Bring support for earray and v2 B-trees from revise_chunks branch to
trunk.
Tested on:
MacOSX/64 10.11.4 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Add 'update' operation to v2 B-trees, which will insert a new record, or
modify an existing one, depending on if the record exists or not.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
Revert most of r27549, since revise_chunks code requires debugging contexts
for v2 B-trees. Also, misc. warning cleanups and alignments w/changes on
revise_chunks branch.
Tested on:
MacOSX/64 10.11.1 (amazon) w/serial & parallel
(h5committest forthcoming)
Update the file format debugging routines to match the recent changes to
the metadata cache, along with a few other cleanups and miscellaneous
enhancements.
Tested on:
MacOSX/64 10.10.5 (amazon)
(h5committest forthcoming)
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 (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
Finish refactoring v2 B-trees so that they can have client callback
context provided to the encode/decode callbacks.
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 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Remove old shim H5B2 routines from refactoring, rename new routines to
old routine names and switch all users of the H5B2 interface back to the old
routine names now that the switch to using the more current open -> <operation>
-> pattern is used for all the H5B2 code. This is the final change before
adding a context to the H5B2 client encode/decode callbacks.
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 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Further refactoring v2 B-trees so that they can get context to the
encode/decode client callbacks:
- Switch tests to using refactored routines
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
Further refactor v2 B-tree code toward being able to pass context info
down to encode/decode client callbacks:
- Separate H5B2_create call to return H5B2_t structure
- Make loading the v2 B-tree header pick up the client class from the
ID stored in the file. Simplify some internal API calls as a
result.
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
Further refactor v2 B-tree code to bring it closer to modern data
structure designed in the library, mainly by introducing a H5B2_t type so that
the v2 B-tree could be held open, but not require the B-tree header to be
protected the whole time. A few other minor tweaks as well.
Also, remove unused 'dirty' flag from fractal heap header.
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
Refactor v2 B-tree code to take creation parameters to H5B2_create() as
a struct (instead of individual arguments), call the client's class "cls"
instead of "type" internally, and add client class name to client class struct.
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
Refactor the v2 B-tree code to use an open & close call internally, in
preparation for making those part of the library private APIs for dealing with
v2 B-trees.
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
Bring work from "compress group's fractal heap" branch back to trunk:
reove unnecessary v2 B-tree 'retrieve' callback from v2 B-tree clients.
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
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
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)
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.
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.
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)
Add first pass of "dense" attribute storage to objects. Lots of parts of
this are stubbed out, but all the tests are passing and I'll work on the corner
cases soon.
Eliminated several unused parameters from object header message callback
routines.
Other, miscellaneous code cleanups, etc. (and probably some things I've
forgotten about... :-)
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
AIX/32 5.? (copper)
Finish implementation of H5Literate() [still needs real tests]
Clean up datatype macro warnings a bit more.
Unify iterator callback macros and put up in public header file, with the
iterator directions.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
This feature is still in progress; Shared Object Header Messages are not
complete as a feature and are not thoroughly tested. There are still
"TODO" comments in the code (comments with the word "JAMES" in them,
so as not to be confused with other TODO comments).
Hopefully this checkin will reduce the liklihood of conflicts as I finish
implementing this feature.
All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
File format is not stable, don't keep files produced!
Description:
First stage of checkins modifying the format of groups to support creation
order. Implement "dense" storage for links in groups.
Try to clarify some of the symbols for the H5L API.
Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest
file format options (including "dense" link storage in groups)
Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation
order tracking in groups (although no index on creation order yet).
Remove --enable-group-revision configure flag, as file format issues are
now handled in a backwardly/forwardly compatible way.
Clean up lots of compiler warnings and other minor formatting issues.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-v1.6 compa
Mac OSX/32 10.4.8 (amazon)
AIX 5.3 (copper) w/parallel & FORTRAN
Improve density of the B-tree further. For greater depths of B-trees,
the gains are over 100%...
