----------------------
./config/irix64
The old (-32) compiler is now supported by setting envrionment
CC='cc -32'. The -64 compiler is the default or you can set
CC='cc -64'.
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5G.c
./src/H5I.c
./src/H5Ocomp.c
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5T.c
./src/H5Tbit.c
./src/H5Tconv.c
./src/H5Z.c
./src/H5detect.c
./test/big.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/enum.c
./test/mtime.c
./test/ohdr.c
./tools/h5ls.c
Fixed lots of warnings on Irix64. Mailed a few remaining
warnings in H5S to Quincey and a few in the dumper to
Ruey-Hsia.
Bug Fixes
Problem:
Warnings given during compilation on some machines.
Solution:
Take care of various Compiler Warnings such as:
1) uninitialized variables;
2) unreachable statements.
Platforms tested:
Solaris2.5, Linux, Irix6.5
----------------------
./configure.in
./acconfig.h
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5public.h
./src/H5Omtime.c
Check for <stddef.h>
Checks for `__tm_gmtoff' in `struct tm' because old versions
of GNU libc are different than recent versions. This fixes the
failing mtime test.
./bin/config.guess
./config/freebsd2.2.7 [REMOVED]
./config/freebsd [ADDED]
Changed the name so it works with all versions of FreeBSD.
./src/H5.c
Moved H5F after H5T and H5G in H5_term_library() to satisfy
dependencies.
./src/H5G.c
Fixed a bug that caused H5Gcreate() to fail if the group name
had trailing slashes.
./src/H5Gpublic.h
Changed `group_name' to `name' in a prototype.
./src/Makefile.in
Dynamic library on Linux, but needs for work to be generally
useful.
./src/H5HG.c
./src/H5HGprivate.h
Fixed alignment problems when using old GCC compilers (like
the one shipped with RedHad Linux).
./tools/h5ls.c
Fixed a bug where the contents of the root group could be
listed twice if there was a link back to the root
group. Similarly for groups that are mentioned on the command
line.
Fixed a bug where unknown types were printed with a random
type class number.
./src/H5T.c
./src/H5Tconv.c
./src/H5Tprivate.h
Fixed O(log N) conversion bugs.
Bug fix
Problem:
Did a H5get_type() on a dataset of committed type without doing
the associated H5Tclose(). This caused an abort to occur during the
atexit() phase of the h5toh4 converter.
Solution:
Execute the associated H5Tclose().
Platform tested:
Solaris2.5
Bug fix
Problem:
The hdp dumper output files used in the h5toh4 converter test
program have the result of the latest changes to the HDF4 library,
but the converter was to maintain compatability with HDF4.1r2.
Solution:
Regenerate the HDF4.1r2 version of the hdp dumper ouput files to
be used for the h5toh4 converter test program.
Platform tested:
Solaris2.5
New feature
Solution:
Modified h5dumptst.c to generate more single dimension
datasets of H5T_STRING type held in file tstr2.h5.
Platform tested:
Solaris2.5
New feature
Solution:
Changes to support conversion of 1-dimensional HDF5 datasets of
H5T_STRING type into HDF4 Vdatas. Also, support conversion of
HDF5 attribute of string type into HDF4 attribute of INT8 type.
Dimensional information is lost.
Platform tested:
Solaris2.5
----------------------
./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:
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
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
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.
New feature
Solution:
Testing of Extendable Dataset support in h5toh4 converter when
extendable dimension is first dimension.
Platform tested:
Solaris2.5
----------------------
./doc/html/Datatypes.html
./src/H5.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tpublic.h
./src/H5detect.c
./test/chunk.c
./test/dtypes.c
./test/h5test.c
./test/mtime.c
./test/tattr.c
./test/th5s.c
./tools/h5dump.c
./tools/h5dumputil.c
./tools/h5import.c
./tools/h5ls.c
./tools/h5toh4.c
./tools/h5tools.c
Renamed the old H5T_NATIVE_CHAR type to H5T_NATIVE_SCHAR to
denote that it is always signed.
Added a new H5T_NATIVE_CHAR type which has the same range,
representation, and behavior as either H5T_NATIVE_SCHAR or
H5T_NATIVE_UCHAR depending on the compiler and its
command-line switches for the application source file which
references H5T_NATIVE_CHAR. If source files are compiled with
different switches then each source file will resolve
H5T_NATIVE_CHAR appropriately so it matches the C type `char'
in that source file.
NOTE: THERE ARE OTHER DOCUMENTATION FILES THAT I DIDN'T CHANGE
BECAUSE I CAN'T MODIFY THE SOURCE.
./test/extend.c
Swapped two lines to prevent diagnostic messages from messing
up the formatted output.
