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Feature
Description:
Adding support for NBIT compression to dumper
Solution:
Platforms tested:
arabica, verbena, copper64
Misc. update:
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Purpose:
bug fix, new test file
Description:
h5dump was not properly displaying array indices > 3D
Solution:
added the same algorythm and data structure that h5diff uses to calculate the array index
from a element number position
Platforms tested:
linux
solaris
Misc. update:
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Bug fix.
Description:
When building h5dumpgentest.c with Visual C++ 6.0, I got the following warning message:
h5dumpgentest.c(4528) : warning C4013: 'h5tools_can_encode' undefined; assuming extern returning int
Solution:
Add the header file h5tools.h into h5dumpgentest.c.
Platforms tested:
Heping (Linux)
Visual C++ 6.0 on Windows XP/2000.
.NET on Windows XP.
(Tested with SZIP-with-encoder and SZIP-without-encoder).
Misc. update:
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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:
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Fix SZIP filter to dynmically detect encoder.
Description:
Solution:
See:
http://hdf.ncsa.uiuc.edu/RFC/SZIP/Szip_dynamic_12_Oct.pdf
Changes to h5dump tests, contingent on detecting SZIP encoder.
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Refactor code
Description:
Refactor common code for determining the native type for using in the
tools into separate routine.
Also, reduce diffs between the two branches and bring back some fixes from
the development branch to the release branch.
Platforms tested:
FreeBSD 4.10 (sleipnir)
too minor to require h5committest
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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:
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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:
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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:
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Description:
the original code that showed a name for HARDLINK was reassigning that name to a name
made in the dump traversal (made by concatenation by nested objects)
Solution:
removed this reassigmnet
now the name showed after HARDLINK is always the first name found for that object
(this object is printed once interely; subsequent printings show the word HARDLINK
and the first name )
Platforms tested:
linux
AIX
solaris
Misc. update:
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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:
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changed the name of one dataset, it was confusing
Description:
Solution:
Platforms tested:
linux (small)
Misc. update:
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h5dump new feature, bug fix
Description:
added the dump of unmamed types to the file contents
fixed a bug in the type array, it was printing invalid characters with the array indices option on
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
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dumper new features
Description:
1) added options for not printing : datasets, groups, datatypes, links
2) added a section for the user block
3) in the traversal routine, added the printing of an arrow for soft links and t
he word HARDLINK for hardlinks
the print of the file contents is made during traversal , instead of at the e
nd of it (this is helpful
for very large files, where the wait time can be very long)
4) changed the description of the fill value properties
5) added a colon after the printing of the array indices
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
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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:
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h5dump new feature
Description:
add processing of tab characters (in the context of the new option process CR/LF)
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
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h5dump update
Description:
updated the h5dump test files generator , so that it coincides with the 1.6 branch
Solution:
Platforms tested:
linux (small)
Misc. update:
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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:
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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:
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Description: Add null dataspace to h5dump and h5ls.
Platforms tested: h5committest
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Description: h5dump and h5ls failed an assertion check when a dataset's
datatype is enumerate type and there are special characters in the names
of these values.
Platforms tested: h5committest
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Bug fix
Description:
Variable length strings and sequences with NULL pointers were not handled
by library, causing problems access the data. This also affected fill values
for variable-length datatypes.
Solution:
Address the issues in the library by detecting NULL sequences/strings
and avoid trying to convert them.
Patched up dumper to display NULL sequences/strings.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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Bug fixes and code cleanup
Description:
Changes to h5dump code:
- Dump shared datatypes for any class of datatype, not just compound
datatypes.
- Cleaned up formatting to greatly reduce the amount of trailing
whitespace emitted in output. Also removed some spurious blank
lines from named datatype output.
Added code to generate named datatype attribute test file.
Added tests for dumping named datatypes in attributes for both DDL and
XML output.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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Code cleanup
Description:
Remove various "fixtype" routines which duplicate (and actually pre-date)
the functionality in H5Tget_native_type in favor of having the tools call
H5Tget_native_type(). This provides the same functionality (actually better
functionality, since the old "fixtype" routines didn't handle alignment of
compound fields correctly) and reduces the amount of code to maintain.
Add additional tests to dump out a "complex" compound datatype which
exercises more code in the library for aligning compound fields correctly.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Code cleanup
Description:
Clean up varios compiler warnings flagged by SGI compiler and gcc 3.3
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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added writing more attributes to one test file
Description:
added the writing of 3D attributes to one test file of h5ls
Solution:
Platforms tested:
Windows 2000 (octopus)
Linux 2.4 (rockaway)
SunOS 5.7 (arabica)
IRIX 6.5 (modi4)
Misc. update:
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Bug fix
Description:
This would sometimes coredump in machines like PSC Alpha cluster
or linux icc if -g is not used.
Solution:
The real problem was because char string arrays were declared
without including space for the null terminator. E.g.,
char s[5][2]={ "s1", "s2", ...}
is not correct. Increased the size and also need to change
the H5S... definitions too.
Platforms tested:
"h5committested"--the h5dumpgentest passed without problem though
it failed in Fortran but that is a current known problem.
Tested in verbena using icc and also in PSC's cluster.
Misc. update:
Can't find this error in the v1.5 know problem list.
