----------------------
./src/H5Flow.c
./src/H5Fprivate.h
./src/H5Fsplit.c
Changed the allocation size request from `size_t' to `hsize_t'
because it was overflowing for the `big' test.
./src/H5detect.c
If `long double' and `double' are the same size then we define
H5T_NATIVE_LDOUBLE to be the same as H5T_NATIVE_DOUBLE.
Similarly for `long' vs. `long long' and `unsigned long' vs.
`unsigned long long'.
./test/Makefile.in
Added `big' to the list of tests to normally run.
./test/big.c
Added a check to see if the file system supports holes and if
it doesn't then the test is skipped.
----------------------
./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.
----------------------
./src/H5Tbit.c
./MANIFEST
./test/Makefile.in
./test/bittests.c NEW
Finished the bit vector operations and added test cases.
./src/H5Tconv.c
./test/dtypes.c
Finished integer->integer general conversion and added test
cases. Overflows and underflows are handled by substituting
the closest possible value. Examples:
(unsigned)0xffff -> (unsigned) 0xff
( signed)0xffff -> (unsigned)0x0000
(unsigned)0xffff -> ( signed)0x7fff
( signed)0x7fff -> ( signed) 0x7f
( signed)0xbfff -> ( signed) 0xbf
( signed)0x8000 -> ( signed) 0x80
./src/H5private.h
Added definitions for MIN and MAX that take 3 or 4 arguments:
MIN3(), MIN4(), MAX3(), MAX4(). Also added MIN2() and MAX2()
as aliases for MIN() and MAX().
./test/tattr.c
Removed some redundant `&' operators.
./configure.in
./src/H5config.h.in [regenerated]
./src/H5.c
Fixed warnings on DEC where long double is the same as
double.
----------------------
./html/Datasets.html
Fixed a couple of typos.
./src/H5.c
Added the `Z' modifier to HDfprintf() for `size_t' sizes. Use
it like this:
HDfprintf(stderr,"size is %Zd\n", (size_t)x);
./src/H5AC.c
./src/H5F.c
./src/H5Fprivate.h
The maximum number of meta data objects that can be cached can
be set from the application (but the library might not honor
it every time; it's a hint).
./src/H5D.c
Changed a warning message so it's not so alarming.
./src/H5Fistore.c
Chunks can be cached.
./src/H5O.c
./src/H5Oprivate.h
Added H5O_copy() and H5O_free() to copy and free messages.
./src/H5P.c
./src/H5Ppublic.h
Added H5Pset_cache() and H5Pget_cache() and changed lots of
"template" to "property list".
./src/H5Z.c
./src/H5Zpublic.h
Miscellaneous little things to clean up. Mostly just removed
H5Z_MAXVAL and added H5Z_USERDEF_MIN and H5Z_USERDEF_MAX.
./MANIFEST
./test/Makefile.in
./test/chunk.c [NEW]
Added a performance test for chunk caching. It looks at the
amount of I/O instead of timing because timing is partly
dependent on the chunk size and I wanted a measurement that
was a function of only the cache size. Run `chunk' with no
arguments and then say `gnuplot x-gnuplot' to see the plots
(press return between plots). Postscript files are created for
each plot.
./test/big.c
./test/cmpd_dset.c
./test/extend.c
./test/external.c
./test/gheap.c
Added H5F_ACC_DEBUG so we can see cache performance
statistics.
----------------------
./html/H5.format.html
./src/H5E.c
./src/H5Epublic.h
./src/H5F.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5Gprivate.h
./src/h5ls.c
./test/Makefile.in
Symbolic links are now supported. The ./test/links program
will create a `links.h5' file that demonstrates hard links,
soft links, dangling links, and recursive links. A symbolic
link is a symbol table entity and doesn't have an object
header. It's format is described in H5.format.hml.
./src/H5G.c
./src/H5Gpublic.h
./src/h5ls.c
Implemented H5Gstat() and H5Gget_linkval() as documented by
Quincey. The `H5G_type_t type' field of `H5G_stat_t' was
changed to `int type' because H5G_type_t was already used and
the `type' data type should be open-ended.
