| Commit message (Collapse) | Author | Age | Files | Lines |
... | |
|
|
|
|
|
|
|
|
|
|
| |
Purpose:
New feature
Description:
Fill-value's behaviors for contiguous dataset have been redefined.
Basicly, dataset won't allocate space until it's necessary. Full details
are available at http://hdf.ncsa.uiuc.edu/RFC/Fill_Value, at this moment.
Platforms tested:
Linux 2.2.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Purpose:
H5Dset_extent API function
Description:
1 new public function: H5Dset_extent, that allows shrinking a dataset
several private functions that free the previously allocated chunks
H5F_istore_prune_by_extent, H5B_prune_by_extent : removes the chunks
H5F_istore_initialize_by_extent : initializes them with the fill value
H5S_select_fill is used to fill the selection in the memory buffer
Platforms tested:
Windows 2000
SUN( arabica)
LINUX (eirene)
IRIX64 (modi4)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
New Feature
Description:
Added new H5Dfill() routine to fill the elements in a selection for a
memory buffer with a fill value. This is a user API wrapper around some
internal routines which were needed for the fill-value modifications
from Raymond as well as Pedro's code for reducing the size of a chunked
dataset.
Platforms tested:
FreeBSD 4.5 (sleipnir) [and IRIX64 6.5 (modi4) in parallel, in a few
minutes]
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Description:
modified the below files to inlude a new public function H5Dset_extend, similar
to H5Dextend, but it can lower the dimension
this function requires 2 more new private functions:
H5D_set_extend
H5S_set_extend
Platforms tested:
|
|
|
|
|
|
|
|
|
| |
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)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
Update
Description:
Changed
#include <hdf_file.h>
construct to
#include "hdf_file.h"
so that the GNU compiler can more easily pick up the dependencies
which it places in the .depend and Dependencies files. Also
regenerated the Dependencies to go along with this.
Platforms tested:
Linux
|
|
|
|
|
|
|
|
| |
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)
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
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.
|
| |
|
|
|
|
|
|
|
| |
to add tests
for now. Also, I revised some of the code for hyperslab I/O, which should
provide a modest speedup in situations with lots of hyperslabs.
|
|
|
|
|
|
| |
currently working
is H5Tvlen_create().
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./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.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./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.
|
|
|
|
| |
also exported all globals and non static functions to the dll
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./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'.
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./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.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
mode to use for data transfer. Currently, INDEPENDENT transfer
is the default mode. Collective is supported for files opened
via the MPIO driver. Specific changes to individual files follow.
H5D.c:
Replaced previous kludge of passing xfer_mode via the file access_mode
with xfer_mode function parameter all the way to the low level I/O
drivers.
H5Dprivate.h:
The H5D_xfer_t.xfer_mode is now used in serial and parallel modes.
Removed the "HAVE_PARALLEL" macro condition to support it.
H5Dpublic.h:
Added H5D_XFER_DFLT as a new value for H5D_transfer_t and removed
the HAVE_PARALLEL condition macro to make the H5D_transfer_t
definition available to both serial and parallel version.
H5B.c:
H5F.c:
H5Farray.c:
H5Fcore.c:
H5Ffamily.c:
H5Fistore.c:
H5Flow.c:
H5Fmpio.c:
H5Fsec2.c:
H5Fsplit.c:
H5Fstdio.c:
H5Gnode.c:
H5HG.c:
H5HL.c:
H5O.c:
H5Sprivate.h:
H5Ssimp.c:
debug.c:
Added xfer_mode to the argument lists of the following routines to
specify data transfer mode. Then updated calls to these routines
with appropriate transfer mode. Whenever cases that collective
mode is inappropriate (e.g. object header read-write, flush),
H5D_XFER_DFLT is used. The H5D_XFER_DFLT mode is currently
acting the same as the independent mode.
H5F_block_read
H5F_block_write
H5F_arr_read
H5F_arr_write
H5F_core_read
H5F_core_write
H5F_fam_read
H5F_fam_write
H5F_mpio_read
H5F_mpio_write
H5F_low_write
H5F_low_read
H5F_sec2_read
H5F_sec2_write
H5F_split_read
H5F_split_write
H5F_stdio_read
H5F_stdio_write
H5S_simp_fgath
H5S_simp_fscat
H5S_simp_read
H5S_simp_write
H5Fprivate.h:
H5P.c:
Removed access_mode field from struct H5F_access_t type.
