----------------------
./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'.
----------------------
./tools/h5tools.c
Strings are not converted to null-padding before being
printed; they are printed with whatever byte values appear in
the file.
Bug fix
Problem:
When -with-hdf4 option is selected during configure,
no machine type found for HDF4 header file hdfi.h.
Solution:
Modify hdf5/config/linux file:
-D__i386 to be added to CPPFLAGS.
Platform tested:
linux(penfold)
----------------------
./INSTALL
./doc/html/Compression.html
./doc/html/Filters.html
Disassociated GNU from zlib. Did not change the introduction
which incorrectly states that compression in hdf5 is available
only if GNU gzip is available (should read zlib).
Changed a typo in INSTALL to match what is documented in
various other places: that zlib 1.1.2 (not 1.0.2) or better is
required for compression.
Added a reference to the main zlib web page in various places.
./src/H5Fistore.c
Fixed a typo in a comment.
./src/H5Flow.c
Removed carriage returns from the end of lines.
./test/dsets.c
The deflate compression tests are still run but `-SKIP-' is
printed instead of `PASSED' if the zlib library was not
detected at configuration time. The tests check that the
compression layer (H5Z) is correctly bypassed.
Bug fix
Problem:
Segmentation fault when attempting to free NULL or uninitialized pointers.
Problem noticed on Linux and HPUX10.20 platforms.
Solution:
Initialialize the pointer to NULL. Execute the "free" statement
upon the condition that the pointer is not equal to NULL (i.e. after the
allocation has taken place.)
Platform tested:
Linux, HPUX10.20, Solaris2.5
----------------------
./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/H5.c
./src/H5private.h
Renamed `library_initialize_g' to `H5_libinit_g' to make it
conform to our naming scheme.
./src/H5I.c
Fixed a bug in H5I_dec_ref() that caused the return value to
always be zero instead of the new reference count.
./src/H5.c
./src/H5Odtype.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5Tpublic.h
Added support for enumeration data types.
./src/H5RA.c
Renamed H5T_insert() to H5T_struct_insert() and added
H5T_enum_insert().
./src/H5RA.c
./src/H5Shyper.c
Added casts to size_t for the third argument of memcpy() to
shut up a warning message from insure++.
./src/H5T.c
Changed "can't" to "unable to" in some error messages to be
more consistent.
./src/H5detect.c
If fork() or waitpid() are unavailable then we assume no
alignment constraints. Hopefully this is the case only on NT
and Intel CPU's don't have alignment constraints.
./src/H5public.h
Include <limits.h> because the H5T_NATIVE_CHAR macro needs the
definition for CHAR_MIN.
----------------------
./MANIFEST
Removed some ddl files from tools/testfiles that are no longer
part of CVS. Added new enum.c test.
./configure [REGENERATED]
./configure.in
Changed printf long long format detection to favor `L' over
`ll'.
Conform closer to other test print-out.
Solution:
Added "All h5dump tests passed." statement to output
of testh5dump.sh when appropriate. Similarly, added
"All h5toh4 tests passed." statement to output of
testh5toh4 when appropriate.
Also, added the testing of converting H5 files with
loop pathways into H4 files with recursive references.
Platforms tested:
Solaris2.5, Digital Unix 4.0
Conform closer to other test print-out.
Problem:
Multiple "PASSED" statements for single test results when test involves
conversion of multiple files. Should be single "PASSED" statement for
test results.
Solution:
"*FAILED*" statement given if conversion fails for any file. Differences
given between expected results and actual results for each file that fails.
"PASSED" statement given when conversion is successful for all files.
Platform tested:
Solaris2.5
New feature, Documentation
Solution:
Changed h5toh4 testing output to more closely resemble other HDF5
testing output.
Also added documentation to describe the puposes of the
conversion test files.
Platform tested:
Solaris2.5
been checked into "HDF5 Development" branch.
General
=======
Various "copy edit" types of repairs.
Revisions to document cross-linking.
Added structural links tying all docs together (banners
at top and bottom of documents, similar to Reference Manual
banners of the Beta release).
Set background color to white in all documents.
NCSAfooterlogo.gif
hdf2.jpg
New image files to make the documents more self-contained
(i.e., to prevent loading images from NCSA and HDF home servers).
index.html
Redesigned to isolate links external to the installation
in a single location.
Intro to HDF5
=============
H5.intro.html
Fixed banner linking Intro to other docs.
Set all URLs to be relative within the distribution; nothing
points back to the HDF server.
Updates to "Limits of the Current Release" and "Changes in
the Current Release."
HDF5 User's Guide
=================
Changed several User Guide section titles such that all
sections that are primarily about a particular interface
are now titled in the format "The xxxxx Interface (H5x)".