./src/H5Ffamily.c
Removed an incorrect diagnostic message.
./test/big.c
Added read/write calls to test partial I/O to big contiguous
datasets. With no arguments it writes to a dataset and prints
the list of points written which should be redirected to a
file. With an argument (the name of a file containing the
stdout of a run with no arguments) values are read from the
dataset. One would typically say `big >x && big x'.
----------------------
./src/H5Osdspace.c
./html/H5.format.html
In the past we were allowed to have >2GB files on a 32-bit
machine as long as no dataset within the file was larger than
4GB (or whatever sizeof(size_t) is). That's been fixed now.
All dataset size calculations are done with `hsize_t' which is
normally defined as `unsigned long long'.
./src/H5F.c
./src/H5Ffamily.c
./src/H5Fprivate.h
./src/H5P.c
./src/H5Ppublic.h
The file family member size can now be set/queried. The
default is still 64MB, but it can be set to 1GB by saying:
H5Pset_family (plist, 30, H5P_DEFAULT);
When opening an existing file family the specified
bits-per-member is ignored and the first member of the family
determines the bits-per-member, which can be retrieved with
H5Pget_family().
./acconfig.h
./configure.in
./src/H5config.h
./src/H5public.h
Added `--disable-hsizet' so that those with old GCC compilers
(<2.8.1) can still compile the code.
./src/H5.c
./src/H5private.h
Added HDfprintf() which works just like fprintf() except you
can give `H' as a size modifier for the integer conversions
and supply an `hsize_t' or `hssize_t' argument without casting
it. For instance:
hsize_t npoints = H5Sget_npoints(space);
HDfprintf(stdout,"Dataset has %Hd (%#018Hx) points\n",
npoints, npoints);
You can now give `%a' as a format to print an address, but all
formating flags are ignored and it causes the return value of
HDfprintf() to not include the characters in the address (but
who uses the return value anyway :-). Example:
H5G_t *grp;
HDfprintf(stdout, "Group object header at %a\n",
&(grp->ent.header));
Added HDstrtoll() which works exactly like [HD]strtol() except
the result is an int64.
./src/debug.c
Large addresses can now be entered from the command-line. Use
either decimal, octal (leading `0') or hexadecimal (leading
`0x') when giving the address.
./src/h5ls.c
The printf format for dataset dimensions was changed to `%Hu'
to support large datasets.
./test/big.c [NEW]
A test for big datasets on 32-bit machines. This test is not
run by default. Don't try to run it on an nfs-mounted file
system or other file system that doesn't support holes because
it creates two 32GB datasets of all zero.
----------------------
./MANIFEST
./test/Makefile.in
./test/shtype.c [NEW]
Added some tests for shared data types.
./configure.in
Removed MF and HL from the default debug list since. MF
because it hasn't been implemented yet and HL because it
produces lots of annoying messages about adjusting the size of
local heaps.
./src/H5F.c
./src/H5T.c
./src/H5Tprivate.h
Fixed a bug with opening the same file twice. The first close
on the file_id incorrectly closed shared data structs.
Closing a file now correctly unshares data types that might be
pointing into that file.
./src/H5T.c
./src/H5Tpublic.h
Added an H5Tis_shared(). The caller supplies a file and a
data type and the function returns true if the data type is
currently marked for sharing in that file.
./src/H5AC.c
./src/H5F.c
./src/H5HL.c
./src/H5HG.c
./src/H5MF.c
./src/H5O.c
We now detect errors sooner when writing to a read-only
file. In the past, the error might not show up until the
cached item was flushed, and it was sometimes possible to not
even get an error!
./src/H5I.c
./src/H5Iprivate.h
If the search function fails then H5I_search() returns
failure. Also, the first argument for the search function
isn't const anymore because we might want the search to have
side effects (like calling H5T_unshare() for all shared data
types whose file just closed).
