Lots of performance improvements & a couple new internal API interfaces.
Description:
Performance Improvements:
- Cached file offset & length sizes in shared file struct, to avoid
constantly looking them up in the FCPL.
- Generic property improvements:
- Added "revision" number to generic property classes to speed
up comparisons.
- Changed method of storing properties from using a hash-table
to the TBBT routines in the library.
- Share the propery names between classes and the lists derived
from them.
- Removed redundant 'def_value' buffer from each property.
- Switching code to use a "copy on write" strategy for
properties in each list, where the properties in each list
are shared with the properties in the class, until a
property's value is changed in a list.
- Fixed error in layout code which was allocating too many buffers.
- Redefined public macros of the form (H5open()/H5check, <variable>)
internally to only be (<variable>), avoiding innumerable useless
calls to H5open() and H5check_version().
- Reuse already zeroed buffers in H5F_contig_fill instead of
constantly re-zeroing them.
- Don't write fill values if writing entire dataset.
- Use gettimeofday() system call instead of time() system when
checking the modification time of a dataset.
- Added reference counted string API and use it for tracking the
names of objects opening in a file (for the ID->name code).
- Removed redundant H5P_get() calls in B-tree routines.
- Redefine H5T datatype macros internally to the library, to avoid
calling H5check redundantly.
- Keep dataspace information for dataset locally instead of reading
from disk each time. Added new module to track open objects
in a file, to allow this (which will be useful eventually for
some FPH5 metadata caching issues).
- Remove H5AC_find macro which was inlining metadata cache lookups,
and call function instead.
- Remove redundant memset() calls from H5G_namei() routine.
- Remove redundant checking of object type when locating objects
in metadata cache and rely on the address only.
- Create default dataset object to use when default dataset creation
property list is used to create datasets, bypassing querying
for all the property list values.
- Use default I/O vector size when performing raw data with the
default dataset transfer property list, instead of querying for
I/O vector size.
- Remove H5P_DEFAULT internally to the library, replacing it with
more specific default property list based on the type of
property list needed.
- Remove redundant memset() calls in object header message (H5O*)
routines.
- Remove redunant memset() calls in data I/O routines.
- Split free-list allocation routines into malloc() and calloc()-
like routines, instead of one combined routine.
- Remove lots of indirection in H5O*() routines.
- Simplify metadata cache entry comparison routine (used when
flushing entire cache out).
- Only enable metadata cache statistics when H5AC_DEBUG is turned
on, instead of always tracking them.
- Simplify address comparison macro (H5F_addr_eq).
- Remove redundant metadata cache entry protections during dataset
creation by protecting the object header once and making all
the modifications necessary for the dataset creation before
unprotecting it.
- Reduce # of "number of element in extent" computations performed
by computing and storing the value during dataspace creation.
- Simplify checking for group location's file information, when file
has not been involving in file-mounting operations.
- Use binary encoding for modification time, instead of ASCII.
- Hoist H5HL_peek calls (to get information in a local heap)
out of loops in many group routine.
- Use static variable for iterators of selections, instead of
dynamically allocation them each time.
- Lookup & insert new entries in one step, avoiding traversing
group's B-tree twice.
- Fixed memory leak in H5Gget_objname_idx() routine (tangential to
performance improvements, but fixed along the way).
- Use free-list for reference counted strings.
- Don't bother copying object names into cached group entries,
since they are re-created when an object is opened.
The benchmark I used to measure these results created several thousand
small (2K) datasets in a file and wrote out the data for them. This is
Elena's "regular.c" benchmark.
These changes resulted in approximately ~4.3x speedup of the
development branch when compared to the previous code in the
development branch and ~1.4x speedup compared to the release
branch.
Additionally, these changes reduce the total memory used (code and
data) by the development branch by ~800KB, bringing the development
branch back into the same ballpark as the release branch.
I'll send out a more detailed description of the benchmark results
as a followup note.
New internal API routines:
Added "reference counted strings" API for tracking strings that get
used by multiple owners without duplicating the strings.
Added "ternary search tree" API for text->object mappings.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Other platforms/configurations tested?
FreeBSD 4.7 (sleipnir) serial & parallel
Solaris 2.6 (baldric) serial
Code cleanup
Description:
Added more test datafiles to clean directive.
Platforms tested:
FreeBSD 4.6 (sleipnir) w and w/o parallel
Linux 2.2.x (eirene) w/FORTRAN & C++
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
Purpose:
New API functions
Description:
Added API functions to return pointer to low-level file handle
(H5Fget_vfd_handle and H5FDget_vfd_handle) and related property list
setting functions(H5Pset_family_offset and H5Pset_multi_type).
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
Purpose:
Added 'ID to name' support
Description:
There is a new API function H5Iget_name
Most of the changes are on H5G.c , regarding the symbol table entry struct H5G_entry_t
which has 2 new fields 'name' and 'old_name'
A new private function was introduced H5G_ent_copy, that does a deep copy
between 2 symbol table entries
The test file is getname.c
Platforms tested:
windows 2000, Linux, Solaris
Code cleanup/More tests
Description:
Cleaned up some compiler warnings and wrote additional tests for space
allocation and storage size routines.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/serial & parallel. Will be testing on IRIX64
6.5 (modi4) in serial & parallel shortly.
Additional regression tests & bug fixes
Description:
There was no testing for the H5Dget_storage_size function and it seemed to
be having problems with compressed, chunked datasets, so write some tests
to verify that its working correctly.
Also, fix case for allocating storage early for chunked datasets
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel
Bug Fix
Description:
H5Dcreate and H5Tcommit allow "empty" compound and enumerated types (i.e.
ones with no members) to be stored in the file, but this causes an assertion
failure and is somewhat vapid.
Solution:
Check the datatype "makes sense" before using it for H5Dcreate and
H5Tcommit.
Platforms tested:
FreeBSD 4.5 (sleipnir)
Test Bug Fix
Description:
Under certain [obscure] circumstances, an object header would get paged out
of the metadata cache, and when it was accessed again and brought back into
the cache, and immediately had additional metadata added to it (an
attribute, usually, or perhaps adding an object to a group), and needed to
be extended with a continuation message, but there was no room in any
existing object header chunks for the continuation message and an existing
object header message needed to be moved to the new object header chunk (I
told you it was obscure :-), the object header message moved to the new
chunk (not the new metadata being added) would get corrupted. *whew* :-)
Solution:
Actually copy the "raw" object header message information of the object
header message being moved to the new chunk, instead of relying on the
"native" object header message information being re-encoded when the object
header is flushed. This is because when an object header is paged out of
the metadata cache and subsequently brought back in, the "native"
information pointer in memory is reset to NULL and only the "raw"
information exists.
[Actually, this additional testing doesn't trigger the bug, which needs
_lots_ of objects to be created and accessed, but it does execise the
object header continuation code more than other tests in the library.]
Platforms tested:
Solaris 2.7 (arabica) & FreeBSD 4.5 (sleipnir)
Bug fix
Description:
$(LT_RUN) was used to execute ./H5detect in src/Makefile.in.
