on the order of the -L flags in the compile line to
specify which libraries to look into first before going on to
look into the system libraries. If some compiler doesn't honor
the this order, yikes...
Platforms tested:
Linux
Purpose:
h4toh5 converter tool under tools
Description:
put flag h4toh5 and testh4toh5 into the configure file.
Solution:
[details about the changes, algorithm, etc...]
[Please as detail as you can since your own explanation is
better than others guessing it from the code.]
Platforms tested:
at eirene and arabica.
[machines you have tested the changed version. This is absolute
important. Test it out on at least two or three different platforms
such as Big-endian-32bit (SUN/IRIX), little-endian-32(LINUX) and
64-bit (IRIX64/UNICOS/DEC-ALPHA) would be good.]
Libtool bug
Description:
The AR macro wasn't being propagated to the libtool file
correctly. When libtool was being generated, it wasn't
recoginizing the AR that was set in the configure script.
Solution:
export the AR macro after it's set.
Platforms tested:
Linux
I introduced a small bug when trying to fix the zlib stuff.
Description:
-lz wouldn't be specified with the compile flags if it was found
while checking for the HDF4 library.
Solution:
Removed my bad check and replaced with a better one.
Platforms:
Linux, Solaris
Added new option --with-Stream-VFD.
Description:
The configure option --with-Stream-VFD[={yes}|{no}] is used
to configure HDF5 to build the Stream Virtual File Driver.
The default is not to build it.
Platforms:
all platforms
Cleaned up the configure file a bit.
Description:
There were a few small bugs having to do with checking if strings
were empty. Also needed to force paths to be absolute instead of
relative.
Solution:
I standardized string checking (test -z for an empty string and
test -n for a non-empty string). Also, if the user specifies a
relative path for any of the options, the configure now makes it
into an absolute path for both CPPFLAGS and LDFLAGS macros.
Platforms:
Solaris, Linux
macro didn't work on all systems. This fixes it.
This also introduces the ability to configure for fortran and c++. This
is not to be implemented yet, though!
command form (e.g., cc, gcc) and put that in the libhdf5.settings
file. This would help show exactly which compiler was used during
the configure stage. It may not be 100% "correct" in some cases
such as "configure done in one machine but compiling done in another."
Makefile.in:
acconfig.h:
src/H5F.c:
src/H5FDdpss.c:
src/H5FDdpss.h:
src/H5config.h.in:
test/dpss_read.c:
test/dpss_write.c:
Changed the name DPSS to GRIDSTORAGE since that is the real name
of the API from ANL. DPSS is just one of the protocols it can use.
Changed a bug in the --with-ssl option.
Makefile.in:
Removed the copying of Makefile.dist since it caused problems
when doing a make distclean in a --srcdir configured directory.
Configuration improvement
Problem:
Arabica has a zlib library that is a dynamic lib in /usr/ncsa/lib.
Binary generated would fail to run with a missig libz.so complain
if /usr/ncsa/lib is not in $LD_LIBRARY_PATH. This exposed the
problem that if the binary is linked with -L$mylibpath -lxyz
where libxyz is a dynamic type, the binary can't run if $mylibpath
is not in $LD_LIBRARY_PATH (or equivalent) or as part of the
system default library paths (e.g., /usr/lib, /usr/local/lib).
This problem also caused failures during configure (when trying
to see what format to print long long) and during H5detect.
The base cause is because libtool does not "transfer" the
knowledge of -L$mylibpath to the wrapper file its mode=link
generates.
Solution:
bin/ltmain.sh:
Changed it so that it transfers the libpaths from -Llibpaths
to the wrapper generated. I used the already defined variable
finalize_shlibpath. Not sure it is correct to use it this way.
Need to check on this.
configure.in:
Put in a patch to transfer information from LDFLAGS to LD_LIBRARY_PATH
right before the AC_TRY_RUN. The above fix for ltmain.sh does not
work here because libtool is generated later than this point.
There should be a cleaner way to do this.
Removed the hardcode of NCSA_LT_LINK_EXE because it is no longer
needed.
commence.in:
Removed the hardcode of NCSA_LT_LINK_EXE because it is no longer
needed.
Makefile.in:
Another patch of LDFLAGS to LD_LIBRARY_PATH because I could not
make it to generate H5detect in the wrapper form of libtool.
Need to make it to use the libtool correctly. Later.
Platform tested:
arabica (solaris 2.7)
baldric (solaris 2.6)
** configure.in
** configure [REGENERATED]
** src/H5private.h
** src/H5public.h
** src/Makefile.in
Generates an H5pubconf.h file which is just like H5config.h except all
the preprocessor symbols have `H5_' prepended. This was done so that
the configuration results can be used in public header files without
polluting the namespace.
** src/H5.c
Added H5I_REFERENCE and H5I_VFL to the API tracing code so their names
are printed instead of just numbers.
** src/H5FDstdio.c
** tools/h5import.c
** tools/h5repart.c
** tools/pdb2hdf.c
Changed to use the `H5_' versions of configure results since these
files include only the public API.
** test/big.c
Removed a compiler warning.
** test/h5test.c
Removed unused code.
** config/depend1.in
We don't regenerate the Dependencies files if we're compiling in the
source tree because `gcc -MM' doesn't output enough information to
make the result usable when compiling outside the source tree.
** src/H5config.h.in
Regenerated to include HAVE_LIBMPI and HAVE_LIBMPIO because of recent
changes to configure.in
New feature
configure.in:
When just --enable-parallel is used, will try to test if MPI and MPI-IO
library codes are linkable. If not, try -lmpi and -lmpio as the most
commonly used library names for them.
Also, set default value for RUNPARALLEL if not set.
Now, for systems, like SGI Crays where there are the system supported
MPI libraries, "./configure --enable-parallel" would configure
correctly.
Configure:
Derived from configure.in via autoconf.
Platform tested:
SGI O2K.
----------------------
./MANIFEST
./configure.in
./configure [REGENERATED]
Added more checking for `make' features.
./Makefile.in
./doc/Makefile.in
./doc/html/Makefile.in
./doc/html/Tutor/Makefile.in
./examples/Makefile.in
./pablo/Makefile.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
./config/commence.in
./config/conclude.in
./config/depend.in [REMOVED]
./config/depend1.in [NEW]
./config/depend2.in [NEW]
./config/depend3.in [NEW]
./config/depend4.in [NEW]
./config/dependN.in [NEW]
The directory search stuff was moved into commence.in, thereby
shortening the Makefile.in prologues.
./doc/html/Dependencies [NEW]
./doc/html/Tutor/Dependencies [NEW]
./examples/Dependencies [NEW]
./src/Dependencies [NEW]
./test/Dependencies [NEW]
./testpar/Dependencies [NEW]
./tools/Dependencies [NEW]
The `.distdep' files were all renamed to `Dependencies' to make them
more obvious. They are required (but may be empty) in every directory
that has a Makefile.in that ends with @CONCLUDE@ (you'll get an
obvious error from make if you forgot to create one).
./bin/trace
./src/H5.c
Added H5E_major_t and H5E_minor_t although tracing only prints the
integer value.
./src/H5E.c
./src/H5Epublic.h
Added tracing information.
./src/H5FDcore.c
./src/H5FDfamily.c
./src/H5FDgass.c
./src/H5FDmpio.c
./src/H5FDsec2.c
./src/H5FDstdio.c
Fixed places where FUNC_LEAVE() evaluated it's argument more than
once.
