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Backward compatibility code
Description:
Add in code to allow the library to emulate the v1.2 API and behavior.
Platforms tested:
FreeBSD 4.2 (hawkwind)
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----------------------
This extensive change is the virtual file layer implementation. I've
ported and tested the sec2, family, and core drivers and only ported
the mpio driver (Albert will test it). So if you need MPIO I would
recommend sticking with the previous version for a while.
You will get a few compile warnings about split and stdio drivers not
being implemented and possibly tracing information not inserted in
some of the drivers. You can safely ignore them but I plan to fix
them.
I'm still working on the split driver because I just realized that it
needs a part of the VFL that isn't written yet.
Documentation is being updated also because there were some minor
changes (mostly just name changes). It should be available on my web
site later this week.
./MANIFEST
./src/Makefile.in
./src/hdf5.h
./src/H5Flow.c [REMOVED]
./src/H5Fstdio.c [REMOVED]
./src/H5Fsec2.c [REMOVED]
./src/H5Fsplit.c [REMOVED]
./src/H5Fmpio.c [REMOVED]
./src/H5Ffamily.c [REMOVED]
./src/H5Fcore.c [REMOVED]
./src/H5MFpublic.h [REMOVED]
./src/H5FD.c [NEW]
./src/H5FDcore.c [NEW]
./src/H5FDcore.h [NEW]
./src/H5FDfamily.c [NEW]
./src/H5FDfamily.h [NEW]
./src/H5FDmpio.c [NEW]
./src/H5FDmpio.h [NEW]
./src/H5FDprivate.h [NEW]
./src/H5FDpublic.h [NEW]
./src/H5FDsec2.c [NEW]
./src/H5FDsec2.h [NEW]
Removed/added files for virtual file layer.
./bin/trace
./src/H5.c
Removed unused public datatypes and added new VFL public
datatypes.
Changed an error message.
./config/BlankForm
./config/dec-flags
./config/gnu-flags
./config/hpux10.20
./config/hpux9.03
./config/irix5.x
./config/irix6.x
./config/solaris2.x
./config/unicosmk
Removed the H5F_OPT_SEEK and H5F_LOW_DFLT constants from the
configuration since they're no longer applicable. The default
file driver is always the sec2 driver and it always optimizes
calls to lseek() or lseek64().
./config/depend.in
C preprocessor errors generated during automatic dependency
building are sent to /dev/null to prevent them from appearing
twice in the make output.
./src/H5AC.c
./src/H5B.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Oshared.c
./src/H5T.c
./src/H5detect.c
./test/ohdr.c
Changed H5F_ADDR_UNDEF to HADDR_UNDEF to be more consistent
with the `haddr_t' datatype which is now a public type.
./src/H5D.c
./src/H5P.c
./src/H5Ppublic.h
./src/H5Tconv.c
./test/cmpd_dset.c
./test/dsets.c
./test/overhead.c
./test/tselect.c
./test/tvltypes.c
The H5P_DATASET_XFER constant was changed to H5P_DATA_XFER
because the properties apply to all types of I/O operations,
not just datasets.
./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5Dpublic.h
./src/H5F.c
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5R.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Spoint.c
./src/H5Sprivate.h
./test/big.c
./test/h5test.c
./test/istore.c
./testpar/t_dset.c
./testpar/t_file.c
./tools/h5debug.c
./tools/h5ls.c
Modified to work with the virtual file layer by calling H5FD_*
functions instead of H5F_low_* functions and by passing file
access and data transfer properties by object ID instead of
pointer.
Changed H5D_transfer_t to H5FD_mpio_xfer_t since the
COLLECTIVE vs. INDEPENDENT transfer mode is specific to the
MPIO file driver.
Moved MPIO-specific stuff into the MPIO driver.
./src/H5B.c
./src/H5D.c
./src/H5Fprivate.h
The H5F_mpio_* private functions were renamed and placed in
the H5FDmpio driver except those which appeared in H5Smpio.c.
./src/H5E.c
./src/H5Epublic.h
Added major error number H5E_VFL for virtual file layer
related errors.
./src/H5F.c
./src/H5Fprivate.h
Changed the logic that controls whether the boot block is
written. Instead of assuming that the first call to write the
boot block is only to allocate space, I've added a function
argument which makes this explicit.
Changed the way files are compared so that a driver-defined
comparison function can be called. Files which belong to
different drivers are always considered different.
Removed H5F_driver_t since file drivers are now identified by
object ID instead of a special non-user-extendible datatype.
Removed all the hard-coded low-level file properties which
have been replaced by the various file drivers.
./src/H5I.c
./src/H5Iprivate.h
Added the H5I_inc_ref() which was removed a few months ago
since we finally have a use for it.
./src/H5Ipublic.h
Added the H5I_VFL object ID type to identify file drivers in
the virtual file layer.
./src/H5MF.c
./src/H5MFprivate.h
Moved all the allocation/deallocation code into the virtual
file layer which allows file drivers to override much of it.