$RUNTEST was set to $(LT_RUN) which was used to execute sequential
executable. $(LT_RUN) is "../libtool --mode=execute". But libtool
invokes some commands that are not supported in the Tflops machine.
That caused failures during the build and check processes.
Solution:
Upon investigation, there does not seem to be need to use $(LT_RUN)
any more. The "libtool --mode=link" now generates a "fake" executable
that is actually a command-script file that can regenerate the real
executable with dynamic libraries hooks setup properly.
Undo all those $LT_RUN substitute and let $RUNSERIAL execute those
sequential executables.
Platforms tested:
Eirene(serial), modi4(parallel)
Bug fix
Description:
When several level deep nested compound & VL datatypes are used, the data
in the nested compound datatypes is incorrectly sharing the same "background
buffer", causing data corruption when the data is written to the file.
Solution:
Allocate a separate background buffer for each level of the nested types
to convert. (Also allocate temporary background buffers for array
datatypes, where this sort of problem could occur also)
Added more regression tests to check for these errors.
Platforms tested:
FreeBSD 4.5 (sleipnir) & Solaris 2.6 (baldric)
Bug Fix
Description:
Regression test for following bug:
The H5Gget_objinfo() function was not setting the 'fileno' field in the
H5G_stat_t struct passed in.
Solution:
Added a "file serial number" to each file currently open in the library
and put that in the 'fileno' field. If a file is opened twice (with
H5Fopen) and the VFL driver detects that it is the same file (i.e. the
two file structures have the same "shared file info" in the library's
memory structures), they will have the same serial number.
This serial number has two drawbacks:
- If a VFL driver doesn't/can't detect that two calls to H5Fopen with
the same file actually _are_ the same file, each will get a
different serial number
- If the same file is closed and re-opened, the serial number will be
different.
It is be possible to fix the second drawback for many VFL drivers, but it
would be a lot of effort and probably isn't worth it until we've got a
good reason to do it. Dunno if we'll ever be able to fix the first
drawback...
Platforms tested:
FreeBSD 4.5 (sleipnir)
VS: ----------------------------------------------------------------------
Cleanup
Description:
Added set_extend.h5 file to the CLEANUP macro in the Makefile so that
it'll be removed when the other temp files are removed.
Platforms tested:
Linux
Bug Fix
Description:
When file space was returned to the file space free-list for reuse,
occasionally raw data allocations which used space from the free-list
would overlap with the metadata accumulator and get over-written with
the cached information in the accumulator, corrupting the data.
Solution:
Check if the space about to be recycled on the free-list is going to be
used for raw data and also overlaps with the metadata accumulator cache,
avoiding using space that fits those criteria.
This fixes bug #701
Platforms tested:
FreeBSD 4.5 (sleipnir)
Removing the DPSS (gridstorage) driver source code.
Description:
The DPSS (using Grid-Storage) driver is retired.
Removed the configure option with-gridstorage from configure.in.
Cvs remove the following files
./src/H5FDdpss.c
./src/H5FDdpss.h
./test/dpss_read.c
./test/dpss_write.c
Regenerated Dependencies files (some had to be hand-edited since
'make depend' did not cover them.)
Removed reference to DPSS Virtual file driver from H5F.c.
Platforms tested:
modi4 (Parallel; -with-gass=...), eirene, arabica (fortran, cxx).
New feature.
Description:
Added a test to verify the correctness of information provided by
configure in H5config.h. Some information, such as SIZEOF some
types can be hardcoded by config/<machine>. This test verified
the information is indeed correct.
Currenly, only size of C language types are verified.
Platforms tested:
Eirene, regular, arabica.
New Feature
Description:
Added array datatype tests to the regression tests. These datatype
combinations are tested currently:
1-D array of atomic datatypes
3-D array of atomic datatypes
array of array of atomic datatypes
array of compound of atomic datatypes
array of compound of array datatypes
array of VL of atomic datatypes
array of VL of array datatypes
Also added a test to verify that the older style compound datatype with
array fields works correctly.
Platforms tested:
FreeBSD 4.1.1 (hawkwind)
Bug fix
Description:
"Time" datatypes (H5T_UNIX_D*) were not being stored and retrieved in
the datatype object header message correctly.
Solution:
Store endian-ness and precision in the datatype object header message and
added test to continue to track them working correctly.
This fixes bug #512.
Platforms tested:
FreeBSD 4.1.1 (hawkwind)
zlib, and zlib isn't in our LD_LIBRARY_PATH or in a standard system
library place (/usr/lib or /lib), then the tests can't run. This fixes it
if the person configures the source with the flag:
--with-zlib=/usr/fnord/include,/usr/fnord/lib
This only works if you're pointing to the shared library version in the
above flag...
that all HDF5 API functions are protected by a mutex lock. Basically,
serialized all API calls. To use it, use
configure --enable-threadsafe --with-pthread
----------------------
./MANIFEST
./configure.in
./configure [REGENERATED]
Added more checking for `make' features.
./Makefile.in
./doc/Makefile.in
./doc/html/Makefile.in
./doc/html/Tutor/Makefile.in
./examples/Makefile.in
./pablo/Makefile.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
./config/commence.in
./config/conclude.in
./config/depend.in [REMOVED]
./config/depend1.in [NEW]
./config/depend2.in [NEW]
./config/depend3.in [NEW]
./config/depend4.in [NEW]
./config/dependN.in [NEW]
The directory search stuff was moved into commence.in, thereby
shortening the Makefile.in prologues.
./doc/html/Dependencies [NEW]
./doc/html/Tutor/Dependencies [NEW]
./examples/Dependencies [NEW]
./src/Dependencies [NEW]
./test/Dependencies [NEW]
./testpar/Dependencies [NEW]
./tools/Dependencies [NEW]
The `.distdep' files were all renamed to `Dependencies' to make them
more obvious. They are required (but may be empty) in every directory
that has a Makefile.in that ends with @CONCLUDE@ (you'll get an
obvious error from make if you forgot to create one).
./bin/trace
./src/H5.c
Added H5E_major_t and H5E_minor_t although tracing only prints the
integer value.
./src/H5E.c
./src/H5Epublic.h
Added tracing information.
./src/H5FDcore.c
./src/H5FDfamily.c
./src/H5FDgass.c
./src/H5FDmpio.c
./src/H5FDsec2.c
./src/H5FDstdio.c
Fixed places where FUNC_LEAVE() evaluated it's argument more than
once.
Added tracing information.
Wrapped long lines.
./config/gnu-flags
Fixed a syntax error when we don't have a gnu compiler.
Minor changes done to test/gass_xxx.c so that they print the
test skip message when GASS driver is not available.
This change is the implementation of GASS within HDF5-1.3 (HDF5 with Virtual
File Layer). The GASS driver gives the facility of accessing HDF files on
remote ftp servers. To use the GASS driver, the option --with-gass=<GASS path>
shoud be specified with configure. An example of the command line used to
test the distribution was:
./configure --disable-shared --without-hdf4
--with-gass=/afs/ncsa/projects/hdf/v5/bagchi/globus/GLB/development/sparc-sun-solaris2.6_nothreads_standard_debug/include,/afs/ncsa/projects/hdf/v5/bagchi/globus/GLB/development/sparc-sun-solaris2.6_nothreads_standard_debug/lib
--disable-parallel
The user should change the path to point to his local GASS installation.
