| Commit message (Collapse) | Author | Age | Files | Lines |
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Fix error introduced into driver info block size computation, which caused
the test/big test to fail.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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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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The problem
came from the EOA for the whole MULTI file. It's taken out because it's
meaningless for MULTI file. Instead, each individual file has its EOA.
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haven't
been run in a while, so many of the source files were updated with
tracing macros, etc. No code changes by me.
Tested on kagiso and smirom.
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Clean up some of the warnings on 64-bit Linux...
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Too minor to require h5committest
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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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Code cleanup
Description:
Clean up unused variables & use portability macros better
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Platforms tested: Not needed.
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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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Bug fix & code cleanup
Description:
Don't unmount child files from a parent file if the parent file is
being held open by an object.
Also, moved the mounting routines into their own source file and the
superblock routines into their own file also.
Solution:
Moved the code for unmounting child files down in the H5F_close routine
and also add checks to the file and group mounting code to unmount child
files when the last object holding open a file closes.
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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Description: After recent fix of family driver bug(#213), some failure
was discovered on sol and kelgia in daily test. Family files can't be
opened by hdf5/tools/misc/repart_test.c. It turned out to be the
destination size of "off_t" type wasn't passed in through H5Pset()
correctly.
Solution: In tools/misc/h5repart.c, copy the destination size to a
variable of "hsize_t" type and pass in to H5Pset().
Platforms tested: sol and kelgia where the failure was discovered.
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Description: See details from Bug #213. Family member file size wasn't saved
anywhere in file. When family file is opened, the first member size determine
the member size.
Solution: This is the fourth step of checkin. A test suit is added for h5repart,
including a program to generate the test files, a script file to run h5repart,
and a program to verify repartitioned files can be opened by the library.
There's a change from the first step of checkin. Family name template is no
longer saved in the superblock because different pathname can make the name
different.
In the third step of checkin, h5repart has been modified. If h5repart is used
to change the size of family member file, the new size(actual member size) is saved
in the superblock.
In the second step of checkin, multi driver is checked against the driver
name saved in superblock. Wrong driver will result in a failure with an error message indicating
multi driver should be used. This change includes split driver because it's a special case for multi
driver.
In the first step of checkin. Family member size and name template(unused at this stage) are saved
in file superblock. When file is reopened,the size passed in thrin superblock. A different size
will trigger a failure with an error message indicating the right size. Wrong driver to open family
file will cause a failure, too.
Platforms tested: h5committest and fuss.
Misc. update: MANIFEST
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Description: See details from Bug #213. Family member file size wasn't saved
anywhere in file. When family file is opened, the first member size determine
the member size.
Solution: This is the third step of checkin. h5repart has been modified. If h5repart is used
to change the size of family member file, the new size(actual member size) is saved in the superblock.
In the second step of checkin, multi driver is checked against the driver
name saved in superblock. Wrong driver will result in a failure with an error message indicating
multi driver should be used. This change includes split driver because it's a special case for multi
driver.
In the first step of checkin. Family member size and name template(unused at this stage) are saved
in file superblock. When file is reopened,the size passed in thrin superblock. A different size
will trigger a failure with an error message indicating the right size. Wrong driver to open family
file will cause a failure, too.
Platforms tested: h5committest and fuss
Misc. update: RELEASE.txt
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Description: See details from Bug #213. Family member file size wasn't saved
anywhere in file. When family file is opened, the first member size determine
the member size.
Solution: This is the first step of fixing this bug. Member size and name
template(unused at this stage) are saved in file superblock. When file is reopened,
the size passed in through H5Pset_fapl_family is checked against the size saved
in superblock. A different size will trigger a failure with an error message
indicating the right size. Wrong driver to open family file will cause a failure,
too.
The second step will change multi driver that wrong driver will cause a failure.
Platforms tested: fuss and h5committest
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Code cleanup
Description:
Clean up various warnings reported by the Windows team.
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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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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Purpose: Correction to previous bug fix. This checkin is mainly to let user
test his program.
Description: For family driver bug(#213), the previous fix was imperfect. The problem
was when user create family file, the member size information wasn't saved in file. When
the file was re-opened, the library simply use the size of 1st member file as member size.
Solution:
When file is re-opened, member size passed in from access property
is checked to see if it's reasonable. If there is only 1 member
file, member size can't be smaller than current member size.
If there are at least 2 member files, member size can only be equal
to the 1st member size.
Platforms tested: h5committest and fuss
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Description: H5Pset_fapl_family sets family member size only for creating
new file. The file doesn't keep this size information. When the file is
re-opened, the size of first member file is used as the member size.
Solution: Assume user knows the original member size and sets it through
H5Pset_fapl_family. That will be the member size. User can pass in value 0
as member size if he doesn't know the original member size. Library will
choose the size of current first member size as the member file size.
Platforms tested: h5committest and fuss.
