| Commit message (Collapse) | Author | Age | Files | Lines |
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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
./tools/h5tools.c
Added support for printing bitfields and opaque data.
./test/dsets.c
Added bitfield and opaque datasets to the output file so h5ls
has something interesting to print.
./test/trefer.c
Resync'd
./src/H5Tconv.c
Fixed bitfield conversion which resulted in possible garbage
in high-order bits of destination when the destination type is
larger than the source type. Thanks for spotting it, Quincey.
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----------------------
./tools/h5tools.c
Finished code which prints references (object and dataset
region). Patrick, if you tell me how h5dump should (or might
want to) print references I can make some changes to support
various formats...
You can try it out with:
cd test
env HDF5_NOCLEANUP=yes ./testhdf5
../tools/h5ls -dvr trefer1.h5
../tools/h5ls -dvr trefer2.h5
(run h5ls with no arguments if you forgot what the switches do)
./test/trefer.c
Call calloc instead of malloc in one place to prevent
uninitialized data from being written into the file.
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----------------------
./tools/h5ls.c
./tools/h5tools.c
./tools/h5tools.h
Finished the `-x' or `--hexdump' switch, which causes all data
to be printed in hexadecimal format with no translation from
file to memory data type.
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----------------------
./doc/html/Datatypes.html
./test/dtypes.c
Added documentation and tests for opaque types.
./tools/h5ls.c
Added a `-x' or `--hexdump' argument which is not fully
implemented (because I want to synchronize h5tools.c first)
but which will eventually print raw data in hexadecimal format
without any translation from disk. This would be useful for
debugging references and VL types.
./tools/h5tools.c
Added support for references (not quite finished yet, but
compiles -- I wanted to sync up this file before Patrick and I
got too far apart...)
./src/H5R.c
Checked for error return value from H5R_get_object_type()
./src/H5A.c
./src/H5D.c
Changed error return values from NULL to FAIL
./test/Makefile.in
./test/trefer.c
Creates trefer1.h5 and trefer2.h5 so that the second test
doesn't clobber the first file since the files might be useful
for debugging.
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fixed the number of parameters to h5dump_fixtype.
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added a new variable to the tools lib that keeps track of what program is using
the library. h5ls.c and h5dump.c needed to init the variable to the correct
value for the programtype variable. this variable will hopefully only be temporary
until the lib gets combined farther
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incorportated all
the constants and from dumputil to to the tools lib and merged h5dump_fixtype
together. I had to add an extra parameter to the function to specify what action
should be taken when it hits H5T_STRING in the case statement. if the parameter
(strDUAction) is true then it does what it use to do in dumputil but if it is false
then it will do what it originally did in this file.
I also put the h5dump_sprint functions into the same file. it isn't really merged yet.
i just wanted to get everything into a file and then worry about the merging of this
function. The toolslib way of h5dump_sprint takes an extra parameter. If this
parameter is set to NULL then it will do the dumputil's version of this function.
like i said this is just the first step i am taking. it will be merged better later.
the rest of the changes to the other files were related to the above changes.
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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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----------------------
./tools/h5tools.c
./tools/h5tools.h
Finally fixed a long-standing bug that caused core dumps if
a compound datum rendered to more than some number of
characters (we kept bumping up the limit at the risk of
violating stack size limits on some machines). The fix works
only on systems that have the vsnprintf() function (otherwise
a 4kB limit is imposed, which if violated probably dumps
core). If vsnprintf() is present then the library dynamically
allocates space for the output string.
Also made it possible to control how compound data is rendered
across multiple lines of output by allowing the caller to
specify where optional line-breaks get inserted. The output
functions split up the value at one or more optional
line-breaks to prevent it from wrapping around the screen.
If a datum doesn't fit on the current line but would fit on
the next line then it is printed on the next line regardless
of whether optional line-breaks would have prevent wrapping
around the screen. This makes it easier to find the beginnings
of compound data values. This feature is disabled by default
but can be enabled by the application.
If a datum doesn't fit on the current line and the previous
datum also occupied more than one line then we move to the
next line before printing. This makes it easier to find the
beginnings of compound data values but prevents the output
from looking fragmented if there are only a few long values
among mostly short values. This feature is disabled by
default but can be enabled by the application.
The application can control the printf() formats used for all
the native data types. The defaults are what the library used
to use: %g, %ld, %lu, %d, and %u
./tools/h5ls.c
Compound datatype values can now be split across multiple
lines of output instead of just wrapping. Also, when lots of
compound values are too long they all start at the beginning
of a line. This only required about 10 lines of changes in the
setup for tools library calls (I didn't modify the h5dump
program because it uses its own version of the tools library
that forked off long ago).
