| Commit message (Collapse) | Author | Age | Files | Lines |
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Changes since 19990616
----------------------
./src/H5T.c
./src/H5Tconv.c
All conversion functions take an extra argument called
`stride' which is the number of bytes to advance the source
and destination pointers after each element is converted. If
the value is zero then the old behavior is preserved (source
and destination values are packed). This feature was necessary
to implement the compound datatype conversion optimizations
and it causes a minor change to the API (application-defined
type conversion functions take an extra size_t stride
argument).
./src/H5Tconv.c
An additional compound data type conversion function was added
which is applied unless the destination type is larger than
the source type. I'm measuring significant performance
increases for certain operations:
Test Name Struct-Conv Noop-Conv
New(Old) MB/s New(Old) MB/s
---------- ------------- -------------
Reordering 2.062(0.3936) 54087(0.9047)
Subsetting 2.901(0.6581) 40192(1.1100)
Shrinking 1.976(0.3925) 33628(1.1500)
---------- ------------- -------------
./test/dtypes.c
Added various compound datatype conversion tests.
Fixed return values from functions.
./src/H5T.c
Conversion timers are updated only if H5T debugging is turned
on a runtime (in addition to compile time). This allows the
data type layer to be compiled with debugging support without
having to pay a big runtime penalty if the debugging isn't
actually used.
./src/H5A.c
./src/H5D.c
./src/H5Ofill.c
./src/H5P.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5Tpublic.h
Added the stride argument to the H5T_convert() calls. The
stride is always zero, which means that the source and
destination data values are packed.
./configure.in
./configure [REGENERATED]
If API tracing is turned off then libhdf5.settings will say
`no' instead of nothing.
./test/flush1.c
./test/flush2.c
Added better error messages in a couple places.
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Changes since 19990614
----------------------
./src/H5D.c
Changed the way the plist_id argument of H5Dvlen_reclaim() is
checked so that it's more specific and works when debugging is
turned off.
./src/H5TB.c
Removed an unused local variable.
./test/fillval.c
./test/h5test.c
./test/h5test.h
Changed `basename' variables to `base_name' to prevent a
warning about a global with the same name.
./tools/h5ls.c
Changed `indent' variables to `ind' to prevent a warning about
a global with the same name.
./tools/h5toh4.c
Commented out declarations for things that normally appear in
system header files since our definitions might be
incompatible with the system and prevent h5toh4 from
compiling. If all looks good on other systems then we can
permanently remove these declarations...
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Changes since 19990611
----------------------
./doc/html/H5.format.html
Added documentation for opaque data types (bitfield types were
already documented but they were out of order).
./src/H5E.c
Fixed a bug with glibc2 on linux systems where `stdout' is an
extern and can't be used to initialize static data.
./src/H5T.c
./src/H5Tpkg.h
./src/H5Tpublic.h
./src/H5detect.c
Removed the `_T' from the new C9x types I just added so the
names are consistent with existing types. Besides, the fact
that something is a datatype is obvious because it starts with
H5T_NATIVE_.
./tools/h5ls.c
Added the new C9x data types. H5ls prints one of these types
only if it doesn't match one of the builtin C types.
Prints the OID for shared data types.
Fixed a formatting bug with symbolic links which was
introduced a few changes ago.
The commandline has been changed so that objects from multiple
files can be listed with a single command. Instead of
specifying a file name and an optional list of objects, each
thing to print is a file name and object concatenated. H5ls
figures out how to devide the name into a file name and object
name even when the file name part doesn't correspond to an
actual Unix file.
Old syntax: h5ls [OPTIONS] FILE [OBJECTS]
New syntax: h5ls [OPTIONS] FILE[/OBJECT] [FILE[/OBJECT]]...
Example ({X,Y} is expanded by the shell)
Old command: h5ls -d ../test/x.data dir1 dir2
New command: h5ls -d ../test/x.data/{dir1,dir2}
The filename is printed as part of the object name when full
names are requested (--full or --recursive). If people really
don't like this they can undefine a constant at the top of
h5ls.