----------------------
./MANIFEST
./src/Makefile.in
./test/Makefile.in
Added new files.
./config/linux
./src/H5HL.c
./src/H5HLprivate.h
./src/H5MF.c
./src/H5MFprivate.h
Added `-DH5HL_DEBUG -DH5MF_DEBUG' to the debug list.
./html/H5.format.html
Updated shared object message information.
./src/H5D.c
Datasets can now share data types.
./src/H5F.c
Updated a comment that referred to H5ACC_WRITE.
./src/H5HG.c
./src/H5HGprivate.h
Moved a few things around. Made debugging better so you can
now give a collection address to ./src/debug and it shows some
useful stuff.
./src/H5O.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Olayout.c
./src/H5Oname.c
./src/H5Onull.c
./src/H5Oprivate.h
./src/H5Osdspace.c
./src/H5Oshared.c [NEW]
./src/H5Ostab.c
Supports shared messages.
./src/H5T.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5Tpublic.h
The H5Tshare() function allows the user to give the library
hints about how a data type will be used.
./test/shtype.c
Tests the H5Tshare() function.
./test/gheap.c
Tests the global heap.
./configure.in
./config/BlankForm [NEW]
./config/alpha-dec
./config/freebsd2.2.1
./config/hpux10.20
./config/irix6.2
./config/irix64
./config/linux
./config/powerpc-ibm-aix4.2.1.0
./config/rs6000-ibm-aix4.1.4.0
./config/solaris2.5
Cleaned up lots of configuration stuff and made the site
configuration files lots easier and more uniform. To make a
new file grab the BlankForm and modify it.
By default, debugging is turned on for most packages. Within
a package one can use `#ifdef H5AC_DEBUG' to wrap debugging
code. Other options are:
--enable-debug
--enable-debug=yes
The default, most but not all packages.
--disable-debug
--enable-debug=no
--enable-debug=none
The symbol NDEBUG is defined and none of the package
debug symbols.
--enable-debug=all
Debugging is turned on for all packages. This might
produce lots of output.
--enable-debug=g,d
Debugging is turned on for H5G and H5D.
A compile mode is also now supported
--enable-production
--enable-production=yes
The library is compiled with optimizations turned on.
The compiler flags are augmented by adding PROD_CFLAGS
and PROD_CPPFLAGS which are defined in the site config
file.
--disable-production
--enable-production=no
The default. The library is compiled for development
by including DEBUG_CFLAGS and DEBUG_CPPFLAGS defined in
the site config file. This is usually just `-g'.
--enable-production=profile
--enable-production=pg
Builds a library for profiling by including the flags
from PROFILE_CFLAGS and PROFILE_CPPFLAGS defined in the
site config file. This is usullay just `-pg' but it
could include optimization flags as well depending on
the type of profile one wants.
In summary, configure by saying `./configure' and you'll get a
development version of the library. Configure by saying
`./configure --enable-production --disable-debug' and you'll
get a production version with no debugging code.
----------------------
./configure.in
./configure
./test/iopipe.c
Added check for system(3)
./config/freebsd2.2.1
./config/linux
Added -DH5D_DEBUG to the debug flags.
./src/H5D.c
./src/H5Dprivate.h
./src/H5P.c
./src/H5Ppublic.h
./src/H5Sprivate.h
./src/H5Ssimp.c
./html/Datasets.html
Finally implemented strip mining in the I/O pipeline, placing
a user-defined upper bound on the amount of temporary memory
used by the pipeline. The default is 1MB type conversion and
background buffers allocated/freed on demand. However, the
size can be changed and/or application-allocated buffers
supplied with H5Pset_buffers() called on the data transfer
property list passed to H5Dread() and H5Dwrite().
Minor optimizations to H5Dread() and H5Dwrite(). More coming
later...
./test/dsets.c
Added calls to H5Pset_buffer() to test application-defined
temporary buffers in the I/O pipeline.
