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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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Update
Description:
A few generic changes to the FPHDF5 code. Some error messages
reworked a bit. Cleaning up in case of failure improved in some
cases. Added another field to the synchronization messages...
Platforms tested:
Linux
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FPHDF5 Fixups
Description:
- Stopped using API calls in the H5FPclient code. It now uses
internal library calls.
- Removed some FIXME comments because they've been fixed.
- Small fix for an enum starting at 37 for no reason :-)
Platforms tested:
Eirene (only affects FPHDF5, so no need to test 3 platforms just yet).
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Code cleanup
Description:
Added some comments and made some minor code cleanups
Platforms tested:
minor change, only testing on FreeBSD 4.7 (sleipnir) w/parallel
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Update
Description:
Added code which performs an update when there's a dataset creation.
Commented on some FIXMEs which were in the code.
Platforms tested:
Eirene PP
Arabica Fortran
Modi4 PP Fortran
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New Feature. Support for new FPHDF5 Feature
Description:
More support for the FPHDF5 feature. This splits the H5D_create
function into separate parts which update the metadata cache. It was
necessary to split apart the H5O_create function to do a similar
thing since it would allocate real space on the hard disk.
I'm checking this up now so that I don't get too far away from what
the CVS repository has and so that others may look at the code and
retch^H^H^H^H^Hmarvel at it. If there are any comments, send them my
way.
There is one outstanding issue, though. I need to use non-API
functions in the FPHDF5 stuff. I'm using some APIs right now and
should migrate to using others. At the moment, I'm putting that on
the back burner until I'm more along in the implementation.
Platforms tested:
Arabica (C++)
Eirene (Parallel)
Modi4 (Parallel)
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Code cleanup
Description:
Add more comments and clean up small bits of the FPH5 code.
Platforms tested:
FreeBSD 4.7 (sleipnir), changes too minor to affect other platforms.
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Oops
Description:
The H5FPprivate.h file was being #included even if PARALLEL was
turned off.
Solution:
put the #include of the H5FPprivate.h file within the #ifdef block so
that it doesn't get included if H5_HAVE_FPHDF5 isn't defined.
Platforms tested:
Linux...
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Feature Add
Description:
New files for the Flexible Parallel HDF5 stuff.
H5FP.c - Module housing the APIs to FPHDF5
H5FPclient.c - Module housing the internal client APIs
H5FPserver.c - Module housing the internal server APIs
H5FPpublic.h - Header for public APIs
H5FPprivate.h - Header for private APIs
H5Ofphdf5.c - Way of serializing FPHDF5 information to and from the
SAP
H5Oplist.c - Way of serializing a generic property list.
Solution:
[details about the changes, algorithm, etc...]
[Please as detail as you can since your own explanation is
better than others guessing it from the code.]
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}?
[If no, why not?]
Other platforms/configurations tested?
Misc. update:
Update MANIFEST if you add or remove any file.
Update release_docs/RELEASE for bug fixes, new features, etc.
Update applicable document files too.
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