Errors from the hdf5 library are turned off.
Commandline switches of the form `--width 80' are accepted in
addition to `--width=80'. This is more symmetric with
single-letter switches that take two forms: `-w 80' and
`-w80'.
./src/H5D.c
Added tracing instrumentation for H5Dvlen_reclaim().
./src/H5private.h
Added casts to int for the isalpha() et al macros to shut up
solaris warnings about char subscripts.
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----------------------
./tools/h5ls.c
Added a `--address' (`-a') switch which causes h5ls to display
file addresses for raw data. For contiguous datasets it's just
a nice simple number, but for chunked datasets it's a list of
logical dataset coordinates, file addresses, filter masks, and
storage sizes.
Changed `--dump' switch to `--data'.
./src/H5D.c
./src/H5F.c
./src/H5Fprivate.h
Enhanced the indexed-storage B-tree iterator so it can dump
raw data addresses (and other info) to the standard error
stream.
Added H5Ddebug() so h5ls has a way to dump addresses for
datasets. I'm not sure what else this API function should do,
so I think we should discuss it before we document it. So far,
h5ls is the only thing that uses it, and we can easily change
that.
./src/H5Tconv.c
./test/dtypes.c
Finally had a chance to verify Paul's H5T_conv_s_s (general
string to string conversions) bug fixes and incorporate them
into H5T_conv_f_f (general floating-point to floating-point
conversions) and H5T_conv_i_i (general integer to integer
conversons). Thanks Paul.
./src/H5D.c
./src/H5S.c
./src/H5Sprivate.h
Added performance timers around data space read and write
callbacks. They were already there for the gather/scatter
callbacks.
The timings for read/write callbacks are displayed along with
gather/scatter when data space debugging is turned on.
./bin/iostats
Updated to print totals. Added a `--fast' option that doesn't
do any output except the totals and is much faster.
./bin/trace
Changed __unused__ to UNUSED to match source code.
./config/gnu-flags
Updated error message for pgcc. I've sent bug reports to the
pgcc people but the new version still has the same bug.
./configure.in
./config/conclude.in
./config/depend.in
Fixed dependencies for non-GNU makes when run in a directory
other than the hdf5 source tree.
Updated GNU `make dep' rules to copy the distributed
dependencies for non-GNU makes into the source tree when run
in some other directory.
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----------------------
./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.
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./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.
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----------------------
./config/*-aix4.* [REMOVED]
./config/*-aix4.x [NEW]
./config/solaris2.5 [REMOVED]
./config/solaris2.x [NEW]
./configure.in
./configure [REGENERATED]
./MANIFEST
Changed the names of the IBM-SP2 config files by replacing the
minor version numbers with an `x'. The solaris config warns
about old versions of gcc.
The RUNSERIAL value is set to the empty string by default. The
config/* file (or user) can override it by setting it to some
other value.
The `--enable-parallel' with no flags turns on the
HAVE_PARALLEL constant in the source code but doesn't add any
MPI or MPI-IO libraries to the link line.
If we are compiling for parallel then configure checks that we
can actually link a very simple program. This has the benefit
of detecting config errors before we waste time compiling the
entire library.
Configure recognizes `mpcc_r' as a parallel compiler.
./src/H5A.c
./src/H5Apublic.c
Fixed some compiler warnings. Changed the return type of
H5Aget_name() from hssize_t to ssize_t because the name can
never be larger then memory.
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----------------------
./INSTALL
Added warnings and a disclaimer about GNU, DEC, Irix64, and NT
compilers that generate incorrect machine code.
./configure.in
./src/H5private.h
Detects and includes <sys/param.h> which is needed on FreeBSD
before <sys/proc.h> even though we only really using anything
from <sys/proc.h> on the DEC Alpha.
./config/irix64
Turned off warnings for duplicate definitions from the linker
because -lnsl on irix has the same stuff in it as -lc.
./config/irix6.x
Split up the CC and CFLAGS settings like with irix64 so that
compilers besides `-n32' can be used.