New Feature
SOLUTION:
h5toh4 is an H5 utility which converts HDF5 files into
HDF4 files. It converts only those H5 objects which have
have mappings into H4 objects.
Some H5 objects that may be converted into H4 objects are:
1) H5 group objects may be converted into H4 Vgroup objects.
2) H5 dataset objects of integer or floating point datatype
may be converted into H4 SDS objects.
3) H5 dataset objects of compound datatype and rank 1 may
be converted into H4 Vdata objects. Field members of the
compound datatype are constrained to be single dimensional.
Platforms tested:
Solaris2.5, HP10.20
New feature
Solution:
This file contains routines to find all shared objects and
committed types and store them in tables. These routines
are made available in the library hdf5/tools/libh5tools.a
Platform tested:
Solaris2.5, HP10.20
New Feature
Solution:
These files are the expected results of the HDF4 hdp dumper,
which has been executed in the following order:
hdp dumpvg file.hdf > file.dmp
hdp dumpvd file.hdf >> file.dmp
hdp dumpsds file.hdf >> file.dmp
Platform tested:
Solaris2.5, HP10.20
New Feature
Solution:
This is a tester for the h5toh4 converter. It is implemented
on different HDF5 files to produce HDF4 files. After each HDF4
file is produced, the file is run through the HDF4 dumper hdp.
The dumper results are compared with expected results and any
differences are noted.
Note: The "/hdf4/bin" directory needs to be part of the tester's
$PATH.
Platform tested:
Solaris2.5, HP10.20
----------------------
./test/flush2.c
./test/overhead.c
Removed carriage-returns inserted by a broken operating system.
./test/big.c
./test/mtime.c
./test/ragged.c
./tools/h5ls.c
Removed inclusion of <H5config.h>, system header files, and definition
of __unused__ since this all happens in <H5private.h>.
./test/chunk.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/extend.c
./test/external.c
./test/fillval.c
./test/flush1.c
./test/flush2.c
./test/iopipe.c
./test/links.c
./test/mount.c
./test/overhead.c
./test/shtype.c
./test/unlink.c
./tools/h5import.c
./tools/h5repart.c
Removed inclusion of <H5config.h> since <hdf5.h> includes it.
./test/flush1.c
Includes <stdlib.h>, protects inclusion of <unistd.h> by using
HAVE_UNISTD_H instead of STDC_HEADERS.
----------------------
./src/H5.c
./src/H5Smpio.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpublic.h
./src/H5detect.c
./src/H5private.h
./src/H5public.h
./test/big.c
The `long long' type isn't quite as prevalent as we had hoped;
there is at least one system that defines `__int64' but not
`long long'. Therefore, I've temporarily changed all
occurrences of `long long' to `long_long' and then #define
that in H5private.h based on the existence of `long long' or
`__int64'. This gets rid of some #ifdef's in other parts of the code.
The semantics of the hdf5 types are:
*int8_t Exactly one byte
*int16_t At least two bytes. We favor 32-bit integers over
16-bit integers if the 16-bit integer is 4-bytes wide
(Cray)
*int32_t At least four bytes.
*int64_t At least eight bytes
long_long The widest integral integer type
The H5Smpio.c contains debugging code which is non-portable.
./tools/h5ls.c
Changed the order native types are detected so we favor the name `int'
over `short' or `long' if two of them are the same.
./config/conclude.in
Added a rule to make test programs depend on the hdf5 library. This
fixes a minor bug where changing H5detect.c and then running `make
test' caused H5Tinit.c to not be recompiled and therefore the test
files are not relinked.
----------------------
./INSTALL.parallel [NEW]
We're beginning to unify some of the parallel installation
steps. This file will contain general information for
installing the parallel library. It's not complete yet.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Check for xdr_int() in libnsl required on Solaris when linking
with hdf4. It's found on the Irix system I tested which
complains that `-lnsl' didn't resolve any symbols. Oh well.
Fixed the order of searching for libdf and libmfhdf for hdf4
linking.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5Z.c
Check for compress() in libz in order to find older versions
of the library that will still work for hdf4. Added a
separate check for compress2() that hdf5 will use.
./configure.in
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
./src/H5.c
./src/H5private.h
./src/H5A.c
./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5F.c
./src/H5Farray.c
./src/H5Fcore.c
./src/H5Ffamily.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fprivate.h
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./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/H5Oprivate.h
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5R.c
./src/H5RA.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Snone.c
./src/H5Spoint.c
./src/H5Sprivate.h
./src/H5Sselect.c
./src/H5T.c
./src/H5Tbit.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5V.c
./test/bittests.c
./test/gheap.c
./test/hyperslab.c
./test/istore.c
./test/tmeta.c
./test/trefer.c
./test/tselect.c
./tools/h5debug.c
./tools/h5tols.c
Added checks for Posix.1g types like `int8_t'. If not defined
then H5private.h defines them. Changed all `int8' etc. to
`int8_t'.
