| Commit message (Collapse) | Author | Age | Files | Lines |
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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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Code cleanup
Description:
Clean up some compiler warnings
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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Bug fix
Description:
Add some "safety net" sort of assertions and sanity checks contributed by
user.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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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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Bug fix
Description:
Fix code to allow --debug-enable=all option to work correctly.
Solution:
Update some ifdef'ed code with recent changes.
Platforms tested:
Linux 2.4 (heping) w/--enable-debug=all
Too minor to require h5committest
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Purpose:
Bug Fix
Description:
If an HDF5 file grows larger than its address space, it dies and is unable to
write any data. This is more likely to happen since users are able to change
the number of bytes used to store addresses in the file.
Solution:
HDF5 now throws an error instead of dying. In addition, it "reserves" address
space for the local heap and for object headers (which do not allocate space
immediately). This ensures that after the error occurs, there is enough address
space left to flush the entire file to disk, so no data is lost.
A more complete explanation is at /doc/html/TechNotes/ReservedFileSpace.html
Platforms tested:
sleipnir, copper (parallel), verbena, arabica, Windows (Visual Studio 7)
Solution:
Platforms tested:
Misc. update:
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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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Code cleanup & small optimization
Description:
Eliminate redundant recomputation of native key pointer offsets.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
too minor to require h5committest
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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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performance.
Description:
Replaced the old metadata cache with a cache with a modified LRU
replacement policy. This should improve the hit rate.
Solution:
Since we want to flush cache entries in increasing address order, I
used the threaded binary B-tree code to store the cache entries.
There is a fair bit of overhead here, so we may want to consider
other options.
While the code is designed to allow the support of other replacement
algorithms, at present, only a modified version of LRU is supported.
The modified LRU algorithm requires that a user selectable portion
of the cache entries be clean. The clean entries are evicted first
when writes are not permitted. If the pool of clean entries is used
up, the cache grows beyond its user specified maximum size. The
cache can also exceed its maximum size if the combined size of the
protected (or locked) entries exceeds the maximum size of the cache.
Platforms tested:
eirene (serial, parallel, fp), h5committested
Misc. update:
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Code cleanup
Description:
Some code cleanups before starting serious optimization efforts.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
Too minor to require h5committest
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Code cleanup & minor optimization
Description:
Re-work the way interface initialization routines are specified in the
library to avoid the overhead of checking for them in routines where there is
no interface initialization routine. This cleans up warnings with gcc 3.4,
reduces the library binary size a bit (about 2-3%) and should speedup the
library's execution slightly.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/gcc34
h5committest
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Code optimizations
Description:
Eliminate memset() call in H5S_set_extent_simple().
Use malloc() instead of calloc in H5B<mumble>.
Change global heap code to track heap objects that are in use in order to
allocate new objects more quickly and also to avoid memset() and calloc() calls.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Code optimization
Description:
Avoid pushing errors on error stack when an object is not found in a B-tree.
Sometimes we are just checking if the object exists before we insert it into
the B-tree and the higher levels in the library should be responsible for
determining if not finding the object in B-tree is really an error.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
too minor to require h5committest
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Code optimization
Description:
Eliminate the B-tree "split_ratios" as a parameter and pull it from the
DXPL instead.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir) w/parallel
too minor to require h5committest
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Code optimization
Description:
Move handling for free list arrays that have no maximum size to separate
set of routines and optimize computations for free list arrays with maximum
size to avoid re-computing sizes all the time.
Platforms tested:
h5committest
Solaris 2.7 (arabica)
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Add note about B-tree not being balanced during deletion operations,
pointing interested readers at the Yao & Lehman paper.
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Add tests & docs
Description:
Added tests for the recent B-tree bug fixes & document their fix in the
release notes.
Platforms tested:
FreeBSD 4.9 (sleipnir)
Too minor to require h5committest
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Bug fix.
Description:
Fix problems in B-tree deletion routine that were corrupting the data
structure when the B-tree had several levels and the right-most item from a
leaf node that was the right-most child of an internal node was removed.
Also address similar problems when a complete internal or right-most node
was removed.
NOTE: The B-tree deletion routines are still _NOT_ maintaining the B-tree
properties correctly, that will be addressed in a future (hopefully soon) fix.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too obscure to require h5committest
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Code cleanup
Description:
Clean up compiler warnings, especially the 'FUNC' variable not used which
comes out in production mode.