Documentation about the features of GASS and the HDF-GASS design is available
separately and till it is put up on the official web site, anyone interested
may contact me.
Test programs to read, write or append remote files have been provided in the
test directory as "gass_read.c", "gass_write.c", "gass_append.c". The test
programs have the ftp site to access #define-d at the top of the file which
the user can change accordingly.
./src/H5Epublic.
Added new error type for file close.
./src/H5F.c
Added hooks for the GASS driver.
./src/H5public.h
Added header files for GASS & Globus.
./src/Makefile.in
Added dependancy on GASS driver in LIB_SRC.
./src/hdf5.h
Included header file for GASS driver.
./src/H5FDgass.c [NEW]
Routines for the GASS driver.
./src/H5FDgass.h [NEW]
Header file for the GASS driver.
./test/Makefile.in
Added dependancy on the gass test routines.
./test/gass_read.c
File to test remote file reading using GASS.
./test/gass_write.c
File to test remote file writing using GASS.
./test/gass_append.c
File to test remote file appending using GASS.
----------------------
./MANIFEST
./src/H5FDmulti.c [NEW]
./src/H5FDmulti.h [NEW]
./src/Makefile.in
./src/hdf5.h
The split driver was reimplemented as a more general "multi"
driver which is capable of splitting data into multiple files
like the family driver except the partioning is done by memory
usage type instead of address. The H5Pset_fapl_split()
function just calls H5Pset_fapl_multi() with arguments which
prepare to split the address space into two files: meta and
raw data.
This is the first version. I plan to allow the open() call to
relax a bit which would allow one to open an hdf5 file when
only the meta-data file is present. This would allow a very
large file to be split and stored on tape and the relatively
small meta file to be mirrored on disk to allow limited
browsing of the file (any request for raw data would fail).
./src/H5private.h
./src/H5F.c
./src/H5FD.c
./src/H5FDprivate.h
./src/H5FDpublic.h
./src/H5FDcore.c
./src/H5FDfamily.c
./src/H5FDmpio.c
./src/H5FDsec2.c
Added the ability for a file driver to store information in
the superblock which would be needed if the file were opened
again later for reading. The format is driver-defined which
allows users to extend it however they like.
./doc/html/H5.format.html
Added information about the new driver information block of
the superblock. This is where file drivers store information
they need in order to reopen the file later.
./src/H5F.c
./src/H5Fprivate.h
./src/H5FD.c
./src/H5FDprivate.h
./src/H5FDpublic.h
./src/H5FDcore.c
./src/H5FDfamily.c
./src/H5FDmpio.c
./src/H5FDsec2.c
./src/H5Fistore.c
./src/H5R.c
The file access properties and the file access property list
were decoupled, which allows the property list to more cleanly
contain properties for various levels of the file and which
allows the property list to be modified more cleanly when
opening files.
./src/H5.c
./src/H5FDpublic.h
Removed H5FD_MEM_META and H5FD_MEM_GROUP since they're never
used.
./src/H5D.c
Changed the way we detect the MPIO driver in all these special
cases.
./src/H5F.c
./src/H5Rpublic.h
./test/tfile.c
The default file sizeof(offset) was changed to be a function
of haddr_t instead of hsize_t.
THE H5RPUBLIC.H DEFINITIONS WILL HAVE PROBLEMS IF THE USER
CREATES A FILE WITH NON-DEFAULT OFFSET AND SIZE SIZES!
./src/H5F.c
Fixed an uninitialized memory access bug in file closing
related to the VFL.
./src/H5T.c
./src/H5Tpublic.h
Added an H5T_NATIVE_HADDR predefined datatype which
corresponds to the `haddr_t' type.
./test/Makefile.in
Reformatted long lines.
./test/big.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/extend.c
./test/external.c
Removed the H5F_ACC_DEBUG flag from file creation/open calls.
./test/big.c
Plugged a memory leak.
./test/h5test.c
Added support for the `multi' driver.
Removed #warning about not having the stdio driver. Plans are
to not implement it since the sec2 driver serves the same
purpose and testing didn't show any difference in execution
times between the two.
----------------------
./Makefile.in [1.3]
./examples/Makefile.in [1.3]
./pablo/Makefile.in [1.3]
./src/Makefile.in [1.3]
./test/Makefile.in [1.3]
./testpar/Makefile.in [1.3]
./tools/Makefile.in [1.3]
./config/commence.in [1.3]
./config/conclude.in [1.3]
./config/depend.in [1.3]
Added a `.PATH' target for Irix pmake which is identical to
the VPATH used by most other `make' programs. Irix 6.5 (or
6.4?) and later `make' ignores VPATH.
Started all beginning-of-line comments with `##' instead of
just `#' because Irix `pmake' barfs on things like the
following because it sees the `# if' as a directive:
# make will barf on the following line
# if running Irix pmake
./config/commence.in [1.3]
Added empty definitions for optional `make' macros because
Irix pmake complains if it sees a macro which has never been
defined. The main body of the Makefiles can redefine these
macros to whatever they need.
----------------------
./doc/html/Datatypes.html
./test/dtypes.c
Added documentation and tests for opaque types.
./tools/h5ls.c
Added a `-x' or `--hexdump' argument which is not fully
implemented (because I want to synchronize h5tools.c first)
but which will eventually print raw data in hexadecimal format
without any translation from disk. This would be useful for
debugging references and VL types.
./tools/h5tools.c
Added support for references (not quite finished yet, but
compiles -- I wanted to sync up this file before Patrick and I
got too far apart...)
./src/H5R.c
Checked for error return value from H5R_get_object_type()
./src/H5A.c
./src/H5D.c
Changed error return values from NULL to FAIL
./test/Makefile.in
./test/trefer.c
Creates trefer1.h5 and trefer2.h5 so that the second test
doesn't clobber the first file since the files might be useful
for debugging.
----------------------
./config/commence.in
./examples/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
Fixed some dependency problems in Makefiles. If the library
version is updated then everything gets recompiled.
./src/H5G.c
./src/H5R.c
Failure return value for object type functions is now
H5G_UNKNOWN as documented.
./src/H5Shyper.c
./src/H5Spoint.c
Fixed an unused argument warning.
./tools/h5debug.c
Fixed a call to H5F_block_read() since the 4th argument is
different now.
./tools/h5ls.c
Added a space between the object name and class to make the
output readable when the object name is longer than 24
characters.
C
----------------------
./config/commence.in
./config/conclude.in
./test/Makefile.in
./tools/Makefile.in
Fixed so private libraries are not installed publicly.
The installation directories `bin', `include', and `lib' are
created mode 755.