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5I.c
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
./src/H5TB.c
./src/H5Z.c
Calling H5*_term_interface() resets interface_initialize_g to
FALSE so a subsequent call to H5open() (implied or explicit)
reinitializes global variables properly.
./src/H5private.h
./src/H5Oefl.c
./src/H5S.c
Changed MAX_SIZET, MAX_SSIZET, MAX_HSIZET, and MAX_HSSIZET to
SIZET_MAX, SSIZET_MAX, HSIZET_MAX, and HSSIZE_MAX to they
match the Posix.1 constants in <limits.h>.
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5detect.c
Added 36 more integer hardware conversion functions to the
type conversion table for conversions to/from `long long' and
`unsigned long long'. The `long long' names will be changed
shortly to make them portable to Win32.
Changed H5T_init() to H5T_native_open() and added an
H5T_native_close() to open and close the predefined native
data types.
Increased the initial size of the type conversion table from
64 to 128 entries.
Reordered the 90 new integer conversion functions so the names
that are printed favor `int' over `short' or `long' when two
of them are the same.
./test/dtypes.c
Added hardware and software integer conversion tests for the
56 functions I added recently but not the additional 36
checked in this time. That will come next.
Call H5close() after each test so type conversion statistics
are easier to follow. Try this: $ HDF5_DEBUG=t ./dtypes
Added more debugging output for when things go wrong.
./src/H5private.h
Removed trailing carriage-returns inserted by broken operating
system ;-)
----------------------
./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.
----------------------
./tools/h5ls.c
The chunk dimensions and total size is printed for chunked datasets.
./examples/h5_attribute.c
./examples/h5_select.c
./test/chunk.c
./test/iopipe.c
./test/ragged.c
./src/H5.c
./src/H5private.h
./src/H5public.h
Removed extra carriage-return characters inserted by a broken
OS :-)
Reformatted strange-looking comments.
Removed C++ comments.
Wrapped long lines.
./examples/h5_attribute.c
./examples/h5_select.c
Removed inclusion of private headers.
Changed `uint32' (originally `uint') to `unsigned' because
`int32' is not exported as part of the API.
./src/H5Fmpio.h
Removed includes for <sys/types.h> and <sys/stat.h> since
they're already included by H5private.h. All system include
files should be included in H5private.h so we can wrap them
with appropriate feature macros.
./tools/h5import.c
./tools/h5repart.c
Included header files like all other programs in that
directory.
./tools/h5tools.c
Better type checking for `hsize_t' and `hssize_t'.
----------------------
./configure.in
./acconfig.h
./configure [REGENERATED]
./src/H5config.h.in [REGENERATED]
Added checks for functions, structs, constants, and header
files used in h5ls.c to determine the output width with
various Windows compilers and Unix variants.
Added check for <sys/stat.h> and defined
HAVE_SYS_STAT_H. Included <sys/stat.h> in H5private.h outside
the Posix.1 #include's section.
./src/H5RA.c
Less aggressive about failing -- rather returns false, which
allows type detection to continue.
./src/h5ls.c
Data types are displayed for datasets and named data types when
`-v' or `--verbose' is specified on the command-line. The
algorithm is a little different than the dumper because we're
trying to be human-friendly, not necessarily machine-friendly.
* Any data type which matches a native C type gets printed
something like `native double'.
* A floating point type that matches one of the IEEE standard
types but not one of the native types gets printed like `IEEE
64-bit big-endian float'.
* Other floating point values have information about sign bit
location; exponent size, location, and bias; and significand
size, location, and normalization.
* Padding and offsets are displayed for types that have
padding (precision != size), including internal padding for
some floating point data types.
* Non-native integer types are displayed like `32-bit
little-endian unsigned integer'.
* Compound data types have each member displayed including the
member name, byte offset within the struct, dimensions, index
permutation, and data type.
* String types are displayed like `256-byte null-terminated
ASCII string'.
* References are displayed like `8-byte unknown reference'
until the reference interface stabilizes a little.
* All other types including types not yet defined will be
printed like `4-byte class-9 unknown'.
The dimensionality of scalar datasets is printed like `{SCALAR}'
instead of just `{}'.
If external raw files are used to store a dataset then the offsets,
sizes, and file names of each are printed if `-v' or `--verbose'
was given on the command-line.
If an object is found and h5ls can't determine the object type then
it still tries to print the number of hard links, the OID, and any
comment that might be present if `-v' or `--verbose' was specified.
If the `-d' or `--dump' switch is turned on then ragged arrays will
report that the data can only be dumped by dumping the component
datasets explicitly. I'm not planning to implement this since
we're going to eventually change the whole way ragged arrays are
stored.