Added code for Win32 which is unable to cast `unsigned long
long' to `double'. If the dataset size exceeds (2^63)-1 then
the percent utilization is not displayed (this is easily
possible with chunked datasets). This is untested yet.
./configure.in
./src/H5config.h.in
./src/H5.c
./src/H5private.h
Check for vsnprintf() and provide a simple, stupid definition
if it isn't available. The stupid definition just calls
vsprintf() and ignores the second argument. This can result in
buffer overflows in h5ls and h5dump since vsprintf() is an
unsafe function (and anyone can create an hdf5 file that runs
an arbitrary command from h5ls and h5dump in that case)!
./config/conclude.in
Remove more *.o files for `make clean'
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
./src/H5TB.c
Cleaned up a memory leak during H5_term_library() by allowing
H5I_clear_group() to skip items that couldn't be freed. This
allows the item to remain in the group until we can free it
later.
./src/H5F.c
The H5F_close_all() function fails if a file cannot be closed.
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----------------------
./config/commence.in
./examples/Makefile.in
./test/Makefile.in
./testpar/Makefile.in
./tools/Makefile.in
Fixed some dependency problems in Makefiles. If the library
version is updated then everything gets recompiled.
./src/H5G.c
./src/H5R.c
Failure return value for object type functions is now
H5G_UNKNOWN as documented.
./src/H5Shyper.c
./src/H5Spoint.c
Fixed an unused argument warning.
./tools/h5debug.c
Fixed a call to H5F_block_read() since the 4th argument is
different now.
./tools/h5ls.c
Added a space between the object name and class to make the
output readable when the object name is longer than 24
characters.
C
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----------------------
./config/depend.in
Fixed automatic dependencies. We were storing dependencies for
*.o files instead of *.lo files after shared libraries were
added.
./config/gnu-flags
./config/linux-gnulibc1
Moved `-march=pentiumpro -mcpu=pentiumpro -malign-double' from
the linux file to this file and caused it to depend on the CPU
name. This fixes one of Elena's bugs.
./src/H5B.c
./src/H5Bprivate.h
./src/H5D.c
./src/H5Dprivate.h
./src/H5Dpublic.h
./src/H5F.c
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fmpio.c
./src/H5Fprivate.h
./src/H5Fpublic.h
./src/H5Gnode.c
./src/H5P.c
./src/H5RA.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Spoint.c
./src/H5Sprivate.h
./src/H5Tpublic.h
./test/istore.c
Added an H5Dget_storage_size() function that reports the
amount of storage allocated for raw data in a dataset.
Changed H5D_xfer_* to H5F_xfer_* because these properties are
more general than datasets. This also allows some of the
lower-level I/O functions to get this information easier.
./src/H5S.c
./src/H5Sall.c
Added two new functions H5S_all_read() and H5S_all_write()
which are optimizations that copy data directly between file
and memory without having to go through the scatter gather
step. This knocks quite a bit of time off the I/O and
reading/writing entire datasets is a fairly common operation.
./tools/h5ls.c
Reports the logical size of data, the allocated size of data,
and the percent utilization.
./MANIFEST
Removed old pablo files, added new files. Snapshots should now
start to work again.
./src/H5D.c
./src/H5Fmpio.c
Removed two warnings signed vs. unsigned comparisons and check
for overflow.
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----------------------
./config/commence.in
./config/conclude.in
./test/Makefile.in
./tools/Makefile.in
Fixed so private libraries are not installed publicly.
The installation directories `bin', `include', and `lib' are
created mode 755.
./src/H5.c
./src/H5A.c
./src/H5F.c
./src/H5Fcore.c
./src/H5Fistore.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fsec2.c
./src/H5Fstdio.c
./src/H5G.c
./src/H5Gent.c
./src/H5Gnode.c
./src/H5HG.c
./src/H5HL.c
./src/H5O.c
./src/H5Oattr.c
./src/H5Ocomp.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
./src/H5Ofill.c
./src/H5Olayout.c
./src/H5Omtime.c
./src/H5Oname.c
./src/H5Osdspace.c
./src/H5Oshared.c
./src/H5Ostab.c
./src/H5R.c
./src/H5Sall.c
./src/H5Shyper.c
./src/H5Smpio.c
./src/H5Snone.c
./src/H5Spoint.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Vprivate.h
./src/H5Z.c
./src/H5detect.c
./src/H5private.h
./test/chunk.c
./test/dsets.c
./test/dtypes.c
./test/h5test.c
./test/overhead.c
./test/ragged.c
./test/tattr.c
./tools/h5dump.c
./tools/h5findshd.c
./tools/h5ls.c
Changed `__unused__' to `UNUSED' to fix a conflict with GNU
header files.