./src/H5.c
./src/H5A.c
./src/H5F.c
./src/H5Fcore.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fsec2.c
./src/H5Fstdio.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Ocomp.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Ofill.c
./src/H5Olayout.c
./src/H5Omtime.c
./src/H5Oname.c
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5R.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Snone.c
./src/H5Spoint.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Vprivate.h
./src/H5Z.c
./src/H5detect.c
./src/H5private.h
./test/chunk.c
./test/dsets.c
./test/dtypes.c
./test/h5test.c
./test/overhead.c
./test/ragged.c
./test/tattr.c
./tools/h5dump.c
./tools/h5findshd.c
./tools/h5ls.c
Changed `__unused__' to `UNUSED' to fix a conflict with GNU
header files.
./src/H5Tpkg.h
./test/h5test.h
Removed __unused__ from forward function declarations.
./src/H5P.c
Removed a comment about restrictions for the type conversion
temporary buffers. Thanks to Quincey, the comment no longer
applied.
./src/H5T.c
Relaxed the H5Tpack() a little so it would pack compound data
structures that had non-transient atomic members.
./tools/h5ls.c
Added a `-g' (or `--group') flag that causes information to be
printed about the specified group instead of the group's
contents. (sort of like Unix's `ls -d'). The `-g' can be used
in combination with `-r' to print information about the group
and its contents.
----------------------
./Makefile.in
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./config/commence.in
./config/conclude.in
./config/dec-osf4.x
./config/depend.in
./config/freebsd
./config/linux-gnu
./config/linux-gnulibc1
./config/linux-gnulibc2
./config/solaris2.x
./examples/Makefile.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
./tools/testh5dump.sh
Changes that allow hdf5 to be configured and compiled in a
directory other than the source directory. This is especially
useful if you want to concurrently compile with different
compilers and/or compile flags, or if the hdf5 source is on
read-only media like a CDROM. The changes were surprisingly
easy ;-) Here's what you can do now...
$ mkdir /tmp/build1 # or something
$ cd /tmp/build1
$ /cdrom/hdf5/configure # where ever the source is
$ make
Paul, you'll have to change the testh5toh4 script similar to
the way I changed testh5dump.sh. I started working on it but
then gave up because of a number of problems: (1) I had to
comment out all the tests that let h5toh4 choose the output
file name because it always tried to put the output file in
the same directory as the input file, (2) if path names are
used during the h4 dump then they interfere with the
diff. The test works fine when run in the source directory,
but try this instead:
$ gunzip <hdf5-1.1.67.tar.gz |tar xf -
$ chmod -R ugo-w hdf5-1.1.67
$ mkdir build
$ cd build
$ ../hdf5-1.1.67/configure
$ make check
Dan, I didn't modify the pablo/Makefile.in because I have no
way to test it. I think all you need to do is add a couple
lines before the @COMMENCE@ line and add a couple search
directories for header files. Anyway, it seems like almost an
exact duplicate of the src/Makefile.in, so it shouldn't be a
problem...
./Makefile.in
Removes a few more temporary files during make clean and
distclean.
./configure.in
I fixed the creation of the time-stamp files so that the
initial make doesn't have to regenerated all the makefiles
(only GNU make users will see any change).
./src/H5R.c
Changed a return type from `intn' to `int' for an API
function.
./src/H5detect.c
Added the volatile qualifier to a couple more variables.
./tools/h5tools.c
Fixed a compiler warning about an unused local.
./tools/h5toh4.c
Initialized `optind' to 1 because it's zero on my system. It
should always be one on a unix system.
./tools/testh5toh4
Redirected "broken pipe" messages to /dev/null so outut is
formatted correctly.
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5private.h
Temporarily commented out the code that tries to link a simple
MPI-IO application because I'm not sure how to pass $LDFLAGS
and $LIBS to the compiler.
Removed the `--enable-parallel=ibm' switch because the library
we link with is either -lmpcc or -lmpcc_r but not both. The
only way to tell is to see what compiler was specified (mpcc
or mpcc_r) but if that compiler is specified then we don't
need any libraries (the compiler script supplies them). That
leaves just two choices: the user must use a compiler script:
CC=mpcc ./configure
or the user must state which library is desired:
LDFLAGS='-lmpcc' ./configure --enable-parallel
Checks for <setjmp.h>, longjmp(), and signal(). We don't check
for setjmp() because it could be a macro (in fact, Posix
requires it to be a macro) and if longjmp() is present then
setjmp() is probably present too ;-)
./src/H5detect.c
The alignment detection loop uses SIGBUS and setjmp/longjmp
instead of fork/wait in order to get around bugs with forking
in conjunction with mpich. This hasn't been tested on the
SP-2 yet but it does work on the DEC Alpha.
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
Changed the order that libraries are linked so -lhdf5 is
always before $LDFLAGS.
----------------------
./INSTALL
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Improvements for parallel library. If you have a properly
working mpicc you should be able to just say:
$ CC=mpicc ./configure
and you will see
checking for mpirun... /usr/local/mpi/bin/mpirun
checking for parallel support files... skipped
checking how to run on one processor...
/usr/local/mpi/bin/mpirun -np 1
checking how to run in parallel...
/usr/local/mpi/bin/mpirun -np $$NPROCS
To quote from the INSTALL file....
*** Parallel vs. serial library
The HDF5 library can be configured to use MPI and MPI-IO for
parallelizm on a distributed multi-processor system. The easy
way to do this is to have a properly installed parallel
compiler (e.g., MPICH's mpicc or IBM's mpcc) and supply that
executable as the value of the CC environment variable:
[NOTE: mpcc is not tested yet]
$ CC=mpcc ./configure
$ CC=/usr/local/mpi/bin/mpicc ./configure
If no such wrapper script is available then you must specify
your normal C compiler along with the distribution of
MPI/MPI-IO which is to be used (values other than `mpich' will
be added at a later date):
$ ./configure --enable-parallel=mpich
If the MPI/MPI-IO include files and/or libraries cannot be
found by the compiler then their directories must be given as
arguments to CPPFLAGS and/or LDFLAGS:
$ CPPFLAGS=-I/usr/local/mpi/include \
LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \
./configure --enable-parallel=mpich
If a parallel library is being built then configure attempts
to determine how to run a parallel application on one
processor and on many processors. If the compiler is mpicc
and the user hasn't specified values for RUNSERIAL and
RUNPARALLEL then configure chooses `mpirun' from the same
directory as `mpicc':
RUNSERIAL: /usr/local/mpi/bin/mpirun -np 1
RUNPARALLEL: /usr/local/mpi/bin/mpirun -np $${NPROCS:=2}
The `$${NPROCS:=2}' will be substituted with the value of the
NPROCS environment variable at the time `make check' is run
(or the value 2).
./testpar/Makefile.in
Saying `make check' (or `make test') will run the tests on two
processors by default. If you define NPROCS then that many
processors are used instead:
$ NPROCS=4 make check
./configure.in
Fixed (hopefully) bugs with detecting whether __attribute__
and __FUNCTION__ are special keywords for the compiler.
./Makefile.in
Saying `make install' from the top level directory shows
instructions for using shared libraries.
