Remove feature
Description:
Retire threaded, balanced binary tree code from HDF5 use. Requiescat in
pace...
Also, regenerate dependencies files.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require full h5committesting (the code is already
disconnected from everything except its tests)
Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
Modify the cache code (H5C) to support automatic cache resizing to
adapt to the work load at run time.
Description:
Different applications require different sized caches to maintain
an acceptable hit rate. This set of changes attempts to provide the
ability to adjust to circumstances automatically.
Solution:
Added highly configurable code to allow the user to either set a
fixed cache size, or allow the cache to grow and shrink according to
conditions.
If enabled, cache size increases are triggered when the hit rate
drops below a user specified threshold in a user specified interval.
Cache size reductions (if enabled) are triggered when either the
hit rate exceeds some user specified threshold over a user specified
interval, when the cache contains "enough" entries that haven't been
accessed for a user specified interval, or some mix of the above.
See the header comments on the H5C_auto_size_ctl_t structure in
H5Cprivate.h for further details.
At present, the cache resize configuration options are not
accessible via the user API. Must add this.
Platforms tested:
h5committested, hepingi (serial), and copper (parallel)
Misc. update:
Port
Description:
Initial work for supporting GNU FORTRAN/F95 on FreeBSD. I think I've
got things mostly set up correctly, but I'm getting an internal compiler
error on one of the FORTRAN sources, so I'm not going to add this configuration
to the daily tests yet.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/GNU FORTRAN
Not tested in h5committest
add hl fortran
Description:
Solution:
Platforms tested:
linux (absfot and pgf90)
solaris (32 and 64 bit)
AIX
note : HP gives a compiling error , to be fixed in the future
Misc. update:
Add new internal data structure
Description:
Add an implementation of skip lists to the library (see comment in
src/H5SL.c for references to the papers describing them) as a potential
replacement for our current threaded, balanced binary tree container.
Skip lists are much simpler to implement and should be faster to use.
Also, added new error codes to release branch, so bump the minor version
number to indicate that the library is no longer perfectly compatible with
the 1.6.3 release.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
Too minor to require further testing (the skip lists aren't actually
used by any library code yet)
bug fix
Description:
the Makefile.in of the hl tests was not including a "srcdir" include path
the test table .c file was missing also the srcdir path
Solution:
add it
Platforms tested:
Misc. update:
insert high level library into main library
Description:
configure.in has a new entry (--enable-hl, disable-hl) it is on by default
the configure message prints info regarding if hl is enabled or not
the tree is
/hl
/hl/src
/hl/test
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Fix SZIP filter to dynmically detect encoder.
Description:
Solution:
See:
http://hdf.ncsa.uiuc.edu/RFC/SZIP/Szip_dynamic_12_Oct.pdf
Platforms tested:
verbena, arabica, cobalt.
Note RE testing:
All automatic tests work as before.
The feature is a configuration thing, so the tests are manual.
Tested with the following configs:
pre-release version of SZIP, with dynamic library,
1. no SZIP
2. SZIP, decoder only
3. SZIP, encoder+decoder
released (static lib) SZIP
4. no SZIP
5. SZIP, decoder only
6. SZIP, encoder+decoder
after build, switch szip in LD_LIBRARY_PATH at run time
7. SZIP decoder
8. SZIP encoder
Misc. update:
Manifest updated
bug fix
Description:
Description:
one case was not handled in the combination of input options (layout and filters)
Solution:
redo the algorythm that handles all cases
Solution:
Platforms tested:
linux
Misc. update:
Refactor and update fortran configuration
Description:
Changed configure.in to include the production, debugging and profiling
flags for FORTRAN in the command line.
Added '-flags' files for PGI and Intel C compilers
Added '-fflags' files for PGI and Intel FORTRAN compilers
Updated 'gnu-flags' file for GNU C compiler to not modify compiler flags
when gcc is not being used.
Make detection of the correct FORTRAN compiler a bit smarter for Linux
platforms. (And carried over some of the minor changes to other affected
machines)
Platforms tested:
Linux 2.4 (tungsten) w/PGI and Intel C & FORTRAN compilers.
Changes not tested by h5committest
Bug fix & code cleanup
Description:
More dataset cleanups to get to a point where we can fix the chunked I/O
bug.
Also fix a couple of errors in the recent file object resurrection changes
which should hopefully address the recent daily test failres (H5T.c)
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
h5committest
new test
Description:
added a test that generates and copies a file with a dataset with fill value
(this is to test the property list function H5Pequal)
Solution:
Platforms tested:
linux
solaris
aix
Misc. update:
Code cleanup
Description:
Fix another batch of minor differences between the development and release
branches.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
Code cleanup
Description:
Clean up collective chunking code a bit.
Also, add '--enable-instrument' configure flag to have a mechanism for
determining that optimized operations happened correctly in the library (instead
of just the "normal" way) by allowing 'flag' properties to be set outside the
library and set when the "right" thing happens. This is mainly for debugging
and regression checks, so we make certain we don't break optimized I/O by
accident. It's enabled by default when --enable-debug is on (which is on by
default in the development branch and off by default in the release branch),
but can also be independently controlled with its own configure flag.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
IBM p690 (copper) w/parallel
h5diff and h5repack changes
Description:
h5diff
introduced the following four modes of output:
Normal mode: print the number of differences found and where they occured
Report mode: print the above plus the differences
Verbose mode: print the above plus a list of objects and warnings
Quiet mode: do not print output (h5diff always returns an exit code of 1 when differences are found)
h5repack
added an extra parameter for SZIP filter (coding method)
the new syntax is
-f SZIP=<pixels per block,coding>
(pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN')
Example of use:
./h5repack -i file1 -o file2 -f SZIP=8,NN -v
updated usage messages, test scripts and files accordingly
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
Purpose:
Bug Fix
Description:
If an HDF5 file grows larger than its address space, it dies and is unable to
write any data. This is more likely to happen since users are able to change
the number of bytes used to store addresses in the file.