./src/H5P.c
./src/H5Ppublic.h
Moved file driver-specific code into the various file driver
files.
The H5Pcopy() and H5Pclose() functions make calls into the
virtual file driver to manage the memory for driver-specific
file access and data transfer properties.
./src/H5private.h
./src/H5public.h
The `haddr_t' type is now public.
./test/tfile.c
Added a few more comments.
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----------------------
./config/depend.in
Fixed automatic dependencies. We were storing dependencies for
*.o files instead of *.lo files after shared libraries were
added.
./config/gnu-flags
./config/linux-gnulibc1
Moved `-march=pentiumpro -mcpu=pentiumpro -malign-double' from
the linux file to this file and caused it to depend on the CPU
name. This fixes one of Elena's bugs.
./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5Dprivate.h
./src/H5Dpublic.h
./src/H5F.c
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fmpio.c
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5Gnode.c
./src/H5P.c
./src/H5RA.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Spoint.c
./src/H5Sprivate.h
./src/H5Tpublic.h
./test/istore.c
Added an H5Dget_storage_size() function that reports the
amount of storage allocated for raw data in a dataset.
Changed H5D_xfer_* to H5F_xfer_* because these properties are
more general than datasets. This also allows some of the
lower-level I/O functions to get this information easier.
./src/H5S.c
./src/H5Sall.c
Added two new functions H5S_all_read() and H5S_all_write()
which are optimizations that copy data directly between file
and memory without having to go through the scatter gather
step. This knocks quite a bit of time off the I/O and
reading/writing entire datasets is a fairly common operation.
./tools/h5ls.c
Reports the logical size of data, the allocated size of data,
and the percent utilization.
./MANIFEST
Removed old pablo files, added new files. Snapshots should now
start to work again.
./src/H5D.c
./src/H5Fmpio.c
Removed two warnings signed vs. unsigned comparisons and check
for overflow.
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also exported all globals and non static functions to the dll
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----------------------
./tools/h5tools.c
Strings are not converted to null-padding before being
printed; they are printed with whatever byte values appear in
the file.
./tools/h5ls.c
Now able to display attribute data type and data.
Added a `-f' or `--full' switch which causes the full name of
each object to be displayed instead of just the base name.
Added a `-r' or `--recursive' switch that recursively prints
the contents of groups, avoiding cycles.
More bulletproofing for non-printable characters in things
like object names, attribute names, and comment strings. We
don't want listing a file to send termal escape sequences
because it's sometimes possible to execute commands that way.
Since h5ls doesn't usually use quotes around object names we
must sometimes escape space characters.
External files are listed in a table to make the output less
confusing.
./tools/h5tools.c
./tools/h5tools.h
Changed h5dump() to h5dump_dset() and added h5dump_mem(). Also
make h5dump_fixtype() public.
./test/dtypes.c
Wrote some data to an attribute to test h5ls attribute
printing.
./src/H5ACprivate.h
./src/H5Apublic.h
./src/H5Dprivate.h
./src/H5Dpublic.h
./src/H5Epublic.h
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5Gprivate.h
./src/H5HLprivate.h
./src/H5Oprivate.h
./src/H5Ppublic.h
./src/H5RApublic.h
./src/H5Rpublic.h
./src/H5Spublic.h
./src/H5Tpkg.h
./src/H5Tpublic.h
./src/H5Vprivate.h
./src/H5Zpublic.h
./src/H5private.h
./src/H5public.h
Reindented function prototypes after `HDF5API' was added. Also
rewrapped long lines.
./src/H5Flow.c
Added an `#ifdef WIN32' around an unused variable.
./src/H5api_adpt.h
Removed extra carriage returns inserted by "broken" operating
system.
./src/H5Dprivate.h
./src/H5Oprivate.h
./src/H5Vprivate.h
./src/H5private.h
Removed extraneous inclusion of H5api_adpt.h since it's
included in H5public.h which is included by everything.
./src/Makefile.in
Added H5api_adpt.h to the list of public header files to fix
broken `make install'.
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TRUE/FALSE/FAIL, hbool_t is now strictly for true boolean values.
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----------------------
./src/H5F.c
./src/H5Fpublic.h
Added H5Freopen() as documented in earlier e-mails. This is
really just a wrapper around H5F_new().
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----------------------
./bin/trace
./src/H5.c
./src/H5F.c
./src/H5Fprivate.h
./src/H5Fpublic.h
Added a `scope' argument to H5Fflush() which should be either
H5F_SCOPE_LOCAL or H5F_SCOPE_GLOBAL and determines which files
are flushed (just the specified file or the entire virtual
file).
./src/H5F.c
Added reference counts to the H5F_t struct so we get the
correct behavior between H5Funmount() and H5Fclose().
./src/H5O.c
Fixed a memory leak that happens during error handling.
./test/cmpd_dset.c
./test/unlink.c
Fixed a memory leak.
./test/mount.c
Enabled the H5Fclose() test.