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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 & 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 cleanup
Description:
Clean up lots of warnings based on those reported from the SGI compilers
as well as gcc.
Platforms tested:
SGI O3900, IRIX64 6.5 (Cheryl's SGI machine)
FreeBSD 4.9 (sleipnir) w/ & w/o parallel
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 & 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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New Feature
Description:
Added support for the lock and unlock function calls for file
drivers. Only FPHDF5 uses this feature. All of these drivers don't
define lock or unlock methods.
Platforms tested:
Linux, Modi4, Sol
Misc. update:
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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 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
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:
Cleaned up a few warnings from compiling with --disable-hsizet on Linux
Platforms tested:
Linux 2.2.x (eirene)
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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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New feature.
Description:
Added a "small data" block allocation mechanism to the library, similar to
the mechanism used for allocating metadata currently.
See the RFC for more details:
http://hdf.ncsa.uiuc.edu/RFC/SmallData/SmallData.html
This reduces the number of I/O operations which hit the disk for my test
program from 19 to 15 (i.e. from 393 to 15, overall).
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
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Purpose:
Bug Fixing
Description:
In H5FD_family_write and H5FD_family_read, size_t is checked against
hsize_t for overflow, which fails on IA32 architecture machine supporting
large files.
Solution:
Use temporary variable which won't pass the limit of size_t.
Platforms tested:
Linux 2.4(platinum) and IRIX64 6.5(modi4)
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Code cleanup
Description:
Broke the FUNC_ENTER macro into several macros, with more specialized
uses (which followup mail will describe). This was designed to move
most/all of the checks which could be done at compile time to that point,
instead of needlessly performing them (over & over :-) at run-time.
This reduces the library's size (and thus staticly linked binaries) and
has a minor speedup effect also.
Platforms tested:
IRIX64 6.5 (modi4) with parallel & FORTRAN enabled, and additional testing
on FreeBSD and Solaris immediately after the checkin.
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New feature
Description:
Add 'closing' parameter to H5FDflush and VFL "flush" functions, per
http://hdf.ncsa.uiuc.edu/RFC/VFLFlush/VFLFlush.html
Platforms tested:
IRIX64 6.5 (modi4)
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Back out changes.
Description:
Back out changes to VFL 'flush' API function, pending review.
Platforms tested:
IRIX64 6.5 (modi4)
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New Feature
Description:
The VFL flush function is called immediately before a file is closed.
This can cause duplicate syncronization actions to occur, if the VFL
close function also performs them.
Solution:
Added 'closing' parameter to VFL 'flush' operation. This allows the VFL
flush function to bypass operations that will be duplicated within the VFL
close function.
Additionally, use the 'closing' parameter to bypass calls to MPI_File_sync()
when set. Since MPI_File_close() also syncronizes the file, this avoids
the terrible performance hit taken when calling MPI_File_sync() as the file
is closing.
Platforms tested:
IRIX64 6.5 (modi4)
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Code cleanup
Description:
Clean up warnings from gcc 3.1
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code cleanup
Description:
Cleanup compiler warnings found by the SGI compiler and gcc 3.0
Platforms tested:
FreeBSD 4.5 w/gcc 3.0 (hack) && IRIX64 (modi4)
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Purpose:
Modify H5Fclose behavior
Description:
The HDF5 actual file close behaves in several ways in terms of if there
are still objects(dataset, group, datatype) opened in file.
Solution:
Added a new file access property, file close degree. It has four values,
H5F_CLOSE_DEFAULT
H5F_CLOSE_WEAK
H5F_CLOSE_SEMI
H5F_CLOSE_STRONG
The way a file is closed is decided by these values.
Platforms tested:
IRIX64 6.5, SunOS 5.6, FreeBSD 4.4
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Code cleanup
Description:
Windows is generating hundreds of warnings from some of the practices in
the library. Mostly, they are because size_t is 32-bit and hsize_t is
64-bit on Windows and we were carelessly casting the larger values down to
the smaller ones without checking for overflow.
Also, some other small code cleanups,etc.
Solution:
Re-worked some algorithms to eliminate the casts and also added more
overflow checking for assignments and function parameters which needed
casts.
Kent did most of the work, I just went over his changes and fit them into
the the library code a bit better.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Bug fix
Description:
Fix deep copies of property lists with H5P_DEFAULT values.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Code cleanup
Description:
Get rid of IDs from internal function calls and some small cleanups from
the old-stype => generic property list conversion.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Code cleanup
Description:
Clean up various compiler warnings from generic property updates.
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Purpose:
Switch from old property list to new generic property list.
Description:
Mainly changed H5Pcreat, H5Pclose, H5Pcopy.
Platforms tested:
IRIX64 6.5, FreeBSD, SunOS 5.7.
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Purpose:
Generic Property List Change
Description:
Changed file access list to the new generic list.
Platforms tested:
IRIX64, SunOS5.7, FreeBSD
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