Solution:
Had to add a new FUNC_ENTER_NOAPI_NOINIT_NOFUNC macro for those non-API
functions which don't need the 'FUNC' variable defined. (This will be _so_
much easier when C99 is standard on all our supposed platforms, since it has a
__FUNC__ macro... )
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor for h5committest (although there were lots of files changed, the
change was minor in each one)
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Update
Description:
A lot of modifications for the FPHDF5 stuff:
H5AC.c
H5ACprivate.h - Removed AC_find (it's replaced with AC_protect
and AC_unprotect). Added flushing if it's an FPHDF5 driver and
we're doing an AC_set or AC_unprotect with the dirty flag set.
H5B.c - Split up the B_flush function into different functions
since the one function was doing serialization which is better
left as a separate entity.
H5D.c - Removed some FPHDF5 code that was incorrect
H5F.c - Split up the F_flush function so that it no longer
allocates file space. Created new functions (F_init_superblock,
F_read_superblock, and F_write_superblock) for greater modularity
and so that the FPHDF5 non-captain processes can read the
superblock after the captain process writes it.
H5FD.c - Error message correction.
H5FDfphdf5.c - Removed MPI barrier call that wasn't needed.
H5FPclient.c
H5FPserver.c - Modified so that if a process requests data that
isn't exactly aligned, we can return it if we have the block that
contains the requested address.
H5G.c
H5Gent.c
H5Gnode.c
H5HL.c
H5HLpkg.h
H5HLprivate.h
H5Oefl.c - Removed the H5HL_peek function since it was doing a
(now unsafe) holding of the information in the cache. Replaced
with protect and unprotect calls.
H5TB.c - Error fix. The TB_dless function wasn't working
properly.
H5Gstab.c - Format change.
H5err.txt
H5Edefin.h
H5Einit.h
H5Epubgen.h
H5Eterm.h - Added new error code.
Platforms tested:
Modi4 (paralle, Fortran)
Sol (Fortran)
Linux (C++, Fortran)
Copper (Parallel, Fortran)
Misc. update:
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Code cleanup
Description:
Patch up a few places where the metadata cache could ask for a read lock
instead of a write lock and other minor code cleanups.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to need h5committest
Misc. update:
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Update
Description:
Added extra parameter to the H5AC_protect() function that indicates
if the cache being asked for is going to be written to or just read
from. Those AC_protect calls that were H5AC_find calls are now
read-only. The rest are writes.
Platforms tested:
Linux (h5committest not needed due to size and small impact)
Misc. update:
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Removal of H5AC_find()
Description:
The H5AC_find() function is mostly redundant and with the new
Flexible Parallel HDF5 stuff, we need to do locking on metadata
returned from the H5AC_find() anyway. So, all of the locking stuff
will be placed in the H5AC_{un}protect() functions. The H5AC_find()
is no longer needed.
Solution:
Replaced all H5AC_finds with H5AC_protects and H5AC_unprotects.
Platforms tested:
Linux (Fortran & C++)
Solaris (Fortran)
Irix (Parallel & Fortran)
Misc. update:
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Code cleanup/bug fix
Description:
Move metadata cache calls around a bit so they protect the usage of the
metadata better.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too small to need h5committest
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Fix, of a sort
Description:
Some of the code would get an object from the cache via the
H5AC_find() function and then modify the returned object. This
behavior is incorrect as the pointer returned via the H5AC_find()
function is supposed to be read only.
Solution:
Changed the H5AC_finds to H5AC_protect() instead and added the
appropriate H5AC_unprotect() function.
Platforms tested:
(simulated h5committest by hand since it doesn't work for me)
Linux (Fortran, C++)
Solaris (Fortran)
AIX (Fortran, C++)
SGI (Parallel, Fortran)
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Code cleanup
Description:
More linting...
Platforms tested:
FreeBSD 4.8 (sleipnir)
too minor to need h5committest
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Bug fix
Description:
The metadata cache 'destroy' callback routines need the file handle in
order for certain callback routines (currently just the H5HG one) to perform
extra cleanups. The recent change to call the 'destroy' callback from the
'clear' callback omitted this parameter.