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----------------------
./doc/html/H5.format.html
./src/H5HG.c
Fixed a bug in the global heap that caused H5HG_read() to
write past the end of the buffer in certain cases.
./test/big.c
The test is skipped if hdf5 was configured with
`--disable-hsizet'.
./src/H5Ofill.c
Data type conversions are implemented for the fill value.
./src/H5.c
Tracing prints one of H5P_FILE_CREATE, H5P_FILE_ACCESS,
H5P_DATASET_CREATE, H5P_DATASET_XFER, or H5P_MOUNT instead of
the more cryptic H5I_TEMPLATE_* constants.
./src/H5D.c
Removed prototype for H5D_find_name().
./src/H5I.c
The GROUP_MASK and ID_MASK are both calculated from GROUP_BITS
instead of being set by hand.
We don't use the sign bit of hid_t; all valid hid_t values are
positive so we can say things like `if ((file=H5Fopen(...))<0)'.
Changed `(int)pow(2.0,x)' to `1<<x' so we don't have to worry
about rounding.
Fixed H5I_get_type() so it doesn't always fail an assertion.
./src/H5E.c
./src/H5Epublic.h
Added minor error H5E_MOUNT
./src/H5F.c
./src/H5Fprivate.h
Added H5Fmount() and H5Funmount(). Mounting and unmounting
works as documented but some of the other things aren't
implemented yet, the biggest being current working groups
always acting on the root of the mount tree, and H5Fclose()
closing the entire tree. The rest of the stuff will be added
shortly...
./src/H5P.c
./src/H5Ppublic.h
Added the H5P_MOUNT property list but haven't implemented any
particular properties for it yet.
./src/H5Gstab.c
Hard links across files return an error instead of failing an
assertion.
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----------------------
./COPYING
Reformatted as text instead of C. Removed zlib crew from the
list of contributors since no zlib code is actually in the
hdf5 library.
./INSTALL
./INSTALL.ascired
./MANIFEST
Minor updates for Beta release including version number
change.
./INSTALL_MAINT
Added information about making a release.
./RELEASE
Updated function list based on public header files.
./bin/checkposix
Got rid of complaints about some obvious things.
./doc/html/H5.api.html
./doc/html/RM_H5F.html
./src/H5F.c
./src/H5Fpublic.h
./test/tfile.c
Changed H5Fget_create_template() and H5Fget_access_template()
to H5Fget_create_plist() and H5Fget_access_plist() since that
conforms better to lots of other names.
./doc/html/Datatypes.html
./doc/html/ExternalFiles.html
./doc/html/Files.html
./doc/html/H5.api.html
./doc/html/H5.sample_code.html
./doc/html/RM_H5F.html
./doc/html/RM_H5Front.html
Changed `template' to `property list', etc.
./doc/html/Ragged.html [NEW]
Documentation for ragged arrays.
./src/H5Iprivate.h
./src/H5Ipublic.h
./src/H5I.c
Changed the scope of some symbols to be more local.
./src/H5.c
./src/H5AC.c
./src/H5D.c
./src/H5E.c
./src/H5F.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5G.c
./src/H5Gnode.c
./src/H5HG.c
./src/H5I.c
./src/H5O.c
./src/H5Ocomp.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Omtime.c
./src/H5Oname.c
./src/H5P.c
./src/H5S.c
./src/H5Shyper.c
./src/H5Tbit.c
./src/H5Tconv.c
./src/H5V.c
./src/H5Z.c
./src/H5private.h
Fixed some violations of our naming scheme by adding HD to the
beginning of all Posix functions.
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H5Gget_objinfo
and renamed internal functions to match up with the renamed API functions.
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----------------------
./config/solaris2.5
Hopefully set up now so it honors the CC and CFLAGS variables
and understands solaris cc flags.
./test/big.c
Checks to see if creating lots of large sparse files exceeds
the user disk quota and skips the test. It also checks that
we can actually open ~64 files at once.
./doc/html/Files.html
./src/H5A.c
./src/H5Aprivate.h
./src/H5F.c
./src/H5Fpublic.h
Added the H5Fflush() function which takes any object as an
argument as long as the object is in some way associated with
a file. This required an H5A_entof()
./src/H5.c
./src/H5Flow.c
The `%a' format of HDfprintf() now allows a field width and
justification flag etc, like the other formats. The old
H5F_addr_print() was recoded to call HDfprintf() instead of
vice versa.
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----------------------
./src/H5.c
Handle hid_t of type H5_TEMPBUF, arguments usually called tbuf_id.
Added array tracing where the array rank is stored in a simple
data space. Just use the name of the data space argument when
declaring the array argument:
herr_t
H5Sselect_hyperslab (hid_t space_id, H5S_seloper_t op,
const hssize_t start[/*space_id*/],
const hsize_t _stride[/*space_id*/],
const hsize_t count[/*space_id*/],
const hsize_t _block[/*space_id*/])
and when the program runs you'll see array values printed:
H5Sselect_hyperslab(space=218103813, op=H5S_SELECT_SET,
start=0xbfffef4c {0}, _stride=NULL,
count=0xbfffef44 {64},
_block=NULL) = SUCCEED;
Added more symbolic data types to the tracing output.