./config/commence.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
Moved the @top_srcdir@ into the makefiles because it was
expanded too early and had the wrong value.
./INSTALL
Added a warning that if the wrong version of hdf4 tools are
installed then `make check' will fail in the tools directory.
----------------------
./INSTALL
Reorganized and added some additional examples.
./MANIFEST
./aclocal.m4 [NEW]
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./bin/ltconfig [NEW]
./bin/ltmain.sh [NEW]
Added tests to determine how to compile shared libraries and
how to link programs with them before the libraries are
installed. Also how to install and uninstall shared
libraries. The configure step also prints the names of the
config files it's trying to load for easier debugging.
./bin/config.guess
./bin/config.sub
Replaced with a newer version from GNU. The changes we made
to that file to report `irix6.x' and `FreeBSD' without version
numbers have been incorporated into configure.in instead. In
the future, do not change these two files (see the top of
configure.in instead). By the way, this update was required to
get shared libraries working.
./config/linux [REMOVED]
./config/linux-gnulibc1 [NEW]
./config/linux-gnu [NEW]
./config/alpha-dec [REMOVED]
./config/alpha-dec-osf4.0 [REMOVED]
./config/dec-osf4.x [NEW]
./config/irix5.3 [REMOVED]
./config/irix5.x [NEW]
./config/irix64 [REMOVED]
./config/freebsd
Moved config files around to agree with output from the new
config.guess. The linux file was split into gnu (RedHat),
gnulibc1, and gnulibc2 versions. The alpha-dec file was
removed (I think it was unused) and the alpha-dec-osf4.0 was
changed to dec-osf4.x. The irix5.3 file renamed to irix5.x and
the irix64 file was renamed to irix6.x. The freebsd file was
changed to point to linux-gnulibc1. These changes were tested
on:
Linux 2.0
Linux 2.1
FreeBSD 3.2
Irix 5.3
Irix64 6.2
Irix64 6.4
HP/UX 10.20
OSF1 4.0
./config/alphaev56-dec-osf4.x
./config/irix64
Added warnings similar to linux/freebsd about using compilers
with known bugs.
./config/commence.in
./config/conclude.in
./src/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
Added definitions for shared libraries. This has been tested
on the following systems:
Linux 2.0
Linux 2.1
FreeBSD 3.2
Irix 5.3
Irix64 6.2
Irix64 6.4
HP/UX 10.20 static only
OSF1 4.0
If you want to disable use of shared libraries (you probably
do for development purposes since it takes a lot longer to
compile and because you have to run dynamically linked
programs in a special way if the library hasn't been
installed) then add `--disable-shared' to the configure
command line. This is all documented in the INSTALL file.
./bin/release
Temprarily commented out the MANIFEST checking when running
under svf since svf is about to be replaced by a newer
version. This change only affects error checking during the
release process.
./Makefile.dist
./Makefile.in
Added `make check' which does the same thing as `make _test'
since the former is endorsed by the GNU coding style and
people are used to it. The old `make _test' still works too
(and so does `make test' if you use GNU make).
----------------------
./test/dtypes.c
./test/enum.c [NEW]
Added support for enumeration data types.
./test/fillval.c
./test/istore.c
Fixed memory leaks during error handling.
----------------------
./src/H5T.c
Fixed a typo in the registration of the `unsigned char' to
`unsigned long long' type conversion that caused it to not be
registered, falling back to software whenever that conversion
path was taken.
./MANIFEST
./test/Makefile.in
./test/testhdf5.c
./test/testhdf5.h
./test/theap.c [REMOVED]
./test/lheap.c [NEW]
./test/tohdr.c [REMOVED]
./test/ohdr.c [NEW]
./test/tstab.c [REMOVED]
./test/stab.c [NEW]
Removed the `t' from the front of these names and made each
test a stand-alone program following the format of most of the
other tests.
./test/big.c
Uses libh5test.a but always sets the low-level driver to 1GB
file family.
The `#if' near the top to set the data space to 8GB has been
simplified now that `long_long' is always defined and the
error message is improved when `long_long' isn't wide enough.
Cleanup code was added to the error handling.
./test/gheap.c
./test/istore.c
Uses libh5test.a. Added error cleanup code.
./test/dtypes.c
./test/h5test.c
Added 68 new tests that check hardware and software
conversions between `long long' and `unsigned long long' and
the other integer types. The tests only run on machines where
sizeof(long_long)!=sizeof(long). We test a total of 180
different integer conversions, half in hardware and half in
software.
Cut down the number of times each test is run from 5 to 1 so
it doesn't take so long. If you want to run more times
there's a constant that can be changed at the top of the file.
./test/extend.c
Removed unused variable.
./test/h5test.c
./test/h5test.h
./test/external.c
./test/fillval.c
The h5_cleanup() returns true/false so it can be used in an `if'
statement to clean up additional files.
./doc/html/Environment.html
Indented. Added HDF5_PREFIX and HDF5_DRIVER descriptions.
./src/H5P.c
Changed the trace type for the second argument from `Iu' to
`x' since it's an output parameter.
./INSTALL
Added a warning that the GNU zlib that comes with the latest
version of HDF4 is too old to use with HDF5 and must be
renamed so configure doesn't see it when `--enable-hdf4' is
used.
----------------------
./MANIFEST
./test/Makefile.in
./test/shtype.c [REMOVED]
Removed shtype.c because it was all commented out. Besides,
these tests are done in dtypes.c now anyway.
./test/external.c
./test/fillval.c
./test/flush1.c
./test/flush2.c
./test/links.c
./test/mount.c
./test/mtime.c
./test/unlink.c
The tests that check the HDF5 API use the h5test support
functions. For one thing, that means that you can specify the
file driver that thay use by the HDF5_DRIVER environment
variable. Possible values are:
HDF5_DRIVER='sec2' Use read() and write()
HDF5_DRIVER='stdio' Use fread() and fwrite()
HDF5_DRIVER='core' Use malloc() and free()
HDF5_DRIVER='split' Split meta and raw data
HDF5_DRIVER='family N' Use file families with each
member being N megabytes (N
can be fractional, defaults to
one).
Some tests might fail for certain drivers: for instance, the
mount and link tests fail for the `core' driver because
they must be able to close and then reopen a file.
----------------------
./src/H5.c
./src/H5A.c
./src/H5AC.c
./src/H5B.c
./src/H5D.c
./src/H5E.c
./src/H5F.c
./src/H5Farray.c
./src/H5Fcore.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5Gstab.c
./src/H5HG.c
./src/H5HL.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5MF.c
./src/H5MM.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Ocomp.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Ofill.c
./src/H5Olayout.c
./src/H5Omtime.c
./src/H5Oname.c
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Snone.c
./src/H5Spoint.c
./src/H5Sselect.c
./src/H5T.c
./src/H5TB.c
./src/H5Tbit.c
./src/H5Tconv.c
./src/H5V.c
./src/H5Z.c
./src/H5detect.c
./src/H5private.h
Most of these changes are because the `interface_initialize_g'
variable change from hbool_t to int. It's a one line change.