./src/H5Tpkg.h
./test/h5test.h
Removed __unused__ from forward function declarations.
./src/H5P.c
Removed a comment about restrictions for the type conversion
temporary buffers. Thanks to Quincey, the comment no longer
applied.
./src/H5T.c
Relaxed the H5Tpack() a little so it would pack compound data
structures that had non-transient atomic members.
./tools/h5ls.c
Added a `-g' (or `--group') flag that causes information to be
printed about the specified group instead of the group's
contents. (sort of like Unix's `ls -d'). The `-g' can be used
in combination with `-r' to print information about the group
and its contents.
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./configure [REGENERATED]
./src/H5D.c
./src/H5O.c
Removed H5AC, H5B, and H5T from the default list of packages
to debug (because they're pretty expensive debugging), and
added H5O. Also fixed a bug for undefined variable in H5D when
H5S debugging is turned on but H5T debugging is turned off.
./config/conclude.in
Fixed installation of header files for building in a directory
other than the source directory. This fixes a bug where
H5config.h wasn't being installed.
./src/H5.c
./src/H5A.c
./src/H5D.c
./src/H5F.c
./src/H5G.c
./src/H5I.c
./src/H5Iprivate.h
./src/H5P.c
./src/H5R.c
./src/H5RA.c
./src/H5S.c
./src/H5T.c
./src/H5TB.c
./src/H5Tprivate.h
./src/H5Z.c
./src/H5detect.c
./src/H5private.h
Changed the way the library shuts down again. Now it handles
cycles between packages and isn't so sensitive to dependencies
between packages. A package might shut down only to be
restarted to process a request from some other package being
shut down. Loops are detected after 100 iteractions and the
shutdown is aborted with a message on standard error. This
also makes it a lot easier to debug.
./src/H5A.c
Fixed H5A_write() and H5A_read() so they pass a non-null
background buffer to the conversion functions. This is
necessary when an attribute has a compound data type.
./src/H5Flow.c
./src/H5Fprivate.h
./src/H5Fsec2.c
Reindented new Win32 stuff.
./src/H5Odtype.c
Fixed a bug when enumeration types are used in a compound data
type. The byte pointer wasn't incremented after the type
information was written.
./tools/h5ls.c
Compound data types display their total size because it's not
always obvious from looking at the members.
Scalar attributes show their space as `scalar' instead of
`{}'.
The index value is not printed for attributes that have only a
few values. Instead the word `Data:' is printed on the first
line of attribute data.
Named types display their data type only if verbose output was
requested.
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----------------------
./configure.in
./configure [REGENERATED]
The path for a command is calculated explicitly the hard way
because `type -path' isn't portable.
./config/freebsd
./config/linux-gnu
./config/linux-gnulibc2
Changed the way files reference each other.
./config/gnu-flags [NEW]
./config/dec-flags [NEW]
These files figure out what flags to pass to certain compilers
so we can reuse code in more than one config/* file. They
also have better warning messages when old compilers are used.
./config/linux-gnulibc1
./config/dec-osf4.x
These files use the new *-flags files.
./src/H5D.c
./src/H5Onull.c
./src/H5Tconv.c
./tools/h5ls.c
Fixed a compiler warning.
./src/H5detect.c
Added a better comment to the top of the generated file.
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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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----------------------
./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.
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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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----------------------
./tools/h5ls.c
Displays enumeration type information.
./tools/h5tools.c
Displays enumerated data using symbol names.
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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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| |
----------------------
./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.
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| |
----------------------
./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.
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----------------------
./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'.
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----------------------
./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.
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----------------------
./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.
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| |
----------------------
./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....
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Changed usage message.
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H5Gget_objinfo
and renamed internal functions to match up with the renamed API functions.
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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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| |
----------------------
./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
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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| |
----------------------
./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().
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----------------------
./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.
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----------------------
./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)
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----------------------
./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,
...
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----------------------
./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.
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----------------------
./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.
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----------------------
./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.
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----------------------
./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.
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----------------------
./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.
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----------------------
./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.
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