./src/H5A.c
./src/H5Apublic.h
./src/H5D.c
./src/H5Dpublic.h
./src/H5F.c
./src/H5Fpublic.h
./src/H5G.c
./src/H5Gpublic.h
./src/H5P.c
./src/H5Ppublic.h
./src/H5S.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Spoint.c
./src/H5Spublic.h
./src/H5Sselect.c
./src/H5Ssimp.c
./src/H5TB.c
./src/H5V.c
Changed some API argument names to be more consistent with
other API functions and to produce better tracing output.
Reformatted some long lines. Indented printf statements.
./tools/h5ls.c
Fixed warnings about unsigned vs. signed comparisons.
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flags
of H5Fmpio via the MPI_Info parameter to H5Fcreate and H5Fopen.
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----------------------
./bin/release
./src/H5.c
./src/H5private.h
./src/H5public.h
./src/H5Fpublic.h
Changed the version number constants to names that begin with
H5_VERS_ and added macros that check that the version numbers
in the include files match the version number of the library.
./MANIFEST
./html/H5.user.html
./html/Version.html [NEW]
./html/version.obj [NEW]
./html/version.gif [NEW]
Documented version numbers and the macros, constants, and
functions associated with them.
./bin/versinc
A perl script that increments the minor version number and
sets the patch level back to zero. This is intended to be
invoked from the top of the source tree by a cvs commit
anywhere in the source tree. Quincey?
./src/H5O.c
./src/H5Oprivate.h
Added H5O_count() to count the number of object header
messages of a particular type. Quincey needs this for the
attribute package.
./test/dsets.c
Fixed warnings. Enabled the small strip-mine buffer test.
./config/linux
Added optimizations for the Pentium-Pro for production mode.
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used to open an HDF5 file with MPIO access. The design has changed
to provide access-mode controll (independent or collective access)
as an argument in the H5D read/write calls.
Also removed the macros H5FACC_INDEPENDENT and H5FACC_COLLECTIVE.
The original thinking was to define how a file is independent or
collective access. They are replaced by the enum H5D_transfer_t
with values of H5D_XFER_INDEPENDENT and H5D_XFER_COLLECTIVE.
These values are used in the H5Pset_xfer to setup a data transfer
property list to be used during the H5D read/write calls.
The original access_mode field in the File access structure is
still there. It would be removed soon once the transfer control
can be passed down to the low level I/O routines.
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----------------------
./src/H5B.c
./src/H5D.c
./src/H5Dprivate.h
./src/H5Dpublic.h
./src/H5F.c
./src/H5Farray.c
./src/H5Fcore.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5HG.c
./src/H5HL.c
./src/H5MF.c
./src/H5MFprivate.h
./src/H5O.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Olayout.c
./src/H5Oname.c
./src/H5Oprivate.h
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5P.c
./src/H5Ppublic.h
./src/H5S.c
./src/H5Sprivate.h
./src/H5Spublic.h
./src/H5Ssimp.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5V.c
./src/H5Vprivate.h
./src/H5private.h
./src/H5public.h
./src/h5ls.c
./test/cmpd_dset.c
./test/dsets.c
./test/extend.c
./test/external.c
./test/hyperslab.c
./test/iopipe.c
./test/istore.c
./test/shtype.c
./test/tfile.c
./test/th5s.c
Anything having to do with the size of a dataset now uses the
types `hsize_t' and `hssize_t' which must be the same size and
at least as large as `size_t'. This isn't fully tested yet,
so hsize_t and hssize_t are defined as size_t and ssize_t in
H5public.h. Setting them to larger values will trip up gcc
versions less than 2.8.1 on x86 platforms.
Documented unused function formals with `__unused__' before
the formal name. This also has the effect of supressing
warning messages for gcc since it's defined to be
`__attribute__((unused))' in the H5private.h file.
./src/debug.c
./src/h5ls.c
If the file name contains a `%' then the file is opened as a
file family with H5P_DEFAULT for the file member access
property list.
./src/h5ls.c
The group name is optional, defaulting to `/'.
./src/hdf5.h
Added some missing public header files.
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----------------------
./configure.in
Moved setting of compiler warning switches earlier in the file.
Turned on more warning switches to gcc.
./config/linux
Prints a warning if the gcc version is less than 2.8.1 since
that version has problems with register allocation for `long
long'.
./html/Datatypes.html
Documented sharing of data types between datasets.
./src/H5G.c
./src/H5Gpublic.h
Implemented H5Gmove(), H5Glink() and H5Gunlink() for hard
links. Still have soft links to do.
