Bring some of Neil's changes to help support SWMR access in the v1
B-tree code from the revise_chunks branch back to the 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 (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
Fix nightly build error on non-linux platforms related to
the Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option. (r19633)
Description:
- Updated to use standard C functions instead of strndup() due to failure on non-linux platforms.
- Changed to Use HDxxx macros for future reference.
- Correct indentation.
Tested:
jam, amani, heiwa, linew
Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.
Description:
Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed.
Tested:
jam, amani, heiwa
Modified test code in t_mdset to use H5Dopen2() instead of H5Dopen1().
This should fix the compile failure when we used --disable-deprecated-symbols
Cursory commit test
- Fix a bug in each of the metadata accumulator source and test code
Description:
- In accum.c test file, switch dxpl_id used in H5F_accum_*
function calls to H5P_DATASET_XFER_DEFAULT (instead of
H5AC_dxpl_id), to fix compilation on windows.
- Changed boundary checking from <= to < when checking
if a read from disk with overlapping dirty metadata in the
accumulator has the read ending such that it aligns exactly
with the dirty accumulator (line 234 of H5Faccum.c).
Tested:
- h5committested
of the H5Ocache.c code to update its image of the on disk representation
of the object header on a call to the clear callback.
This wasn't an issue as long as all flushes of the object header were
made from the same process, but if an object header is modified, and
then flushed on one process and cleared on the rest, the changes were
not be reflected in the images of the on disk representation on all
processes where the object header was cleared rather than flushed.
If one of these processes did the next flush, the changes were lost in
the on disk representation.
Fixed this by causing all dirty messages and to be written to the copy
of the on disk image maintained by the object header code on both flush
and clear.
Also added associated test code in t_mdset.c.
Also checking in some cache debug code developed while chasing this bug.
Commit tested and tested (parallel) on phoenix.
Merge accum_tests branch back to the trunk.
Description:
Changes consist of addition of tests for H5Faccum.c source code,
as well as some fixes that address some discovered bugs in the
metadata accumulator on several corner cases.
Tested:
h5committested
Backout the previous changes (r19598):
(Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.)
Description:
Some failure occurred on talwit, so backout the changes and will put it back
after the fix.
(Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed.
Merged from hdf5 trunk r19598.)
Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.
Description:
Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. Expected to be failed.
Tested:
jam, amani, heiwa
FAILED. Rejected by the xlc compiler.
Solution: changed it to reutrn NULL.
Tested: UP make passed. serial passed but some parallel tests failed. The
parallel tests failed were not related to this fix.
RUNSERIAL=${RUNSERIAL="env LDR_CNTRL=MAXDATA=0x20000000@DSA"}
kind of mess things up for the parallel HDF5 configure.
Changed it to
RUNSERIAL=${RUNSERIAL="env LDR_CNTRL=MAXDATA=0x20000000@DSA MP_PROCS=1 MP_TASKS_PER_NODE=1 poe"}
if --enable-parallel.
Also merge powerpc-ibm-aix5.x with ibm-aix by making powerpc-ibm-aix5.x to
source ibm-aix just like ibm-aix6.x. This is in preparation that all AIX
platforms will eventually just use ibm-aix directly.
Fixed a small problme in ibm-flags: some older xlc (e.g. v7.1) prints the
version information with a leading blank. So, accommodate this pattern by
removing the "^".
Tested: LLNL uP, 32/64bits, serial/parallel. (parallel has tests failed
but this change is mainily for configure issues.)
Also tested BP, 32/64bits but serial only.
(Forgot to commit this file when bin/config.guess was committed.)
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 HDF5 can build shared lib for AIX 6.X systems
but it still could not install the proper library as in AIX 5.X
systems. Also, bin/config.sub should be updated too.
Tested: BP which is the AIX 6.1 system that exposed this problem.
Address issue with object headers being created getting evicted from
the metadata cache cache before they are completely initialized. This is
done by pinning the object header in the cache until it is completely
initialized and attached to a group.
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
with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2
set through H5Eset_auto. I changed the structure H5E_auto_t. I added a IS_DEDAULT flag in
it. Both H5Eprint1/2 are the default now. If the user sets his/her own printing function.
Then a call to H5Eget_auto1/2 will have to match H5Eset_auto1/2.
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.
unknown versions of the C Intel compilers.
Modified apple config file to display Intel compiler information.
Updated RELEASE.txt notes accordingly.
Platfroms tested: jam, amani and dubna (Mac 64-bit) with Intel C, Fortran and C++ compilers.
Patch for metadata accumulator bug
Description:
Linew failed one of the randomly seeded fheap tests
due to a corner case bug in the metadata accumulator code.
This patch fixes the corner case.
Tested:
used same random seed in fheap tests to reproduce and
verify on linew; plus full make check on jam.
unit tests for accumulator code coming soon.
flag IS_DEDAULT in the H5E_auto_t structure. Both H5Eprint1/2 are the default now. If the user
sets his/her own printing function. Then a call to H5Eget_auto1/2 will have to match
H5Eset_auto1/2.
Tested on jam, heiwa, and amani.
Optimize the vector-vector memcpy() routine even further, for a total
of ~2x speedup. :-)
Make a generic vector-vector operation routine and convert other
vector-vector read & write routines to use generic routine instead of multiple
copies of the basic algorithm.
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
Update help page for exclude-path feature.
Description:
Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19406)
Tested:
jam, amani, heiwa
Speed up hyperslab sequence generation routine some more, giving
about a 10% improvement in Ger Van Diepen's LOFAR benchmark.
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
Quincey Koziol
Jonathan Kim
John Mainzer
Mike McGreevy
Allen Byrne
Albert Cheng
Raymond Lu
HDF Tester
Elena Pourmal
Larry Knox