Compound data values do not have the component names displayed by
default when `-v' or `--verbose' is turned on. Instead, the names
can be displayed with `-l' or `--label'.
The output width is determined by the first rule that applies:
* If the `-wN', `-w N' or `--width=N' switch appeared on
the command line then use N for the output width.
* Query the OS for the tty width in a highly unportable way
borrowed from GNU `less' depending on what functions and
data structures were found during configuration (if any):
_getvideoconfig(), gettextinfo(), _srcsize(), ioctl(),
GetConsoleScreenBufferInfo(), struct videoconfig, struct
text_info, the TIOCGWINSZ ioctl, the TIOCGETD ioctl.
* If the `COLUMNS' environment variable is set then use
its value.
* Use the value 80.
Just for kicks, run Mark and Jim's test_vbt and then say `h5ls -dlsv
test.vbt'. You can also try it on the various *.h5 files in the
test/example directories.
./config/linux
Removed turning on parallel by default on Robb's macine.
----------------------
./bin/snapshot
Made same fix as for the release script yesterday.
./src/H5D.c
./src/H5Dprivate.h
./src/H5G.c
./src/H5Gprivate.h
./src/H5Gpublic.h
./src/H5O.c
./src/H5Oprivate.h
./src/H5RA.c
./src/H5RAprivate.h
./src/H5T.c
./src/H5Tprivate.h
Improved object type checking. Instead of determining the
object type by trying to open each of the possible types, we
keep a table of associations between object type number (like
H5G_GROUP, H5G_DATASET, H5D_TYPE, and H5D_RAGGED) and an `isa'
function that returns true if the object header has the right
messages to make the object a particular type. This mechanism
also allows specialization of object types by permitting an
object to satisfy more than one `isa' function.
Added `isa' functions for groups, datasets, ragged arrays, and
committed data types.
./src/H5config.h.in
Added HAVE_STAT_ST_BLOCKS. I thought this had already been
added, but apparently not.
./tools/h5ls.c
Removed system include files since they're already included by
H5private.h and since I wasn't including them portably anyway.
By default, 1-byte integer types are printed as integer values
instead of ASCII characters. However, the `-s' or `--string'
command-line switch causes the data to be interpretted as
ASCII. String data types are always printed as character
data.
Ragged arrays are now identified as ragged arrays and h5ls
doesn't descend into the group automatically. This uses the
new object type specialization stuff.
./tools/h5tools.c
./tools/h5tools.h
Added the ability to print 1-byte integer types as either
ASCII or numeric data instead of always ASCII. The default is
to print as numeric data.
----------------------
./MANIFEST
Added new Pablo files HDF5record_RT.h and ProcIDs.h
./acconfig.h
./configure [REGENERATED]
./configure.in
./src/H5.c
./src/H5Vprivate.h
./src/H5config.h.in [REGENERATED]
./src/H5private.h
./src/H5public.h
./test/big.c
Added more configuration stuff for the Win32 environment. Removed all
the #ifdef WIN32 from the source and replaced them with OS-independent
stuff. Specifics follow:
Check for non-Posix.1 `st_blocks' field in `struct stat' which is used
by the big file test to decide if the file system supports holes. If
the st_blocks field isn't present then we just skip the test.
Configure checks for <io.h> <sys/resource.h> <sys/time.h> and
<winsock.h> and defines HAVE_IO_H, HAVE_SYS_RESOURCE_H,
HAVE_SYS_TIME_H and HAVE_WINSOCK_H when they're found.
Configure checks whether both <sys/time.h> and <time.h> can be
included and defines SYS_TIME_WITH_TIME if so. Otherwise include only
<sys/time.h> or <time.h> even if both exist.
Configure checks sizeof(__int64) and defines SIZEOF___INT64 to the
result or to zero if __int64 isn't defined. The source uses `long
long' in preference to `__int64'.
Removed null WIN32 definition for `inline' since such a definition
already exists in H5config.h
Protected gettimeofday() calls in debugging code with
HAVE_GETTIMEOFDAY instead of WIN32.
./src/H5F.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fsec2.c
./src/H5Fstdio.h
./src/H5P.c
./src/H5Tconv.c
./src/H5private.h
Removed #include of system files from library source files and
consolodated them into H5private.h where they're protected by various
configuration macros (most of them were duplicated there already
anyway).
./test/big.c
./test/chunk.c
./test/cmpd_dset.c
./test/dsets.c
./test/dtypes.c
./test/extend.c
./test/external.c
./test/fillval.c
./test/flush1.c
./test/flush2.c
./test/iopipe.c
./test/links.c
./test/mount.c
./test/mtime.c
./test/overhead.c
./test/ragged.c
./test/shtype.c
./test/unlink.c
Protected system #include's with #ifdef's from H5config.h.