Changed the way the library is closed so we have more control
over the order the interfaces are shut down. Instead of
registering an atexit() function for every interface in some
haphazard order we just register one: H5_term_library() which
then calls the H5*_term_interface() functions in a
well-defined order.
If the library is closed and then reopened repeatedly by
calling H5close() and H5open() in a loop we only add one copy
of the library termination functions with atexit().
Termination is a two-step process in order to help detect
programming errors that would cause an infinite loop caused by
the termination of one interface waking up some other
previously terminated interface. The first step terminates
the interface and *marks it as unusable*. After all
interfaces are terminated then we mark them all as usable
again. The FUNC_ENTER() macro has been modified to return
failure or to dump core (depending on whether NDEBUG is
defined) if we try to call an interface while it's shutting
down.
./src/H5.c
The H5dont_atexit() function returns failure if it's called
more than once or if it's called too late. However, the error
stack is not automatically printed on failure because the
library might not be initialized yet
./test/chunk.c
./test/flush1.c
./test/flush2.c
./test/iopipe.c
./test/overhead.c
./test/ragged.c
Changed the extra cast for Win32 so we do floating point
division again -- it was just confusion about precedence and
associativity of casting and the C coercion rules. Removed
extra carriage returns inserted by broken operating system.
./src/H5Ffamily.c
Fixed an bug where H5F_fam_write() lowered the EOF marker for
one of the family members causing H5F_fam_read() to read
zeros.
./test/h5test.h [NEW]
./test/h5test.c [NEW]
./test/Makefile.in
./test/bittests.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/extend.c
./test/external.c
Support library for test files. This isn't done yet but
Katie's contractions are ~10 minutes apart so I figured I
better back this stuff up just in case I'm not here next
week...
Eventually all test files will understand HDF5_DRIVER to name
the low level file driver and parameters so we can easily test
various drivers. They will also understand HDF5_PREFIX to
prepend to the beginning of file names which is necessary for
testing ROMIO with various drivers. Also, the cleanup function
will know how to use the file name prefix and will understand
different file driver naming schemes like file families. I'm
not sure they'll understand the `gsf:' type prefixes yet.
Note, the external test is completely commented out because
I'm in the middle of modifying it. It will still compile and
run but it doesn't test anything at the moment.
----------------------
./config/conclude.in
./test/Makefile.in
./tools/Makefile.in
The Makefile $TESTS variable has finally been split into
$TEST_PROGS and $TEST_SCRIPTS with the latter being the names
of shell scripts that need to be run with `/bin/sh'. Now we
don't have to copy each shell script before we run it. NOTE:
THIS CHANGE DOES NOT AFFECT THE PABLO MAKEFILE SINCE THAT FILE
IS A COPY OF A PREVIOUSLY GENERATED MAKEFILE.
./src/Makefile.in
Added H5Snone.c to the source list.
./src/H5G.c
Plugged a memory leak by emptying the object type "isa" table
when the library is closed.
./src/H5Tconv.c
./src/H5Tpkg.h
Added 48 new type functions to take advantage of hardware for
integer type conversions. These functions are not registered
in the conversion table yet because I haven't fully tested
them.
./src/H5Tpkg.h
Removed __unused__ qualifiers from prototypes.
----------------------
./INSTALL
Added instructions about specifying a path for GNU zlib and
HDF4 headers and library.
Added comments for each of the tool names. Added h5toh4 as a
tool name.
./configure.in
./conigure [REGENERATED]
./src/H5config.h.in [REGENERATED]
The config/* scripts get invoked with $CC_BASENAME set the
base name of the compiler in order to make it easier to handle
setting compiler flags for different compilers in a big case
statement. For instance, if $CC has the value
/usr/local/mpi/bin/mpicc -ansi -64
then $CC_BASENAME will be `mpicc'. The $CC_BASENAME is not
set if $CC is not set.
Fixed alignment in `configure --help'.
An include and/or library path can be specified for GNU zlib
if configure can't find it in normal places. The "normal"
means wherever your compiler normally searches, including
search paths you've added through environment variables like
CPPFLAGS and LDFLAGS. The INSTALL file has instructions.
The `-ljpeg' library is detected.
If `ssize_t' is not found then a #define is added to
H5config.h similar to what we already do for `size_t'.
We detect the hdf5 header file `mfhdf.h' and libraries
`-lmfhdf' and `-ldf' and if found define the H5TOH4 and
TESTH5TOH4 Makefile variables. The user can specify an
include and/or library path. The INSTALL file has
instructions.
The `RUNTEST' variable has been split into `RUNSERIAL' and
`RUNPARALLEL' because these are different commands. The
makefile still uses `RUNTEST', which defaults to the RUNSERIAL
value. The new testpar/Makefile.in sets RUNTEST to the
RUNPARALLEL value. The default RUNSERIAL value is empty and
the default RUNPARALLEL value is `mpirun -np 2'. These can
both be overridden in the config/* files. To make the value
the empty string set it like `RUNPARALLEL=none' in the
config/* file.
The new testpar/Makefile is generated from testpar/Makefile.in
./config/commence.in
Added the RUNSERIAL and RUNPARALLEL makefile definitions.
./src/Makefile.in
The `H5detect' program is run with RUNSERIAL, which is empty
on all platforms except intel-osf1 (ASCI/Red)
./config/conclude.in
Removed the `.c.a:' implicit rule -- we don't use it any more.
./config/BlankForm
./config/alpha-dec
./config/alpha-dec-osf4.0
./config/freebsd2.2.7
./config/hpux10.20
./config/hpux9.03
./config/intel-osf1
./config/irix5.3
./config/irix6.2
./config/irix64
./config/linux
./config/powerpc-ibm-aix4.2.1.0
./config/rs6000-ibm-aix4.1.4.0
./config/solaris2.5
All of these files have been updated to hande multiple
compilers. Most of them assume `cc' if CC is not set. The
documentation in `BlankForm' has been updated and
documentation in the other files refer to `BlankForm'.
The intel-osf1 uses LDFLAGS instead of LIBS to specify the extra
library search paths.
./examples/Makefile.in
./test/Makefile.in
./tools/Makefile.in
Simplified by grouping some dependency information together
more succinctly.
The tools Makefile.in has been modified to work with the
`h5toh4' and `testh5toh4' programs. Until Paul checks these
in you may have problems compiling. If so, just create files
h5toh4.c and testh5toh4.c that contain:
#include <stdio.h>
int main(int argc, char *argv[]) {
fprintf(stderr, "%s: not implemented\n", argv[0]);
return 1;
}
./src/H5public.h
Removed definition for `ssize_t' since this is now handled by
configure in H5config.h with a #define.
./MANIFEST
./testpar/Makefile.in [NEW]
Added a makefile for parallel tests. As soon as we get this
working properly we can remove the other four makefiles in
that directory and maintain just one.
----------------------
./MANIFEST
./test/Makefile.in
./test/flush1.c [NEW]
./test/flush2.c [NEW]
Test to see if calling H5Fflush() results in a consistent
file.