Added tracing information.
Wrapped long lines.
./config/gnu-flags
Fixed a syntax error when we don't have a gnu compiler.
Updated.
configure.in:
Removed the test for -lxnet in the GASS-driver part. There is
no need for it and it does not exist in other machines like IRIX64.
configure:
Deriverd from configure.in.
----------------------
./configure.in
./src/H5config.h.in [REGENERATED]
The /usr/ncsa/{include,lib} directories are only added if they
actually exist. This fixes a warning on some systems.
Checks for the <pdb.h> header file and also for either the PDB or Silo
library, and if found prepares to compile the pdb2hdf program.
./config/distdep
Relative path names for include files are changed to base names since
the makefile contains the logic for searching and since it's likely
that building the .distdep files happed from a location other than
where they would be used in the file system.
./config/conclude.in
Fixed shell errors when `for' loops iterate over nothing for the
`uninstall' target.
./src/H5D.c
./src/H5Oefl.c
File names for the external files are added to the heap when the
dataset is created instead of when the object header is written. This
fixes a rare infinite recursion bug.
./src/H5FD.c
./src/H5FDpublic.h
Optimization to the free list causes H5FD_alloc() usage to go from >10
seconds to <0.4 second for one example (converting a 30MB equation of
state file from PDB to HDF5 format). The optimization is to simply
keep track of the largest item in the free list and not search the
free list when the largest item is not big enough to satisfy the
request.
./src/H5FDcore.c
./src/H5FDcore.h
./test/h5test.c
If the `backing_store' property is true then a flush causes the entire
contents of memory to be written to the specified file. This is in
preparation for the ASCI/red optimizations and is currently tested by
the pdb2hdf `--cached' switch.
./src/H5Odtypes.c
Wrapped three long lines.
./tools/Makefile.in
./tools/pdb2hdf.c [NEW]
A PDB-to-HDF5 translator. It only translates meta data -- the
resulting HDF5 points into the PDB file for the raw data.
Added the GASS macro definition entry.
configure:
[Generated from configure.in]
configure.in:
Added Globus GASS driver configuation as --with-gass=INC,LIB option.
Default is no => no GASS configured.
src/H5config.h.in:
[Generated from acconfig.h]
Added the checking for zlib and jpeg libraries when doing the -with-hdf4
option. HDF4 applications in general needs lib mfhdf, df, z, and jpeg.
Removed the earlier alone test for jpeg. It conflicted with the hdf4
tests. Also, moved the hdf5-own library test for zlib after the hdf4
tests so that when hdf4 is used, the results would cover the zlib
test.
configure:
derived from configure.in by autoconf.
Platforms tested:
IRIX 6.5, IRIX64 6.5, Solaris 2.6 (with default gcc, tested h5toh4
tool).
Comments:
This still generates compile commands that listed the "-lmfhdf ..."
library list before the -L/usr/ncsa/lib. I traced the problem to
the libtool. (I stopped at the door and dared not to enter this
libtool cave. :-) Most compilers, except solaris' cc, tolerate
the "duplicated" library list.
Changes since 19990618
----------------------
./configure.in
./configure [REGENERATED]
Now that compound struct conversions don't make so many calls
to convert their members I turned the H5T debugging back on by
default (it will still be disabled in a production version).
./src/H5AC.c
./src/H5B.c
Made it possible to turn off messages about debugging these
two packages using the same method as for all other
packages. Just supply an invalid file descriptor number or use
the shell to redirect said descriptor to /dev/null like this:
$ HDF5_DEBUG=99,ac,b 99>/dev/null a.out
./src/H5T.c
Changed the name of the old compound conversion function from
`struct' to `struct(no-opt)' to be more consistent with the
new version named `struct(opt)'.
Fixed a bug in H5T_cmp() that caused any two VL types to
compare as being equal.
Removed duplicate code for bitfield comparisons in H5T_cmp().
./src/H5Tconv.c
Relaxed some constraints in the new compound conversion
function so it applies to more cases. Also eliminated a
memcpy in a tight loop.
./test/cmpd_dset.c
Added a `--noopt' command line switch which unregisters the
optimized compound conversion so we can test the non-optimized
version.
Changes since 19990616
----------------------
./src/H5T.c
./src/H5Tconv.c
All conversion functions take an extra argument called
`stride' which is the number of bytes to advance the source
and destination pointers after each element is converted. If
the value is zero then the old behavior is preserved (source
and destination values are packed). This feature was necessary
to implement the compound datatype conversion optimizations
and it causes a minor change to the API (application-defined
type conversion functions take an extra size_t stride
argument).
./src/H5Tconv.c
An additional compound data type conversion function was added
which is applied unless the destination type is larger than
the source type. I'm measuring significant performance
increases for certain operations:
Test Name Struct-Conv Noop-Conv
New(Old) MB/s New(Old) MB/s
---------- ------------- -------------
Reordering 2.062(0.3936) 54087(0.9047)
Subsetting 2.901(0.6581) 40192(1.1100)
Shrinking 1.976(0.3925) 33628(1.1500)
---------- ------------- -------------
./test/dtypes.c
Added various compound datatype conversion tests.
Fixed return values from functions.
./src/H5T.c
Conversion timers are updated only if H5T debugging is turned
on a runtime (in addition to compile time). This allows the
data type layer to be compiled with debugging support without
having to pay a big runtime penalty if the debugging isn't
actually used.
./src/H5A.c
./src/H5D.c
./src/H5Ofill.c
./src/H5P.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5Tpublic.h
Added the stride argument to the H5T_convert() calls. The
stride is always zero, which means that the source and
destination data values are packed.
./configure.in
./configure [REGENERATED]
If API tracing is turned off then libhdf5.settings will say
`no' instead of nothing.
./test/flush1.c
./test/flush2.c
Added better error messages in a couple places.
----------------------
./configure.in
./configure [REGENERATED]
./src/H5T.c
./src/H5Tpkg.h
./src/H5Tpublic.h
./src/H5config.h.in [REGENERATED]
./src/H5detect.c
./src/H5private.h
Added checks for the C9x integer types like int32_t,
int_least32_t, and int_fast32_t and the unsigned
versions. HDF5 defines H5T_NATIVE_* versions (all caps) to be
the same as the type provided by the C library, otherwise it
defines them as integers exactly the specified size. Hardware
type conversion functions are used when the types
match some C-language type (like `int').
----------------------
./configure.in
./configure [REGENERATED]
./src/libhdf5.settings.in [NEW]
./config/conclude.in
./INSTALL
./MANIFEST
A file called `libhdf5.settings' is installed along with the
libraries and it contains a list of various things that might
be of interest to someone using the library (such as what
compiler/options were used and what other libraries might need
to be linked to satisfy external references). We can add more
things as it becomes necessary. Here's a sample...
SUMMARY OF THE HDF5 CONFIGURATION
=================================
HDF5 Version: hdf5-1.1.106
Configured on: Tue Jun 8 11:38:52 EDT 1999
Configured by: matzke@llnl.gov at Spizella Software
Configure mode: development
Host system: i686-pc-linux-gnulibc1
Byte sex: little-endian
Libraries: static, shared
Parallel support: mpicc
Installation point: /usr/local
Compiler: mpicc (egcs-2.91.66)
Compiler switches: -Wall -g
Extra libraries: -lmfhdf -ldf -lz -ljpeg -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages: d,e,f,g,hg,i,mm,o,p,s,v,z
API Tracing: yes
File addresses: large
----------------------
Remove changes from CVS
./bin/release
Added a `--nocheck' switch which causes the script to not
check the contents of the MANIFEST file against CVS. This is
sometimes useful when you need to make a quick snapshot but
the MANIFEST file is not quite up to date.