Undefined NDEBUG since some of the tests rely on assert() to check
return values.
Removed WIN32 definitions for __unused__ since this can be controlled
by the definition of HAVE_ATTRIBUTE in H5config.h
./test/testhdf5.h
Removed the CLEAN_CMD definition because we no longer use it.
Albert's cleanup() functions replaced it.
./test/fillval.c
Initialized auto hid_t variables to fix warnings in error recovery
code when data flow analysis is turned on in compilers.
./test/h5tools.c
Initialized an auto variable to fix a compiler warning.
./test/chunk.c
./test/ragged.c
The WIN32 had some unsigned variables changed to signed because the
compiler generates warnings when coercing unsigned to double(?). I
changed them back to unsigned because they really are unsigned
quantities. If this the change was just to shut up extraneous warnings
then perhaps a compiler flag can do the same; otherwise if the
compiler generates bad code then we should supply a patch file instead
messing up source code with bug work-arounds.
./src/H5detect.c
Protected system #include's with #ifdef's from H5config.h thereby
removing a WIN32.
If getpwuid() doesn't exist (HAVE_GETPWUID) then we assume that
`struct passwd' doesn't exist either (we don't really need it in that
case).
The H5T_NATIVE_LLONG and H5T_NATIVE_ULLONG are defined in terms of
`long long' or else `__int64' or else `long' depending on what's
available.
./src/H5Flow.c
./src/H5Ofill.c
Added __unused__ to some function arguments that aren't used when
assertions are turned off.
./src/H5V.c
Changed an auto variable name in some hand-inlined code to get rid of
a warning about the variable shadowing a previous auto.
----------------------
./MANIFEST
./test/th5s.h5 [NEW]
./test/th5s.c
Added a test to make sure that creating a data space with too
large a rank fails.
Added a test to make sure that reading a file that has a
dataset with a space with too large a rank fails. Actually,
this one is a little weird: the code that reads the data space
message assumes the space is scalar if the message cannot be
read. Fortunately the layout message fails also, preventing
the dataset from being opened. However, since the data type
message is still visible h5ls will report that the object is a
named data type.
./test/space_overflow.c [NEW]
This is the little program that makes the th5s.h5 file.
./src/H5A.c
./src/H5R.c
./src/H5Sselect.c
Updated trace info.
./src/H5Olayout.c
./src/H5Osdspace.c
Added code to fail if the dimensionality is too large when
decoding a layout or simple data space message.
./src/H5Oprivate.h
Redefined H5O_LAYOUT_NDIMS in terms of H5S_MAX_RANK.
./src/H5P.c
./src/H5S.c
Check for ndims>H5S_MAX_RANK in API function calls, added
assert to internal functions.
./src/H5V.c
Changed a `<' to an `<=' in an assert.
./test/flush2.c
Includes stdlib.h for getenv().
./tools/h5tools.c
Able to handle up to H5S_MAX_RANK dimensions during output.
----------------------
./src/H5F.c
./src/H5Fprivate.h
./src/H5G.c
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5Gpublic.h
./test/istore.c
./test/tstab.c
Removed CWG functionality.
./tools/Makefile.in
Added `_test' where I added `test' last week. Maybe now the
snapshots will start up again...
----------------------
./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.
----------------------
./src/H5D.c
./src/H5Fistore.c
./src/H5Fprivate.h
Fixed a couple things for parallel hdf5 that I broke with the
last checkin.
./src/H5Ofill.c
If no fill value is specified it isn't added to the object
header.
./tools/h5ls.c
Added a line-feed after `Unknown object' is printed.
./tools/h5tools.c
Fixed printing of scalar values. Need to still track down a
failed assertion when H5Sselect_hyperslab() is called with a
zero size....
During make test, it copies the master copy testh5dump.sh
to a temperary copy, testh5dump and run it. Make clean
remove only duplicated version, not the original master.
Platform test:
baldric.
----------------------
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.
----------------------
./Makefile.in
Running `make distclean' will not fail if one of the
subdirectories has already been cleaned.
./config/BlankForm
./config/irix5.3
Cleaned it up more. Added better support/documentation for
systems that have more than one compiler.
./config/alpha-dec-osf4.0 [NEW]
Added a new config file as a result of testing on Jim Reus's
machine.
./test/chunk.c
Scaled down the testing range so we can actually run it
interactively.
./tools/h5import.c
Included <unistd.h> to get rid of warning for close().
./src/H5detect.c
Seg-faults on Linux for some reason when NDEBUG is defined, so
I just undef it at the top of the source.
./test/big.c
Added a fflush().
./tools/h5ls.c
The `-d' flag now works even when `-v' isn't specified.
