| Commit message (Collapse) | Author | Age | Files | Lines |
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Change back to clearing memory buffers by default, but give users option
to disable this, for performance reasons (--disable-clear-file-buffers).
Also, add configure option (--enable-using-memchecker) to conveniently
control making the library "play nice" with memory checking tools like valgrind
and purify.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (kagiso)
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Take further advantage of the readers/writer locking in the metadata cache
and push the locking of the local heap up to the routines which call B-tree
routines, which should drastically lower the number of metadata cache protect/
unprotect calls.
Tested on:
Mac OS X/32 10.4.9 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Initial changes to take advantage of readers/writer locking on metadata
cache entries. Reduce the # of protect/unprotect pairs during B-tree iteration
by holding reader lock on B-tree and symbol table nodes while iteration occurs.
This also has the benefit of preventing an iteration callback from
modifying the B-tree being iterated over (which would probably confuse the
B-tree iteration code terribly)
Tested on:
Mac OS X/32 10.4.9 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Clean up some formatting, comments and error messages.
Tested on:
Mac OS X/32 10.4.9 (amazon)
Too minor to require h5committest
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Fully enable readers/writer locking in metadata cache and correct errors
in cache clients which were modifying a cache entry while only holding a
read lock on it.
Tested on:
Mac OS X/32 10.4.9 (amazon)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
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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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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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Migrate more object header routines to use the H5O_msg_ prefix and put
them into the src/H5Omessage.c code module.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
AIX/32 5.? (copper)
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Finish removing library's internal code that uses H5G_get_objinfo() and
retarget it at either getting the link information or the object information,
as appropriate. (Still need to add user-level tests for H5Oget_info(), but
since several internal components of the library depend on the internal version,
it appears to be working correctly).
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/322.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
Mac OS X/32 10.4.8 (amazon)
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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)
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Basic support for H5Literate() routine. Still needs to be fleshed out and
refactored to simplify. Also, needs tests. :-)
Tested on:
FreeBSD/32 4.11 (sleipnir)
Linux/32 2.4 (heping)
Linux/64 2.4 (mir)
AIX/32 5.? (copper)
Mac OS X/32 10.4.8 (amazon)
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Finish refactoring internal link deletion code, to make it possible to
wrap up the H5Ldelete_by_idx() coding.
Tested on:
Linxu/32 2.6 (chicago)
Linxu/64 2.6 (chicago2)
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Move compact storage routines into separate file, to make room for internal
routines that operate on links within group operations.
Tested on:
Linux/32 2.6 (chicago)
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Finished implementation of H5Lget_info_by_idx for all cases: old vs. new
group formats, compact vs. dense new link storage, increasing vs. decreasing
vs. native iteration order.
Also, refactor symbol table "foo by index" routines to be more generic
and share more code by using a single B-tree iteration callback which makes
callbacks to a specific "get <foo>" callback.
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)
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Clean up code to build name for ID with no name tracked - get rid of
global variable, unused routines, etc.
Tested on:
FreeBSD/32 4.11 (sleipnir)
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Refactor generic property list initialization code to put property list
specific routines in property list modules, instead of scattered to the four
winds. Also, introduce property list class initialization objects, to make
adding new property list classes in the library easier.
Fix daily test failure by using H5Pget_elink_prefix() API routine instead
of looking at the "raw" generic property list information.
Tested on:
Mac OS X/32 10.4.8 (amazon)
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/C++ & FORTRAN
Linux/64 2.4 (mir) w/build-all & 1.6 compat
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handle flush callbacks which can dirty other entries, and
resize and/or rename the target entry.
This feature is needed by the fractal heap code.
Also added associated test code.
H5Commit tested. Test failed on heping, but the
error appears to be a syntax error in an un-related
file.
Tests on copper & sol passed, along with tests on
phoenix.
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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
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Users can create external links using H5L_create_external(). These links
point to an object in another HDF5 file. Users can alter the behavior of
external links or create new kinds of links by registering callbacks
using the H5L interface.
Added tests, tools support, etc.
Also a number of other, minor changes have been made (some restructuring of
the H5L interface, for instance).
Additional documentation and examples are forthcoming.
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Feature
Description:
Revised Link APIs.
Solution:
New link APIs use H5L*
H5*create_expand do not create links to the objects created; this must
be done manually with H5Llink.