./bin/snapshot
The snapshots are tagged with names like hdf5-1_1_52 which is
similar to the way the releases are tagged (cvs doesn't allow
dots in tags).
./test/dtypes.c
./src/H5private.h
./src/H5Tconv.c
Fixed some alignment violations on the DEC when using high
optimization levels. The DEC incorrectly optimizes certain
memcpy() and memmove() calls when the source argument is not
word aligned if the call looks like it's copying an atomic
data type.
./test/hyperslab
Worked around code generation bugs in the Irix64 Mongoose 7.00
compiler by casting some `unsigned long' values to `unsigned'
in an expression.
./src/H5Ocomp.c
Fixed a place where %d was used to print a size_t.
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----------------------
./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.
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----------------------
./src/H5F.c
./src/H5private.h
./src/H5Ipublic.h
./src/H5O.c
Fixed a rather nasty bug with file closing that caused the
file boot block to be updated incorrectly, effectively
truncating the file. The bug I fixed was triggered by:
1. Create a file, F
2. Open an object, X
3. Close file F
4. Reopen file F for read/write.
5. Create and close some objects
6. Close file F
7. Close library (exit).
Step 3 pended the close because object X is still open, but
the file ID was removed from the H5I_FILE ID group. Step 4
created a new file because it didn't see any matching file on
the H5I_FILE ID group. Step 5 extends the file. Step 6 writes
the new file boot block to disk. Step 7 closes object X and
completes the close from step 3, writing the old boot block
information to disk.
The new behavior is that step 3 moves the file from the
H5I_FILE group to the H5I_FILE_CLOSING group. Step 4 searches
both groups and finds the file. Step 5 extends the file using
the same H5F_file_t struct as step 3. Step 6 closes the H5F_t
struct opened in step 3 but not the H5F_file_t struct shared
by steps 1 and 3. Step 7 closes object X which closes the
H5F_file_t from step 1, flushing the boot block which was
shared by all steps.
./src/H5F.c
Added some bulletproofing to file reference counting and
removed comments which no longer apply. Added H5F_flush_all()
and H5F_close_all() which apply to all files.
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
Added the new H5I_free_t data type to describe the function
type to be passed as the `free_func' argument to
H5I_init_group().
./src/H5I.c
Bulletproofed the object removal functions. Removed comments
which no longer apply. Changed global variable names so they
don't violate the naming scheme. Added H5I_debug() that prints
the contents of an ID group. Removed H5I_inc_ref() because it
isn't used. Reindented a couple of functions.
./src/H5.c
./src/H5G.c
./src/H5Ipublic.h
Changed H5I_MAXID to H5I_NGROUPS to better relect the fact
that it's the total number of valid ID groups.
./src/H5Shyper.c
Changed hyperslab offset arrays to signed quantities to get
rid of warnings on DEC cluster.
./src/H5Flow.c
./src/H5Fprivate.h
Changed the objno argument of H5F_addr_pack() to be unsigned
to get rid of warnings on DEC cluster.
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----------------------
./src/H5Shyper.c
Changed hyperslab offset arrays to signed quantities to get
rid of warnings on DEC cluster.
./src/H5Flow.c
./src/H5Fprivate.h
Changed the objno argument of H5F_addr_pack() to be unsigned
to get rid of warnings on DEC cluster.
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----------------------
./src/H5.c
Fixed more dependency problems in H5_term_library(). There was
a bug in the previous version that could cause the wrong EOF
marker to be written to the boot block under certain
circumstances. Hopefully this fixes it although I don't ready
access to a test case (Mark Miller will test it).
./src/H5F.c
./src/H5Fprivate.h
Added an H5F_close_all() that is similar to
H5F_term_interface() but which doesn't close the
interface. Files that don't have open object headers are
closed, others are delayed until all object headers close. All
files are flushed.