./examples/h5_chunk_read.c
./examples/h5_compound.c
./examples/h5_extend_write.c
./examples/h5_group.c
./examples/h5_read.c
./examples/h5_write.c
Indented according to hdf5 standards.
Fixed compiler warnings
----------------------
./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
./src/H5R.c [NEW]
./src/H5Rprivate.h [NEW]
./src/H5Rpublic.h [NEW]
./src/Makefile.in
./src/hdf5.h
./test/ragged.c [NEW]
Preliminary support for 2d ragged arrays for Mark Miller and
Jim Reus. Not fully implemented yet. The test is not actually
part of `make test' because we still have some memory problems.
./src/H5E.c
./src/H5Epublic.h
Added H5E_RAGGED as a major error number.
./bin/release
Checks the MANIFEST file against `svf ls' on systems that have
it.
./bin/trace
Fixed a bug that caused arguments of type `void *x[]' to not
be handled.
./src/H5.c
Removed unused variables and changed a couple types to
fix compiler warnings.
Added tracing support for ragged array object ID's and arrays
of pointers.
./src/H5D.c
H5Dcreate() will complain if either of the property lists are
invalid (instead of using the default).
./src/H5D.c
./src/H5Dprivate.h
Split H5Dget_space() into an API and internal function so it
can be called from the new ragged array layer.
./src/H5Fistore.c
Fixed warnings about unsigned vs. signed comparisons.
./src/H5Flow.c
Fixed a warning about a variable being shadowed in the MPI-IO
stuff.
./src/H5Iprivate.h
./src/H5Ipublic.h
Added the H5_RAGGED atom group.
./src/H5Shyper.c
Fixed some freeing-free-memory errors that resulted when
certain arrays were freed but the pointers were left in the
data structures. I simply set the pointers to null after they
were freed.
./src/H5Sprivate.h
./src/H5Sselect.c
Split the H5Sselect_hyperslab() function into an API and a
private function so it could be called from the ragged array
layer.
Added H5S_SEL_ERROR and H5S_SEL_N to the switch statements to
get rid or compiler warnings.
./src/H5Tconv.c
Removed a misleading comment.
./test/bittests.c
Fixed a warning about a printf().
./test/cmpd_dset.c
Fixed warnings about unused variables because of test #11
being commented out.
./bin/trace
Shortened the right margin for the output to allow room for
the `);' at the end of the TRACE() macros.
Fixed errors
H5.c
Fixed core dump with setvbuf() for debugging.
H5Fistore.c
Fixed bug with sparse datasets.
H5Omtime.c
Found a typo in "Posix Programmer's Guide". The `%z' in the
strftime() should be `%Z' instead.
H5T.c
H5Tpublic.h
Improved api tracing for H5Tinsert_array().
h5tools.c
Doesn't dump core for empty datasets.
Renamed what was called h5dump.c to h5tools.c.
Changed Makefile.in to reflect all the changes.
(Make dependence is to be processed later.)
Tested in Solaris 2.5
----------------------
./MANIFEST
Replaced Compression.html with Filters.html
./doc/html/Filters.html
./src/H5Ocomp.c
./src/H5P.c
./src/H5Ppublic.h
./src/H5Z.c
./src/H5Zprivate.h
Added two extra arguments to H5Pget_filter() in order to
retrieve the filter name. The name is the name registered for
the filter with H5Zregister(), but if the dataset creation
property originally came from an existing file then the name
is that which is stored in the file.
./tools/h5ls.c
The `-v' option now prints the names of the filters.
./src/H5B.c
./src/H5Fistore.c
./src/H5O.c
./src/H5Oefl.c
./src/H5Oprivate.h
./src/H5P.c
Plugged a memory leak.
./src/H5MMprivate.h
H5MM_malloc(0) and H5MM_calloc(0) actually allocate a single
byte in order to be sure that we get a valid pointer.
./src/H5S.c
./src/H5Sselect.c
Fixed pointer->integer conversions in error return values in
three places.
----------------------
./bin/release
Added ./Makefile to the distribution again -- it got lost in
the changes last week although it isn't all that important a
file since it gets clobbered by configure anyway.
./bin/trace
./doc/html/Filters.html
./doc/html/H5.format.html
./doc/html/H5.user.html
./src/H5.c
./src/H5D.c
./src/H5Dprivate.h
./src/H5E.c
./src/H5Epublic.h
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fprivate.h
./src/H5O.c
./src/H5Ocomp.c
./src/H5Oprivate.h
./src/H5P.c
./src/H5Ppublic.h
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Spoint.c
./src/H5Sprivate.h
./src/H5Ssimp.c
./src/H5Z.c
./src/H5Zprivate.h
./src/H5Zpublic.h
./src/hdf5.h
./test/dsets.c
./tools/h5ls.c
Added the data filter pipeline, a generalization of the
compression stuff which allows things like checksums,
encryption, compression, performance monitoring, etc. See
./doc/html/Filters.html for details -- it replaces the
Compression.html doc.
