----------------------
./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).
----------------------
./src/H5D.c
Fill values are working for contiguous datasets now except
there are two things that need more support from the data
space layer, specifically the ability to form a selection from
the difference of two selections. They are (1) extending an
external contiguous dataset, (2) optimization by delaying the
fill until after the first H5Dwrite().
Renamed H5D_allocate() to H5D_init_storage() since allocation
is only part of the story. Added a data space argument so it
doesn't have to query the space from the object header -- the
space is always available in the caller anyway.
Removed `#ifdef HAVE_PARALLEL' from a few places where it
wasn't necessary. We don't need it around code that doesn't
compile anything from mpi.h or mpio.h.
./src/H5Fistore.c
Uncommented H5F_istore_alloc() for non-parallel and moved the
`#ifdef HAVE_PARALLEL' just around Kim's barrier.
./src/H5Fmpio.c
Wrapped a couple long lines.
Got rid of two signed vs. unsigned comparison warnings.
./MANIFEST
./test/Makefile.in
./test/fillval.c [NEW]
Added tests for fill values. The contiguous dataset extend
test is disabled until H5S_SELECT_DIFF is implemented.
./tools/Makefile.in
Fixed a bug where `make test' didn't build the executables
first. This should cause the snapshots to start up again.
./Makefile.in
Changed to build in `test' directory before `tools'
directory. We want the library tests to pass before we even
start considering the tools. You can still build and/or test
the tools independent of the library tests passing.
----------------------
./Makefile.in
Running `make distclean' will not fail if one of the
subdirectories has already been cleaned.
./config/BlankForm
./config/irix5.3
Cleaned it up more. Added better support/documentation for
systems that have more than one compiler.
./config/alpha-dec-osf4.0 [NEW]
Added a new config file as a result of testing on Jim Reus's
machine.
./test/chunk.c
Scaled down the testing range so we can actually run it
interactively.
./tools/h5import.c
Included <unistd.h> to get rid of warning for close().
./src/H5detect.c
Seg-faults on Linux for some reason when NDEBUG is defined, so
I just undef it at the top of the source.
./test/big.c
Added a fflush().
./tools/h5ls.c
The `-d' flag now works even when `-v' isn't specified.
./examples/h5_chunk_read.c
./examples/h5_compound.c
./examples/h5_extend_write.c
./examples/h5_group.c
./examples/h5_read.c
./examples/h5_write.c
Indented according to hdf5 standards.
Fixed compiler warnings
----------------------
./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.
Documentation (mostly)
Solution:
Parallel HDF5 support on Intel TFLOPS machine using PFS file system
and MPIO.
Platform tested:
Intel TFLOPS (ASCI Red)
----------------------
This checkin completes the compression stuff almost two weeks ahead of
schedule. It should now all be working and documented.
./Makefile.in
./config/commence.in
A distclean causes the distribution makefile to be copied to
Makefile again.
./src/H5D.c
Opening a compressed dataset now works properly.
./src/H5P.c
./src/H5Ppublic.h
The H5Pset_compression() and H5Pget_compression() now work as
documented.
./src/H5T.c
Fixed a bug that causes the library to crash sometimes if
debugging is turned on for the `t' package.
./src/H5Z.c
Fixed a bug where the number of bytes attributed to
compression overruns was too low in the debugging output.
./test/dsets.c
More compression tests: reading of uninitialized data, opening
an existing dataset and reading it, partial I/O which isn't
aligned on chunk boundaries, and use of application-defined
compression methods.
./MANIFEST
Removed ./test/dspace.c.
----------------------
./MANIFEST
./configure.in
./configure
./Makefile.in
./bin/distdep [NEW]
./config/conclude.in
./config/depend.in
./src/.distdep [NEW]
./test/.distdep [NEW]
Added some code so non-GNU systems have a list of dependencies
between the .c files and the .h files. Hopefully this works
and y'all don't have to keep saying `make clean' each time you
change a header.