./src/H5ACprivate.h
./src/H5Bprivate.h
./src/H5Dprivate.h
./src/H5Eprivate.h
./src/H5Fprivate.h
./src/H5Gpkg.h
./src/H5Gprivate.h
./src/H5Gpublic.h
./src/H5HGprivate.h
./src/H5HLprivate.h
./src/H5Iprivate.h
./src/H5MFprivate.h
./src/H5MMprivate.h
./src/H5Oprivate.h
./src/H5Pprivate.h
./src/H5Ppublic.h
./src/H5RAprivate.h
./src/H5Sprivate.h
./src/H5Spublic.h
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5Tpublic.h
./src/H5Vprivate.h
./src/H5Zprivate.h
./src/H5private.h
./src/H5public.h
Reindented after __DLL__ was added.
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----------------------
./tools/h5tools.c
Strings are not converted to null-padding before being
printed; they are printed with whatever byte values appear in
the file.
./tools/h5ls.c
Now able to display attribute data type and data.
Added a `-f' or `--full' switch which causes the full name of
each object to be displayed instead of just the base name.
Added a `-r' or `--recursive' switch that recursively prints
the contents of groups, avoiding cycles.
More bulletproofing for non-printable characters in things
like object names, attribute names, and comment strings. We
don't want listing a file to send termal escape sequences
because it's sometimes possible to execute commands that way.
Since h5ls doesn't usually use quotes around object names we
must sometimes escape space characters.
External files are listed in a table to make the output less
confusing.
./tools/h5tools.c
./tools/h5tools.h
Changed h5dump() to h5dump_dset() and added h5dump_mem(). Also
make h5dump_fixtype() public.
./test/dtypes.c
Wrote some data to an attribute to test h5ls attribute
printing.
./src/H5ACprivate.h
./src/H5Apublic.h
./src/H5Dprivate.h
./src/H5Dpublic.h
./src/H5Epublic.h
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5Gprivate.h
./src/H5HLprivate.h
./src/H5Oprivate.h
./src/H5Ppublic.h
./src/H5RApublic.h
./src/H5Rpublic.h
./src/H5Spublic.h
./src/H5Tpkg.h
./src/H5Tpublic.h
./src/H5Vprivate.h
./src/H5Zpublic.h
./src/H5private.h
./src/H5public.h
Reindented function prototypes after `HDF5API' was added. Also
rewrapped long lines.
./src/H5Flow.c
Added an `#ifdef WIN32' around an unused variable.
./src/H5api_adpt.h
Removed extra carriage returns inserted by "broken" operating
system.
./src/H5Dprivate.h
./src/H5Oprivate.h
./src/H5Vprivate.h
./src/H5private.h
Removed extraneous inclusion of H5api_adpt.h since it's
included in H5public.h which is included by everything.
./src/Makefile.in
Added H5api_adpt.h to the list of public header files to fix
broken `make install'.
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----------------------
./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.
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----------------------
./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.
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----------------------
./src/H5HG.c
Fixed a bug in the alignment calculation for the heap free
space. The reference test passes now.
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----------------------
./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.
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----------------------
./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 ;-)
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----------------------
./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.
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----------------------
./src/H5Fistore.c
Improved the hash function so it mixes bits better. This
results in a few percent improvement in raw data chunk cache
efficiency because there are fewer collisions.
./test/chunk.c
Added #define's for chunk preemption `w0' value and number of
slots in cache.
./src/H5B.c
Added some more comments to H5B_insert_helper() and
H5B_remove_helper() and also point to some additional
documentation.
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----------------------
./bin/trace
./src/H5.c
./src/H5F.c
./src/H5Fprivate.h
./src/H5Fpublic.h
Added a `scope' argument to H5Fflush() which should be either
H5F_SCOPE_LOCAL or H5F_SCOPE_GLOBAL and determines which files
are flushed (just the specified file or the entire virtual
file).
./src/H5F.c
Added reference counts to the H5F_t struct so we get the
correct behavior between H5Funmount() and H5Fclose().
./src/H5O.c
Fixed a memory leak that happens during error handling.
./test/cmpd_dset.c
./test/unlink.c
Fixed a memory leak.