./src/H5T.c
Cleaned up debugging output.
./config/linux
Added checks for egcs and pgcc and changed optimization flags
for the compilers.
./src/H5G.c
./tools/h5dump.c
Fixed compiler warnings in these files and others.
./configure.in
./src/H5private.h
./test/mtime.c
Added a check for difftime() and defined HDdifftime() to do
something else on systems that don't have difftime().
----------------------
./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.
----------------------
./tools/h5dump.c
./tools/h5ls.c
./tools/h5tools.h
Able to handle compound data types now. Moved code that
chooses memory data type based on file data type from h5ls to
libh5tools.a(h5dump.o)
----------------------
./src/H5A.c
./src/H5Apublic.h
./test/tattr.c
Switched the order of the second and third argument of
H5Aget_name() to make it consistent with other functions that
take buffers and buffer sizes.
./src/H5G.c
./src/H5Gpublic.h
./src/H5Gprivate.h
The H5Gget_comment() function returns the size of the comment
including the null terminator. If the object has no comment
then zero is returned. If an error occurs then a negative
value is returned.
./MANIFEST
./tools/Makefile.in
./tools/h5tools.h [NEW]
./tools/h5dump.c [NEW]
Created a library for printing values of datasets in a way
that looks nice. It's not done yet, but I needed it for
debugging the contents of files from Jim Reus.
./tools/h5ls.c
Added the `-d' and `--dump' options which cause the contents
of a dataset to be printed. Added `-w N' and `--width=N'
options to control how wide the raw data output should be. If
you want single-column output then say `-w1'.
Printing dataset values can now handle datasets of any integer
or floating point atomic type. As a special case, integers
which are one byte wide are treated a character strings for
now.
Sample output:
$ h5ls --dump --width=60 banana.hdf
ARCHIVE 0:0:0:744 Dataset {52/Inf}
Data:
(0) "U struct complex { double R; double I; };\012V"
(43) " double;\012"
U 0:0:0:2500 Dataset {256/512}
Data: printing of compound data types is not implemented yet
V 0:0:0:3928 Dataset {256/512}
Data:
(0) 0, 0.015625, 0.03125, 0.046875, 0.0625,
(5) 0.078125, 0.09375, 0.109375, 0.125, 0.140625,
(10) 0.15625, 0.171875, 0.1875, 0.203125, 0.21875,
(15) 0.234375, 0.25, 0.265625, 0.28125, 0.296875,
...
----------------------
./src/H5.c
Handle hid_t of type H5_TEMPBUF, arguments usually called tbuf_id.
Added array tracing where the array rank is stored in a simple
data space. Just use the name of the data space argument when
declaring the array argument:
herr_t
H5Sselect_hyperslab (hid_t space_id, H5S_seloper_t op,
const hssize_t start[/*space_id*/],
const hsize_t _stride[/*space_id*/],
const hsize_t count[/*space_id*/],
const hsize_t _block[/*space_id*/])
and when the program runs you'll see array values printed:
H5Sselect_hyperslab(space=218103813, op=H5S_SELECT_SET,
start=0xbfffef4c {0}, _stride=NULL,
count=0xbfffef44 {64},
_block=NULL) = SUCCEED;
Added more symbolic data types to the tracing output.
./src/H5A.c
./src/H5Apublic.h
./src/H5D.c
./src/H5Dpublic.h
./src/H5F.c
./src/H5Fpublic.h
./src/H5G.c
./src/H5Gpublic.h
./src/H5P.c
./src/H5Ppublic.h
./src/H5S.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Spoint.c
./src/H5Spublic.h
./src/H5Sselect.c
./src/H5Ssimp.c
./src/H5TB.c
./src/H5V.c
Changed some API argument names to be more consistent with
other API functions and to produce better tracing output.
Reformatted some long lines. Indented printf statements.
./tools/h5ls.c
Fixed warnings about unsigned vs. signed comparisons.
----------------------
./tools/h5ls.c
If the dataset is of type H5T_NATIVE_CHAR then we print the
value as a string. This is temporary -- I plan to add better
control of this later but needed something now for debugging.
./src/H5Fistore.c
Squashed a bug in the chunk caching code that caused the wrong
chunk to be returned.