H5.user.html
Commented out links to developer docs since they are marked
in MANIFEST as not being for distribution in the release.
Removed 2nd and 3rd indices from page.
Changed "freeform" lists of sections (TOCs) to aligned tables.
Datatypes.html
Removed the sentence "I'm deferring definition until later
since they're probably not as important as the other data
types." from Section 3.3, "Properties of Date and Time
Atomic Types."
Added info regarding 'char' versus 'string' datatypes. Added
as Section 3.7, "Character and String Datatype Issues."
References.html
Commented out substantial material (at end of document) from
References planning document that is not appropriate for
the User Guide but that is worth keeping around.
Groups.html
Final edits from elimination of "current working group."
HDF5 Reference Manual
=====================
Removed "Draft" from the <title>__</title> lines.
RM_H5Front.html
Removed 2nd and 3rd indices from page.
Changed "freeform" lists of sections (TOCs) to aligned tables.
RM_H5F.html
RM_H5P.html
Add file mounting information.
Features of this version of dumper
* loop detection
* data type
** atomic type
-> H5T_INTEGER (H5T_STD_XXXXX)
-> H5T_FLOAT (H5T_IEEE_XXXXX)
-> H5T_STRING (H5T_C_S1, H5T_FORTRAN_S1)
** committed/transient/unamed compound type
* data space
** scalar space
** simple space
* dataset
dumper can display dataset's
** attribute
** type
** space
** data
* group
dumper can display group attributes and group members which include
** named/unamed data type
** group
** dataset
** softlink
* attribute
dumper can display attribute's
** type
** space
** data
* hard link
* soft link
* format of data
** fit on 80 columns
** end of line after each row
(more work will be done on data.)
Problems:
There were three separate bugs in the h5toh4 converter worked on.
They were:
1) When a loop was detected, the H4 file was missing references
to paths which were available in the H5 file.
2) When an H4 SDS or Vdata was created from a H5 dataset, the H4
object was referenced in the root group, instead of the correct
Vgroup.
3) The FIRST path taken to an object for the h5toh4 conversion
could not involve a SOFTLINK.
Solutions:
The bug fixes were:
1) All of the associated references to available paths which
occur in the H5 file, now appear in the H4 file.
2) After an H4 SDS or Vdata is created from a H5 dataset, the H4
object is tag/ref'ed in the appropriate Vgroup.
3) The FIRST path taken to an H5 object for the H5toh4 conversion
may involve a HARDLINK, a SOFTLINK, or neither. The same is
true of any additional paths to the same object.
Platform tested:
Solaris2.5
New feature
Solution:
Added some new new tests to show that paths involving HARDLINKS
and paths involving SOFTLINKS convert existing objects from H5 to
H4 the same way that paths involving no links does.
Platform tested:
Solaris2.5
----------------------
./INSTALL
Added warning that enabling debugging code can adversely
affect performance even when the debugging isn't turned on at
run-time. Performance testing shows that under certain
circumstances (like data type conversions of compound types)
the H5_timer functions, although only a few lines each,
contribute a fairly large percent to the execution time.
./src/H5T.c
./src/H5Tpkg.h
./src/H5Tpublic.h
Improved the H5Tunregister() function to make unregistering
more flexible. It takes the same arguments as H5Tregister()
but also accepts wild cards. All conversion functions that
match the H5Tunregister() search criteria are removed from the
global type conversion table.
The H5Tregister_hard() and H5Tregister_soft() were combined
into a single function called H5Tregister() which is the
counterpart to H5Tunregister(). A new `persistence' argument
was added to differentiate between the two types of conversion
functions.
The application is allowed to register a hard conversion
function for the no-op conversion path although the library
isn't obligated to call it (it usually does). This is mostly
for completeness, but the application might use it to help
determine if the raw data pipeline was able to use the
optimized path for the case when no type conversion is
necessary. The library doesn't allow this path to be
unregistered although the application can redefine it as often
as it likes.
Fixed the type conversion tables in preparation for MT-safety
and to fix previosly-known design bugs wrt. unregistering
conversion functions or changing the C function associated
with a conversion path. The MT-safety stuff is documented in a
separate white paper.
Increased the conversion function debugging name from 9
characters to 31 characters so the output can be more
descriptive.
Moved conversion path statistics from the H5T_cdata_t member
into the conversion path itself. This makes H5T_cdata_t
contain only application-visible data structures.
./src/H5A.c
./src/H5D.c
./src/H5Ofill.c
./src/H5P.c
./src/H5T.c
Improved the way type conversion functions are called so the
caller doesn't have to check for data type debugging and
increment type conversion timers and statistics.