./src/H5D.c
Removed warnings for unused variables
./src/H5Fprivate.h
Removed the WIN32 definition for `uint' and changed the data
type for `eof_written' from `uint' to `uintn'. Shouldn't this
really be `hbool_t'?
./src/H5Odtype.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tpublic.h
./test/dtypes.c
./doc/html/H5.format.html
Added support for bitfields and opaque data types.
----------------------
./tools/h5ls.c
Added a `--address' (`-a') switch which causes h5ls to display
file addresses for raw data. For contiguous datasets it's just
a nice simple number, but for chunked datasets it's a list of
logical dataset coordinates, file addresses, filter masks, and
storage sizes.
Changed `--dump' switch to `--data'.
./src/H5D.c
./src/H5F.c
./src/H5Fprivate.h
Enhanced the indexed-storage B-tree iterator so it can dump
raw data addresses (and other info) to the standard error
stream.
Added H5Ddebug() so h5ls has a way to dump addresses for
datasets. I'm not sure what else this API function should do,
so I think we should discuss it before we document it. So far,
h5ls is the only thing that uses it, and we can easily change
that.
./src/H5Tconv.c
./test/dtypes.c
Finally had a chance to verify Paul's H5T_conv_s_s (general
string to string conversions) bug fixes and incorporate them
into H5T_conv_f_f (general floating-point to floating-point
conversions) and H5T_conv_i_i (general integer to integer
conversons). Thanks Paul.
./src/H5D.c
./src/H5S.c
./src/H5Sprivate.h
Added performance timers around data space read and write
callbacks. They were already there for the gather/scatter
callbacks.
The timings for read/write callbacks are displayed along with
gather/scatter when data space debugging is turned on.
./bin/iostats
Updated to print totals. Added a `--fast' option that doesn't
do any output except the totals and is much faster.
./bin/trace
Changed __unused__ to UNUSED to match source code.
./config/gnu-flags
Updated error message for pgcc. I've sent bug reports to the
pgcc people but the new version still has the same bug.
./configure.in
./config/conclude.in
./config/depend.in
Fixed dependencies for non-GNU makes when run in a directory
other than the hdf5 source tree.
Updated GNU `make dep' rules to copy the distributed
dependencies for non-GNU makes into the source tree when run
in some other directory.
----------------------
./tools/h5tools.c
./tools/h5tools.h
Finally fixed a long-standing bug that caused core dumps if
a compound datum rendered to more than some number of
characters (we kept bumping up the limit at the risk of
violating stack size limits on some machines). The fix works
only on systems that have the vsnprintf() function (otherwise
a 4kB limit is imposed, which if violated probably dumps
core). If vsnprintf() is present then the library dynamically
allocates space for the output string.
Also made it possible to control how compound data is rendered
across multiple lines of output by allowing the caller to
specify where optional line-breaks get inserted. The output
functions split up the value at one or more optional
line-breaks to prevent it from wrapping around the screen.
If a datum doesn't fit on the current line but would fit on
the next line then it is printed on the next line regardless
of whether optional line-breaks would have prevent wrapping
around the screen. This makes it easier to find the beginnings
of compound data values. This feature is disabled by default
but can be enabled by the application.
If a datum doesn't fit on the current line and the previous
datum also occupied more than one line then we move to the
next line before printing. This makes it easier to find the
beginnings of compound data values but prevents the output
from looking fragmented if there are only a few long values
among mostly short values. This feature is disabled by
default but can be enabled by the application.
The application can control the printf() formats used for all
the native data types. The defaults are what the library used
to use: %g, %ld, %lu, %d, and %u
./tools/h5ls.c
Compound datatype values can now be split across multiple
lines of output instead of just wrapping. Also, when lots of
compound values are too long they all start at the beginning
of a line. This only required about 10 lines of changes in the
setup for tools library calls (I didn't modify the h5dump
program because it uses its own version of the tools library
that forked off long ago).
Added code for Win32 which is unable to cast `unsigned long
long' to `double'. If the dataset size exceeds (2^63)-1 then
the percent utilization is not displayed (this is easily
possible with chunked datasets). This is untested yet.
./configure.in
./src/H5config.h.in
./src/H5.c
./src/H5private.h
Check for vsnprintf() and provide a simple, stupid definition
if it isn't available. The stupid definition just calls
vsprintf() and ignores the second argument. This can result in
buffer overflows in h5ls and h5dump since vsprintf() is an
unsafe function (and anyone can create an hdf5 file that runs
an arbitrary command from h5ls and h5dump in that case)!
./config/conclude.in
Remove more *.o files for `make clean'
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
./src/H5TB.c
Cleaned up a memory leak during H5_term_library() by allowing
H5I_clear_group() to skip items that couldn't be freed. This
allows the item to remain in the group until we can free it
later.
./src/H5F.c
The H5F_close_all() function fails if a file cannot be closed.
./configure [REGENERATED]
./src/H5D.c
./src/H5O.c
Removed H5AC, H5B, and H5T from the default list of packages
to debug (because they're pretty expensive debugging), and
added H5O. Also fixed a bug for undefined variable in H5D when
H5S debugging is turned on but H5T debugging is turned off.
./config/conclude.in
Fixed installation of header files for building in a directory
other than the source directory. This fixes a bug where
H5config.h wasn't being installed.
./src/H5.c
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
./src/H5TB.c
./src/H5Tprivate.h
./src/H5Z.c
./src/H5detect.c
./src/H5private.h
Changed the way the library shuts down again. Now it handles
cycles between packages and isn't so sensitive to dependencies
between packages. A package might shut down only to be
restarted to process a request from some other package being
shut down. Loops are detected after 100 iteractions and the
shutdown is aborted with a message on standard error. This
also makes it a lot easier to debug.
./src/H5A.c
Fixed H5A_write() and H5A_read() so they pass a non-null
background buffer to the conversion functions. This is
necessary when an attribute has a compound data type.
./src/H5Flow.c
./src/H5Fprivate.h
./src/H5Fsec2.c
Reindented new Win32 stuff.
./src/H5Odtype.c
Fixed a bug when enumeration types are used in a compound data
type. The byte pointer wasn't incremented after the type
information was written.
./tools/h5ls.c
Compound data types display their total size because it's not
always obvious from looking at the members.
Scalar attributes show their space as `scalar' instead of
`{}'.
The index value is not printed for attributes that have only a
few values. Instead the word `Data:' is printed on the first
line of attribute data.
Named types display their data type only if verbose output was
requested.
----------------------
./configure.in
./configure [REGENERATED]
./config/commence.in
A few tweaks to the makefile rules for rebuilding makefiles.
./src/H5detect.c
Fixed a really stupid mistake: resetting the signal handler
after a longjmp(). This should fix Bob's SIGBUS on Solaris.
----------------------
./Makefile.in
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./config/commence.in
./config/conclude.in
./config/dec-osf4.x
./config/depend.in
./config/freebsd
./config/linux-gnu
./config/linux-gnulibc1
./config/linux-gnulibc2
./config/solaris2.x
./examples/Makefile.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
./tools/testh5dump.sh
Changes that allow hdf5 to be configured and compiled in a
directory other than the source directory. This is especially
useful if you want to concurrently compile with different
compilers and/or compile flags, or if the hdf5 source is on
read-only media like a CDROM. The changes were surprisingly
easy ;-) Here's what you can do now...
