| Commit message (Collapse) | Author | Age | Files | Lines |
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Clean up warnings, switch library code to use Standard C/POSIX wrapper
macros, remove internal calls to API routines, update checkapi and checkposix
scripts.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
Big-Endian Linux/64 (ostrich)
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iteration process over datasets, groups, and files as Quincey suggested. I also removed H5I_search that I introduced in last commit but didn't actually used it.
Tested on jam and koala - simple change.
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followup commit. Quincey
reviewed my previous commit and suggested me to use H5I_iterate to iterate through
all opened objects in H5Z_unregister. I changed it in this commit.
Tested with h5committest.
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protection measures:
1. If any opened object uses the filter, let it fail.
2. Flush all opened files to push any cached data to files.
Tested with h5committest.
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More misc. cleanups, but main change is to make an "extern" header file
for the plugin interface.
Tested on:
Mac OSX/64 10.8.3 (amazon)
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Bring r23542 from desy_1_8 branch to trunk:
Further revisions to dynamic library loading code, to clean it up.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/parallel
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during data reading.
Tested on koala and jam.
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Review & cleanup code.
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of loading dynamically filter libraries and a simple test for it.
Tested on koala.
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Refactor function name macros and simplify the FUNC_ENTER macros, to clear
away the cruft and prepare for further cleanups.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
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say which filter isn't registered. This is the follow-up commit. In my first checkin, I took out the line "H5Z_SZIP->encoder_present = SZ_encoder_enabled()" by
mistake. It caused SZIP test to fail. I'm puting it back now.
Tested on jam - simple change.
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say which filter isn't registered. The fix is simple. Most of the effort is on the test. The file with filter enabled is created in gen_filter.c. The verification of the error message is in test_error.c. The output is compared against the standard output.
Tested on jam, koala, and heiwa.
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Clean up the internal usage H5I_dec_ref() to eliminate the sequence of
flags that has been creeping in.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
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couldn't close (bug 1260). The fix releases all resources and closes
the dataset but returns a failure.
Tested with h5committest - jam, heiwa, amani.
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should return htri_t not
herr_t. To minimize the change of the library's behavior, in the function
H5Z_prelude_callback of H5Z.c, if the return value of can_apply is FALSE and
the filter is MANDATE, this function returns a FAILURE. If the return value is FALSE
but the filter is OPTIONAL, this function returns a SUCCEED. During the IO, the filter
will fail and return a size of zero. But the pipeline will skip this filter.
Tested on jam, lnew, and amani. Tested on jam with szip.
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Bring "compress group's fractal heap" feature from branch back to
trunk.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.1 (amazon) in debug mode
Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Simplify out dataspace cleanup code.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Description:
Previously, when H5Z_filter_info was called for a filter that was not present,
it would succeed and return the information from one position past the end of
the pipeline, possibly causing a segfault. This affected at least
H5Pget_fitler_by_id1/2, and possibly other API functions. Fixed to properly
return failure.
Tested: jam, linew, smirom (h5committest)
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Tested: jam (--disable-deprecated-symbols)
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Embed the content of libhdf5.settings into the hdf5 executables so that an
"orphaned" executables can display (via the Unix strings command, for example)
the library settings used to build the executables.
This is a prototype implementation. Much improvement is needed.
configure.in:
Added the --disable-embedded-libinfo option to disable this feature.
configure:
src/H5config.h.in:
Generated by autotools like automake.
src/H5detect.c:
Implement insert_libhdf5_settings() to insert the contents of
libhdf5.settings into the library as an extern string variable so that it
is included in all HDF5 executable. Much improvement is needed.
fortran/src/Makefile.in:
Auto-generated by bin/reconfigure. (i.e., I did make any changes to cause
its direct regeneration).
Tested:
Jam serial, using default and --disable-embedded-libinfo, configure options.
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Description:
Previously, there was no versioning for H5Z_class_t. This prevented applications
written for 1.6 using custom filters from being able to use the 1.8 library.
There is now an H5Z_class1_t and H5Z_class2_t to enable compatibility. H5Zregister is
*not* versioned, it determines which version of the struct has been passed in by the
value of the first field (id or version, both are ints).
Tested: jam, linew, smirom (h5committest), jam (--with-default-api-version=v16)
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Remove another call to H5E_clear_stack() from within the library.
Clean up lots of compiler warnings.
Tested on:
Mac OS X/32 10.5.6 (amazon)
(followup on other platforms forthcoming)
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Bring revision 16278 back from revise_chunks branch:
Update layout information in DCPL to unify all information in one
underlying property and switch to using H5O_layout_t for storing it, which
simplifies things considerably.
Also, fix many compiler warnings.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(Original patch tested on many machines)
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Fix a few typos introduced in r15510.