On systems with GNU make, GCC, and Perl, the dependency
information is generated automatically from rules in
config/depend.in as has always been done. But now extra files
called `.distdep' (for `distributable dependencies) are left
in each directory and these are part of CVS and thus
releases. (A `make dep' will create dependencies on demand
without doing anything else.)
On systems lacking one or more of the tools above, the various
`.distdep' files are inserted into the end of the Makefiles.
If you do developement on one of these systems you'll have to
update the `.distdep' and/or Makefile by hand, or wait until
you have access to a GNU system and do a `make dep'.
New feature
Problem:
"make H5Tinit.c" from toplevel not supported.
Solution:
added in the lines
H5Tinit.c:
(cd src && $(MAKE) $@)
This and other changes already committed allow the sequential HDF5
library to be compiled and tested for the ASCI Red machine in the
following steps:
sasn100: configure -v tflop
janus: make H5Tinit.c #made possible by this check-in
sasn100: make >&! comp.out
janus: make _test >&! test.out
The name: indicates which machine the command line must be run from.
Platform tested:
ASCI Red machine: janus
----------------------
./INSTALL
./Makefile.dist
./Makefile.in
./config/conclude.in
Some stupid make's don't know what PHONY means. I added
changed config to _config in the default makefile and added
_test to the other makefiles.
./src/H5Psim.c
A `file_offset' argument got changed to `int' accidently that
causes tests to fail on 64-bit machines. I changed it back to
size_t.
./src/H5T.c
Changed a couple printf formats.
----------------------
./Makefile.in
./config/commence.in
With GNU make you can now use `-j' and `-l' options and things
get built correctly. I can do a `make -j -l6 test' from a
clean hdf5 source tree (after configure) in 45 seconds (8 to
build dependencies, 26 to compile everything, and 11 to run
the tests).
./src/H5Gnode.c
Removed a comment that no longer applies.
./src/H5P.c
./src/H5Pprivate.h
./src/H5Ppublic.h
Changed H5Pselect_hyperslab() to H5Pset_hyperslab() and added
H5Pget_hyperslab() and H5P_get_hyperslab().
Replaced a couple short memset() calls with a for loop.
Removed `if (foo!=NULL)' from around H5MM_xfree() calls.
Clear hslab_def when the hyperslab disappears.
./src/H5Tpublic.h
Removed trailing enum comma.
----------------------
./Makefile.in
Added more dependencies to .PHONY.
./src/H5D.c
The write side of the I/O pipeline is implemented now too.
Things are looking good for the prototype and it's just a
matter of populating the library with the data type and data
space conversion functions.
./src/H5Farray.c
./src/H5Fprivate.h
./test/istore.c
Changed the order of the arguments for H5F_arr_read() and
H5F_arr_write().
./src/H5P.c
./src/H5Pprivate.h
Changed the names of the arguments of H5P_find(). Fleshed out
the mgath and fscat callback types.
./src/H5Psimp.c
Added stubs for H5P_simp_mgath() and H5P_simp_fscat() that
operate on the entire data space. Quincey, once you have the
data space hyperslab stuff in place let me know and I'll
finish the H5P_simp_*() functions to do partial I/O. Or you
can take a look at it too if you like; there's some comments
in there for you.
./src/H5V.c
./src/H5Vprivate.h
Changed dimensionality arguments from `size_t' to `intn' to be
consistent with the rest of the library and to get rid of
warnings on 64-bit Irix.
----------------------
./config/depend.in
Fixed backslashes in sed script because the H5Gnode.c
dependency info was disappearing. You'll have to rerun
config.status to rebuild the Makefiles unless you use gnu
make.
./config/conclude.in
Also removes emacs backup files, TAGS, and svf backup files.
./config/linux
Grouped gcc flags and added provisions for debugging vs. production.
./html/H5.format.html
Updated messages 0x0008, 0x0009, and 0x000A.
./html/storage.html
Documentation describing storage schemes.
./src/Makefile.in
./test/Makefile.in
New source files.
./src/H5A.c
./src/H5Apublic.h
./src/H5C.c
Changed VOIDP to void* in a couple places.