Solution:
HDF5 now throws an error instead of dying. In addition, it "reserves" address
space for the local heap and for object headers (which do not allocate space
immediately). This ensures that after the error occurs, there is enough address
space left to flush the entire file to disk, so no data is lost.
A more complete explanation is at /doc/html/TechNotes/ReservedFileSpace.html
Platforms tested:
sleipnir, copper (parallel), verbena, arabica, Windows (Visual Studio 7)
Solution:
Platforms tested:
Misc. update:
h5repack changes
Description:
there were some requests to change some minor h5repack features
h5repack only made a warning about a non available filter in verbose mode ( -v )
without -v it kept silent, and users sometimes missed this warning
the request was that it should print this warning always. so, the new format, is e.g
./h5repack -i test_szip.h5 -o out.h5
Warning: dataset </dset_szip> cannot be read, SZIP filter is not available
due to this, and to avoid a lot of these messages in the shell test script, I modified
the script h5repack.sh so that it detects the presence of all filters in the environment
(previously it only detected SZIP)
the test files were also divided in more files , to make the script code easier to
follow
Solution:
Platforms tested:
linux
AIX (no szip)
solaris (no szip, no gzip )
Misc. update:
h5dump new tests
Description:
added new tests for the print of array indices (nested objects, several ranks)
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
Bug fix
Description:
The "shared" raw B-tree node can get freed before all the B-tree nodes
had been flushed out to disk and released by the cache.
Solution:
Implement a simple reference counting wrapper for objects in the library
and use it to hold the shared raw B-tree nodes so they aren't freed before all
references to them in memory are released.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir)
IRIX64 6.5 (modei4)
h5dump new tests
Description:
added more tests for the escape/not escape feature for string data (with vlen, with
compound, with char data)
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
h5dump new tests
Description:
added new tests for the -p option, superblock, file contents, fill values, array indices.
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
Description:
Replaced the old metadata cache with a cache with a modified LRU
replacement policy. This should improve the hit rate.
Solution:
Since we want to flush cache entries in increasing address order, I
used the threaded binary B-tree code to store the cache entries.
There is a fair bit of overhead here, so we may want to consider
other options.
While the code is designed to allow the support of other replacement
algorithms, at present, only a modified version of LRU is supported.
The modified LRU algorithm requires that a user selectable portion
of the cache entries be clean. The clean entries are evicted first
when writes are not permitted. If the pool of clean entries is used
up, the cache grows beyond its user specified maximum size. The
cache can also exceed its maximum size if the combined size of the
protected (or locked) entries exceeds the maximum size of the cache.
Platforms tested:
eirene (serial, parallel, fp), h5committested
Misc. update:
Purpose:
HDF5 now supports SZIP with no encoder.
Description:
SZIP can be configured to have both encoder and decoder or just to have the decoder. HDF5 can now query the configuration of any filter, and will throw errors if users try to write using a filter with encoding disabled.
Solution:
Added H5Zget_filter_info function, changed API for H5Pget_filter and H5P_get_filter_by_id. See SZIP RFC.
Platforms tested:
Copper (fortran, C++, parallel), Sleipnir (C++), Arabica (fortran, C++), Verbena (fortran, C++)
Misc. update:
Description: Added new API H5Fget_name and new test program called filename.c. This function
returns the name of the file by object ID(file, group, dataset, named datatype, and attribute)
which belongs to the file.
Platforms tested: h5committest and fuss.
Misc. update: MANIFEST and RELEASE.txt
h5dump output change, new tests
Description:
the storage layout output format the storage layout output format had some changes
same for the user defined filter
add an option (-y) for not printing the array indices (default is print indices )
the option for escaping non printable characters covers all characters (default is not escape)
(this might be not very portable, the test files are tstring.ddl and tstringe.ddl )
add tests for the new options
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Description: This is the second effort to correct XML dumper after adding null
dataspace test for attribute and dataset. Since XML schema hasn't been updated
for null space, took out null space test from tdset.h5 and tattr.h5 and put it
into a seperate file, tnullspace.h5. Only h5dump tests this null space file;
XML dumper doesn't do it at this moment. We'll wait until XML schema is updated
first.
Platforms tested: h5committest and RH 8(fuss)
Misc. update: MANIFEST(added two new files in tools/testfiles, tnullspace.h5
and tnullspace.ddl)
Description:
added the code for print strings with new line and display the path of references (new source files h5tools_ref.c and .h )
added a test suite in testh5dump.sh.in for
( note : to create testh5dump.sh , one must redo ./configure; this detects the availability of filters
and generates testh5dump.sh accordingly)
1) storage layout
2) fill value
3) print reference with path
4) print strings with new lines
5) filters
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
Update shell scripts
Description:
Switch to generating the testh5dump.sh script at configure time, so we can
determine which filters are available to test.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too small to require h5committest
h5dump new version
Description:
added the changes already made for 1.6
support for dumping of
1) filters
2) storage layout
3) fill value
4) comments
5) superblock
6) file contents
7) array indices
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