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added a new test for h5ls
Description:
Solution:
Platforms tested:
Misc. update:
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Bug fix
Description:
A few groups were left open after they were used.
Solution:
Closed them. :-)
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committested
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Feature Add
Description:
It's now possible to print out characters as actual characters
instead of their decimal equivalent numbers. It's the same thing that
h5ls does. The flag to do this is "--string" or "-r".
Platforms tested:
Verbena (Fortran & C++)
Arabica (Fortran)
Modi4 (Fortran & Parallel)
Misc. update:
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Code cleanup
Description:
Various code cleanups to allow the development branch to be compiled with
a C++ compiler (i.e. CC=g++ )
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) C++
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Lots of performance improvements & a couple new internal API interfaces.
Description:
Performance Improvements:
- Cached file offset & length sizes in shared file struct, to avoid
constantly looking them up in the FCPL.
- Generic property improvements:
- Added "revision" number to generic property classes to speed
up comparisons.
- Changed method of storing properties from using a hash-table
to the TBBT routines in the library.
- Share the propery names between classes and the lists derived
from them.
- Removed redundant 'def_value' buffer from each property.
- Switching code to use a "copy on write" strategy for
properties in each list, where the properties in each list
are shared with the properties in the class, until a
property's value is changed in a list.
- Fixed error in layout code which was allocating too many buffers.
- Redefined public macros of the form (H5open()/H5check, <variable>)
internally to only be (<variable>), avoiding innumerable useless
calls to H5open() and H5check_version().
- Reuse already zeroed buffers in H5F_contig_fill instead of
constantly re-zeroing them.
- Don't write fill values if writing entire dataset.
- Use gettimeofday() system call instead of time() system when
checking the modification time of a dataset.
- Added reference counted string API and use it for tracking the
names of objects opening in a file (for the ID->name code).
- Removed redundant H5P_get() calls in B-tree routines.
- Redefine H5T datatype macros internally to the library, to avoid
calling H5check redundantly.
- Keep dataspace information for dataset locally instead of reading
from disk each time. Added new module to track open objects
in a file, to allow this (which will be useful eventually for
some FPH5 metadata caching issues).
- Remove H5AC_find macro which was inlining metadata cache lookups,
and call function instead.
- Remove redundant memset() calls from H5G_namei() routine.
- Remove redundant checking of object type when locating objects
in metadata cache and rely on the address only.
- Create default dataset object to use when default dataset creation
property list is used to create datasets, bypassing querying
for all the property list values.
- Use default I/O vector size when performing raw data with the
default dataset transfer property list, instead of querying for
I/O vector size.
- Remove H5P_DEFAULT internally to the library, replacing it with
more specific default property list based on the type of
property list needed.
- Remove redundant memset() calls in object header message (H5O*)
routines.
- Remove redunant memset() calls in data I/O routines.
- Split free-list allocation routines into malloc() and calloc()-
like routines, instead of one combined routine.
- Remove lots of indirection in H5O*() routines.
- Simplify metadata cache entry comparison routine (used when
flushing entire cache out).
- Only enable metadata cache statistics when H5AC_DEBUG is turned
on, instead of always tracking them.
- Simplify address comparison macro (H5F_addr_eq).
- Remove redundant metadata cache entry protections during dataset
creation by protecting the object header once and making all
the modifications necessary for the dataset creation before
unprotecting it.
- Reduce # of "number of element in extent" computations performed
by computing and storing the value during dataspace creation.
- Simplify checking for group location's file information, when file
has not been involving in file-mounting operations.
- Use binary encoding for modification time, instead of ASCII.
- Hoist H5HL_peek calls (to get information in a local heap)
out of loops in many group routine.
- Use static variable for iterators of selections, instead of
dynamically allocation them each time.
- Lookup & insert new entries in one step, avoiding traversing
group's B-tree twice.
- Fixed memory leak in H5Gget_objname_idx() routine (tangential to
performance improvements, but fixed along the way).
- Use free-list for reference counted strings.
- Don't bother copying object names into cached group entries,
since they are re-created when an object is opened.
The benchmark I used to measure these results created several thousand
small (2K) datasets in a file and wrote out the data for them. This is
Elena's "regular.c" benchmark.
These changes resulted in approximately ~4.3x speedup of the
development branch when compared to the previous code in the
development branch and ~1.4x speedup compared to the release
branch.
Additionally, these changes reduce the total memory used (code and
data) by the development branch by ~800KB, bringing the development
branch back into the same ballpark as the release branch.
I'll send out a more detailed description of the benchmark results
as a followup note.
New internal API routines:
Added "reference counted strings" API for tracking strings that get
used by multiple owners without duplicating the strings.
Added "ternary search tree" API for text->object mappings.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Other platforms/configurations tested?
FreeBSD 4.7 (sleipnir) serial & parallel
Solaris 2.6 (baldric) serial
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Purpose:
bug fix.
Description:
h5dump cannot dump data and datatype for VL string.
Platforms tested:
eirene, arabica
Misc. update:
MANIFEST, RELEASE.txt
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Renamed h5dumptst.c to h5dumpgentest.c.
Added a test to run h5dumpgentest to make it can run without error. Note
that this does not verify if it is generating the correct test files.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}? YES
Misc. update:
Update MANIFEST if you add or remove any file. YES
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