Added APIs to link an object given its ID (H5Llink), to copy links (H5Lcopy),
and changed creation APIs (H5Lcreate_hard and H5Lcreate_soft) and query
API (H5Lget_linkinfo instead of H5Gget_objinfo).
All old APIs are still supported in H5Gdeprec.c .
Platforms tested:
sol, mir, copper
Misc. update:
Forgot to update MANIFEST and release docs. Will do after checkin.
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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
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New feature
Description:
Check in Peter's code to add support for "shallow copy", "create
intermediate groups", "no attributes" and "expand soft links" support.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (chicago) w/ & w/o group-revision enabled
h5committest
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"Hide" file format changes (for now)
Description:
Add ifdef's (controlled by the --enable-group-revision configure flag)
to disable group revision changes to the file format, in order to allow alpha
release to go ahead without releasing an unsupported version into the wild.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 32-bit (heping)
Linux 2.4 64-bit (mir)
Solaris 2.9 (shanti)
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New/expanded features
Description:
Check in Peter's changed for the object copy code:
- Allow/fix copying datasets using named variable-length datatypes
- Start adding framework for property list to control how object
copying occurs.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Bug fix
Description:
Retrieving an object's name could fail (in various ways) under certain
circumstances (mostly having to do with mounted files).
Solution:
Re-write & simplify "get object name" code to fix error in a better way
than adding yet another hack to the previous pile of hacks... :-)
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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New feature
Description:
Check in baseline for compact group revisions, which radically revises the
source code for managing groups and object headers.
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
This initiates the "unstable" phase of the 1.7.x branch, leading up
to the 1.8.0 release. Please test this code, but do _NOT_ keep files created
with it - the format will change again before the release and you will not
be able to read your old files!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
Solution:
There's too many changes to really describe them all, but some of them
include:
- Stop abusing the H5G_entry_t structure and split it into two separate
structures for non-symbol table node use within the library: H5O_loc_t
for object locations in a file and H5G_name_t to store the path to
an opened object. H5G_entry_t is now only used for storing symbol
table entries on disk.
- Retire H5G_namei() in favor of a more general mechanism for traversing
group paths and issuing callbacks on objects located. This gets us out
of the business of hacking H5G_namei() for new features, generally.
- Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t
- Lots more...
Platforms tested:
h5committested and maybe another dozen configurations.... :-)
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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
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Bug fix
Description:
Fix "double root open" bug and apply same fix to datasets & named datatypes.
Also fix bug in symbol table entry lookup code that would "transfer" an
object from one file handle to another file handle when the two file handles
were opened on the same actual file.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Code cleanup/reorganization
Description:
Merge back some more changes extracted from the "compact group" set.
This bunch cleans up and prepares the H5G_* routines for eventual import of
new features.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Mac OS X.4
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Code cleanup
Description:
Clean up internals of group creation & iteration code.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Mac OS X (nile)
Too minor to require h5committest
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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
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Big fix
Description:
A group opened by dereferencing a object reference would not work for
H5Giterate(), due to the local heap & B-tree information not being cached.
Solution:
Get the local heap & B-tree info & point to that structure instead of
the group entry for the group.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Bug fix
Description:
Correct problems when querying information about a group that was opened
by dereferencing an object reference.
Solution:
Read in symbol table information instead of rely on it being cached.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Code cleanup
Description:
Refactor metadata cache to merge "dirtied" flag in with other flags for
H5AC_unprotect and H5C_unprotect.
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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Interim checkin of code changes moving management of the is_dirty flag
into the cache code.
Description:
Prior to this checkin, management of the is_dirty flag was handled
above the level of the metadata cache. This can no longer be allowed,
as it introduces a race condition in the proposed fix for a cache
coherency bug in PHDF5.
Solution:
Move management fo the is_dirty flag to the cache code proper.
Entries are now marked as dirty via a flag on the unprotect call.
Platforms tested:
h5committested
Misc. update:
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Bug
Description:
Assertion failure
Solution:
don't call decrement when the object doesn't exist.
Platforms tested:
shanti,verbena
Misc. update:
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Description: Removed PABLO from the source
Solution:
Platforms tested: arabica with 64-bit, copper with parallel,
heping with GNU C and C++ and PGI fortran (but
I disabled hl, there is some weird problem only
on heping: F9XMODFLAG is not
propagated to the Makefile files
Misc. update:
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1) Provide facilities in cache to allow us to avoid a potential cache
consistency bug in the parallel case.
2) Clean up a off by one sanity checking bug.
3) Turn off execution of long running tests in debug mode.