$ mkdir /tmp/build1 # or something
$ cd /tmp/build1
$ /cdrom/hdf5/configure # where ever the source is
$ make
Paul, you'll have to change the testh5toh4 script similar to
the way I changed testh5dump.sh. I started working on it but
then gave up because of a number of problems: (1) I had to
comment out all the tests that let h5toh4 choose the output
file name because it always tried to put the output file in
the same directory as the input file, (2) if path names are
used during the h4 dump then they interfere with the
diff. The test works fine when run in the source directory,
but try this instead:
$ gunzip <hdf5-1.1.67.tar.gz |tar xf -
$ chmod -R ugo-w hdf5-1.1.67
$ mkdir build
$ cd build
$ ../hdf5-1.1.67/configure
$ make check
Dan, I didn't modify the pablo/Makefile.in because I have no
way to test it. I think all you need to do is add a couple
lines before the @COMMENCE@ line and add a couple search
directories for header files. Anyway, it seems like almost an
exact duplicate of the src/Makefile.in, so it shouldn't be a
problem...
./Makefile.in
Removes a few more temporary files during make clean and
distclean.
./configure.in
I fixed the creation of the time-stamp files so that the
initial make doesn't have to regenerated all the makefiles
(only GNU make users will see any change).
./src/H5R.c
Changed a return type from `intn' to `int' for an API
function.
./src/H5detect.c
Added the volatile qualifier to a couple more variables.
./tools/h5tools.c
Fixed a compiler warning about an unused local.
./tools/h5toh4.c
Initialized `optind' to 1 because it's zero on my system. It
should always be one on a unix system.
./tools/testh5toh4
Redirected "broken pipe" messages to /dev/null so outut is
formatted correctly.
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5private.h
Temporarily commented out the code that tries to link a simple
MPI-IO application because I'm not sure how to pass $LDFLAGS
and $LIBS to the compiler.
Removed the `--enable-parallel=ibm' switch because the library
we link with is either -lmpcc or -lmpcc_r but not both. The
only way to tell is to see what compiler was specified (mpcc
or mpcc_r) but if that compiler is specified then we don't
need any libraries (the compiler script supplies them). That
leaves just two choices: the user must use a compiler script:
CC=mpcc ./configure
or the user must state which library is desired:
LDFLAGS='-lmpcc' ./configure --enable-parallel
Checks for <setjmp.h>, longjmp(), and signal(). We don't check
for setjmp() because it could be a macro (in fact, Posix
requires it to be a macro) and if longjmp() is present then
setjmp() is probably present too ;-)
./src/H5detect.c
The alignment detection loop uses SIGBUS and setjmp/longjmp
instead of fork/wait in order to get around bugs with forking
in conjunction with mpich. This hasn't been tested on the
SP-2 yet but it does work on the DEC Alpha.
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
Changed the order that libraries are linked so -lhdf5 is
always before $LDFLAGS.
----------------------
./config/*-aix4.* [REMOVED]
./config/*-aix4.x [NEW]
./config/solaris2.5 [REMOVED]
./config/solaris2.x [NEW]
./configure.in
./configure [REGENERATED]
./MANIFEST
Changed the names of the IBM-SP2 config files by replacing the
minor version numbers with an `x'. The solaris config warns
about old versions of gcc.
The RUNSERIAL value is set to the empty string by default. The
config/* file (or user) can override it by setting it to some
other value.
The `--enable-parallel' with no flags turns on the
HAVE_PARALLEL constant in the source code but doesn't add any
MPI or MPI-IO libraries to the link line.
If we are compiling for parallel then configure checks that we
can actually link a very simple program. This has the benefit
of detecting config errors before we waste time compiling the
entire library.
Configure recognizes `mpcc_r' as a parallel compiler.
./src/H5A.c
./src/H5Apublic.c
Fixed some compiler warnings. Changed the return type of
H5Aget_name() from hssize_t to ssize_t because the name can
never be larger then memory.
----------------------
./configure.in
./configure [REGENERATED]
The path for a command is calculated explicitly the hard way
because `type -path' isn't portable.
./config/freebsd
./config/linux-gnu
./config/linux-gnulibc2
Changed the way files reference each other.
./config/gnu-flags [NEW]
./config/dec-flags [NEW]
These files figure out what flags to pass to certain compilers
so we can reuse code in more than one config/* file. They
also have better warning messages when old compilers are used.
./config/linux-gnulibc1
./config/dec-osf4.x
These files use the new *-flags files.
./src/H5D.c
./src/H5Onull.c
./src/H5Tconv.c
./tools/h5ls.c
Fixed a compiler warning.
./src/H5detect.c
Added a better comment to the top of the generated file.
----------------------
./INSTALL
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Improvements for parallel library. If you have a properly
working mpicc you should be able to just say:
$ CC=mpicc ./configure
and you will see
checking for mpirun... /usr/local/mpi/bin/mpirun
checking for parallel support files... skipped
checking how to run on one processor...
/usr/local/mpi/bin/mpirun -np 1
checking how to run in parallel...
/usr/local/mpi/bin/mpirun -np $$NPROCS
To quote from the INSTALL file....
*** Parallel vs. serial library
The HDF5 library can be configured to use MPI and MPI-IO for
parallelizm on a distributed multi-processor system. The easy
way to do this is to have a properly installed parallel
compiler (e.g., MPICH's mpicc or IBM's mpcc) and supply that
executable as the value of the CC environment variable:
[NOTE: mpcc is not tested yet]
$ CC=mpcc ./configure
$ CC=/usr/local/mpi/bin/mpicc ./configure
If no such wrapper script is available then you must specify
your normal C compiler along with the distribution of
MPI/MPI-IO which is to be used (values other than `mpich' will
be added at a later date):
$ ./configure --enable-parallel=mpich
If the MPI/MPI-IO include files and/or libraries cannot be
found by the compiler then their directories must be given as
arguments to CPPFLAGS and/or LDFLAGS:
$ CPPFLAGS=-I/usr/local/mpi/include \
LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \
./configure --enable-parallel=mpich
If a parallel library is being built then configure attempts
to determine how to run a parallel application on one
processor and on many processors. If the compiler is mpicc
and the user hasn't specified values for RUNSERIAL and
RUNPARALLEL then configure chooses `mpirun' from the same
directory as `mpicc':
RUNSERIAL: /usr/local/mpi/bin/mpirun -np 1
RUNPARALLEL: /usr/local/mpi/bin/mpirun -np $${NPROCS:=2}
The `$${NPROCS:=2}' will be substituted with the value of the
NPROCS environment variable at the time `make check' is run
(or the value 2).
./testpar/Makefile.in
Saying `make check' (or `make test') will run the tests on two
processors by default. If you define NPROCS then that many
processors are used instead:
$ NPROCS=4 make check
./configure.in
Fixed (hopefully) bugs with detecting whether __attribute__
and __FUNCTION__ are special keywords for the compiler.
./Makefile.in
Saying `make install' from the top level directory shows
instructions for using shared libraries.
./config/commence.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
Moved the @top_srcdir@ into the makefiles because it was
expanded too early and had the wrong value.
./INSTALL
Added a warning that if the wrong version of hdf4 tools are
installed then `make check' will fail in the tools directory.
----------------------
./INSTALL
Reorganized and added some additional examples.