./src/H5AC.c
./src/H5ACprivate.h
./src/H5D.c
./src/H5E.c
./src/H5Eprivate.h
./src/H5F.c
./src/H5Farray.c
./src/H5Fcore.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5Fsec2.c
./src/H5Fstdio.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5HG.c
./src/H5HL.c
./src/H5HLprivate.h
./src/H5I.c
./src/H5Iprivate.h
./src/H5MM.c
./src/H5MMprivate.h
./src/H5O.c
./src/H5Oefl.c
./src/H5Oprivate.h
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5P.c
./src/H5S.c
./src/H5Ssimp.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Tprivate.h
./src/H5Tpublic.h
./src/H5V.c
./src/H5Vprivate.h
./src/H5detect.c
./src/h5ls.c
./test/cmpd_dset.c
./test/dsets.c
./test/external.c
./test/hyperslab.c
./test/iopipe.c
./test/istore.c
./test/shtype.c
./test/tstab.c
Fixed comparisons between signed and unsigned values. Fixed
warnings about unused function arguments.
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is more consistent with other names like STDIO.
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----------------------
./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.
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----------------------
./bin/release
Changed default to not tag CVS sources.
./src/H5F.c
Replaced a constant switch with preprocessor directives.
Removed a local variable which was set but not used.
./src/H5Fprivate.h
Changed `long long' to `int64' to get rid of ansi warnings in
a few places.
Fixed bugs in INT64DECODE() and UINT64DECODE() for big-endian
architectures. This fixes all the bugs with the Irix -64
compile.
./src/H5F.c
The default address and length sizes are set according to the
sizeof(size_t) now that the bugs have been fixed.
./src/H5Fpublic.h
Removed a trailing comma in an enumerated type.
./src/H5Fstdio.c
./src/H5Fsec2.c
Added two more calls to fseek64() and lseek64(). Removed `long
long' in place of `int64' to suppress -ansi warnings.
./src/H5P.c
Replaced a FAIL with H5F_LOW_ERROR.
./src/H5private.h
./configure.in
Increased version number to hdf5-1.0.1a since we've already
released hdf5-1.0.0a. Include <sys/types.h>. Fixed
indentation. Fixed detection of off64_t for old Irix systems
where it might be a struct.
./src/Makefile.in
Moved a comment from the shell to the makefile since some
versions of sh barf on interactive comments.
./config/linux
Allow overriding of the CC variable from the command-line. It
still defaults to gcc but this allows us to specify a complete
path from test scripts by saying:
CC=/usr/local/tools/gnu/gcc sh configure
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----------------------
./html/Files.html
Added a few details for some of the new H5Pset/get functions.
./src/H5F.c
./src/H5Fpublic.h
Fixed automatic closing of files on exit().
Added public H5F_ACC_DEBUG. Using it to create or open a file
turns on debugging for that file, which currently just prints
cache statistics when the file is closed.
./src/H5G.c
An error is returned if one tries to set the current working
group to something other than a group.
./src/H5Gnode.c
Fixed a symbol table bug. Under certain circumstances it was
possible to enter a symbol in such a way that lookup of that
symbol failed. A bug report was sent to hdf5dev.
./src/H5P.c
./src/H5Ppublic.h
Added the H5Pget_...() functions for file drivers. The
H5Pget_mpi() is a no-op that always fails.
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from H5C to H5P
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----------------------
./configure.in
./src/H5Fprivate.h
./src/H5Fsec2.c
We now detect and use lseek64() on systems that have it (e.g.,
Irix64) and are able to generate >2GB files on Irix XFS file
systems (and anything else that supports large files). This
change also removed some warning messages from the Irix `-64'
compiler.
> $ ls -l istore.h5
> -rw-r--r-- 1 matzke meshtv 8605436856 Feb 17 14:03 istore.h5
./configure.in
./src/H5Fprivate.h
./src/H5Fstdio.h
We now detect and use fseek64() on systems that have it (e.g.,
Irix64) and are able to generate >2GB files on Irix XFS file
systems (and anything else that supports large files). This
change also removed some warning messages from the Iris `-64'
compiler.
./src/H5E.c
./src/H5Epublic.h
Added the H5E_OVERFLOW error to signal file address overflow.
./src/H5Fpublic.h
./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
./html/Datasets.html
./html/Files.html
./html/H5.api.html
./html/H5.intro.html
./html/H5.sample_code.html
./html/ph5example.c
./html/review1.html
./test/cmpd_dset.c
./test/dsets.c
./test/extend.c
./test/tfile.c
./test/th5p.c
./test/theap.c
./test/tohdr.c
./test/tstab.c
./testpar/phdf5.c
Renamed file access constants to follow the naming scheme.
Also changed the base names a little to be more accurate as to
what they do. The old names H5ACC_WRITE and H5ACC_OVERWRITE
will temporarily work.