./src/H5.c
./src/H5A.c
./src/H5D.c
./src/H5Fistore.c
./src/H5I.c
./src/H5S.c
./src/H5Shyper.c
./src/H5Sselect.c
./src/H5TB.c
Changed comparisons against SUCCEED and FAIL to >=0 and <0 in
about 15 places.
./src/H5.c
./src/H5V.c
./src/H5detect.c
./src/H5private.h
./src/H5public.h
./test/big.c
./test/chunk.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/external.c
./test/fillval.c
./test/iopipe.c
./test/links.c
./test/mount.c
./test/mtime.c
./test/ragged.c
./test/shtype.c
./test/unlink.c
Removed ^M from the end of lines inserted on broken OS's ;-)
./src/H5private.h
Changed c++ comments to c comments.
./src/H5R.c
Added tracing macros.
----------------------
./src/H5.c
Fixed a signed vs. unsigned comparison.
./src/H5D.c
Setting a fill value of all zeros will cause the fill value to
be written to the dataset instead of relying on the low-level
file driver initializing unwritten areas with zero.
./src/H5D.c
./src/H5F.c
./src/H5Fprivate.h
./src/H5G.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5O.c
./src/H5T.c
More file mounting stuff.
./src/H5I.c
Fixed a bug where trying to close an invalid object id caused
a core dump. For instance, H5Gclose(-1).
./MANIFEST
./test/Makefile.in
./test/mount.c [NEW]
Mounting tests.
./src/H5R.c
Fixed a couple (herr_t)NULL casts.
----------------------
./src/H5D.c
Fill values are working for contiguous datasets now except
there are two things that need more support from the data
space layer, specifically the ability to form a selection from
the difference of two selections. They are (1) extending an
external contiguous dataset, (2) optimization by delaying the
fill until after the first H5Dwrite().
Renamed H5D_allocate() to H5D_init_storage() since allocation
is only part of the story. Added a data space argument so it
doesn't have to query the space from the object header -- the
space is always available in the caller anyway.
Removed `#ifdef HAVE_PARALLEL' from a few places where it
wasn't necessary. We don't need it around code that doesn't
compile anything from mpi.h or mpio.h.
./src/H5Fistore.c
Uncommented H5F_istore_alloc() for non-parallel and moved the
`#ifdef HAVE_PARALLEL' just around Kim's barrier.
./src/H5Fmpio.c
Wrapped a couple long lines.
Got rid of two signed vs. unsigned comparison warnings.
./MANIFEST
./test/Makefile.in
./test/fillval.c [NEW]
Added tests for fill values. The contiguous dataset extend
test is disabled until H5S_SELECT_DIFF is implemented.
./tools/Makefile.in
Fixed a bug where `make test' didn't build the executables
first. This should cause the snapshots to start up again.
./Makefile.in
Changed to build in `test' directory before `tools'
directory. We want the library tests to pass before we even
start considering the tools. You can still build and/or test
the tools independent of the library tests passing.
----------------------
./MANIFEST
Changed freebsd2.2.1 to freebsd2.2.7 to match change in file name.
Added a few missing files. Are all of these supposed to be
distributed?
./tools/testfiles/h5dumptst.c
+ ./tools/testfiles/tall-1.ddl
+ ./tools/testfiles/tall-2.ddl
+ ./tools/testfiles/tall-3.ddl
./tools/testfiles/tall.ddl
./tools/testfiles/tall.h5
+ ./tools/testfiles/tattr-1.ddl
+ ./tools/testfiles/tattr-2.ddl
+ ./tools/testfiles/tattr-3.ddl
+ ./tools/testfiles/tattr-4.ddl
./tools/testfiles/tattr.ddl
./tools/testfiles/tattr.h5
+ ./tools/testfiles/tdset-1.ddl
+ ./tools/testfiles/tdset-2.ddl
+ ./tools/testfiles/tdset-3.ddl
+ ./tools/testfiles/tdset-4.ddl
./tools/testfiles/tdset.ddl
./tools/testfiles/tdset.h5
+ ./tools/testfiles/tgroup-1.ddl
+ ./tools/testfiles/tgroup-2.ddl
+ ./tools/testfiles/tgroup-3.ddl
./tools/testfiles/tgroup.ddl
./tools/testfiles/tgroup.h5
+ ./tools/testfiles/tslink-1.ddl
+ ./tools/testfiles/tslink-2.ddl
./tools/testfiles/tslink.ddl
./tools/testfiles/tslink.h5
./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5Dprivate.h
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fprivate.h
./src/H5Gstab.c
./src/H5P.c
./src/H5Ppublic.h
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Spoint.c
./src/H5Sprivate.h
./test/istore.c
Implemented split ratios as documented in previous
e-mails. Frank, the new API functions are H5Pget_btree_ratios()
and H5Pset_btree_ratios().
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Spoint.c
./src/H5Sprivate.h
Added more type checking for the data transfer property list
passed to these functions.
./src/H5D.c
Added a dataset transfer property list as an argument to
H5D_allocate() for the parallel version in order to pass split
ratios down to H5F_istore_lock(). Eventually we won't need
the split ratios for H5D_allocate() because we'll build a
completely full B-tree from the leaves up, but it might be
useful to have other transfer properties at that level
anyway. I always caled H5D_allocate() with &H5D_dflt_xfer.
./MANIFEST
./test/Makefile.in
./test/overhead.c [NEW]
Added an `overhead' test run by `make timings'.
----------------------
./MANIFEST
./src/H5B.c
./src/H5Bprivate.h
./src/H5G.c
./src/H5Gnode.c
./src/H5Gprivate.h
./test/Makefile.in
./test/unlink.c [NEW]
Finished H5Gunlink() and H5Grename().
./src/H5F.c
./src/H5Fistore.c
./src/H5Fprivate.h
Removed the last memcpy() from the chunk cache.
./src/H5Fistore.c
The offset of a chunk within a dataset is an 8-byte quantity
per dimension instead of 4 bytes.
./src/H5HL.c
Fixed infinite loops in H5HL_remove().
----------------------
This checkin is to fix a couple bugs for Jim Reus. Some features are
not fully implemented but it shouldn't break anything.
./config/conclude.in
./test/Makefile.in
`make clean' removes object files from the test directory as
well as a couple more *.h5 temp files.
./config/hpux9.03 [NEW]
New config file for HP/UX 9.03
./src/H5B.c
./src/H5Bprivate.h
./src/H5Fistore.c
./src/H5G.c
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5Gstab.c
Not-yet-complete version of object removal.
./src/H5Fistore.c
./src/H5Fprivate.h
Experimental optimizations, disabled by default.
./src/H5Fprivate.h
Default low-level driver was changed to H5F_LOW_SEC instead of
H5F_LOW_STDIO because the sec2 driver is much easier to debug.
./src/H5Fsplit.c
./src/H5G.c
./src/H5Z.c
Changed a couple return statements to HRETURN.
./src/H5Odtype.c
Removed a check for nested compound data types from back when
they weren't implemented that raised an error.