Also, don't split internal nodes with 3->4 splits, use a 1->2 split
instead, so that the density of the nodes around a split is maximized.
Tested:
Mac OS X/PPC 10.4 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Split edge nodes in the tree with a 1->2 node split, instead of a 2->3 node
split, which creates a more dense tree when a pattern of record insertions
occurs (because it leaves behind full nodes instead of 2/3 full nodes).
Tested:
FreeBSD/32 4.11 (sleipnir)
Linux/64 2.4 (mir)
Linux/32 2.4 (heping)
Solaris/64 2.9 (shanti)
Revert passing the v2 B-tree class to callbacks, it turns out to be
unnecessary. Also revert have a "class private" pointer for each v2 B-tree
class.
Add in support for the different flavors of fractal heap 'huge' objects
also.
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/64 2.4 (mir)
Solaris/64 2.9 (shanti)
Update code formatting a little and refactor to add a better mechanism
for performing callbacks when removing records from the B-tree or deleting
entire B-tree.
Testing:
FreeBSD 4.11 (sleipnir)
Linux/64 2.4 (mir)
Linux/32 2.4 (heping)
Mac OS 10.4 (amazon)
Code cleanup
Description:
Trim trailing whitespace in Makefile.am and C/C++ source files to make
diffing changes easier.
Platforms tested:
None necessary, whitespace only change
Maintenance
Description:
Remove half-built (half-baked? :-) implementation of B+tree, block tracker
and segmented heaps. (In preparation for starting the new heap coding)
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (heping)
New feature
Description:
Add in baseline "object copy" code from Peter [in the form of a new API
routine: H5Gcopy()]. There's still some work to do (like handling variable-
length datatypes and possibly support for references) and it hasn't been tested
on mounted files yet, but the core functionality is there and working
correctly.
I've also got a set of patches to update the 1.6 branch with tweaks to
keep the branches mostly in sync, but Elena will kill me if I import them
before the 1.6.5 release is out... :-)
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committested
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
New feature
Description:
Add new "block tracker" data structure to library, for tracking blocks of
bytes in a file. Block trackers will be used to keep track of the blocks
belonging to the soon-to-be-implemented "segmented heap" which is designed to
replace the current local & global heaps (starting with the local heap).
Block trackers will also keep track of the free space in the segmented heap
and someday could be used to track the free space in the entire HDF5 file.
They are implemented as a small header of information to cache the state
of the blocks (max & min sizes of blocks tracked, etc.) and the records of
the blocks themselves are stored in a v2 B-tree.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
h5committest
Bug fix & New feature
Description:
Correct some situations where a write lock on the data in the metadata
cache was requested, but only a read lock is necessary.
Add routine to find nearest neighbor record < or > to a query key.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
New features & refactor
Description:
Add basic record removal (only handles level-0 B-trees currently)
Add query routine to check the number of records in a B-tree
Add debugging routine to check the address of the root node in the B-tree
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
Bug fix & new feature
Description:
Fix errors in tracking the total number of records "below" a node.
Add feature to find the n'th record in a B-tree
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
New feature, refactor code
Description:
Add call to search for a record in a B-tree by key value
Refactored some of the existing callbacks to simplify them.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
New feature & code cleanup
Description:
Change some references from 'keys' to 'records', which is more correct for
this implementation.
Added feature to allow preemptive 3 node record redistributions (for leaves
only currently)
Added feature to perform preemptive 3->4 node splits (for leaves only
currently)
Platforms tested:
FreeBSD 4.11 (sleipnir) w/parallel
Solaris 2.9 (shanti) w/purify
Too minor to require h5committest
New feature
Description:
Expand v2 B-tree code to support splitting the root node when enough
records are inserted and move metadata cache callbacks into their own source
file.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/parallel
Too minor for h5committest
New feature
Description:
Add basic code for new B-tree implementation. They don't do much yet,
aren't hooked up to anything yet and the format may change, but I'd like to
start getting them into the daily tests.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/parallel
Too minor to require h5committest