./test/Makefile.in
Removed `iopipe' from the list of confidence tests. Saying
`make timings' in the test directory runs timing tests. I did
this because (1) they don't really test anything new, and (2)
they can take a long time to run.
----------------------
./MANIFEST
New files
./html/extern1.gif [NEW]
./html/extern1.obj [NEW]
./html/extern2.gif [NEW]
./html/extern2.obj [NEW]
./html/Datasets.html
Documented external raw data storage.
./html/Datasets.html
./html/chunk1.gif [NEW]
./html/chunk1.obj [NEW]
Added a picture and better description for chunking since it
seems that people are thinking chunks are fixed-size at the
file level instead of at the array level.
./src/H5D.c
./src/H5Dpublic.h
./test/external.c
Changed H5Dget_create_parms() to H5Dget_create_plist().
./src/H5D.c
./src/H5Farray.c
./src/H5Fprivate.h
./src/H5Oefl.c
./src/H5Oprivate.h
./src/H5Sprivate.h
./src/H5Ssimp.c
./test/external.c
./test/istore.c
External raw data file I/O for contiguous storage is now
working. The library supports segments of various sizes which
can be scattered throughout multiple files in any order.
./test/Makefile.in
Remove more temporary files.
----------------------
./html/Dataspaces.html
./html/Errors.html
./html/Files.html
./html/H5.api.html
./html/review1.html
./src/H5private.h
./src/H5public.h
./test/dsets.c
./test/dtypes.c
Removed all the types like `int32' and `intn' into private
headers since they violate the naming scheme and pollute
application name space. Besides, our test files only use them
in a handful of places and it's probably useless to export
them to the app. The app is always written in terms of
standard numeric types or its own numeric types and probably
never in terms of HDF5 numeric types. If it were, then the
user would have to copy from their type to hdf5 type for
almost every hdf5 API function call! Same goes for return
values. I also removed SUCCEED/FAIL from the API since apps
should be checking against zero anyway.
if (FAIL==(space=H5Screate_simple(...))) /*wrong*/
if ((space=H5Fcreate_simple(...)<0)) /*right*/
./src/H5.c
Changed arguments of H5version() from `uintn' to `unsigned'.
./src/H5Tpublic.h
./src/H5T.c
Changed return type of H5Tget_nmembers() from `intn' to `int'
./src/H5A.c
./src/H5Aprivate.h
./src/H5Apublic.h
Changed `H5Asearch_func_t' to `H5A_search_func_t' and moved
its definition from the public to the private header file.
./html/H5.format.html
Documented changes made to the external file list (H5O_EFL)
message.
./src/H5D.c
./src/H5Dprivate.h
./src/H5E.c
./src/H5Epublic.h
./src/H5O.c
./src/H5Oefl.c
./src/H5Oprivate.h
./src/H5P.c
./src/H5Ppublic.h
Added partial support for external raw data files. HDF5 can
now describe external raw data files by listing the file
names, offsets, and size for a dataset. However, we will
restrict a dataset to be stored "contiguously" when the
external file list is viewed as a single address space. The
current implementation is unable to read/write to external
files--that will come later this week as will documentation.
For now, take a look at ./test/external.c, particularly the
calls to H5Pset_external().
./test/Makefile.in
./test/external.c [NEW]
./MANIFEST
Added tests for external storage. Note: the read test is
supposed to fail at this point since reading external datasets
is not implemented yet. There is no write test.
./src/H5S.c
./src/H5Sprivate.h
./src/H5Ssimp.c
Added H5S_get_npoints_max() to return the maximum possible
number of data points in a data space.
Added an extra argument to H5S_get_dims() which returns the
maximum dims.
./src/H5F.c
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5M.c [DEPRICATED]
./src/H5Mpublic.h [DEPRICATED]
Changed `template' to `property list' in lots of places.
./src/H5Osdspace.c
Removed an extra `\n' from a print statement.
./src/H5S_public.h
Changed H5S_UNLIMITED to the maximum size_t value.