The access-mode was the initial design to control independent
or collective I/O mode. It is now supported by the data
transfer mode.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./html/Compression.html [NEW]
./html/Datasets.html
./html/H5.format.html
./html/H5.user.html
Documented compression. A couple of the H5P functions aren't
quite implemented yet but they're coming soon...
./src/H5Dprivate.h
./src/H5E.c
./src/H5Epublic.h
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fprivate.h
./src/H5MF.c
./src/H5MFprivate.h
./src/H5O.c
./src/H5Ocomp.c [NEW]
./src/H5Oprivate.h
./src/H5P.c
./src/H5Ppublic.h
./src/H5Sprivate.h
./src/H5Ssimp.c
./src/H5Z.c [NEW]
./src/H5Zprivate.h [NEW]
./src/H5Zpublic.h [NEW]
./src/Makefile.in
./src/hdf5.h
./test/dsets.c
./test/istore.c
Compression is now mostly working. Don't try to open a
compressed dataset though because the compression message
won't be read.
./html/Datatypes.html
./html/H5.api.html
./src/H5.c
./src/H5private.h
./src/H5D.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5Tpublic.h
Added timing support. When compiled with H5T_DEBUG defined
the library will print conversion bandwidths when the library
closes. The H5Tregister functions take a string as the first
argument so the statistics output is meaningful.
./MANIFEST
Added new files.
./configure.in
./src/H5config.h.in
Check for getrusage(). Check for compress2() in libz.a and
the zlib.h header file. Added `z' to the debug list.
./src/H5B.c
./src/H5Bprivate.h
./src/H5Gnode.c
./src/debug.c
Cleaned up some indentation and added support to print istore
B-trees. From the debugger, give the B-tree address and the
dimensionality from the layout message of the object header.
./src/h5ls.c
The oid is printed as w:x:y:z where w and x are the file ID
and y and z are the OID within the file. You can give z or
y*2^32+z as an argument to the debugger to print the object
header for the object.
./src/H5AC.c
Cleaned up statistics and made them match those reported by
H5T and H5Z.
./src/H5MM.c
./src/H5MMprivate.h
./src/H5Fistore.c
Finally got rid of a couple of long-standing const cast
warnings.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
H5D.c
Changed H5D_write and H5D_read to recognize collective transfer
requests. Current algorithm puts the xfer-mode in the file->mpio
structure. Not thread safe. Need to revise it to pass transfer
parameter as a function parameters to the lower levels.
H5Dprivate.h
H5Dpublic.h
Added xfer_mode to the transfer property list structure.
Added defination of transfer modes, H5D_XFER_INDEPENDENT and
H5D_XFER_COLLECTIVE.
H5Farray.c
Added code to handle collective access requests. Currently
works for one contiguous block at a time. Need to revise
it with the MPIO low level calls to combine all blocks as
one truely collective call.
H5P.c
H5Ppublic.h
Added H5Pset_xfer and H5Pget_xfer routines that can set and get
the transfer mode of a data transfer property list.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./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.
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./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.
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./src/H5C.c
./src/H5Cprivate.h
./src/H5D.c
./src/H5Dpublic.h
Added H5Dget_create_parms(), trying to stay one step ahead of
Elena ;-)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./MANIFEST
Added H5Fmpio.c. One way to check that you've properly
included new files is to run `./bin/release none', then unpack
the resulting tar file somewhere and try to compile it. The
tar file will be ./releases/hdf-5.0.0a.tar.
./config/freebsd2.2.1
./config/linux
Added `-ansi'
./acconfig.h
Added definitions for PHDF5 and HAVE_PARALLEL.
./configure.in
Added minimal support for parallel build. Kim and Albert will
have to flesh this out or I can do it if they're more specific
about what they need.
./config/commence.in
Added default value for $(RUNTEST)
./config/conclude.in
`make test' uses value of $(RUNTEST) to run test cases.
./src/Makefile.in
Added PARALLEL_SRC for conditional compilation of H5Fmpio.c
./src/H5D.c
./src/H5Dpublic.h
Added H5Dget_type() for Elena
NOTE: These changes require that configure be rerun. If you're using
GNU make it will happen automatically, otherwise do it by
hand.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./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.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./src/H5D.c
./src/H5Dpublic.c
Added H5Dget_space().