Description:
1) In the parallel case, all writes to metadata must be collective,
but reads may not be. In pricipal, this allows us to different
contents in different caches. This isn't a problem as long as the
correct data is always on disk, but unless we can force certain
writes immediately, that need not be the case.
2) & 3) should need no further explanation.
Solution:
1) Add code allowing us to mark cache entries, and then force
these entries to be flushed at a later time.
Note that to actually avoid the bug, we will have to modify
existing code to use these new features.
2) & 3) should need no further explanation.
Platforms tested:
heping (serial debug and production)
committest (copper, sol, and heping). test failed on heping in the
c++ portion of the build, but at Quincey's siggestion, I am proceeding
with the checkin.
Misc. update:
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Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
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Code optimization
Description:
Switch a few more malloc/free pairs over to using internal free list code,
to avoid abusing system memory allocator as badly.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
Too minor to require h5committest
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Code cleanup
Description:
Clean up minor warnings and align with release branch.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & FPH5
Solaris 2.7 (arabica) w/production mode
Linux 2.4 (heping) w/C++ and FORTRAN
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Bug fix/code cleanup
Description:
Clean up raw data I/O code to bundle the I/O parameters (dataset, DXPL ID,
etc) into a single struct to pass around through the dataset I/O routines,
since they are always passed together, until very near the bottom of the I/O
stack.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
IRIX64 6.5 (modi4)
h5committest
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Description: Restore 6 old error API functions back to the library to be backward
compatible with v1.6. They are H5Epush, H5Eprint, H5Ewalk, H5Eclear, H5Eset_auto,
H5Eget_auto. These functions do not have error stack as parameter.
Solution: Internally, these functions use default error stack.
Platforms tested: h5committest and fuss.
Misc. update: RELEASE.txt
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Code cleanup, sorta
Description:
Added ifdef sections for "H5_USING_PURIFY" in various places in the code,
which are designed to reduce the spurious "uninitialized memory read" warnings
from purify which are actually OK. Note that this macro will have to be
turned on by adding it to the CFLAGS for the build - I didn't think it was
important enough to add a configure flag for.
Also, the changes in H5HG.c optimize the walks through the objects in a
heap to only look at the 'used' entries instead of all the 'allocated' entries.
Platforms tested:
Solaris 2.7 (arabica) w/purify
Not tested by h5committest
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Bug fix
Description:
Correct problems with "resurrecting" a dataset in a file. (This occurs
when a dataset which is open gets unlinked from the group hierarchy (making it
"dead" and marked for deletion in the file) and then is re-linked to the group
hierarchy). Note that the current solution applies only to datasets, further
work will fix this for groups and named datatypes also.
Also, fix the "debug" routines to be a little more helpful in certain
situations.
Additionally, fix a locking bug in the symbol table node splitting routine
which could be [one of] the cause[s] of the file corruption in flexible
parallel operation.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
h5committested
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Code optimization
Description:
Re-work the insertion of a new child into an existing node, to exploit
some speedups for adding the rightmost child, since this is a very common case
when appending records to an unlimited size dataset.
Also, hoist the checks for the tree's 'K' value into a field in the shared
information about the tree, instead of re-calculating them all the time.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Code optimization
Description:
Refactor B-tree code to extract all common information for a B-tree into a
shared structure that is pointed to by all the nodes in tree (instead of being
included in each node).
Also re-order B-tree node comparison checks for chunked datasets to
check for >= the upper node first, since the comparison is a bit "heavy" and
this check is more likely to succeed when you are adding records to the
dataset.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
(also, recent h5dump commits have broken testing...)
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Bug fix
Description:
The "shared" raw B-tree node can get freed before all the B-tree nodes
had been flushed out to disk and released by the cache.
Solution:
Implement a simple reference counting wrapper for objects in the library
and use it to hold the shared raw B-tree nodes so they aren't freed before all
references to them in memory are released.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir)
IRIX64 6.5 (modei4)
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Code optimization
Description:
Since the raw B-tree nodes are the same size and only used when reading in
or writing out a B-tree node, move raw B-tree node buffer from being per node
to a single node that is shared among all B-tree nodes of a particular tree,
freeing up a lot of space and eliminating lots of memory copies, etc.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Code cleanup
Description:
Fix problems when compiling with C++ compiler.
Also clean up some warnings with gcc 3.4.x
Platforms tested:
FreeBSD 4.10 (sleipnir)
Too minor to require h5committest
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