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:
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:
for the file contents dump and for hardlinks, one arrow "->" is printed, followed
by the first found name for that object
options for not printing specific types of objects were postponed
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
bug fix
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
solaris
AIX
Misc. update:
Code cleanup
Description:
Clean up almost all warnings from Windows builds.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
bug fix
Description:
an if statment was wrongly placed before a swith-case statment, causing the
fall to the next case
this error was only detected by the C99 compiler (gcc 3.44)
Solution:
put if after the case
Platforms tested:
sleipnir with gcc 3.4
linux
Misc. update:
bug fix
Description:
the indentation was not made properly for nested objects when printing array indices
Solution:
added the indentation to h5tools_simpple_prefix
Platforms tested:
linux
AIX
solaris
Misc. update:
h5dump new feature
Description:
added the dump of unamed datatypes for the file contents
added a colon as separator for the indices array option
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
dumper new feautures
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 the word HARDLINK for hardlinks
the print of the file contents is made during traversal , instead of at the end 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:
Misc. update:
Code cleanup
Description:
Reduce compiler warnings on SGI IRIX
Platforms tested:
FreeBSD 4.10 (sleipnir)
SGI IRIX6 (Cheryl's machine)
Too minor to require full h5committest
h5dump new features
Description:
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)
add tests for the new options
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
h5dump new features
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:
bug fix
Description:
the output of array indices for the array datatype case was not done correctly
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
h5dump new features
Description:
added the code for new features. dump of
1) filters
2) storage layout
3) fill value
4) comments
5) file super block
6) file contents
7) array indices
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
Code cleanup
Description:
Clean up lots of warnings based on those reported from the SGI compilers
as well as gcc.
Platforms tested:
SGI O3900, IRIX64 6.5 (Cheryl's SGI machine)
FreeBSD 4.9 (sleipnir) w/ & w/o parallel
h5committest
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
Fix bug.
Description:
Wrong parameter in subroutine call.
Note: this only affects '--xml', and only affects the value of
the fill value that is reported.
Solution:
put correct parameter in subroutine call
Platforms tested:
verbena
Misc. update:
bug fix
Description:
On windows debug/debugdll; somehow: a crash happened by free() function
although that string is "allocated".
Make some efforts to fix without success.
Suspect a compiler bug.
Solution:
Use #ifdef WIN32 #endif comment out that free function for the time being.
Hopefully h5dump debug version is not used.
Platforms tested:
windows 2000, linux 2.4(no need for more platforms because of win-specified).
Misc. update:
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
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
bug fix
Description:
On windows, rindex is not supported. strrchr is used instead.
Solution:
Platforms tested:
linux 2.4, windows 2000
(since the change is minimal and three other platforms have been used to
test for 1.7 branch, so no needs to test more).
Misc. update:
1. Address Bug 888
2. Update h5dump xml to 1.6
Description:
This is an omnibus update to the h5dump tool.
1. Bug 888: Added '-A', suppress data in dataset, but give values of attr.
2. Many changes to update the XML output. See:
http://hdf.ncsa.uiuc.edu/RFC/XMLSchema/
3. The XML dumper tests have been split off. The standard 'make check'
no longer runs the XML tests.
'make check-xml' runs the XML tests manually. (Some tests
may fail on some platforms, e.g., on 64bit.)
'make check-all' runs regular and then xml tests.
Solution:
Platforms tested:
verbena, arabica, copper (64bit)
Misc. update:
MANIFEST updated.
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:
Code cleanup
Description:
Clean up miscellaneous warnings which have crept into the code.
Fix "_POSIX_C_SOURCE not defined" warning on FreeBSD.
Adjust gcc compiler flags to be more concise for production mode.
Refactor the H5O code so that there is a stronger boundary between code
in the H5O package and code in the library which just calls H5O routines.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel and gcc 2.95.4 & gcc 3.2.2
Misc. update:
Update MANIFEST if you add or remove any file.
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
Improvement
Description:
Moved the code parsing for missing file name in the parse_command_line
routine.
Added a test checking if the tool fails as expected when no file name is
given.
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, added nofilename.ddl
Bug fix (ID 765 and part of ID 841)
Description:
"h5dump -H" would core dump. It was because the code was not
checking if there was any file argument after option parsing.
It referred to an non-existing filename argument.
There was also some very old but not commented code which allowed
the use of back slash to escape a filename begun with '-'. The
'--' option is better and more common practice.
Solution:
Added code to check if there is still a filename argument after parsing.
(This checking probably should goto inside the option_parsing routine.
Also removed that old code mentioned above.
