| Commit message (Collapse) | Author | Age | Files | Lines |
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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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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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mounted files.
Description:
Moved mount table from top file structure to shared file structure. Moved
parent out of mount table and back into top file structure. Mounted files can
now be accessed from any handle of the parent file. Changes to how files are
closed. Stricter cycle checking on mounted files. Removed unused function
H5F_has_mount().
Tested:
committest in 1.8 branch. Committing now due to the urgency of the fix. No
changes here are specific to the trunk, but I will keep an eye on the daily
tests.
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large entry, or to a large increases in the size of an existing entry.
This required some additions to the cache configuration structure, and
thus will require changes in the metadata cache documentation.
The basic idea is to monitor the size of entries as they are loaded,
inserted, or increased in size. If the size of the entry (or increase)
exceeds some user selected fraction of the size of the cache, increase
the size of the cache.
Note that this fix was designed quickly -- while it deals with the
use case that exposed the problem, we may have to revisit the issue
later.
Tested serial and parallel on Phoenix, and 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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Updates from running bin/reconfigure on recent changes, in preparation for
making private snapshot. Also updated tracing information for recent types
added to public API routines.
Tested on:
Linux/32 2.6.x (kagiso)
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Add H5Ovisit() and H5Ovisit_by_name() API routines.
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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Add H5Lvisit_by_name() API routine to library.
Eliminated all (five!) other group traversal routines and changed them
all to use the new API routine.
Cleaned up output of h5ls & h5stat:
- Issue error when requesting recursive traversal of a file
with the "group info" flag, but no group given
- Print info about root group in all(?) appropriate situations
- Don't print "verbose" information about root group until the
root group is in the list of objects to display
(mostly because h5ls & h5stat had a different twist on traversing the
groups in a file that the other utilities)
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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link was opened twice, the library
had some trouble to close in the end. The problem came from the field "holding_file" of
H5O_loc_t. It's used to indicate special links like external links. The fix is to turn it off
whenever H5O_open is called. Later the caller function should turn it on when it needs to.
Tested on kagiso, linew, and smirom.
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Change H5O[gs]et_comment to H5O[gs]et_comment_by_name and re-add simpler
forms of H5O[gs]et_comment.
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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Change H5Llink to H5Olink, which makes more sense.
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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Change H5Oget_info -> H5Oget_info_by_name and re-add H5Oget_info in a
simpler form for querying a particular object, to align with other new API
routines.
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 --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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Make H5Dopen versioned and change all internal usage to use H5Dopen2
Add simple regression test for H5Dopen1
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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Finish deprecating last H5G symbol (H5G_obj_t) - yay!
Lots of misc. library fixes to remove confusion between links and
objects. The tools could still use another pass, to remove h5trav_type_t type
and make the correct distinction between links & objects.
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 2.6 (smirom) 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
AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Add H5O{set|get}_comment routines, which were overlooked before.
Move H5G{set|get}_comment routines to deprecated code section,
replacing internal calls with H5O{set|get}_comment.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
AIX/32 5.3 (copper)
Mac OS X/32 10.4.10 (amazon)
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Add flag to bypass (expensive) B-tree & heap size retrieval for
internal calls to H5O_get_info().
Teted on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
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Various code cleanups and refactor recent changes for h5stat to fit
into the existing library data structures better.
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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New feature.
Description:
Added routines to report on the amount of storage for:
1) 1.6 btree and heap storage info for groups
2) 1.8 btree, fractal heap storage info for groups, attributes and SOHM table
3) btree storage for chunked datasets
4) 1.8 superblock extension size.
Platform tested:
h5committested.
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Fix possible file corruption when using "new" format object headers and the
size of chunk #0 for an object header transitions between needing 1->2->4->8-
byte encoding for the size and there are "clean" messages in the object header
already. (Usually triggered by flushing the file while adding attributes to
an object)
Tested on:
Mac OS X/32 10.4.9 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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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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Fix H5O_msg_iterate() and H5O_link() to protect cache entries with
better permissions.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
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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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Change H5[D|G|T]<foo>_expand() "temporary" API routines to
H5[D|G|T]<foo>2() "versioned" routines. Also added
H5[D|G|T](create|commit)_anon() routines to continue to allow "anonymous"
objects to be created in a file.
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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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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Reduce size of "default" link message storage.
Tested on:
FreeBSD/32 6.2 (duty)
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Whitespace/formatting cleanup.
Tested on:
None, just eyeballed.
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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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Make certain to use the later version of the object header format if
creation order is tracked on attributes.
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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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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Add new object header message to track attribute information (unused
currently).
Tested on:
Mac OS X/32 10.4.8 (amazon)
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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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Minor code rearrangements and comment cleanups, in preparation for moving
attribute tracking information out of object header prefix.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Fix bug in external links when "strong" file close degree is used.
Make external link callbacks use standard error reporting mechanisms.
Other minor code cleanups...
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
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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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Revise latest form of superblock format pretty drastically, to
eliminate unused fields and move rarely used fields into superblock extension.
Finished removing last vestiges of references to (never used) i"shared"
object header message ID.
Added object header messages for non-default v1 B-tree 'K' values
and for driver info.
Updated testfiles to reflect size changes, etc.
Various minor cleanups, etc.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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Make H5O_protect/H5O_unprotect use pinned cache entries instead of
protected entries (allowing the object header routines to be semi-reentrant).
Tested on:
FreeBSD 6.2 (duty)
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Checkpoint progress on H5Aiterate2().
Mark H5Aiterate() as deprecated.
Various code cleanups.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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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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object header
information, rather than storing it directly in the superblock.
This should make future updates to the superblock much less painful.
Tested on Windows, kagiso, and smirom.
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Add API routines for tracking & indexing the creation order on
attributes.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
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More cleanups on the object header message handling code, to make it
easier to work with and move forward on the creation order coding.
Various other minor cleanups & warning fixes.
Tested on:
FreeBSD/32 6.2 (duty)
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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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Final tweaks before the big twist to fix shared message method calling.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 6.2 (duty)
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