| Commit message (Collapse) | Author | Age | Files | Lines |
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h5committested.
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Review Vailin's "metadata retry" code and make various cleanups to it.
Also, disallow SWMR access for non-latest format and for non-POSIX VFDs.
Tested on:
Mac OSX/64 10.9.0 (amazon) w/gcc 4.8 and make check-vfd
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checksum.
Implement new public routine H5Fget_metadata_read_retries_info().
h5committested.
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is opened with SWMR access.
There are debugging printfs which will be removed when coding is finalized.
Also some bug fixes:
1) accum.c--clean up some warning messages and use new_argv/new_envp for the call to execve.
2) hl/tools/h5watch--clean up some warning messages and a bug fix for h5watch.c.
This checkin is awaiting code review feedback.
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1) H5O_load() in H5Ocache.c: when reading a block that is > spec_read siez, read the whole block in again and possibly decode the header.
2) H5F_accum_write() in H5Faccum.c: for a large write that is >= H5F_ACCUM_MAX_SIZE, flush the metadata in the accumulator first before the write.
Tests are added to test/ohdr.c and test/accum.c. h5committested.
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Description:
Added flush dependencies between object header chunks. Also added a new object
header proxy object, which is a child dependency of all object header chunks.
All objects which are child dependencies of an object header should set up a
flush dependency on the object header proxy, so the dependency applies to all
object header chunks.
Tested: ummon; jam (fails ph5diff -v, unrelated), koala, ostrich (h5committest)
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Bring r22599:22634 from trunk to revise_chunks branch
Tested on:
Mac OSX/64 10.7.4 (amazon) w/gcc 4.7.x, C++ & FORTRAN
(No need for h5committest yet on this branch)
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Bring r20557:22085 from trunk to this branch, also fixing some other
issues/failures in the branch simultaneously. The h5repack tests are still
failing, but Neil will be checking into those, so the branch can be fully
functional again.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug
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Bring r19542:19639 from trunk to revise_chunks branch.
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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Bring r18704:19049 from trunk to revise_chunks branch.
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, in production 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 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Bring r18638:18704 from trunk to revise_chunks branch.
Tested on:
Mac OS X/32 10.6.3 (amazon) w/debug & production
(h5committest not required on this branch)
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Bring r18600:18619 from trunk to revise_chunks branch
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, 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 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Bring r18533:18581 from trunk to revise_chunks branch.
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, 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 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Bring r18446:18533 from trunk to revise_chunks branch.
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, 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
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Bring r17986:18172 from trunk to revise_chunks branch.
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, 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
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Bring r17299:17346 from trunk to revise_chunks branch (including
rerunning bin/reconfigure, after the autotools update in 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/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-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
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Bring r17265:17269 from trunk to revise_chunks branch
Tested on
FreeBSD/32 6.3 (duty)
(h5committest not required on this branch)
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Bring r16618:16633 back from trunk to revise_chunks branch.
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/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 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Merge r16440:16500 from trunk into revise_chunks branch.
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/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 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Bring r16367:16391 back from trunk into revise_chunks branch.
Tested on:
FreeBSD 6.3/32 (duty)
(h5committest not required on this branch)
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Add detection of C99 "designated initializers" to configure script and
use new H5_HAVE_C99_DESIGNATED_INITIALIZER macro to conditionally compile
default layout variables in src/H5Pdcpl.c
Also, minor code cleanups, etc.
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/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
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 10.5.6 (amazon) in debug mode
Mac OS X/32 10.5.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Bring file free space branch changes through r15795 into trunk, which
includes a fair bit of code cleanup & rearrangement along with a couple of
bug fixes also.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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
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Centralize all macros for declaring "magic numbers"/signatures for
objects in the file into src/H5Fprivate.h, so it's easier to know what values
have already been defined, etc.
Tested on:
Mac OS X/32 10.5.4 (amazon) in debug mode
Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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
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Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Tested on:
Mac OS X/32 10.5.5 (amazon)
No need for h5committest, just whitespace changes...
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Omnibus compiler warning cleanup & some reformatting also.
Tested on:
Mac OS X/32 10.5.4 (amazon)
Too minor to require h5committest
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files with incorrect
datatype versions are encountered.
Description: The library now recognizes some problems with datatype versions in
H5O_decode_helper(), and, if not performing strict format checks, automatically
corrects them. Framework added for other message decode routines to
automatically correct file errors. Datatype version information added to
h5debug.
