| Commit message (Collapse) | Author | Age | Files | Lines |
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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 cleanup
Description:
Various minor tweaks to clean code up and bring it into closer
syncronization with the release branch.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
h5committested
IRIX64 6.5 (modi4)
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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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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 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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allow users to register IDs and ID types at runtime.
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Code optimization
Description:
Allow global heap collections to grow in size (up to a 64K limit) if they
are able to. This allows them to grow to a more reasonable size than the 4K
minimum size.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Bug fix
Description:
Correct potential file corruption from mis-setting the metadata accumulator
address. (Bugfix contributed by Sean Monner <seanm@quadrus.com>)
Solution:
When the new metadata overlaps with the end of the metadata accumulator and
the accumulator grows in size, don't reset the address of the accumulator, since
it hasn't moved.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Checkpoint checkin of FP bug fixes. FP is still quite
buggy, but I must go deal with other matters.
Description:
Fixed two major bugs:
1) H5FPserver.c was clobbering meta data in its care.
2) H5FPserver.c was allocating the same space multiple
times, causing both data and meta data corruption.
Also made minor fixes, added debugging code, and familiarized
myself with the FP code.
All development work with FP enabled was done on Eirene.
On this platform, FP now passes its test reliably with
up to 9 processes. At 10 processes it seg faults every
time. I haven't looked into this issue.
There are also several known locking bugs which have to
be fixed. However, they are of sufficiently low probability
that I didn't bother with them on this pass.
FP has not been tested with deletions -- this should be
done.
Also, need to test FP chunked I/O.
Solution:
1) Modified cache in H5FPserver.c to merge changes correctly.
Found and fixed a bug in H5TB.c in passing.
2) Multiple space allocation was caused by a race condition
with set eoa requests.
Most of these eoa requests appeared to be superfluous, so
I deleted them.
Those issued during the superblock read seemed necessary,
so I inserted a barrier at the end of the superblock read,
to prevent races with allocations.
Platforms tested:
h5committested
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Fix build with C++ compiler
Description:
Add file driver header files for prototypes.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/CC=g++
too obscure to require h5committest
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Code cleanup
Description:
Add destructor to match constructor fr VFLs when they are shut down by the
library.
Solution:
Added H5FD_*_term() routines to "undo" changes made in H5FD_*_init()
routines.
Platforms tested:
IBM p690 (copper)
too minor to require h5committest
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Bug fix/optimization
Description:
Address slowdown in MPI-I/O file metadata operations that was introduced
mid-stream. We now _require_ a POSIX compliant parallel file system for the
MPI-I/O file driver (as well as for the MPI-POSIX file driver).
Also optimized file open operation when the file is being created by
reducing the number of collective & syncronizing calls.
Additionally, refactor the MPI routines into a common place, eliminating
duplicated code.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
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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Warning cleanup
Description:
Make a parameter 'const' to clean up a warning during compiles.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Code cleanup
Description:
Refactored handlier of VFL drivers in file access and data transfer property
lists in order to simplify and unify the code dealing with them.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Add feature
Description:
Add H5Fget_freespace() routine, to check the amount of free space in a
file. This information is only valid until the file is closed currently,
however (until we start recording the free space information in the file
itself).
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest
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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 & bug fix
Description:
More de-linting...
Also correct a bug that lint exposed which was incrementing the incorrect
driver ID of a file driver and also no saving the correct driver ID for the
newly opened file.
Platforms tested:
FreeBSD 4.8 (sleipnir)
too minor for h5committest
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Code cleanup
Description:
More linting...
Platforms tested:
FreeBSD 4.8 (sleipnir)
too minor to need h5committest
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Added some comments, etc.
Platforms tested:
FreeBSD 4.8 (sleipnir)
too trivial for 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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Feature change & code cleanup
Description:
Changed fileno field in H5FD_t struct from 'unsigned long[2]' to just
'unsigned long'.
Changed over code to handle the fileno change.
Chased error API changes
Platforms tested:
h5committested
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Code cleanup
Description:
Correct name of H5FD_term_interface function in FUNC_ENTER macro.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Bug fix.
Description:
Corrected fencepost error which was incorrectly checking for merging
metadata at the front of the metadata accumulator. This now allows the
metadata cache to cache I/O operations more efficiently.
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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Update & Bug Fix
Description:
The "free" protocol was missing. Added that to the server side.
When doing a "create" of a file (with no other data structures
created), the freespace in the file wasn't being reclaimed.
Solution:
After adding the free protocol, we put the burden of running through
the FD_free function on the SAP instead of each client.
Platforms tested:
Linux
Misc. update:
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Bug Fix & Update
Description:
FPHDF5 was creating files which didn't have the EOA field in the
superblock set correctly. It turns out that the SAP was keeping this
information to itself instead of giving it to the client processes.
Naughty SAP!
Solution:
Have the SAP send this information back to the clients so that they
can update the superblock as necessary. This now creates a file (with
just the root group) that looks correct! Only problem is that there's
extra file space being allocated. Also, at program termination,
there's an infinite loop...
Platforms tested:
H5committests (run by hand on burrwhite, arabica, and modi4)
Misc. update:
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Bug fix and Update
Description:
From Quincey's comments on the code I checked in last night:
- In H5F_close call, the "private" processes should call the
H5F_flush with the "CLEAR_ONLY" flag.