./test/extend.c
"Extendable" is spelled "extendible".
./src/H5Farray.c
./src/H5V.c
./src/H5Vprivate.h
./test/hyperslab.c
Strides are now type ssize_t instead of int. These have
nothing to do with the sample granularity arguments for
hyperslabs, which are also called "strides" in the code.
./test/tstab.c
Changed assumptions about default address and length sizes.
----------------------
./INSTALL
Added instructions for which C flags to set for debugging.
./src/H5C.c
./src/H5Cpublic.h
H5Cset_chunk() takes const pointer.
./src/H5D.c
./src/H5Dprivate.h
./src/H5Dpublic.h
Added H5Dextend() to extend the dimensions of a dataset.
./src/H5Osdspace.c
./src/H5P.c
./src/H5Pprivate.h
./src/H5Ppublic.h
./test/cmpd_dset.c
./test/dsets.c
./test/th5p.c
Added the optional `maxdims' argument to H5Pcreate_simple()
and defined constant H5P_UNLIMITED which can appear in the
maxdims. Added `const' to arguments.
Implemented H5Pcopy()
Removed the unused file argument from H5P_modify.
Added H5P_extend().
Removed the `flags' field from simple data types and we
determine if the `max' or `perm' arrays are valid by looking
at the pointer. Cleaned up the H5O_sdspace_debug output.
./src/H5T.c
Fixed a printf format.
./MANIFEST
./test/Makefile.in
./test/extend.c [NEW]
Added a test for multi-dimensional unlimited dimensions.
----------------------
./config/conclude.in
The maintainer-clean target removes Emacs backup files,
mirroring backup and contrib files, core files, and profile
output files in addition to what it used to remove.
./src/H5D.c
Fixed a buffer allocation bug in the output pipeline.
./src/H5Gnode.c
Fixed a comparison against size_t
./test/Makefile.in
Added the other temporary h5 files to the `MOSTLYCLEAN' var.
./test/cmpd_dset.c
Added four tests for partial I/O. Don't you just love it when
something works on the first try!
Problem: Some *.h5 files are left behind after tests.
Solution: Added the MOSTLYCLEAN line for those few .h5 to be removed
if "make clean" is called. Did not use "*.h5" because of concern that
it may blow away legitimate .h5 files. Though it is possible to put
legitimate .h5 in a subdirectory, it is better to play it safe this
way.
----------------------
./MANIFEST
Added new files.
./src/H5D.c
Added support for partial datatype I/O which is needed when
merging struct members between file and disk. This isn't the
efficient version because the merge requires an extra gather
(step 1b in my pipeline diagram) that isn't turned off when it
isn't needed.
./src/H5T.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5Tpublic.h
Conversion functions take an extra argument which is a pointer
to a blob of private data that can be used by the conversion
function to save anything that's expensive to compute and
is constant for a particular conversion path.
./src/H5Tconv.c
Compound data type conversion is beginning to work! We can
handle conversions between compound types that have members
which are not arrays. It also supports partial conversion so
we can omit certain members of the source and not clobber
extra members in the destination.
./test/Makefile.in
./test/cmpd_dset.c [NEW]
Added a test case that demonstrates how to use compound data
types in a dataset. The output doesn't match the output of
the other test cases yet, the the entire example is more
readable and written entirely with the API.
Added new tests.
./test/dsets.c NEW
Tests datasets.
./test/dspace.c NEW
Tests data spaces.
./test/dtypes.c NEW
Tests data types.
./test/istore.c
./test/tfile.c
./test/th5p.c
./test/theap.c
./test/tohdr.c
Changed to work with new function names.
./test/testhdf5.c
Removed the data type and dataset tests since they're now in
their own files. They had to be rewritten because of extensive
changes to those interfaces.
----------------------
./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.
to int64 encode/decode to fix purify on 32-bit systems, changes to
H5O_modify, changes to H5D.c to use H5F_open/close(), etc.
Documentation will be mailed shortly...