./bin/trace
./src/H5.c
Added support for printing values of array arguments when the
size of the array is supplied by some previous argument. You
must declare the argument as an array in order for the
automatic tracing stuff to work. For instance, the third
argument of H5Pset_chunk() is an array whose size is
determined by the second argument `ndims'. Here's how you
should declare it:
herr_t
H5Pset_chunk(hid_t plist_id, intn rank, hsize_t dims[/*rank*/])
The comment inside the `[]' is the name of some previous
integer argument (int, unsigned, size_t, ssize_t, hsize_t,
hssize_t). The trace output will look something like:
H5Pset_chunk(plist=1234567, rank=2, dims=0x112233 {11, 22})
Changed tracing so that data types are printed out
symbolically when possible.
Changed tracing so data type initializations are not printed.
This used to be confusing because lots of H5Tcopy() and
H5Tregister...() calls showed up before the applications first
explicit API call.
./src/H5Ipublic.h
Changed the file atom group from zero to one so printing of
atoms during tracing is more consistent -- they're all big
numbers now.
./src/H5A.c
./src/H5E.c
./src/H5F.c
./src/H5G.c
./src/H5Sselect.c
./src/H5T.c
./src/H5TB.c
./src/H5Z.c
Accidently modified these when working on the tracing, but
nothing should have changed.
./src/H5P.c
Changed the definition of H5Pset_chunk() for tracing.
./src/H5S.c
./src/H5Spublic.h
Changed the definitions of H5Sset_extent_simple() and
H5Screate_simple() for tracing. Changed the FUNC_ENTER() name
for H5Screate_simple() so tracing shows the correct name.
----------------------
./src/H5Gpublic.h
./src/H5Gprivate.h
./src/H5G.c
./test/dsets.c
./doc/html/Groups.html
Added the H5Gset_comment() and H5Gget_comment() functions
described in an earlier e-mail.
./src/H5.c
Fixed a bug in the tracing code that caused certain data space
enum types to not be printed. Nested case statements can get
confusing to the eyes!
./tools/h5ls.c
Prints the first 50 bytes or so of object comments.
----------------------
./bin/release
The archive names have only three parts to a version number.
Instead of `hdf5-1.2.3d.tar.gz' they will be named like
`hdf5-1.2.3.tar.gz'.
./src/H5public.h
./src/H5.c
Dropped the patch level from the version number. The version
number is now a major number, a minor number, and a release
number.
./doc/html/Version.html
Updated to get rid of patch numbers.
./tools/h5repart.c
Added a `-V' flag like for `h5ls' that prints the version number.
----------------------
./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.
./RELEASE
Added a couple minor details details about API tracing and
symbolic links.
./src/H5public.h
Added comments about the use of hbool_t. Fixed a comment
spelling error.
./test/testhdf5.h
Changed the way the version number is printed. The old method
was `hdf5-1.2.3d' and the new method is `hdf5 version 1.2
release 3'
./tools/h5ls.c
Only prints the max dimension if it differs from the current
dimension or if verbose mode is enabled. Added switches `-?',
`-h', and `--help' to print a usage message. Added switches
`-v' and `--verbose' to generate more verbose output. Added
switches `-V' and `--version' to print the version number and
exit. The version number is printed like: This is h5ls
version 1.0 release 24'
./bin/h5vers [NEW]
This script prints, sets, and/or increments the hdf5 version
number. It can be run from the top directory or any of the
child directories like src, tools, test, etc. Some examples:
$ h5vers # Display current version
1.0.24
$ h5vers -v
version 1.0 release 24 # Display current version.
$ h5vers -s 5.2.8 # Set version and display
5.2.8
$ h5vers -s 2.1
2.1.0
$ h5vers -s hdf5-1.0.24a.tar.bz2
1.0.24
$ h5vers -s 'version 2.0 release 8'
2.0.8
$ h5vers -s 'junk 22 junk 33 more junk 66 and 99 junk'
33.66.99
$ h5vers -i major # Increment from 1.0.24
2.0.0
$ h5vers -i minor # Increment from 1.0.24
1.1.0
$ h5vers -i release # Increment from 1.0.24
1.0.25
$ h5vers ~/hdf5/src/H5public.h # Use an alternate file
1.0.24
./bin/checkapi [NEW]
Run from the src directory with arguments H5[A-Z]*.c and it
will print the locations of each place where an API function
was called from within the library. Use it as the compile or
grep command under Emacs and you can C-x ` through the list.
./bin/debug-ohdr [NEW]
Keeps track of H5O_open() and H5O_close() debugging messages
and lists the file addresses of the object headers that are
opened but never closed. You must enable the `o' debugging at
configuration time and pipe stderr into this script.
./bin/errors
Added a note to indicate that this script no longer works
because of changes in the HRETURN_ERROR() and HGOTO_ERROR()
macros.
./bin/iostats [NEW]
Watches output from the Linux strace program and accumulates
statistics about low-level access to an hdf5 file. The output
is a list of 2d data points which can be plotted by gnuplot to
show file seeking behavior.
./MANIFEST
Added new files.
----------------------
./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.