H5ACC_DEFAULT --> H5F_ACC_RDONLY for H5Fopen()
H5ACC_DEFAULT --> H5F_ACC_EXCL for H5Fcreate()
H5ACC_WRITE --> H5F_ACC_RDWR
H5ACC_OVERWRITE --> H5F_ACC_TRUNC
Albert or Kim: The H5ACC_INDEPENDENT and H5ACC_COLLECTIVE
macros in H5Fpublic.h should be an enum typedef and have names
more like H5F_MPIO_INDEPENDENT and H5F_MPIO_COLLECTIVE. Also
change the access_mode argument of H5Cset_mpio().
H5Fcreate() and H5Fopen() are more strict now about which
flags are acceptable for the operation.
./src/H5Fprivate.h
./src/H5F.c
./src/H5C.c
Changed the file access template to make it more general. A
union contains a struct for each type of low-level driver and
the default template is initialized at run-time.
./src/H5Fpublic.h
./src/H5F.c
Added H5Fget_access_template() and cleaned up
H5Fget_create_template().
./src/H5C.c
The H5Cset_mpi() no longer trashes the file access template
when an error is detected. We check for errors and *then*
update the file access template.
Added H5C_close() so Albert and Kim have a place to release
the MPI communicator and info from the file access property
list.
Kim or Albert: I notice in H5Cset_mpi() you copy the MPI
communicator. Do you need to do something similar in
H5C_copy()?
./src/H5F.c
Added more error checking for the file creation and access
property lists because it used to be possible to make the
library dump core by swapping the creation and access property
list ID numbers of H5Fcreate().
./test/istore.c
./test/tfile.c
./test/th5p.c
./test/theap.c
./test/tohdr.c
./test/tstab.c
./testpar/testphdf5.c
One must pass H5C_DEFAULT as the file creation or access
property list in order to get the default property list. It
is no longer possible to pass zero or any other arbitrary bad
object ID.
./src/H5Fcore.c
./src/H5Ffamly.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5MF.c
The file access property list is passed to all H5F_low_...()
functions and to the drivers.
./src/H5Fcore.c
The block size can be set at run time on a per-file basis
instead of at compile time across all files. The "5000 items in
a group test" now takes 1.6 seconds.
./src/H5private.h
Removed inclusion of mpi.h and mpio.h since they're included
from H5public.h.
./src/H5Cpublic.h
./src/H5C.c
Added H5Cset_stdio(), H5Cset_sec2(), H5Cset_core(),
H5Cset_split(), and H5Cset_family() in addition to the
H5Cset_mpio() that Kim and Albert already wrote. We still
need the H5Cget_driver() and an H5Cget...() counterpart for
each of those functions. The split and family drivers still
need a little work but I'm checking this in anyway.
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MPIO lower interface layer (H5Fmpio.c) has been commited by Kim already.
All PHDF5 codes are "bracket'ed" by #ifdef HAVE_PARALLEL macro.
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----------------------
./src/*.h
Fixed indentation where indent(1) screwed up. This isn't by
any means the final say, but it's better than it was.
./src/H5A.c
./src/H5Aprivate.h
./src/H5Apublic.h
./src/H5C.c
./src/H5D.c
./src/H5E.c
./src/H5F.c
./src/H5G.c
./src/H5M.c
./src/H5P.c
./src/H5T.c
./src/H5Tconv.c
./src/debug.c
./test/dtypes.c
./test/istore.c
./test/theap.c
./test/tohdr.c
./test/tstab.c
Removed some atom functions from the API and made them
library-scope. Also changed some names by removing the
redundant `atom' from the name and by adding a `_' after the
`H5A'.
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Removed the interface initialization argument from
FUNC_ENTER() and made it a locally-defined preprocessor
symbol, INTERFACE_INIT.
Changed `offset' to `address' and `length' to `size' in
documentation so it's more consistent. `Offset' still appears
occassionally when it refers to a byte offset within some
other data structure.
Moved interface termination function prototypes from public
header files to .c files and made them static.
./src/H5.c
./src/H5public.h
Added H5init() because it's possible that the predefined data
types are not initialized. This happens only if the first
call to the hdf5 library passes a predefined data type symbol
as an argument. There should be some way to fix this...
./src/H5A.c
./src/H5Aprivate.h
./src/H5Apublic.h
The free_func returns SUCCEED or FAIL, although the return
value is ignored by H5A. This is so we can use the various
H5*_close() functions to free things.
H5Ainc_ref() and H5Adec_ref() are no longer public. Many of
the other atom functions should also be made private, but I'll
save that for later...
Added additional template groups called H5_TEMPLATE_0 through
H5_TEMPLATE_7 that are used by the various template
subclasses.
Increased the number of bits used for atom groups to prevent
negative atoms.
./src/H5AC.c
./src/H5ACprivate.h
Changed H5AC_new() to H5AC_create() to make names more consistent.
./src/H5B.c
./src/H5Bprivate.h
Changed H5B_new() to H5B_create() to make names more consistent.
./src/H5C.c
./src/H5Cprivate.h
./src/H5Cpublic.h
Now supports multiple subclasses of templates, although it's
done with big switch statements. The default values for
templates are defined in the source file to which that
template belongs. This got rid of lots of needless
preprocessor constants.
