| Commit message (Collapse) | Author | Age | Files | Lines |
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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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Code cleanup
Description:
Clean up a few more warnings and update dependencies.
Platforms tested:
Linux 2.2.18smp (eirene) serial & parallel
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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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corrected a typo--H5Fget_obj_counts should be H5Fget_obj_count.
Platforms tested:
Eirene only since it is just a string typo.
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Purpose:
New feature to H5Dget_offset
Description:
If user block is set, H5Dget_offset should be able to return the absolute
offset from the beginning of file.
Platforms tested:
eirene, arabica
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Code cleanup/Bug Fix
Description:
Re-do the ID->name code again, taking into account many more weird and
wonderful special cases stumbled across during the last set of test
writing.
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:
a bug fix
Description:
modify the condition check for the file close degree.
Platforms tested:
Linux 2.2(eirene), Solaris 2.7(arabica), IRIX64 6.5(modi4)
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Purpose:
a bug fix
Description:
When a file is opened for a second time, file close degree is supposed to
be either the same as the first open, or default as the first open is also
default.
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
Description:
Clean up ID->name code:
- Reformat to better match library coding standard
- Changed several algorithms to be more efficient
- Integrated into library more smoothly
Platforms tested:
eirene w/FORTRAN & C++
arabica w/FORTRAN
modi4 w/FORTRAN & parallel
sleipnir
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Purpose:
bug fix
Description:
memory leak regarding the ID to name buffer
Solution:
added a new function H5G_free_ent_name that is called on several places of the library
Platforms tested:
windows 2000
linux, with cpp
solaris, with fortran, cpp
irix64, with parallel, fortran
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Purpose:
Added 'ID to name' support
Description:
There is a new API function H5Iget_name
Most of the changes are on H5G.c , regarding the symbol table entry struct H5G_entry_t
which has 2 new fields 'name' and 'old_name'
A new private function was introduced H5G_ent_copy, that does a deep copy
between 2 symbol table entries
The test file is getname.c
Platforms tested:
windows 2000, Linux, Solaris
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Purpose:
Design for compact dataset
Description:
Compact dataset is stored in the header message for dataset layout.
Platforms tested:
arabica, eirene.
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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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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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Code cleanup
Description:
Re-alphabetized header includes.
Platforms tested:
FreeBSD 4.6 (sleipnir) w/parallel & C++
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Code cleanup
Description:
Make the sieve buffer managed by the free-list code.
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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Bug fix.
Description:
"strong" file closing feature was re-using free'd memory for objects which
were still open in the file.
Solution:
Used the "dmalloc" tools to determine where the memory was being
re-used and re-arranged the code to avoid these cases.
Platforms tested:
FreeBSD 4.6 (sleipnir)
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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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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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Bug fix.
Description:
Added extra check to locations where metadata and "small data" blocks were
being returned to the file's list of free space to avoid freeing 0-sized
blocks. This should fix the problems in last night's daily tests.
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Code cleanup/bug fix
Description:
Unused space in the file was being "dropped on the floor" when the metadata
or "small data" block was moved to a new location in the file and there was
unused space in the old block.
Solution:
Put the space left in the allocation block into the free list of space for
the file. This allows it to be [potentially] reused and sometimes allows
the file to be smaller.
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
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Code improvement.
Description:
Added boot block and driver info block checksumming feature to the shared
file information. This prevents these blocks from being written out
multiple times when they haven't changed.
This reduces the number of I/O operations which hit the disk for my test
program from 15 to 14 (i.e. from 393 to 14, overall).
Platforms tested:
Solaris 2.7 (arabica) w/FORTRAN and FreeBSD 4.5 (sleipnir) w/C++
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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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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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Code cleanup.
Description:
Took Robb's recent ideas for improving the FUNC_ENTER/FUNC_LEAVE macros
equivalents in the SAF library and adapted them to our library. I added
an additional macro which is equivalent to FUNC_ENTER:
FUNC_ENTER_NOINIT - Has the API tracing code, etc. from FUNC_ENTER but
none of the library or interface initialization code. This is to
be used _only_ for static functions and those which explicitly
cannot have the library or interface initialization code enabled
(like the API termination routines, etc.).
This allowed many more of the functions in the library [but not all yet :-(]
to be wrapped with FUNC_ENTER[_NOINIT]/FUNC_LEAVE pairs.
It also reduced the size of the library and executables (by cutting out a
bunch of code which was never executed), I'll e-mail the exact results when
I've finished editing it.
Platforms tested:
IRIX64 6.5 (modi4)
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Purpose:
eliminating the compiler warnings in Windows
Solution:
I am eliminating the compiler warnings in Windows.
the last 2 were:
1)
if((oid_list = H5MM_malloc(oid_count*sizeof(hid_t)))==NULL)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL,
"memory allocation failed");
D:\disk_w\hdf5\src\H5F.c(2590) : warning C4047: '=' : 'int ' differs in levels
of indirection from 'void *'
on the HGOTO_ERROR call , I replaced the NULL with FAIL
2)
*((float*)d) = *((double*)s);
D:\disk_w\hdf5\src\H5Tconv.c(6426) : warning C4244: '=' : conversion from 'double ' to 'float ', possible loss of data
I added the type cast
*((float*)d) = (float) *((double*)s);
we have now 0 errors 0 warnings on Windows !
