[svn-r19472] Description: Create a new, more streamlined method of generating I/O sequences when there is only a single block defined by a hyperslab. This improves the performance of Ger Van Diepen's (LOFAR team) benchmark by about 20%.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
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
...
[svn-r19471] Bug fix: 1961-- AIX 6.1 --enable-share did not work.Description:
The AIX platform does not install the lib*.so for some reason but libhdf5.a
acts like a shared library. Until we can find out how to fix this, patch
up tetlibinfo.sh to not look for an lib*.so in AIX. (Note the test results
look wierd as it says libhdf5.a passed and skipped.)
Tested: NCSA BP for both enable and disable-shared.
[svn-r19470] Bug fix: 1961-- AIX 6.1 --enable-share did not work.Description:
In an AIX 6.1 system, configure --enable-shared could not build a shared
HDF5 library. The problem was because the version of config.guess was too
old to recongnize AIX 6.X and also configure.in had a local fix which did
not recognize AIX 6.X.
Solution:
1. Mike McGreevy updated bin/config.guess to handle AIX 6.X.
2 Albert fixed configure.in to recognize AIX 6.X.
Note that though ...
[svn-r19469] Bug fix for 1707 - My previous checkin wasn't complete. I left out the case when the deprecated symbols were disabled. I made a different definition for H5E_auto_op_t when the deprecated symbols were disabled.Tested on jam - a simple change.
[svn-r19461] Purpose: Fix bug 1864Description:
Library versions 1.6.3 and earlier contain a bug which causes them to be unable
to perform certain operations on a group if that group's symbol table
information is not cached in the parent group's symbol table. Versions 1.8.0
to 1.8.5 did not cache this information. Modified library to cache this
information.
Tested: jam, amani, heiwa (h5committest)
[svn-r19457] Bug fix for 1707 - H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2 set through H5Eset_auto. I changed the union in the structure H5E_auto_t. Another change is to make H5Eget_auto fail if H5Eset_auto is called to set the printing function. I'll write a document f...Tested on heiwa, jam, and amani.
The property change in configure.in, config, and Makefile.am came from the merge of the 1.8
library change.
[svn-r19443] Purpose: Fix for group comparison with exclude-path case. Use relative path.Description:
Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19406)
Tested:
jam, amani and heiwa
[svn-r19418] On windows, an include bypassed the WIN32_LEAN_AND_MEAN define. Moved the define up. Moved the h5dif.h to after the h5private includeTested: Windows
[svn-r19412] Modified shape same tests to deal with the performance problem on Abe.Problem appears to have been caused by file system contention.
In the chunked dataset case, reshaping the chunks so that only one
process would touch each chunk and setting the alignment equal to the
default Lustre block size more or less dealt with the problem.
For contiguous datasets, the problem was a bit more difficult, as
re-working the test to avoid contention would have been very time...
[svn-r19410] Purpose: Add missing files from the previous checkin.
(Add extra test cases for Bug1975 h5diff - support recursive comparison on group when specified as an object)
[svn-r19409] Purpose: Add extra test cases for bug1975 h5diff - support recursive comparison on group when specified as an object.Description:
Additional tests for combination of group recursive and --follow-symlinks
with multi-linked external links with several files (same name/strucure).
Tested:
jam, amani, heiwa
[svn-r19406] Purpose: Add --exclude-path optionDescription:
Specified path to an object will be excluded from comparing the two files or two groups. If group is specified all the member objects will be excluded.
Related to "1890: h5diff excluding object for file comparison via command line"
Tested:
jam, amani and heiwa
[svn-r19403] Update to H5REPACK tests for layout info required a grep script like runTest.cmake. Update CMakeLists.txt for new h5repack layout tests.Tested: local linux
[svn-r19402] Description: Correct Bz#1968 (Problem when opening new format file with H5F_LIBVER_EARLIEST) by initializing symbol table leaf information in a more universal way. Also cleaned up other superblock initialization a little bit while I'm here.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 (...
[svn-r19400] Purpose: Fix for Bug1975 h5diff - support recursive comparison on group when specified as an objectDescription:
Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly.
Tested:
jam, amani, heiwa
[svn-r19398] Descriptino: 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 (...
[svn-r19396] Description: Bring back various modifications to the v2 B-trees that were introduced in the revise_chunks branch but aren't dependent on any file format or API changes.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 (...