Added H5Ccreate() to create a new template. Changed
H5C_release() to H5Cclose() to make the naming more
consistent.
./src/H5D.c
./src/H5Dprivate.h
./src/H5Dpublic.h
Enhanced to use the new dataset interface, and uses the enhanced
data type and data space interfaces, which haven't been
completely implemented. The dataset interface doesn't handle
non-contiguous storage, compression, or data type and space
conversions yet.
./src/H5F.c
./src/H5Fprivate.h
./src/H5Fpublic.h
Removed H5Fflush() since just calls H5F_flush(), which doesn't
do what the user would probably think it does, namely, flush
everything. It only flushes those things sitting in the H5AC
cache and the boot block.
Changed the `file_create_parms' field of H5F_low_t to just
`create_parms' since the `file' part is obvious.
./src/H5Fistore.c
Added some support for external files. Mostly just in the
file format and not supported much by the library yet. I need
to finish some dataset functions first.
Changed H5F_istore_new() to H5F_istore_create() to make names
more uniform across packages.
./src/H5Flow.c
Flushing a file causes the file to be physically extended to
the logical eof. This prevents H5F_open() from thinking a
file has been truncated. Most of the time the file will
already be that large, and when it isn't Unix will often just
allocate the final block anyway.
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5Gstab.c
Removed H5G_basename()
Removed (temporarily) data type information from symbol table
entries and renamed H5G_CACHED_SDATA to H5G_CACHED_SDSPACE to
reflect that it's a simple data space and has nothing to do
with raw data.
Changed H5G_node_new() to H5G_node_create() and H5G_stab_new()
to H5G_stab_create() to make names more uniform across
packages.
Fixed an undefined address bug that happens when H5G_node_debug()
program doesn't pass enough info to H5G_node_load().
./src/H5H.c
./src/H5Hprivate.h
Changed H5H_new() to H5H_create() to make the names more
uniform across packages.
./src/H5M.c
./src/H5Mprivate.h
./src/H5Mpublic.h
Nulled all the create functions. Most of the other callbacks
are to public functions. Removed H5Mcreate().
Changed hobjtype_t to group_t since it has to be the same
thing anyway.
./src/H5O.c
./src/H5Oprivate.h
./src/H5Osdim.c
./src/H5Osdtyp.c
Changed H5O_SIM_DIM to H5O_SDSPACE (simple data space) since
`simple data space' is its official name, not `simple
dimensions'. Will eventually add H5O_CDSPACE for comples data
spaces. Changed _sim_dim_ to _dspace_.
Replaced H5O_SIM_DTYPE and the compound data type messages
with a single H5O_DTYPE message. Changed _sim_dtype_ to _dtype_.
Changed H5O_STD_STORE to H5O_CSTORE (contiguous storage) since
contiguous storage is not necessarily standard. Changed
_std_store_ to _cstore_ in H5Ocstore.c
Added the H5O_EFL (external file list) message.
Changed H5O_new() to H5O_create() to make names more uniform
across packages.
./src/H5Oefl.c NEW
External file list message for specifying which non-hdf5 files
contain raw data for a dataset.
./src/H5P.c
./src/H5Pprivate.h
./src/H5Ppublic.h
Renamed and moved data structures to make the names conform to
our naming scheme.
./src/H5T.c
./src/H5Tprivate.h
./src/H5Tpublic.h
./src/H5Tpkg.h NEW
Data structures redesigned to be more flexible. The interface
was redesigned to make it more regular and to make some names
more uniform across packages.
./src/H5detect.c
Output was changed to produce a file that conforms to the hdf5
coding standard.
./src/Makefile.in
Generates H5Tinit.c by running H5detect.
./src/debug.c
Moved command argument processing.
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allocated during
runtime. Isolated but can't figure out how to fix bug reported with purify.
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Added H5Fflush() and H5F_flush() which flush (and optionally
invalidate the cache) and flush the file boot block.
H5Fcreate() calls H5F_flush() to output the boot block.
H5Fclose() calls H5F_flush() to update the boot block.
H5F_debug() prints the root symbol table entry.
./src/H5Fpublic.h
Added H5Fflush() prototype.
./src/H5G.c
The name message is removed when an object moves from the root
object position into a directory.
Added H5G_debug() to print a symbol table entry. Most of the
code was just moved from H5G_node_debug().
./src/H5Gnode.c
Moved some debugging code into H5G_debug().
./src/H5Gprivate.c
Added H5G_debug() prototype.
./src/H5O.c
Implemented H5O_remove().
Added identifiers for H5O_SIM_DIM and H5O_SIM_DTYPE so they
can be read from files.
H5O_load() combines adjacent null messages for better memory
management.
./src/H5Oprivate.h
Changed minimum header data block size from 16 to 32 bytes.