./tools/h5tools.c
Increased temp buffer sizes and added a check for buffer
overflow so we fail an assertion (hopefully). This really
needs to be fixed sometime.
Added support for printing H5T_STRING data types.
----------------------
./MANIFEST
./bin/release
./bin/snapshot
The format of the MANIFEST file has been relaxed -- comments
and blank lines should no longer confuse the tools that use
it.
As before, this file should contain a list of *all* files that
are part of HDF5, which means all files which are managed by
CVS/SVF. However, files can be marked so they're not part of
a release by adding _DO_NOT_DISTRIBUTE_ after the file name.
I've removed all the *.obj files from the distribution by
adding _DO_NOT_DISTRIBUTE_ after their names. I also removed
the old white-papers that might not apply to the current
version of the library and documentation about chunking
performance since it's wrong now that chunk caching is
implemented. Everyone please check the files you're
responsible for to make sure that they should really be part
of a release.
To get a list of all files use
grep '^\.' MANIFEST | cut -f1
To get a list of files for distribution use:
grep '^\.' MANIFEST | grep -v _DO_NOT_DISTRIBUTE_
(These commands assume tabs in the MANIFEST file. If the file
might contain spaces then run it through `unexpand' or `tr'
first).
./configure.in
./configure
./src/H5config.h.in
./test/ragged.c
Check for sigaction().
./test/Makefile.in
The `clean' target removes the timing tests.
----------------------
./RELEASE
Updated with important changes I made since the second beta.
./src/H5A.c
./src/H5D.c
./src/H5Dprivate.h
./src/H5G.c
./src/H5Gprivate.h
./src/H5R.c
./src/H5Rprivate.h
./src/H5T.c
./src/H5Tprivate.h
Any API function that used to take an `hid_t loc_id' followed
by a `const char *name' can now take any type of object for
the loc_id as long as the object is somehow associated with a
file. Internally, H5G_loc() was modified to return an
H5G_entry_t* instead of an H5G_t* so it's more general.
Among other things, this allows one to retrieve information
about an object like a named type or dataset without knowing
the name of the type or dataset:
int
get_nlinks (hid_t obj)
{
H5G_stat_t sb;
if (H5Gstat(obj, ".", TRUE, &sb)<0) return -1;
return sb.nlink;
}
./test/gheap.c
./test/istore.c
These files needed a couple of changes because they call some
of the internal functions whose H5G_t arguments changed to
H5G_entry_t.
./src/H5A.c
Got rid of all the switch statements for getting symbol table
entries for varous objects and replaced them with a call to
H5G_loc() allowing attributes to automatically apply to any
type of object that belongs to a file.
./test/Makefile.in
Moved the ragged array tests from the normal list of tests to
the `make timings' target.
./test/ragged.c
Added rewrite tests -- rewrite the rows of a dataset changing
the number of rows and the length of each row.
./test/mtime.c
Added a test that checks that H5Gstat() can be called with a
dataset as the first argument.
./src/H5S.c
Added #ifdef HAVE_PARALLEL around code to check for the
HDF5_MPI_OPT_TYPES environment variable because the global
variable that gets set is #ifdef'd.
./bin/release
bzip2 uses .bz2 as the file extension.
----------------------
./src/H5G.c
Fixed a link count on groups. Groups were always created with
a link count of zero instead of one.
./src/H5Gpublic.h
Added H5G_NTYPES so applications can easily declare arrays
which are indexed by object type.
./src/H5O.c
Calling `H5O_link(&ent,0)' will succeed when the file is open
for read only because it's the only way to get the object's
current link count.
./tools/h5ls.c
Can take non-group object names on the command line (and
multiple objects). Reorganized to be more extendible. The
link count is displayed for `-v'.
./src/H5F.c
Dumping of cache statistics is controlled by only the
HDF5_DEBUG environment variable and not the H5F_ACC_DEBUG flag
for H5Fopen() and H5Fcreate() since this makes it similar to
the other debugging options.
./src/H5R.c
./test/ragged.c
./test/Makefile.in
Tests pass but still a little work left to be done.
----------------------
./MANIFEST
./test/Makefile.in
./test/mtime.c [NEW]
Test for the modification time message.
./src/H5AC.c
./src/H5Fistore.c
Turned off printing of statistics on H5close() if H5AC_DEBUG
isn't defined.
----------------------
./MANIFEST
./doc/html/H5.format.html
./src/H5O.c
./src/H5Oprivate.h
./src/H5Omtime.c [NEW]
./src/H5private.h
./src/Makefile.in
Added the modification time message. If an object header has
this message then it's value is updated with the current time
whenever anything changes in the object header.
./acconfig.h
./configure.in
Alas, there seems to be no standard way to convert a string
time like 19980727122800 in UTC to a time_t since mktime()
only converts local times to time_t. So I've modified the
configuration to check for various ways of getting the time
zone information:
* Added checks for the `tm_gmtoff' field of `struct tm'.
* Added a check for the `timezone' global variable.
* Added a check for `struct timezone'.
* Added a check for BSDgettimeofday().
* Added a check for gettimeofday() although it doesn't
actually set the timezone argument on some systems.
* Added a check to see if `tm_zone' is a member of `struct tm'.
* Added a check to see if `tzname' is a global variable.
* Added a check to see if `struct tm' is defined in time.h
or sys/time.h.
It's not difficult to get the right UTC modification message
into the object header, but some systems might have problems
getting the right time back out (Irix64 is one) and those
systems will report zero for the H5G_stat_t.mtime from an
H5Gstat() call as if the mtime message isn't even present. It
will, however, continue to be updated as normal.
./src/H5G.c
./src/H5Gpublic.h
The H5G_stat_t struct now contains an `mtime' field which will
hold the object modification time. If the object has no
object modification time then the `mtime' will be initialized
to zero.
Fixed a bug in H5G_stat() that caused the `objno' field of the
H5G_stat_t to be set incorrectly on some machines.
./src/H5D.c
Writing to external datasets fail if the hdf5 file is not open
for writing.
A modification time message is added to the dataset object
header when it's created and H5O_touch() is called from
H5D_write() to update that message.
./src/H5T.c
Fixed a bug in H5Tget_member_dims() that caused a segmentation
fault if one of the output array arguments was the null
pointer.
Relaxed the member dimension checking in H5Tinsert_array() so
it can also be used for scalar members.
./test/Makefile.in
Added additional file names to the `mostlyclean' target.
./tools/h5dump.c
./tools/h5tools.h
Increased the temporary buffer size to 1MB.
Added support for printing compound data types with array
members.
When printing H5T_NATIVE_CHAR and H5T_NATIVE_UCHAR we escape
double quote characters.
./tools/h5ls.c
Changed the output format a little because we were starting to
get too much info to fit on a line. Without `--verbose' each
object occupies one line of output. Otherwise, additional
information is printed below the object name: object file
address, comment, and modification time. If `--dump' is given
then the data is printed after the other information.
./test/cmpd_dset.c
Changed the way the dataset is initialized to be more uniform.
----------------------
./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...