- There's no need for a special case for FPHDF5 in the
FD_real_alloc function since FPHDF5 doesn't define an alloc
function.
- The return type of H5Pset_fapl_fphdf5 should be herr_t instead
of hid_t. I don't know how it got that way in the first place.
- The variable names for MPI types and the structure typedefs
should be switched: H5FP_request/H5FP_request_t to
H5FP_request_t/H5FP_request and so on.
- In the H5FP.c module, I was commiting the H5FP_request MPI
datatype but using the wrong offset field...
Platforms tested:
Linux...will test on others, but these are mostly FPHDF5 changes.
Misc. update:
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Update
Description:
When doing an allocation, check to see, if it's an FPHDF5
driver, if only the captain should be performing the allocation
Platforms tested:
Linux, Modi4, Sol
Misc. update:
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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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Refactoring of Flush Logic
Description:
The Flushing logic passed in multiple flags to indicate what type of
flush it was: closing, invalidate, alloc only. This made extending
the function of the flush logic to handle other flags annoying.
Solution:
I changed it to be just one bitmasked flag to indicate what type of
flushing to do. I also added the CLEAR_ONLY flag, which will be used
in the FPHDF5 stuff.
Platforms tested:
h5committest doesn't work for me (my environment isn't setup on the
other machines I guess). I tested it manually:
Linux parallel & C++
Sol Fortran
Modi4 parallel & Fortran.
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Update
Description:
Big change to the H5FD.c module:
- Split apart H5FD_alloc and H5FD_free. H5FD_alloc was huge and
H5FD_free had a freeing of the freelist part which I needed to
call from the SAP.
- Added support for FPHDF5. If it's a client, then it sends the
allocation or free request to the SAP. The SAP will call the
same code, but it'll actually do the allocation/freeing in that
case.
Platforms tested:
Linux & Modi4
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Purpose:
Change feature
Description:
Switch to Fletcher32 from Adler32 checksum
Platforms tested:
arabica, eirene, modi4
Misc. update:
MANIFEST and RELEASE.txt updated.
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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
Description:
Reduce warnings on Windows
Platforms tested:
FreeBSD 4.7 (sleipnir)
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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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Bug Fix
Description:
Free blocks of space in the file which were merged with a block before them
were not updating the free list information correctly, allowing space in
the file to over-allocated and potentially corrupted.
Solution:
Correct address of free block during merging.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir)
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Code cleanup
Description:
Clean up compile warnings.
Platforms tested:
FreeBSD 4.6 (sleipnir) w and w/o parallel
Linux 2.2.x (eirene) w/FORTRAN & C++
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN & parallel
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Purpose:
Performance improvement for compact dataset.
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
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Purpose:
New API functions
Description:
Added API functions to return pointer to low-level file handle
(H5Fget_vfd_handle and H5FDget_vfd_handle) and related property list
setting functions(H5Pset_family_offset and H5Pset_multi_type).
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
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Code cleanup/New Feature
Description:
Improve the space allocation in the file by re-using freed space more
effectively.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/serial & parallel
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Code cleanup
Description:
Combined H5P_isa_class and H5I_object functionality into a new internal
H5P API function: H5P_object_verify, which checks that a property list is
the appropriate class and then returns the property list object associated
with the property list ID.
This reduces the source code by about 200 LOC and trims the library binary
some more.
Platforms tested:
FreeBSD 4.6 (sleipnir)
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Code cleanup
Description:
Changed the last HRETURN* statements in the FUNC_ENTER macros into HGOTO*
macros, which reduces the size of the library binary in certain
configurations by another 10%
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel, IRIX64 6.5 (modi4) serial &
parallel
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Code cleanup
Description:
Change most (all?) HRETURN_ERROR macros to HGOTO_ERROR macros, along with
HRETURN macros to HGOTO_DONE macros. This unifies the error return path
from functions and reduces the size of the library by up to 10% on some
platforms.
Additionally, I improved a lot of the error cleanup code in many routines.
Platforms tested:
FreeBSD 4.6 (sleipnir) serial & parallel and IRIX64 6.5 (modi4) serial &
parallel.
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Code cleanup
Description:
Created a new H5I function which combined the some of the functionality of
H5I_get_type and H5I_object: H5I_object_verify.
Using this new function in the library trims another ~200 lines of code off
the library and makes the resulting binaries smaller and faster also.
Platforms tested:
FreeBSD 4.6 (sleipnir)
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New feature.
Description:
Added MPI-posix VFL driver. This driver uses MPI to coordinate actions, but
performs I/O directly with posix sec(2) I/O functions. This driver should
_NOT_ be used if the file accessed is not on a parallel filesystem.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/parallel & IRIX64 6.5 (modi4) w/parallel
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Code improvement
Description:
Some small code cleanups and took out the code the was turning off the
metadata cache for parallel I/O (!)
Platforms tested:
IRIX64 6.5 (modi4) w/parallel
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Bug fix.
Description:
H5P_get was reading a 'hsize_t' field into a 'size_t' variable, causing
problems on the HP's and Windows.
Solution:
Changed the variable to be an hsize_t
Platforms tested:
HP/UX 11.0 (kelgia)
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Code cleanup
Description:
Allow H5FD_free to return successfully (but ignore) freeing objects with
size 0.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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