./MANIFEST
./aclocal.m4 [NEW]
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./bin/ltconfig [NEW]
./bin/ltmain.sh [NEW]
Added tests to determine how to compile shared libraries and
how to link programs with them before the libraries are
installed. Also how to install and uninstall shared
libraries. The configure step also prints the names of the
config files it's trying to load for easier debugging.
./bin/config.guess
./bin/config.sub
Replaced with a newer version from GNU. The changes we made
to that file to report `irix6.x' and `FreeBSD' without version
numbers have been incorporated into configure.in instead. In
the future, do not change these two files (see the top of
configure.in instead). By the way, this update was required to
get shared libraries working.
./config/linux [REMOVED]
./config/linux-gnulibc1 [NEW]
./config/linux-gnu [NEW]
./config/alpha-dec [REMOVED]
./config/alpha-dec-osf4.0 [REMOVED]
./config/dec-osf4.x [NEW]
./config/irix5.3 [REMOVED]
./config/irix5.x [NEW]
./config/irix64 [REMOVED]
./config/freebsd
Moved config files around to agree with output from the new
config.guess. The linux file was split into gnu (RedHat),
gnulibc1, and gnulibc2 versions. The alpha-dec file was
removed (I think it was unused) and the alpha-dec-osf4.0 was
changed to dec-osf4.x. The irix5.3 file renamed to irix5.x and
the irix64 file was renamed to irix6.x. The freebsd file was
changed to point to linux-gnulibc1. These changes were tested
on:
Linux 2.0
Linux 2.1
FreeBSD 3.2
Irix 5.3
Irix64 6.2
Irix64 6.4
HP/UX 10.20
OSF1 4.0
./config/alphaev56-dec-osf4.x
./config/irix64
Added warnings similar to linux/freebsd about using compilers
with known bugs.
./config/commence.in
./config/conclude.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
Added definitions for shared libraries. This has been tested
on the following systems:
Linux 2.0
Linux 2.1
FreeBSD 3.2
Irix 5.3
Irix64 6.2
Irix64 6.4
HP/UX 10.20 static only
OSF1 4.0
If you want to disable use of shared libraries (you probably
do for development purposes since it takes a lot longer to
compile and because you have to run dynamically linked
programs in a special way if the library hasn't been
installed) then add `--disable-shared' to the configure
command line. This is all documented in the INSTALL file.
./bin/release
Temprarily commented out the MANIFEST checking when running
under svf since svf is about to be replaced by a newer
version. This change only affects error checking during the
release process.
./Makefile.dist
./Makefile.in
Added `make check' which does the same thing as `make _test'
since the former is endorsed by the GNU coding style and
people are used to it. The old `make _test' still works too
(and so does `make test' if you use GNU make).
----------------------
./INSTALL
Added instructions for using other compilers on Irix platforms.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5private.h
The presence of <sys/sysinfo.h> and <sys/proc.h> is only
checked on DEC/Alpha because there are too many problems
including these headers on other systems.
./config/irix6.x
./config/irix64
Removed `-ansi' and added a comment. Converting an ASCII UTC date
and time to a time_t value is not defined by ANSI or Posix but
is available if we don't use `-ansi'. This allows the dataset
modification time messages to be read properly by
H5Gget_objinfo().
./src/H5Tconv.c
Fixed a compiler warning.
./test/dtypes.c
./test/hyperslab.c
./test/istore.c
Fixed compiler warnings in printf() statements.
----------------------
./INSTALL
Added warnings and a disclaimer about GNU, DEC, Irix64, and NT
compilers that generate incorrect machine code.
./configure.in
./src/H5private.h
Detects and includes <sys/param.h> which is needed on FreeBSD
before <sys/proc.h> even though we only really using anything
from <sys/proc.h> on the DEC Alpha.
./config/irix64
Turned off warnings for duplicate definitions from the linker
because -lnsl on irix has the same stuff in it as -lc.
./config/irix6.x
Split up the CC and CFLAGS settings like with irix64 so that
compilers besides `-n32' can be used.
./bin/snapshot
The snapshots are tagged with names like hdf5-1_1_52 which is
similar to the way the releases are tagged (cvs doesn't allow
dots in tags).
./test/dtypes.c
./src/H5private.h
./src/H5Tconv.c
Fixed some alignment violations on the DEC when using high
optimization levels. The DEC incorrectly optimizes certain
memcpy() and memmove() calls when the source argument is not
word aligned if the call looks like it's copying an atomic
data type.
./test/hyperslab
Worked around code generation bugs in the Irix64 Mongoose 7.00
compiler by casting some `unsigned long' values to `unsigned'
in an expression.
./src/H5Ocomp.c
Fixed a place where %d was used to print a size_t.
----------------------
./configure.in
./acconfig.h
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5public.h
./src/H5Omtime.c
Check for <stddef.h>
Checks for `__tm_gmtoff' in `struct tm' because old versions
of GNU libc are different than recent versions. This fixes the
failing mtime test.
./bin/config.guess
./config/freebsd2.2.7 [REMOVED]
./config/freebsd [ADDED]
Changed the name so it works with all versions of FreeBSD.
./src/H5.c
Moved H5F after H5T and H5G in H5_term_library() to satisfy
dependencies.
./src/H5G.c
Fixed a bug that caused H5Gcreate() to fail if the group name
had trailing slashes.
./src/H5Gpublic.h
Changed `group_name' to `name' in a prototype.
./src/Makefile.in
Dynamic library on Linux, but needs for work to be generally
useful.
./src/H5HG.c
./src/H5HGprivate.h
Fixed alignment problems when using old GCC compilers (like
the one shipped with RedHad Linux).
./tools/h5ls.c
Fixed a bug where the contents of the root group could be
listed twice if there was a link back to the root
group. Similarly for groups that are mentioned on the command
line.
Fixed a bug where unknown types were printed with a random
type class number.
./src/H5T.c
./src/H5Tconv.c
./src/H5Tprivate.h
Fixed O(log N) conversion bugs.
----------------------
./MANIFEST
Removed some ddl files from tools/testfiles that are no longer
part of CVS. Added new enum.c test.
./configure [REGENERATED]
./configure.in
Changed printf long long format detection to favor `L' over
`ll'.
----------------------
./MANIFEST
Added tcompound2.{dmp,h5} and tdset2.{dmp,h5} used by the
h5toh4 testing.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Added check for <sys/timeb.h> for Win32.
Determines sizeof(char) just so we have a complete list of
type sizes defined as preprocessor symbols.
./src/H5detect.c
./src/H5T.c
./src/H5Tpkg.h
Detects alignment constraints. In order for this to work the
operating system must not correct unaligned data (for
instance, on the DEC Alpha one might need to say `uac p
sigbus' before running H5detect).
./src/H5private.h
Includes <signal.h> because it's needed by H5detect.c to
detect alignment constraints.
./src/H5Tconv.c
Added extra checks to all hardware conversion functions so
they align data when necessary before the conversion. This
slows down the conversions somewhat but they're still much
faster than the software conversions.
./test/dtypes.c
By setting a constant at the top of the source you can test
conversions where the data is aligned on various byte
boundaries.
By setting a constant at the top of the source you can
simulate architectures that have alignment constraints on
architectures that don't.
Changed typo SIZEOF_LDOUBLE to SIZEOF_LONG_DOUBLE in a few
places.