Tested: kagiso, smirom, linew (h5committest)
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Add work-around to allow reading files that were produced with a buggy
earlier version of the library, which could create objects with the wrong
object header message count. There is now a configure flag
"--enable-strict-format-checks" which triggers a failure on reading a file
with this sort of corruption (when enabled) and allows the object to be read
(when disabled). The default value for the "strict-format-checks" flag is
yes when the "debug" flag is enabled and no when the "debug" flag is disabled.
Note that if strict format checks are disabled (allowing objects with
this particular kind of corruption to be read) and the file is opened with
write access, the library will re-write the object header for the corrupt
object with the correct # of object header messages.
This closes bugzilla bug #1010.
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Clean up ISOHM code further and get rid of several non-optimal ways
of working with object headers.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.9 (amazon)
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Check in "unique, but sharable" optimization to ISOHM code, which
allows object header messages that are only used in one object to remain in
the sole user's header, but migrates messages that are used in more than one
header into the ISOHM heap.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Add "fail if unknown" and "mark if unknown" flags to object header messages.
This gives the library a clean way to tell older libraries that a message should
not be just ignored if it's unknown, but that other actions should occur.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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4294967296LL is not supported by older C like Windows VC6.
Solution:
/* use <= 2**32 -1 to stay within 4 bytes integer range */
HDassert(chunk0_size <= 4294967295UL);
Platforms tested:
kelgia, copper and osage.
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dsets failed on kelgia with assertion failure in H5Ocache.c. Kelgia
could not deal with the comparison of uint64_t variable with 4294967296 constant.
Solution:
By John's suggestions used suffix LL for the constant.
Platforms tested:
kelgia, kagiso, and smirom with icc compiler
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Add some sanity checking to improve the resilience of the object header
decoding in the face of a bad reference, or a corrupted file.
Tested on:
Mac OS X/32 10.4.9 (amazon)
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Avoid storing the # of attributes in the "attribute info" message
and regenerate it when the object is opened.
Tested on:
FreeBSD/32 6.2 (duty)
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Eliminate storing # of links in "link info" message, regenerate it
when the object is opened instead.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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Move ref. count of # of links to an object out of the object header's
prefix and make it a header message instead (since it's a "rare" occurence),
eliminating some more space for each object in the file.
Inserting this "ref. count" message exposed a flaw in the library's
mechanism for locating a message to promote to another chunk and replace
with a continuation message, which required some additional work to fix.
It's still not completely robust, but it's working for more cases now and
detects failures robustly.
Reduced the minimum size of an object header chunk to just enough to
contain a header message prefix and continuation message.
Tested on:
FreeBSD/32 6.2 (duty)
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Fix mis-calculation of chunk #0 size encoding and also catch a few more
places which adjust the size of chunk and have them adjust the encode flags
also. Add some assertions to object header sanity checking routine.
Tested on:
FreeBSD/32 6.2 (duty)
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Reduce the size of the value used to store the # of bytes in the
"payload" for chunk 0 of an object header.
Tested on:
FreeBSD/32 6.2 (duty)
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Eliminate message count from new version of object header prefix -
it can be computed when the header is loaded and the table of messages is
built.
Tested on:
FreeBSD/32 6.2 (duty)
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Move attribute tracking information out of object header prefix and
make it into a message that is inserted only when attributes are present on
the object.
Tested on:
FreeBSD/32 6.2 (duty)
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The main purpose of this checkin was to eliminate the
space used for tracking creation time indices when there is no way they
can be used (i.e. attributes can't be shared in the file and the user hasn't
turned on attribute creation tracking), however there were some other minor
changes which crept in:
- Fix a cache locking deadlock when a shared attribute and one of its
components end up in the same fractal heap direct block.
(This is fixed the "slow" way for right now, until John has time
to add support for readers/writer locking to the cache.
- Optimize attribute copying when a copy will be kept during a v2 B-tree
search.
- When freeing a block on disk, attempt to merge it with the metadata
and "small data" aggregators.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
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Avoid storing the phase change values for attribute storage, unless
they are non-default values.
Tested on:
Mac OS X/32 10.4.8 (amazon)
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Add some extra sanity checking to object header status flags read from
file.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Add object creation property (H5P[s|g]et_obj_track_times) to disable
storing timestamps on objects, which makes the object's header size smaller.
Also, added object header status flags to H5O_info_t struct (for
H5Oget_info/H5Oget_info_by_idx) and cleaned up other field names in the
struct as well.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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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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Add support for inserting attributes into creation order index.
Also, update support for dense link & attribute storage in h5debug.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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More progress on creation order for attribbutes - they are now basically
working for "compact" attribute storage.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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Remove the "scaffolding" for shared message method invocation and
simplify the way shared messages are dealt with in general.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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Move filter pipeline message class to new "shared message interface"
regime, along with minor fixups to implementation of calling that interface.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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