Solution:
Add the file handle to the metadata cache 'clear' callbacks.
Platforms tested:
FreeBSD 4.8 (sleipnir)
too small to need h5committest
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Update
Description:
Added an extra flag to the clear functions that triggers a "destroy"
of the object being cleared if necessary. This is a fix for the
FPHDF5 stuff which had an object sticking around after it was
cleared. (In FPHDF5, some processes are in charge of destroying the
object, but all processes might actually allocate the object.)
Platforms tested:
AIX (Copper: Fortran & C++)
Linux (Verbena: Fortran & C++)
IRIX (Modi4: Parallel & Fortran)
(Sol is down)
Misc. update:
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Code cleanup
Description:
Tail end of B-tree 'K' value conversion to unsigned ints.
Also, lots of misc. code cleanups suggested by lint tool
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Bug fix (backward compatibility)
Description:
Changes we've made during development of the 1.5.x branch had broken the
feature of allowing user's callbacks to H5Giterate to return a value
through the library back to the application which called H5Giterate.
Solution:
Correctly pass along iterator callback return value and adjust internal
library code to conform to this design.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Code cleanup
Description:
Limit the scope on more function prototypes/macros/typedefs.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest not necessary.
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Code cleanup & new feature
Description:
Track changes to H5AC API (code cleanup)
Added routine to delete B-tree in file.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
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Bug fix
Description:
This fixes a bug in the low-level metadata caching code in the library
which could possibly lose metadata during file I/O when a lot of objects are
inserted into a group.
This also fixes a couple of (similar) fencepost bugs in the B-tree
deletion code.
Solution:
For the metadata bug - call the low-level driver's 'write' routine instead
of H5FD_write.
For the B-tree bug - include the correct number of keys.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
(h5committest is still not working for me on burrwhite)
Misc. update:
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Bug fix/code cleanup/new feature
Description:
Fix h5debug to work correctly again, with all the changes over the past
few months.
Improved and cleaned up debugging output available in h5debug.
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Finish code cleanup
Description:
Wrap up the conversion of H5F_flush's multiple boolean flags into a single
bitfield of flags by pushing the flags down into the H5AC_flush and
H5F_istore_flush routines.
Also, changed the flags from H5_FLUSH_<foo> to H5F_FLUSH_<foo> to be more
consistent with rest of library.
And reverted the changes to H5FDflush and H5FD_flush routines.
Platforms tested:
FreeBSD 4.7 (sleipnir)
Solaris 5.8 (sol)
IRIX64 6.5 (modi4) w/parallel
Misc. update:
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Code cleanup
Description:
Add B-tree node debugging routine for symbol table nodes (i.e. groups)
Platforms tested:
FreeBSD 4.7 (sleipnir)
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Bug fix.
Description:
Correct compile errors when configured with --enable-debug=all.
Platforms tested:
FreeBSD 4.7 (sleipnir) serial & parallel
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Bug Fix
Description:
Metadata cache in parallel I/O can cause hangs in applications which
perform independent I/O on chunked datasets, because the metadata cache
can attempt to flush out dirty metadata from only a single process, instead
of collectively from all processes.
Solution:
Pass a dataset transfer property list down from every API function which
could possibly trigger metadata I/O.
Then, split the metadata cache into two sets of entries to allow dirty
metadata to be set aside when a hash table collision occurs during
independent I/O.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel
Misc. update:
Updated release_docs/RELEASE
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Code cleanup/new feature.
Description:
Split FUNC_LEAVE into API and non-API specific versions. This allows a
solution to compiling this branch with C++, as well as reducing the size
of the binaries produced.
Platforms tested:
FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
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Lots of performance improvements & a couple new internal API interfaces.
Description:
Performance Improvements:
- Cached file offset & length sizes in shared file struct, to avoid
constantly looking them up in the FCPL.
- Generic property improvements:
- Added "revision" number to generic property classes to speed
up comparisons.
- Changed method of storing properties from using a hash-table
to the TBBT routines in the library.
- Share the propery names between classes and the lists derived
from them.
- Removed redundant 'def_value' buffer from each property.
- Switching code to use a "copy on write" strategy for
properties in each list, where the properties in each list
are shared with the properties in the class, until a
property's value is changed in a list.
- Fixed error in layout code which was allocating too many buffers.