./src/H5Gstab.c
./src/H5H.c
Fixed a comparison with size_t against <0.
./src/H5P.c
./src/H5Pprivate.h
./src/H5Ppublic.h
Changed `intn' to `int' for public function args and
returns. H5Pget_hyperslab() returns the dimensionality.
./test/testhdf5.h
Clears error stack more frequently.
./src/H5Psimp.c
./test/cmpd_dset.c
Impelementing data space conversion.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./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'.
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./html/Datasets.html
Removed some archaic comments about data spaces. Fixed example
code.
./MANIFEST
./html/H5.format.html
./src/H5O.c
./src/H5Oprivate.h
./src/H5Ocstore.c [DELETED]
./src/H5Oistore.c [DELETED]
./src/H5Olayout.c [NEW]
./src/Makefile.in
./test/istore.c
Replaced H5O_CSTORE and H5O_ISTORE messages with a more
general H5O_LAYOUT message.
./src/H5D.c
./src/H5Dprivate.h
./src/H5Dpublic.h
A little more work on the pipeline. Access to the file data
is through the new H5F_arr_read() and H5F_arr_write() which do
I/O on hyperslabs of byte arrays and don't depend on data
layout. This should simplify the I/O pipeline quite a bit.
I also added another argument to H5Dread() and H5Dwrite() to
describe the hyerslab of the file array on which I/O is
occuring. We discussed this at last week's meeting.
./src/H5Farray.c [NEW]
Added functions that sit on top of H5F_block_read() and
H5F_istore_read() and implement a common set of functions
between all layouts. This means I/O of hyperslabs of
byte-arrays in the file to arrays of bytes in memory. When
operating on arrays of elements (>1byte) then we just add
another dimension. That is, a 10x20 array of int32 becomes a
10x20x4 array of bytes.
[This is the area I'll be working on most of next week to
implement partial I/O for contiguous data and to improve
performance for chunked data.]
./src/H5Fistore.c
./src/H5Fprivate.h
Replaced the H5F_istore_t data type with the layout message
H5O_layout_t which looks almost the same. Eventually I'd like
to rename `istore' to `chunked' everywhere and use `istore'
for 1-d storage where the chunks are all different sizes like
in the small object heap where each object is a chunk.
./src/H5V.c
Changed ISTORE to LAYOUT in one place.
./test/dsets.c
Fixed for extra argument to H5Dread() and H5Dwrite().
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
----------------------
./config/freebsd2.2.1
./config/linux
Added -UH5O_DEBUG to the debug flags. Turn this on to get
lots of lines on stderr to show what objects are opened and
closed.
./src/H5C.o
./src/H5Cpublic.h
./test/dsets.c
./test/tfile.c
Split H5Cget_prop() and H5Cset_prop() into functions for each
property.
./src/H5D.c
./src/H5Dpublic.h
./src/H5Gstab.c
./src/H5O.c
./src/H5Ocont.c
./src/H5Ocstore.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Oistore.c
./src/H5Oname.c
./src/H5Onull.c
./src/H5Oprivate.h
./src/H5Osdspace.c
./src/H5Ostab.c
./src/H5P.c
./src/istore.c
./test/tohdr.c
Object header functions now understand constant
vs. non-constant messages.
./src/H5F.c
./src/H5Fprivate.h
The file OID can be closed before other OID's.
./src/H5Flow.c
H5F_addr_defined() is a macro in this file.
./src/H5G.c
./src/H5Gpublic.h
./test/tstab.c
A current working group cannot be deleted.
./src/H5Gent.c
./src/H5Gpkg.h
Removed unused functionality.
./src/H5public.h
Includes <sys/types.h> for size_t.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
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.
|
| |
|
|
|
|
|
|
| |
allocated during
runtime. Isolated but can't figure out how to fix bug reported with purify.
|
|
|
|
|
|
| |
except writing
a second dataset out to the file seems to loose the first one.
|
|
|
|
|
|
|
| |
to the disk
correctly, but only in "native" format. I'm adding the data-type conversions
and checking the reading later today.
|
|
./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.
|