Tested on:
Mac OS X/32 10.5.4 (amazon)
More testing upcoming
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Clean up warnings & formatting
Tested on:
Mac OS X/32 10.5.4 (amazon)
More tests forthcoming
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reference count
> 1.
Description: Added a new field 'app_count' to H5I_id_info_t struct, to track
the reference count on an id due to the application. the old 'count' field
tracks the total. Generally any id visible to the application gets placed
in app_count. Added app_ref boolean parameter to H5I_inc_ref, H5I_dec_ref,
H5I_register, H5I_clear_type, and a few other functions, to specify whether
the operation(s) being performed on the id(s) are due to the application
(TRUE) or not (FALSE). Test added for this case.
Tested: kagiso, smirom, linew (h5committest)
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Correct another case of using 'size_t' for chunk sizes where 'uint32_t'
was necessary.
Tested on:
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN
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Remove --enable-hdfv1_6 configure flag, now that all dependencies on it
have been removed and new --with-default-api-version=[v16|v18] and
--disable-deprecated-symbols flags have taken its place.
Update types in bin/trace so that bin/reconfigure runs cleanly.
Run bin/reconfigure to regenerate configure script, along with
other associated files, etc.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Remove 1.6 compatibility ifdef's which were masking error from querying
for info on invalid filter.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Fix problem with I/O pipeline messages where the version of the format
for a I/O pipeline message could depend on the "use the latest format" flag from
the file after it was initially created.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Mac OS X/32 10.4.10 (amazon)
Solaris/32 2.10 (linew)
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Fix reference to uninitialized memory, which could trigger a memory
corruption, once in a purple moon.
Tested on:
FreeBSD/32 6.2 (duty) w/valgrind
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running on kagiso.
The static szip libraries are working as intended, but when shared szip
libraries are present and intended for use they cannot be opened. A check
has been implemented to test if shared szip libraries are functional on
current platform. If they are not, and the user is trying to use them,
szip is now disbaled and the user is informed.
This issue occurs on kagiso, and the resolution was tested on kagiso.
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copyright notice.
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
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in DCPLs.
Extended the test so it broke again and then fixed it again.
Tested on kagiso.
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have filter
data.
Added a regression test for this bug.
Tested on kagiso.
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haven't
been run in a while, so many of the source files were updated with
tracing macros, etc. No code changes by me.
Tested on kagiso and smirom.
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Migrate more object header routines to use the H5O_msg_ prefix and put
them into the src/H5Omessage.c code module.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
AIX/32 5.? (copper)
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Reduce memory usage for common cases of I/O pipeline filter memory usage.
Also, clean up some more code...
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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New feature.
Description:
Add the scaleoffset internal library filter.
Solution:
Platforms tested:
heping, copper, arabica
Misc. update:
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Description: Removed PABLO from the source
Solution:
Platforms tested: arabica with 64-bit, copper with parallel,
heping with GNU C and C++ and PGI fortran (but
I disabled hl, there is some weird problem only
on heping: F9XMODFLAG is not
propagated to the Makefile files
Misc. update:
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Adding framework of N-bit filter
Description:
N-bit filter is required for NetCDF project.
To add N-bit filter, configure.in configure, Makefile.in under src and other
filter-related source code needs to be updated.
Currently, N-bit tests are turned off from the library. So the change will affect daily test.
Solution:
Platforms tested:
sol 2.7, linux 2.4, aix 5.1
Misc. update:
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Bug fix.
Description:
When building H5Z.c with Visual C++ 6.0, I got the following warning message:
H5Z.c(1241) : warning C4013: 'SZ_encoder_enabled' undefined; assuming extern returning int
Solution:
The header file szlib.h should be included in H5Z.c in order to use SZ_encoder_enabled() function.
Add the following script into H5Z.c:
#ifdef H5_HAVE_SZLIB_H
# include "szlib.h"
#endif
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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Description: Restore 6 old error API functions back to the library to be backward
compatible with v1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear, H5Eset_auto,
H5Eget_auto. These functions do not have error stack as parameter.
Solution: Internally, these functions use default error stack.
Platforms tested: h5committest and fuss.
Misc. update: RELEASE.txt
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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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Code cleanup & small bug fix
Description:
Regenerate dependency files
Add htri_t as separate type from hbool_t for code tracing purposes.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
too minor to require h5committest
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Code cleanup & minor optimization
Description:
Re-work the way interface initialization routines are specified in the
library to avoid the overhead of checking for them in routines where there is
no interface initialization routine. This cleans up warnings with gcc 3.4,
reduces the library binary size a bit (about 2-3%) and should speedup the
library's execution slightly.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/gcc34
h5committest
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Code optimization
Description:
Don't recompute the internal index value for looking up the chunk in the
hash table, just use the value already computed from iterating through the
chunks.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir) w/parallel
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