./test/mount.c
Enabled the H5Fclose() test.
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----------------------
./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...
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call. Also
checked in H5R skeleton files.
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reference API.
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which were
calling malloc too often. Also, added caching of hyperslab blocks, which
improves performance _significantly_ for hyperslab I/O.
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H5Gget_objinfo
and renamed internal functions to match up with the renamed API functions.
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----------------------
./test/cmpd_dset.c
Uncommented the last test again and there are still bugs.
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----------------------
./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
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----------------------
./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.
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----------------------
./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.
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----------------------
./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.
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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.
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conditionally included at compile time. Tracing and debugging share
the same environment variable. All is documented in Debugging.html.
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----------------------
./src/H5.c
Fixed an argument promotion bug in HDfprintf()
./src/H5Fistore.c
Fixed a array bounds read error.
./src/H5HG.c
Fixed uninitialized (but unused) data appearing in the hdf5
file, a potential security problem.
./src/H5T.c
./src/H5Tpublic.h
Added new data types for hdf5 types: H5T_NATIVE_HSIZE,
H5T_NATIVE_HSSIZE, H5T_NATIVE_HERR, and H5T_NATIVE_HBOOL. I
did not add H5T_NATIVE_HID since I couldn't think of a reason
that it would be stored in a file anyway.
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----------------------
./src/H5Fistore.c
Fixed a bug that caused the wrong number of chunk offsets to
be read or written from the file.
./src/H5Z.c
Fixed a memory bug.
./test/dtypes.c
Removed redundant tests.
./bin/snapshot
Removed Perl code from a shell script. Oops :-)
./src/H5D.c
Removed cvs merge conflicts.
./src/H5Omtime.c
Fixed a typo in the Irix5.3 code.
./src/H5S.c
Fixed a memory leak.
./src/H5Shyper.c
Fixed a bad call to malloc() that didn't allocate enough
memory. Reordered a comparison to eliminate an array bounds
read error.
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----------------------
./MANIFEST
./src/H5Ssimp.c [REMOVED]
./src/Makefile.in
Removed H5Ssimp.c since it was no longer used.
./bin/snapshot
Fixed a few minor things to make it work better.
./src/H5D.c
Cleaned up H5D_read() and H5D_write() by combining some code
in each. Added timing calls around the data space calls when
H5S_DEBUG is defined.
./src/H5S.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Spoint.c
./src/H5Sprivate.h
Changed H5S_find() so it returns a table entry again instead
of copying the data into a caller-supplied buffer. This
allows the timers to be stored in the table and updated by the
caller. Added H5S_register() to register new table entries
and added entry creation to all the H5S selection
methods. Also changed lots of global functions to static
functions.
./src/H5Fistore.c
Fixed a memory bug in the raw data cache.
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----------------------
./doc/html/Datatypes.html
./doc/html/H5.format.html
./src/H5.c
./src/H5Odtype.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tpublic.h
./test/dtypes.c
Changed the values of the H5T_str_t type in order to make a
distinction between C's null terminated strings and strings
which are not null terminated.
The string character set and padding method are saved to the
hdf5 file instead of using defaults.
Added conversion function from one fixed-length string type
to another.
./test/chunk.c
Fixed to work with new filter API
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----------------------
./config/solaris2.5
Hopefully set up now so it honors the CC and CFLAGS variables
and understands solaris cc flags.
./test/big.c
Checks to see if creating lots of large sparse files exceeds
the user disk quota and skips the test. It also checks that
we can actually open ~64 files at once.
./doc/html/Files.html
./src/H5A.c
./src/H5Aprivate.h
./src/H5F.c
./src/H5Fpublic.h
Added the H5Fflush() function which takes any object as an
argument as long as the object is in some way associated with
a file. This required an H5A_entof()
./src/H5.c
./src/H5Flow.c
The `%a' format of HDfprintf() now allows a field width and
justification flag etc, like the other formats. The old
H5F_addr_print() was recoded to call HDfprintf() instead of
vice versa.
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----------------------
./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.
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