Platforms tested:
w2000, linux
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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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Bug Fix
Description:
When H5Freopen is called, the file to reopen's 'intent' (read/write
permissions, etc) is not being copied to the new file's 'intent'
information.
Solution:
Copy it. :-)
Platforms tested:
IRIX64 6.5 (modi4)
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Performance enhancement
Description:
Doing an MPI_File_sync() just before a file is closed causing a large
performance loss.
Solution:
Add flag to MPI file driver to avoid performance the MPI_File_sync() when
the flag is set before a call to H5F_flush().
Platforms tested:
IRIX64 6.5 (modi4)
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Code cleanup
Description:
Restructure H5F_close code to use just one H5F_flush call.
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:
The parallel I/O file driver is optimized to only write metadata with one
process (and broadcast the results to the other processes). This is
currently enabled by a separate call to H5FD_mpio_tas_allsame() before
each metadata write to the file. This can easily lead to problems where
the prelude function call is omitted before the actual write code or, in
a threaded environment, lead to race condititions where the value set is
reset before being used.
Solution:
Since we only want to write metadata from one process, key off of the 'type'
parameter (which has information about whether the data being written it
metadata or raw data) to H5FD_mpio_write() as the method for determining
whether to only write from one process or not.
Platforms tested:
IRIX64 6.5 (modi4)
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Migrate from configure macros of XYZ_ABC to H5_XYZ_ABC
Description:
configure generates many macros definitions on the fly and
were stored in src/H5config.h which is included by H5public.h.
But other software that uses hdf5 may also run their own configure.
There can be a clash in macro name space. We decided awhile ago
to prepend all generated macros with "H5_" to avoid conflicts.
The process has started and this commit completes it (at least attempt
to).
Solution:
Many macros symbols (e.g. SIZEOF_xxx and HAVE_xxx were changed to
H5_SIZEOF_xxx and H5_HAVE_xxx). Then H5private.h no longer includes
H5config.h. This cuts H5config.h away from HDF5 source code.
Pending issues:
The module of fortran and pablo are to be resolved in a different
commit.
Platforms tested:
eirene (parallel), arabica (solaris 7 --enable-fortran, --enable-cxx)
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New Feature
Description:
Added new H5Dfill() routine to fill the elements in a selection for a
memory buffer with a fill value. This is a user API wrapper around some
internal routines which were needed for the fill-value modifications
from Raymond as well as Pedro's code for reducing the size of a chunked
dataset.
Platforms tested:
FreeBSD 4.5 (sleipnir) [and IRIX64 6.5 (modi4) in parallel, in a few
minutes]
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Bug Fix
Description:
The H5Gget_objinfo() function was not setting the 'fileno' field in the
H5G_stat_t struct passed in.
Solution:
Added a "file serial number" to each file currently open in the library
and put that in the 'fileno' field. If a file is opened twice (with
H5Fopen) and the VFL driver detects that it is the same file (i.e. the
two file structures have the same "shared file info" in the library's
memory structures), they will have the same serial number.
This serial number has two drawbacks:
- If a VFL driver doesn't/can't detect that two calls to H5Fopen with
the same file actually _are_ the same file, each will get a
different serial number
- If the same file is closed and re-opened, the serial number will be
different.
It is be possible to fix the second drawback for many VFL drivers, but it
would be a lot of effort and probably isn't worth it until we've got a
good reason to do it. Dunno if we'll ever be able to fix the first
drawback...
Platforms tested:
FreeBSD 4.5 (sleipnir)
VS: ----------------------------------------------------------------------
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Code cleanup
Description:
Added some more assertions to help debug in the future...
Platforms tested:
FreeBSD 4.5 (sleipnir)
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Removing the DPSS (gridstorage) driver source code.
Description:
The DPSS (using Grid-Storage) driver is retired.
Removed the configure option with-gridstorage from configure.in.
Cvs remove the following files
./src/H5FDdpss.c
./src/H5FDdpss.h
./test/dpss_read.c
./test/dpss_write.c
Regenerated Dependencies files (some had to be hand-edited since
'make depend' did not cover them.)
Removed reference to DPSS Virtual file driver from H5F.c.
Platforms tested:
modi4 (Parallel; -with-gass=...), eirene, arabica (fortran, cxx).
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Code cleanup
Description:
Tweaked internal error handling macros to reduce the size of the library's
object code by about 10-20%.
Also cleaned up some compiler warnings...
Platforms tested:
FreeBSD 4.4 (sleipnir)
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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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Code cleanup
Description:
Be more careful when starting up and shutting down APIs, only initialize
variables which are actually shut down already.
Get rid of IDs from internal function calls
Platforms tested:
FreeBSD 4.4 (hawkwind)
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Code cleanup
Description:
Fix a bunch of warnings and also make the linux compilers happy with
some casts.
Platforms tested:
Linux 2.2 (eirene)
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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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