----------------------
./src/H5Tconv.c
With my poor eyesight I missed the definitions of SCHAR_MIN
and SCHAR_MAX in <limits.h> and used CHAR_MIN and CHAR_MAX
incorrectly. I changed all occurrences of the latter to the
former and the new hardware integer type conversions now work
on Irix.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5private.h
./src/H5.c
./test/h5test.c
Added a wrapper for HDsnprintf() that just calls sprintf() if
snprintf() isn't available.
./MANIFEST
Added Paul's new h5toh4 files.
----------------------
./INSTALL.parallel [NEW]
We're beginning to unify some of the parallel installation
steps. This file will contain general information for
installing the parallel library. It's not complete yet.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Check for xdr_int() in libnsl required on Solaris when linking
with hdf4. It's found on the Irix system I tested which
complains that `-lnsl' didn't resolve any symbols. Oh well.
Fixed the order of searching for libdf and libmfhdf for hdf4
linking.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5Z.c
Check for compress() in libz in order to find older versions
of the library that will still work for hdf4. Added a
separate check for compress2() that hdf5 will use.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5.c
./src/H5private.h
./src/H5A.c
./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5F.c
./src/H5Farray.c
./src/H5Fcore.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fprivate.h
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Ocomp.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Ofill.c
./src/H5Olayout.c
./src/H5Omtime.c
./src/H5Oname.c
./src/H5Oprivate.h
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5R.c
./src/H5RA.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Snone.c
./src/H5Spoint.c
./src/H5Sprivate.h
./src/H5Sselect.c
./src/H5T.c
./src/H5Tbit.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5V.c
./test/bittests.c
./test/gheap.c
./test/hyperslab.c
./test/istore.c
./test/tmeta.c
./test/trefer.c
./test/tselect.c
./tools/h5debug.c
./tools/h5tols.c
Added checks for Posix.1g types like `int8_t'. If not defined
then H5private.h defines them. Changed all `int8' etc. to
`int8_t'.
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5I.c
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
./src/H5TB.c
./src/H5Z.c
Calling H5*_term_interface() resets interface_initialize_g to
FALSE so a subsequent call to H5open() (implied or explicit)
reinitializes global variables properly.
./src/H5private.h
./src/H5Oefl.c
./src/H5S.c
Changed MAX_SIZET, MAX_SSIZET, MAX_HSIZET, and MAX_HSSIZET to
SIZET_MAX, SSIZET_MAX, HSIZET_MAX, and HSSIZE_MAX to they
match the Posix.1 constants in <limits.h>.
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5detect.c
Added 36 more integer hardware conversion functions to the
type conversion table for conversions to/from `long long' and
`unsigned long long'. The `long long' names will be changed
shortly to make them portable to Win32.
Changed H5T_init() to H5T_native_open() and added an
H5T_native_close() to open and close the predefined native
data types.
Increased the initial size of the type conversion table from
64 to 128 entries.
Reordered the 90 new integer conversion functions so the names
that are printed favor `int' over `short' or `long' when two
of them are the same.
./test/dtypes.c
Added hardware and software integer conversion tests for the
56 functions I added recently but not the additional 36
checked in this time. That will come next.
Call H5close() after each test so type conversion statistics
are easier to follow. Try this: $ HDF5_DEBUG=t ./dtypes
Added more debugging output for when things go wrong.
./src/H5private.h
Removed trailing carriage-returns inserted by broken operating
system ;-)
----------------------
./INSTALL
Added instructions about specifying a path for GNU zlib and
HDF4 headers and library.
Added comments for each of the tool names. Added h5toh4 as a
tool name.
./configure.in
./conigure [REGENERATED]
./src/H5config.h.in [REGENERATED]
The config/* scripts get invoked with $CC_BASENAME set the
base name of the compiler in order to make it easier to handle
setting compiler flags for different compilers in a big case
statement. For instance, if $CC has the value
/usr/local/mpi/bin/mpicc -ansi -64
then $CC_BASENAME will be `mpicc'. The $CC_BASENAME is not
set if $CC is not set.
Fixed alignment in `configure --help'.
An include and/or library path can be specified for GNU zlib
if configure can't find it in normal places. The "normal"
means wherever your compiler normally searches, including
search paths you've added through environment variables like
CPPFLAGS and LDFLAGS. The INSTALL file has instructions.
The `-ljpeg' library is detected.
If `ssize_t' is not found then a #define is added to
H5config.h similar to what we already do for `size_t'.
We detect the hdf5 header file `mfhdf.h' and libraries
`-lmfhdf' and `-ldf' and if found define the H5TOH4 and
TESTH5TOH4 Makefile variables. The user can specify an
include and/or library path. The INSTALL file has
instructions.
The `RUNTEST' variable has been split into `RUNSERIAL' and
`RUNPARALLEL' because these are different commands. The
makefile still uses `RUNTEST', which defaults to the RUNSERIAL
value. The new testpar/Makefile.in sets RUNTEST to the
RUNPARALLEL value. The default RUNSERIAL value is empty and
the default RUNPARALLEL value is `mpirun -np 2'. These can
both be overridden in the config/* files. To make the value
the empty string set it like `RUNPARALLEL=none' in the
config/* file.
The new testpar/Makefile is generated from testpar/Makefile.in
./config/commence.in
Added the RUNSERIAL and RUNPARALLEL makefile definitions.
./src/Makefile.in
The `H5detect' program is run with RUNSERIAL, which is empty
on all platforms except intel-osf1 (ASCI/Red)
./config/conclude.in
Removed the `.c.a:' implicit rule -- we don't use it any more.
./config/BlankForm
./config/alpha-dec
./config/alpha-dec-osf4.0
./config/freebsd2.2.7
./config/hpux10.20
./config/hpux9.03
./config/intel-osf1
./config/irix5.3
./config/irix6.2
./config/irix64
./config/linux
./config/powerpc-ibm-aix4.2.1.0
./config/rs6000-ibm-aix4.1.4.0
./config/solaris2.5
All of these files have been updated to hande multiple
compilers. Most of them assume `cc' if CC is not set. The
documentation in `BlankForm' has been updated and
documentation in the other files refer to `BlankForm'.
The intel-osf1 uses LDFLAGS instead of LIBS to specify the extra
library search paths.
./examples/Makefile.in
./test/Makefile.in
./tools/Makefile.in
Simplified by grouping some dependency information together
more succinctly.
The tools Makefile.in has been modified to work with the
`h5toh4' and `testh5toh4' programs. Until Paul checks these
in you may have problems compiling. If so, just create files
h5toh4.c and testh5toh4.c that contain:
#include <stdio.h>
int main(int argc, char *argv[]) {
fprintf(stderr, "%s: not implemented\n", argv[0]);
return 1;
}
./src/H5public.h
Removed definition for `ssize_t' since this is now handled by
configure in H5config.h with a #define.
./MANIFEST
./testpar/Makefile.in [NEW]
Added a makefile for parallel tests. As soon as we get this
working properly we can remove the other four makefiles in
that directory and maintain just one.
----------------------
./configure.in
./acconfig.h
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Added checks for functions, structs, constants, and header
files used in h5ls.c to determine the output width with
various Windows compilers and Unix variants.
Added check for <sys/stat.h> and defined
HAVE_SYS_STAT_H. Included <sys/stat.h> in H5private.h outside
the Posix.1 #include's section.
./src/H5RA.c
Less aggressive about failing -- rather returns false, which
allows type detection to continue.