Platforms tested:
eirene, arabica and modi4
updated copyright note.
Copied the UNUSED correction from v1.4.
Added an example to the usage of -- option.
Description:
[describe the bug, or describe the new feature, etc]
Solution:
[details about the changes, algorithm, etc...]
[Please as detail as you can since your own explanation is
better than others guessing it from the code.]
Platforms tested:
arabica (fortran), modi4 (pp, fortran),eirene (fortran, CC).
Migrate from configure macros of XYZ_ABC to H5_XYZ_ABC
Description:
configure generates many macros definitions on the fly and
were stored in src/H5config.h which is included by H5public.h.
But other software that uses hdf5 may also run their own configure.
There can be a clash in macro name space. We decided awhile ago
to prepend all generated macros with "H5_" to avoid conflicts.
The process has started and this commit completes it (at least attempt
to).
Solution:
Many macros symbols (e.g. SIZEOF_xxx and HAVE_xxx were changed to
H5_SIZEOF_xxx and H5_HAVE_xxx). Then H5private.h no longer includes
H5config.h. This cuts H5config.h away from HDF5 source code.
Pending issues:
The module of fortran and pablo are to be resolved in a different
commit.
Platforms tested:
eirene (parallel), arabica (solaris 7 --enable-fortran, --enable-cxx)
Bug Fix
Description:
There was a problem with having a lot of groups nested together. We
could only handle 1024 characters at most, but, in a parallel program
especially, it could occur that there were lots and lots of groups
and would be more than 1024.
Solution:
I made the "objname" part of the obj_t structure a pointer instead of
a fixed size. Added code to allocate/deallocate the memory we need
for it. Had to fix how the "prefix" was being handled in the h5dump
program. It was also set to only 1024 characters in length. I made it
dynamic.
Added a test case...Go me!
Platforms tested:
Linux, Solaris
Purpose:
Feature Add
Description:
Added support for dumping Group Comments. This involved a
modification of the DDL as well.
Solution:
Steal code from h5ls and put it in the h5dump. The ddl.html file was
updated as normal. And a test was created...
Platforms tested:
Dangermouse, Modi4, Kelgia
Code cleanup
Description:
Windows is generating hundreds of warnings from some of the practices in
the library. Mostly, they are because size_t is 32-bit and hsize_t is
64-bit on Windows and we were carelessly casting the larger values down to
the smaller ones without checking for overflow.
Also, some other small code cleanups,etc.
Solution:
Re-worked some algorithms to eliminate the casts and also added more
overflow checking for assignments and function parameters which needed
casts.
Kent did most of the work, I just went over his changes and fit them into
the the library code a bit better.
Platforms tested:
FreeBSD 4.4 (hawkwind)
Code cleanup for better compatibility with C++ compilers
Description:
C++ compilers are choking on our C code, for various reasons:
we used our UNUSED macro incorrectly when referring to pointer types
we used various C++ keywords as variables, etc.
we incremented enum's with the ++ operator.
Solution:
Changed variables, etc.to avoid C++ keywords (new, class, typename, typeid,
template)
Fixed usage of UNUSED macro from this:
char UNUSED *c
to this:
char * UNUSED c
Switched the enums from x++ to x=x+1
Platforms tested:
FreeBSD 4.4 (hawkwind)
Purpose:
Bug Fix
Description:
Some so-called "operating systems" (*cough*Windows*cough*) can't
handle large string sizes.
Solution:
Replace the Usage string with individual strings which all call
fprintf() themselves.
Platforms tested:
Linux
Purpose:
Bug Fix
Description:
Object IDs command-line options weren't being picked up.
Solution:
The wrong flag was being checked for. Changed the flag from "v" to
"i", which is what the documentation says.
Platforms tested:
Linux
Code cleanups, mostly..
Description:
Work on pacifying the SGI compiler to get the generic properties working
correctly with --enable-parallel and --enable-fortran. It's not quite
fixed yet, but I need to head home and these patches help... :-/
Platforms tested:
IRIX64 6.5 (modi4)
Feature shift
Description:
Take out the v1.2.x compatibility stubs and put in the hooks for v1.4.x
compatibility when needed.
Platforms tested:
FreeBSD 4.3 (hawkwind)
Purpose:
Bug Fix/Feature Add
Description:
Added new flag ("-f" and "--family") to allow user to specify which
file driver to use to open the file. If they don't specify anything,
then it defaults to the old behaviour of trying each driver in turn
until one actually opens the file.
If the driver the user specified doesn't succeed in opening the
file, then we do NOT try other file drivers.
Platforms tested:
Linux