Changed check for no-op conversion since it is now
application-definable and there may even be more than one
definition at a time in a multi-threaded application (one
thread might be using the no-op conversion path when some
other thread changes its definition -- the first thread still
sees the original defintion until it's done with the
operation).
./doc/html/Datatypes.html
Updated the user guide to reflect the changes to data type
conversion registration functions.
./bin/trace
./src/H5.c
Added tracing support for the new H5T_pers_t data type.
./test/dtypes.c
Added printf to display alignment value if non-aligned data
types are being tested.
./test/h5test.c
Modified the H5Tunregister() calls to use the new
arguments. All 94 of those calls can be replaced by a single
call to the new H5Tunregister() function.
./src/H5.c
Added HAVE_GETTIMEOFDAY around an auto variable and
initialized the elapsed time to zero when gettimeofday() is
not available.
./src/H5F.c
./src/H5Fprivate.h
./src/H5P.c
Added an H5*_init() functions which do the same thing as
H5*_init_interface() but can be called from other packages and
don't do anything if the interface is already initialized.
This fixes a couple memory leaks in applications that
repeatedly close and open the library with H5close().
./src/H5Tconv.c
Optimized some data alignment code in the hardware conversion
functions.
Hardware conversions accumulate statistics about source and
destination data alignment and print that information when the
conversion function is unregistered (usually when the
application exits) if data type debugging is compiled into the
library and enabled at run-time.
The conversion caching was cleaned up for the compound data
type conversion function. It now caches conversion paths in a
manner that will be MT-safe and is much simpler than the old
method. Also cleaned up some array index maps.
./src/H5detect.c
Fixd mispelling of alingemnt.
./src/H5private.h
Changed `TRUE' to `1' in assignment to interface_initialize_g
in FUNC_ENTER macro definition.
./tools/testh5dump.sh
Completely rewritten to make it shorter, better documented,
and conforming to most of the other test outputs.
The comparison of the actual output with the expected output
is insensitive to differences in white space. The test now
passes for the first time on Linux where the output width
wasn't as expected but the output was otherwise correct.
./tools/testfiles/tall-1.ddl
./tools/testfiles/tall-2.ddl
./tools/testfiles/tall-3.ddl
./tools/testfiles/tattr-1.ddl
./tools/testfiles/tattr-2.ddl
./tools/testfiles/tattr-3.ddl
./tools/testfiles/tattr-4.ddl
./tools/testfiles/tcomp-1.ddl
./tools/testfiles/tcomp-2.ddl
./tools/testfiles/tcomp-3.ddl
./tools/testfiles/tcomp-4.ddl
./tools/testfiles/tdset-1.ddl
./tools/testfiles/tdset-2.ddl
./tools/testfiles/tdset-3.ddl
./tools/testfiles/tdset-4.ddl
./tools/testfiles/tgroup-1.ddl
./tools/testfiles/tgroup-2.ddl
./tools/testfiles/tgroup-3.ddl
./tools/testfiles/tlink-1.ddl
./tools/testfiles/tlink-2.ddl
./tools/testfiles/tlink-3.ddl
./tools/testfiles/tlink-4.ddl
./tools/testfiles/tlink-5.ddl
./tools/testfiles/tslink-1.ddl
./tools/testfiles/tslink-2.ddl
Changed `../h5dump' to just `h5dump'.
./config/alpha-dec-osf4.0
Added more warning and optimization switches to the native
compiler.
----------------------
./MANIFEST
Added tcompound2.{dmp,h5} and tdset2.{dmp,h5} used by the
h5toh4 testing.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Added check for <sys/timeb.h> for Win32.
Determines sizeof(char) just so we have a complete list of
type sizes defined as preprocessor symbols.
./src/H5detect.c
./src/H5T.c
./src/H5Tpkg.h
Detects alignment constraints. In order for this to work the
operating system must not correct unaligned data (for
instance, on the DEC Alpha one might need to say `uac p
sigbus' before running H5detect).
./src/H5private.h
Includes <signal.h> because it's needed by H5detect.c to
detect alignment constraints.
./src/H5Tconv.c
Added extra checks to all hardware conversion functions so
they align data when necessary before the conversion. This
slows down the conversions somewhat but they're still much
faster than the software conversions.
./test/dtypes.c
By setting a constant at the top of the source you can test
conversions where the data is aligned on various byte
boundaries.
By setting a constant at the top of the source you can
simulate architectures that have alignment constraints on
architectures that don't.
Changed typo SIZEOF_LDOUBLE to SIZEOF_LONG_DOUBLE in a few
places.