./src/h5ls.c
Data types are displayed for datasets and named data types when
`-v' or `--verbose' is specified on the command-line. The
algorithm is a little different than the dumper because we're
trying to be human-friendly, not necessarily machine-friendly.
* Any data type which matches a native C type gets printed
something like `native double'.
* A floating point type that matches one of the IEEE standard
types but not one of the native types gets printed like `IEEE
64-bit big-endian float'.
* Other floating point values have information about sign bit
location; exponent size, location, and bias; and significand
size, location, and normalization.
* Padding and offsets are displayed for types that have
padding (precision != size), including internal padding for
some floating point data types.
* Non-native integer types are displayed like `32-bit
little-endian unsigned integer'.
* Compound data types have each member displayed including the
member name, byte offset within the struct, dimensions, index
permutation, and data type.
* String types are displayed like `256-byte null-terminated
ASCII string'.
* References are displayed like `8-byte unknown reference'
until the reference interface stabilizes a little.
* All other types including types not yet defined will be
printed like `4-byte class-9 unknown'.
The dimensionality of scalar datasets is printed like `{SCALAR}'
instead of just `{}'.
If external raw files are used to store a dataset then the offsets,
sizes, and file names of each are printed if `-v' or `--verbose'
was given on the command-line.
If an object is found and h5ls can't determine the object type then
it still tries to print the number of hard links, the OID, and any
comment that might be present if `-v' or `--verbose' was specified.
If the `-d' or `--dump' switch is turned on then ragged arrays will
report that the data can only be dumped by dumping the component
datasets explicitly. I'm not planning to implement this since
we're going to eventually change the whole way ragged arrays are
stored.
Compound data values do not have the component names displayed by
default when `-v' or `--verbose' is turned on. Instead, the names
can be displayed with `-l' or `--label'.
The output width is determined by the first rule that applies:
* If the `-wN', `-w N' or `--width=N' switch appeared on
the command line then use N for the output width.
* Query the OS for the tty width in a highly unportable way
borrowed from GNU `less' depending on what functions and
data structures were found during configuration (if any):
_getvideoconfig(), gettextinfo(), _srcsize(), ioctl(),
GetConsoleScreenBufferInfo(), struct videoconfig, struct
text_info, the TIOCGWINSZ ioctl, the TIOCGETD ioctl.
* If the `COLUMNS' environment variable is set then use
its value.
* Use the value 80.
Just for kicks, run Mark and Jim's test_vbt and then say `h5ls -dlsv
test.vbt'. You can also try it on the various *.h5 files in the
test/example directories.
./config/linux
Removed turning on parallel by default on Robb's macine.
----------------------
./bin/snapshot
Made same fix as for the release script yesterday.
./src/H5D.c
./src/H5Dprivate.h
./src/H5G.c
./src/H5Gprivate.h
./src/H5Gpublic.h
./src/H5O.c
./src/H5Oprivate.h
./src/H5RA.c
./src/H5RAprivate.h
./src/H5T.c
./src/H5Tprivate.h
Improved object type checking. Instead of determining the
object type by trying to open each of the possible types, we
keep a table of associations between object type number (like
H5G_GROUP, H5G_DATASET, H5D_TYPE, and H5D_RAGGED) and an `isa'
function that returns true if the object header has the right
messages to make the object a particular type. This mechanism
also allows specialization of object types by permitting an
object to satisfy more than one `isa' function.
Added `isa' functions for groups, datasets, ragged arrays, and
committed data types.
./src/H5config.h.in
Added HAVE_STAT_ST_BLOCKS. I thought this had already been
added, but apparently not.
./tools/h5ls.c
Removed system include files since they're already included by
H5private.h and since I wasn't including them portably anyway.
By default, 1-byte integer types are printed as integer values
instead of ASCII characters. However, the `-s' or `--string'
command-line switch causes the data to be interpretted as
ASCII. String data types are always printed as character
data.
Ragged arrays are now identified as ragged arrays and h5ls
doesn't descend into the group automatically. This uses the
new object type specialization stuff.
./tools/h5tools.c
./tools/h5tools.h
Added the ability to print 1-byte integer types as either
ASCII or numeric data instead of always ASCII. The default is
to print as numeric data.
----------------------
./MANIFEST
Added new Pablo files HDF5record_RT.h and ProcIDs.h
./acconfig.h
./configure [REGENERATED]
./configure.in
./src/H5.c
./src/H5Vprivate.h
./src/H5config.h.in [REGENERATED]
./src/H5private.h
./src/H5public.h
./test/big.c
Added more configuration stuff for the Win32 environment. Removed all
the #ifdef WIN32 from the source and replaced them with OS-independent
stuff. Specifics follow:
Check for non-Posix.1 `st_blocks' field in `struct stat' which is used
by the big file test to decide if the file system supports holes. If
the st_blocks field isn't present then we just skip the test.
Configure checks for <io.h> <sys/resource.h> <sys/time.h> and
<winsock.h> and defines HAVE_IO_H, HAVE_SYS_RESOURCE_H,
HAVE_SYS_TIME_H and HAVE_WINSOCK_H when they're found.
Configure checks whether both <sys/time.h> and <time.h> can be
included and defines SYS_TIME_WITH_TIME if so. Otherwise include only
<sys/time.h> or <time.h> even if both exist.
Configure checks sizeof(__int64) and defines SIZEOF___INT64 to the
result or to zero if __int64 isn't defined. The source uses `long
long' in preference to `__int64'.
Removed null WIN32 definition for `inline' since such a definition
already exists in H5config.h
Protected gettimeofday() calls in debugging code with
HAVE_GETTIMEOFDAY instead of WIN32.
./src/H5F.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fsec2.c
./src/H5Fstdio.h
./src/H5P.c
./src/H5Tconv.c
./src/H5private.h
Removed #include of system files from library source files and
consolodated them into H5private.h where they're protected by various
configuration macros (most of them were duplicated there already
anyway).
./test/big.c
./test/chunk.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/extend.c
./test/external.c
./test/fillval.c
./test/flush1.c
./test/flush2.c
./test/iopipe.c
./test/links.c
./test/mount.c
./test/mtime.c
./test/overhead.c
./test/ragged.c
./test/shtype.c
./test/unlink.c
Protected system #include's with #ifdef's from H5config.h.
Undefined NDEBUG since some of the tests rely on assert() to check
return values.
Removed WIN32 definitions for __unused__ since this can be controlled
by the definition of HAVE_ATTRIBUTE in H5config.h
./test/testhdf5.h
Removed the CLEAN_CMD definition because we no longer use it.
Albert's cleanup() functions replaced it.
./test/fillval.c
Initialized auto hid_t variables to fix warnings in error recovery
code when data flow analysis is turned on in compilers.
./test/h5tools.c
Initialized an auto variable to fix a compiler warning.
./test/chunk.c
./test/ragged.c
The WIN32 had some unsigned variables changed to signed because the
compiler generates warnings when coercing unsigned to double(?). I
changed them back to unsigned because they really are unsigned
quantities. If this the change was just to shut up extraneous warnings
then perhaps a compiler flag can do the same; otherwise if the
compiler generates bad code then we should supply a patch file instead
messing up source code with bug work-arounds.
./src/H5detect.c
Protected system #include's with #ifdef's from H5config.h thereby
removing a WIN32.
If getpwuid() doesn't exist (HAVE_GETPWUID) then we assume that
`struct passwd' doesn't exist either (we don't really need it in that
case).