Changed prototype for H5O_remove()
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I commented out a bunch of code in H5D_flush() so I could
compile and link the test cases. If you commit your changes
to that file, whatever they may be, I'll change H5D_flush() to
use the new directory functions described below...
./src/H5G.c
H5G_namei()
-----------
Understands files without directories. The root object
(directory or not) can be found by asking for `/' (or any
equivalent absolute or relative name like `/.//.///' or
`.//.///' (if the cwd is the root)) or by name like `/foo' (or
any other equivalent absolute or relative name) if the object
has a name message with the value `foo'. This function is
used by most of the other H5G functions so they now understand
directory-less files too.
H5G_new()
---------
Creates the root directory implicitly if it doesn't already
exist, moving any previous non-directory root object into the
new root directory before creating the requested directory
within the root. The creation of the root directory happens
first, regardless of whether the requested directory creation
succeeds. Once the root directory is created it never
disappears even if the file later has only one object. This
"feature" can be used to force a file to have a root directory
by saying something like:
H5G_new (..., "/", ...);
H5ECLEAR; /*we don't care about the H5E_EXISTS failure*/
The H5G_new() in the previous example fails because the root
directory is created implicitly before we attempt to create
the requested "/" directory.
H5G_find()
----------
Understands files without directories. If there is no root
object then this function is guaranteed to fail even if the
request is for `/'. As mentioned for H5G_namei(), the root
object can be retrieved with `/' or `/foo' (or equivalent
absolute or relative names).
H5G_insert()
------------
Understands files without directories and attempts to create
such files when there is only one object. The root symbol
table is created implicitly when necessary.
A root object can be given a name message by the caller and
then inserted with the name `/' or it can be inserted with
the name `/foo' in which case H5G_insert() will set the name
message to `foo'.
H5G_modify()
------------
Understands files without directories.
./src/H5Fprivate.h
Removed the root_type field from hdf5_file_t.
./src/H5Fprivate.h
./src/H5F.c
Removed H5F_root_type()
./src/H5Fpublic.h
Removed H5F_root_symtype_t.
./src/H5Oprivate.h
./src/H5O.c
Added H5O_remove() which is currently a no-op.
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./src/H5Aproto.h
./src/H5Bproto.h
./src/H5Cproto.h
./src/H5Dproto.h
./src/H5Eproto.h
./src/H5Fproto.h
./src/H5Gproto.h
./src/H5Hproto.h
./src/H5MFproto.h
./src/H5MMproto.h
./src/H5Mproto.h
./src/H5Oproto.h
./src/H5Pproto.h
./src/H5Tproto.h
./src/H5proto.h
These files were removed from the library and renamed by
changing `proto' to `public'.
./src/H5ACpublic.h NEW
./src/H5Apublic.h NEW
./src/H5Bpublic.h NEW
./src/H5Cpublic.h NEW
./src/H5Dpublic.h NEW
./src/H5Epublic.h NEW
./src/H5Fpublic.h NEW
./src/H5Gpublic.h NEW
./src/H5Hpublic.h NEW
./src/H5MFpublic.h NEW
./src/H5MMpublic.h NEW
./src/H5Mpublic.h NEW
./src/H5Opublic.h NEW
./src/H5Ppublic.h NEW
./src/H5Tpublic.h NEW
./src/H5public.h NEW
These files came from the old H5*proto.h files.
./src/Makefile
./src/Makefile.in NEW
Removed. Now generated automatically from Makefile.in by
running configure.
./src/h5oplat.h
./src/hdf5fort.h
./src/hdf5gen.h
./src/hdf5glob.h
./src/hdf5lims.h
./src/hdf5meta.h
./src/hdf5pabl.h
./src/hdf5plat.h
./src/hdf5port.h
./src/hdf5type.h
Removed. The contents of these files has moved to other
header files or source files depending on it's nature.
./src/H5.c
./src/H5A.c
./src/H5B.c
./src/H5C.c
./src/H5D.c
./src/H5E.c
./src/H5F.c
./src/H5G.c
./src/H5H.c
./src/H5M.c
./src/H5MF.c
./src/H5MM.c
./src/H5O.c
./src/H5Ocont.c
./src/H5Oname.c
./src/H5Onull.c
./src/H5Ostab.c
./src/H5P.c
./src/H5T.c
Fixed include files. Moved some things from old headers into
these files.
./src/H5ACprivate.h
./src/H5Aprivate.h
./src/H5Bprivate.h
./src/H5Cprivate.h
./src/H5Dprivate.h
./src/H5Eprivate.h
./src/H5Fprivate.h
./src/H5Gprivate.h
./src/H5Hprivate.h
./src/H5MFprivate.h
./src/H5MMprivate.h
./src/H5Mprivate.h
./src/H5Oprivate.h
./src/H5Pprivate.h
./src/H5Tprivate.h
./src/H5private.h
./src/debug.c
Fixed include files.
./src/hdf5.h
This is now the top-level *PUBLIC* include file. It should
never appear in the library *.c files.
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