- Redefined public macros of the form (H5open()/H5check, <variable>)
internally to only be (<variable>), avoiding innumerable useless
calls to H5open() and H5check_version().
- Reuse already zeroed buffers in H5F_contig_fill instead of
constantly re-zeroing them.
- Don't write fill values if writing entire dataset.
- Use gettimeofday() system call instead of time() system when
checking the modification time of a dataset.
- Added reference counted string API and use it for tracking the
names of objects opening in a file (for the ID->name code).
- Removed redundant H5P_get() calls in B-tree routines.
- Redefine H5T datatype macros internally to the library, to avoid
calling H5check redundantly.
- Keep dataspace information for dataset locally instead of reading
from disk each time. Added new module to track open objects
in a file, to allow this (which will be useful eventually for
some FPH5 metadata caching issues).
- Remove H5AC_find macro which was inlining metadata cache lookups,
and call function instead.
- Remove redundant memset() calls from H5G_namei() routine.
- Remove redundant checking of object type when locating objects
in metadata cache and rely on the address only.
- Create default dataset object to use when default dataset creation
property list is used to create datasets, bypassing querying
for all the property list values.
- Use default I/O vector size when performing raw data with the
default dataset transfer property list, instead of querying for
I/O vector size.
- Remove H5P_DEFAULT internally to the library, replacing it with
more specific default property list based on the type of
property list needed.
- Remove redundant memset() calls in object header message (H5O*)
routines.
- Remove redunant memset() calls in data I/O routines.
- Split free-list allocation routines into malloc() and calloc()-
like routines, instead of one combined routine.
- Remove lots of indirection in H5O*() routines.
- Simplify metadata cache entry comparison routine (used when
flushing entire cache out).
- Only enable metadata cache statistics when H5AC_DEBUG is turned
on, instead of always tracking them.
- Simplify address comparison macro (H5F_addr_eq).
- Remove redundant metadata cache entry protections during dataset
creation by protecting the object header once and making all
the modifications necessary for the dataset creation before
unprotecting it.
- Reduce # of "number of element in extent" computations performed
by computing and storing the value during dataspace creation.
- Simplify checking for group location's file information, when file
has not been involving in file-mounting operations.
- Use binary encoding for modification time, instead of ASCII.
- Hoist H5HL_peek calls (to get information in a local heap)
out of loops in many group routine.
- Use static variable for iterators of selections, instead of
dynamically allocation them each time.
- Lookup & insert new entries in one step, avoiding traversing
group's B-tree twice.
- Fixed memory leak in H5Gget_objname_idx() routine (tangential to
performance improvements, but fixed along the way).
- Use free-list for reference counted strings.
- Don't bother copying object names into cached group entries,
since they are re-created when an object is opened.
The benchmark I used to measure these results created several thousand
small (2K) datasets in a file and wrote out the data for them. This is
Elena's "regular.c" benchmark.
These changes resulted in approximately ~4.3x speedup of the
development branch when compared to the previous code in the
development branch and ~1.4x speedup compared to the release
branch.
Additionally, these changes reduce the total memory used (code and
data) by the development branch by ~800KB, bringing the development
branch back into the same ballpark as the release branch.
I'll send out a more detailed description of the benchmark results
as a followup note.
New internal API routines:
Added "reference counted strings" API for tracking strings that get
used by multiple owners without duplicating the strings.
Added "ternary search tree" API for text->object mappings.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Other platforms/configurations tested?
FreeBSD 4.7 (sleipnir) serial & parallel
Solaris 2.6 (baldric) serial
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Purpose:
new functions
Description:
H5Gget_num_objs, H5Gget_objname_by_idx and H5Gget_objtype_by_idx.
Platforms tested:
modi4, arabica, eirene
Misc. update:
RELEASE.txt updated.
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Code cleanup.
Description:
Cleaned up compiler warnings & updated a few comments.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir)
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bug fix
Description:
Last change of FUNC_ENTER to FUNC_ENTER_NOAPI did not include
definition of variable ret_value and label done.
Solution:
Added the missing ret_value and label done.
Not sure if the logic is correct since the function will abort
if some assert fails. This fix only takes care of the syntax
error.
Platforms tested:
eirene(pp). Did not test on other machine since the syntax fix
is pretty simple.
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