The H5T_NATIVE_LLONG and H5T_NATIVE_ULLONG are defined in terms of
`long long' or else `__int64' or else `long' depending on what's
available.
./src/H5Flow.c
./src/H5Ofill.c
Added __unused__ to some function arguments that aren't used when
assertions are turned off.
./src/H5V.c
Changed an auto variable name in some hand-inlined code to get rid of
a warning about the variable shadowing a previous auto.
----------------------
./MANIFEST
./bin/release
./bin/snapshot
The format of the MANIFEST file has been relaxed -- comments
and blank lines should no longer confuse the tools that use
it.
As before, this file should contain a list of *all* files that
are part of HDF5, which means all files which are managed by
CVS/SVF. However, files can be marked so they're not part of
a release by adding _DO_NOT_DISTRIBUTE_ after the file name.
I've removed all the *.obj files from the distribution by
adding _DO_NOT_DISTRIBUTE_ after their names. I also removed
the old white-papers that might not apply to the current
version of the library and documentation about chunking
performance since it's wrong now that chunk caching is
implemented. Everyone please check the files you're
responsible for to make sure that they should really be part
of a release.
To get a list of all files use
grep '^\.' MANIFEST | cut -f1
To get a list of files for distribution use:
grep '^\.' MANIFEST | grep -v _DO_NOT_DISTRIBUTE_
(These commands assume tabs in the MANIFEST file. If the file
might contain spaces then run it through `unexpand' or `tr'
first).
./configure.in
./configure
./test/ragged.c
Check for sigaction().
./test/Makefile.in
The `clean' target removes the timing tests.
----------------------
./bin/release
Added ./Makefile to the distribution again -- it got lost in
the changes last week although it isn't all that important a
file since it gets clobbered by configure anyway.
./bin/trace
./doc/html/Filters.html
./doc/html/H5.format.html
./doc/html/H5.user.html
./src/H5.c
./src/H5D.c
./src/H5Dprivate.h
./src/H5E.c
./src/H5Epublic.h
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fprivate.h
./src/H5O.c
./src/H5Ocomp.c
./src/H5Oprivate.h
./src/H5P.c
./src/H5Ppublic.h
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Spoint.c
./src/H5Sprivate.h
./src/H5Ssimp.c
./src/H5Z.c
./src/H5Zprivate.h
./src/H5Zpublic.h
./src/hdf5.h
./test/dsets.c
./tools/h5ls.c
Added the data filter pipeline, a generalization of the
compression stuff which allows things like checksums,
encryption, compression, performance monitoring, etc. See
./doc/html/Filters.html for details -- it replaces the
Compression.html doc.
./src/H5T.c
Cleaned up debugging output.
./config/linux
Added checks for egcs and pgcc and changed optimization flags
for the compilers.
./src/H5G.c
./tools/h5dump.c
Fixed compiler warnings in these files and others.
./configure.in
./src/H5private.h
./test/mtime.c
Added a check for difftime() and defined HDdifftime() to do
something else on systems that don't have difftime().
----------------------
./MANIFEST
./doc/html/H5.format.html
./src/H5O.c
./src/H5Oprivate.h
./src/H5Omtime.c [NEW]
./src/H5private.h
./src/Makefile.in
Added the modification time message. If an object header has
this message then it's value is updated with the current time
whenever anything changes in the object header.
./acconfig.h
./configure.in
Alas, there seems to be no standard way to convert a string
time like 19980727122800 in UTC to a time_t since mktime()
only converts local times to time_t. So I've modified the
configuration to check for various ways of getting the time
zone information:
* Added checks for the `tm_gmtoff' field of `struct tm'.
* Added a check for the `timezone' global variable.
* Added a check for `struct timezone'.
* Added a check for BSDgettimeofday().
* Added a check for gettimeofday() although it doesn't
actually set the timezone argument on some systems.
* Added a check to see if `tm_zone' is a member of `struct tm'.
* Added a check to see if `tzname' is a global variable.
* Added a check to see if `struct tm' is defined in time.h
or sys/time.h.
It's not difficult to get the right UTC modification message
into the object header, but some systems might have problems
getting the right time back out (Irix64 is one) and those
systems will report zero for the H5G_stat_t.mtime from an
H5Gstat() call as if the mtime message isn't even present. It
will, however, continue to be updated as normal.
./src/H5G.c
./src/H5Gpublic.h
The H5G_stat_t struct now contains an `mtime' field which will
hold the object modification time. If the object has no
object modification time then the `mtime' will be initialized
to zero.
Fixed a bug in H5G_stat() that caused the `objno' field of the
H5G_stat_t to be set incorrectly on some machines.
./src/H5D.c
Writing to external datasets fail if the hdf5 file is not open
for writing.
A modification time message is added to the dataset object
header when it's created and H5O_touch() is called from
H5D_write() to update that message.
./src/H5T.c
Fixed a bug in H5Tget_member_dims() that caused a segmentation
fault if one of the output array arguments was the null
pointer.
Relaxed the member dimension checking in H5Tinsert_array() so
it can also be used for scalar members.
./test/Makefile.in
Added additional file names to the `mostlyclean' target.
./tools/h5dump.c
./tools/h5tools.h
Increased the temporary buffer size to 1MB.
Added support for printing compound data types with array
members.
When printing H5T_NATIVE_CHAR and H5T_NATIVE_UCHAR we escape
double quote characters.
./tools/h5ls.c
Changed the output format a little because we were starting to
get too much info to fit on a line. Without `--verbose' each
object occupies one line of output. Otherwise, additional
information is printed below the object name: object file
address, comment, and modification time. If `--dump' is given
then the data is printed after the other information.
./test/cmpd_dset.c
Changed the way the dataset is initialized to be more uniform.
----------------------
./Makefile.in
./config/commence.in
./config/conclude.in
./config/depend.in
./src/Makefile.in
./test/Makefile.in
Tests are no longer installed for `make install'. Added a new
target `make tests' that builds the tests but doesn't run them.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Added detection of fork() and waitpid(). If present the
contants HAVE_FORK and HAVE_WAITPID will be defined in
H5config.h.
./test/dtypes.c
Minor tweaks for systems that don't have fork() or waitpid().
./MANIFEST
./tools [NEW]
./tools/Makefile.in [NEW]
./tools/h5debug.c [NEW]
./tools/h5import.c [NEW]
./tools/h5ls.c [NEW]
./tools/h5repart.c [NEW]
Added a tools directory and moved tools from the src directory
to here.
----------------------
./MANIFEST
Alphabetized. `d' comes before `e' :-)
./bin/release
Added the `-batch' option which causes the script to not ask
questions and to automatically update the minor version
number and set the patch level back to `a'. This is intended
to be used for the daily snapshots:
#! /bin/sh
set -e
cd ~/hdf5
make distclean
make test
bin/release -batch tar compress gzip bzip2
mv ./releases/* /repository
./src/H5Z.c
Removed warnings about unused variables when the zlib.h header
file is present but libz.a isn't.
./INSTALL
./configure.in
./doc/html/tracing.html
Made API tracing the default (you still need to define the
HDF5_TRACE environment variable to get results) and change the
name from `--disable-tracing' to `--disable-trace' to make it
consistent with the other switches.
Changed `site config file' to `host config file' to match the
documentation.
./doc/html/H5.user.html
Added a reference to the `tracing.html' file.
----------------------
./MANIFEST
./configure.in
./examples/Makefile.in [NEW]
Added a Makefile.in for the examples directory. To generate
the Makefile run configure again.