[svn-r19395] Purpose: Fixed bug 1903Description:
After a C++ API object is closed, its id should be reset regardless
of the reference count of the underlying HDF5 object. User reported
the bug for Group, but it's applicable to all other objects. Fixed.
Platforms tested:
Linux/32 2.6 (jam)
FreeBSD/64 6.3 (liberty)
SunOS 5.10 (linew)
[svn-r19392] Purpose: Additional fix for Bug 1821 - h5repack outputs compression information where it is not supposed toDescription:
Remove unnecessary lopping code, which only lowers performance.
Tested:
jam, amani, heiwa
[svn-r19389] Purpose: Fix for Bug1896 h5repack - changing layout to COMPACT does not workDescription:
Make h5repack be able to convert a layout to COMPACT for small size dataset as default. Also add verifying layout changes in our test script.
Tested:
jam, amani, heiwa
[svn-r19386] Purpose: Fix assertion failure caused by fractal heap header file pointerDescription:
The fractal heap header structure keeps a pointer to the file associated with
it. However, it is possible for that file pointer to be closed while the
header is still in cache (through the shared file pointer). Previously, the
header's file pointer was not updated and subsequently pointed to an invalid
file structure. Modified fractal heap code to update the file pointer every
t...
[svn-r19384] Description: Correct an error I convinced Mike to introduce with the phread_once() code, :-( along with another one that wasn't my fault. Also, clean up warnings and restructure code in the thread-safe code a bit.Tested on:
Mac OS X/32 10.6.4 (amazon) w/production + thread-safe
(not a configuration that h5committest tests)
[svn-r19374] [BZ1938] - VS2010 on windows requires stdint.h to compile C++ library. CMake will check if c++ compiler supports stdint.h and set the H5_HAVE_STDINT_H_CXX define.Tested: windows and local linux
[svn-r19369] Update MANIFEST for new m4 directory and macros. Directory and files are for reconfigure and therefore marked _DO_NOT_DISTRIBUTE_.Tested on jam.
[svn-r19367] Purpose: Add windows threads support to HDF5.
Description:
Added calls to the windows threads library to the H5TS layer, and wrapped
most calls to either pthreads or windows threads library with portable
H5TS-style defines. Modified tests to use portable function definitions
as well.
This can be configured via CMake with the HDF5_ENABLE_THREADSAFE
option, and should work o...
[svn-r19366] Updated autoconf to version 2.6.7, libtool to version 2.2.10, and m4 to version 1.4.14. Also added m4 directory for m4 macros according to autoconf suggestion.Tested with h5committest on amani, jam, and heiwa, and on linew.
[svn-r19364] Bug Fix: ID 2019Description:
The development (--disable-production) mode ran a long time, especially on the
testhdf5 (select) that exceeded the wall clock 10 minutes limits and was
terminated. It turned out the development had DEBUG_CFLAG set to "-g -xildoff".\
The -xildoff was added back when h5detect had errors when -g only was used. But
that bug does not exist any more since when only -g is used to build, h...
[svn-r19363] When mandatory filter failed to write data chunks, the dataset couldn't close (bug 1260). The fix releases all resources and closes the dataset but returns a failure.Tested with h5committest - jam, heiwa, amani.
[svn-r19360] Bug fix: ID 2026Description:
testhdf5/select runs very slow when in --disable-production mode using
pgcc compiler. This was caused by the -Mchkfpstk compiler switch added
to the DEBUG_FLAGS in config/pgi-flags file.
Solution:
Removed -Mchkfpstk from both pgi-flags and pgi-fflags.
See Bug 2026 for dettails.
Tested: (no h5committest test since they don't use PGI compilers.)
Jam (linux32): using pgcc/pgf90/pgC...
[svn-r19354] Quincey and I made H5Eset_current_stack also close the stack to be set. This is to avoid H5Eclose_stack clearing the default stack. Please see bug 1799.Tested on jam - simple change.
[svn-r19352] Description: Align w/changes on revise_chunks branchTested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(too minor to require h5committest)
Quincey Koziol
Albert Cheng
Raymond Lu
Neil Fortner
Allen Byrne
Jonathan Kim
Mike McGreevy
John Mainzer
Binh-Minh Ribler
Larry Knox