./src/H5AC.c
./src/H5ACprivate.h
./src/H5B.c
./src/H5Bprivate.h
./src/H5G.c
./src/H5Gnode.c
./src/H5Gprivate.h
./src/H5H.c
./src/H5O.c
Removed `const' from some variables because H5G_node_found() wanted
to modify it's udata argument. Removing const there caused it
to cascade to these other locations.
./src/H5AC.c
./src/H5ACprivate.h
./src/H5B.c
./src/H5Gnode.c
./src/H5Gstab.c
./src/H5H.c
./src/H5O.c
Added an extra argument to H5AC_find_f() and H5AC_protect(). This
arg gets passed to the load() method. Also added an extra
argument to the H5AC_find() macro.
./src/H5B.c
./src/H5Bprivate.h
./src/H5Gnode.c
Extra argument passed to the sizeof_rkey() method.
./src/H5Fprivate.c
./src/H5Fistore.c (new)
Added indexed I/O operations.
./src/H5G.c
./src/H5Gnode.c
./src/H5Gprivate.h
Beginning to add H5G_open/close and related bug fixes.
./src/H5Oprivate.h
./src/H5Oistore.c (new)
Added the H5O_ISTORE messsage (0x0008) for indexed storage of
objects.
./src/H5private.h
Added extra braces around both sides of the FUNC_ENTER() and
FUNC_LEAVE() macros so FUNC_ENTER() can appear before
declarations or after executable statements the second case is
used by H5G_namei() to initialize output arguments to sane
values before FUNC_ENTER() might return failure.
int f ()
{
int decl1;
printf ("This happens before FUNC_ENTER()\n");
FUNC_ENTER (...);
int another_declaration;
./src/H5B.c
./src/H5Bprivate.h
./src/H5Gnode.c
Extra arguments for key encoding and decoding.
./src/H5E.c
./src/H5Epublic.h
./src/H5Fistore.c
./src/H5Oistore.c
./src/H5Oprivate.h
Indexed, chunked, sparse storage (not ready for general consumption
yet).
./src/H5V.c (new)
./src/H5Vprivate.h (new)
./test/hyperslab.c (new)
Vector, array, and hyperslab functions.
./src/H5B.c
./src/H5Bprivate.h
./src/H5Fistore.c
./src/H5Gnode.c
./src/H5V.c
./src/H5Vprivate.h
./test/hyperslab.c
Added functionality for indexed storage.
./src/H5F.c
Fixed problems with seek optimizing. Recommend we disable it
until we can implement it in the file/address class since all
of HDF5 must be aware of it.
./src/H5O.c
Fixed comeent speling erorr :-)
./MANIFEST
Added new files.
./config/conclude.in
Added the word `Testing' to the test cases. So if a test
program is called hyperslab then the make output will contain
the line `Testing hyperslab'.
./config/linux
The default file I/O library is Posix section 2 on my linux
machine so I can do some I/O performance testing.
./src/H5C.c
./src/H5Cprivate.h
./src/H5Cpublic.h
Added ability to set size of indexed-storage B-tree.
./src/H5D.c
./src/H5E.c
./src/H5Epublic.h
./src/H5F.c
./src/H5Fprivate.h
./src/H5G.c
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5Gpublic.h
./src/H5Gshad.c
./src/H5Gstab.c
./test/stab.c
Changed `directory' to `group' in numerous places.
./src/H5private.h
The FILELIB constant can be set on the compile command-line.
./src/istore.c NEW
Tests for indexed storage.
Instructions for end users.
./INSTALL_MAINT NEW
Instructions and hints for maintainers.
./MANIFEST NEW
A list of names of files that are part of the HDF5
distribution.
./Makefile.in NEW
Top-level makefile template. See INSTALL and/or INSTALL_MAINT
for instructions on how to generate the Makefile from this
file.
./configure NEW
./configure.in NEW
Configuration shell script generated from configure.in.
./Makefile
Removed from CVS. This file is now generated by running
configure.
