| Commit message (Collapse) | Author | Age | Files | Lines |
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Add H5Sis_regular_hyperslab() and H5Sget_regular_hyperslab() API routines,
along with tests.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial
(h5committest forthcoming)
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Revert r25273, 25283 & 25439 (the hyperslab improvement changes). They
are buggy and it's taking me a long time to correct the problem. I'll check
in a revised form of the changes when I've got them straightened out.
Tested on:
Mac OSX 10.10.0 (amazon) w/gcc 4.9.x, C++, FORTRAN
Linux 2.6.x (jam) w/parallel
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Correct error in new hyperslab selection test to use the right # of
dimensions for start/stride/count/block arrays. Also, switch H5Sselect_select
to H5Smodify_select.
Tested on:
MacOSX/64 10.9.3 (amazon) w/gcc 4.9.1, OpenMPI, C++, FORTRAN & threadsafe
(Too minor to require h5committest)
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Bring in Chao/Neil/my changes to optimize hyperslab selection operations
further, along with 3 new public API routines: H5Scombine_hyperslab(),
H5Sselect_select() and H5Scombine_select(), along with many minor cleanups to
the code and fixing a few compiler warnings.
Tested on:
Mac OSX/64 10.9.3 w/gcc 4.9.x and parallel w/OpenMPI
(h5commttest forthcoming)
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Improve checks for NULL buffer from user during H5Dread/H5Dwrite calls.
Tested on:
Linux/32 2.4.x (jam) w/gcc
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Clean up more compiler warnings, plus merge a few Coverity bug fixes from
the hdf5_1_8_coverity branch back to the trunk:
r20877:
Purpose: Fix coverity issue 1723
Description:
Modified test_generate in hl/test_image to close file "f" before exit, even if
an error occurs.
r20879:
Issue 63: change check of return of H5Tget_nmembers to <=0. No need to go
futher if call fails as well as empty.
r20881:
Coverity #659 in Run 46: I changed the Line 442 where it tries to check whether
FLAG_PRINTED is TRUE. But it had just been set to FALSE. I took out the
condition check in the print statement.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & Parallel
(too minor to require h5committest)
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Prep work for adding a memory free function, part of HDFFV-8551.
Tested on:
32-bit LE linux (jam)
* with C++, Fortran
* with thread safety on
These are minor changes (almost entirely renaming foo functions
to HDfoo) that don't change functionality. This should not
require a full commit test.
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Create a new, more streamlined method of generating I/O sequences when
there is only a single block defined by a hyperslab. This improves the
performance of Ger Van Diepen's (LOFAR team) benchmark by about 20%.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
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Switch from using "UINT16_MAX" to "64 * 1024" for assert macro.
Tested on:
None, just eyeballed.
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Bring "shape same" changes from LBL branch to trunk. These changes
allow shapes that are the same, but projected into dataspaces with different
ranks to be detected correctly, and also contains code to project a dataspace
into greater/lesser number of dimensions, so the I/O can proceed in a faster
way.
These changes also contain several bug fixes and _lots_ of code
cleanups to the MPI datatype creation code.
Many other misc. code cleanup are included as well...
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Clean up compiler warnings, check error values and fix whitespace.
Tested on:
FreeBSD/32 6.3 (duty) w/debug
(too minor to require h5committest)
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Remove another call to H5E_clear_stack() from within the library.
Clean up lots of compiler warnings.
Tested on:
Mac OS X/32 10.5.6 (amazon)
(followup on other platforms forthcoming)
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Bring file free space branch changes through r15795 into trunk, which
includes a fair bit of code cleanup & rearrangement along with a couple of
bug fixes also.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
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Changed the error check string to match the function being called, changed the string H5Sselect_all to H5Sselect_none
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Correct the prototype for H5Sselect_elements() to take an 'hsize_t *' for
the coordinates, instead of 'hsize_t **'.
Tested on:
Mac OS X/32 10.5.1 (amazon)
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- Avoid trying to update 1-D dataset's chunk indices (they can't change)
- Cache a copy of a dataspace describing a chunk, when doing single
element I/O
- Keep a 'chunk info' struct around, for single element I/O
- Avoid creating a skip list for chunk infos when performing I/O on single
element
Also, minor formatting cleanups to testing code
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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- Changed H5S_select_shape_same routine to handle scalar dataspace
comparisons correctly. (Added regression tests to verify)
- Simplified chunk map creation, now that scalar dataspaces are handled
in same way as "simple" dataspaces.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Add H5Dcreate to API versioned routines, replacing internal usage with
H5Dcreate2
Fix thread-safe error stack initialization for API versioned error
stack printing routines.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Make H5Dopen versioned and change all internal usage to use H5Dopen2
Add simple regression test for H5Dopen1
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Deprecate H5Dextend in favor of H5Dset_extent (without using API
versioning, due to changed behavior) and switch internal usage to H5Dset_extent
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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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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dataspace is not valid, or when dataspace is valid but closed.
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Clean up more compiler warnings, esp. on Linux/64 platform.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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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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Bug fix/Feature
Description:
Modify the library to use rand_r, when available, instead of srand. If
rand_r is not available, it will try to use srandom/random, and then finally
fall back to srand/rand.
Solution:
A couple places in the library use the srand() function to seed the random
number generator. This can cause problems on certain platforms and could theoretically
cause problems for users who expect a certain sequence of random numbers following their
own call to srand().
Most platforms have an implementation of rand_r, which is identical to rand, except that
it allows for explicit storage of the seed value. The configure script will now check
for the existence of rand_r to facilitate its use in the library.
Two new functions are added, to replace the macros HDsrand/HDrand. These functions are HDrand and
HDsrand. HDrand will call rand_r, if available, or random(), if available, and fall back to rand() if neither
of those is available. HDsrand will store the seed value locally, if rand_r is available. Otherwise, it will call
srandom if available, and fall back to srand otherwise.
Platforms tested:
heping, mir. Really need to test on Red Storm, since that platform motivated this fix, but the machine
is currently not available.
Misc. update:
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Code cleanup
Description:
Style fixes for consistency & other minor cleanups
Platforms tested:
FreeBSD 4.11 (sleipnir)
Mac OSX (amazon)
Linux 2.4
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Bug fix
Description:
Check in Kent's fixes to hyperslab rebuilding code that should correctly
detect situation when different sub-hyperslabs exist in a higher dimension.
Solution:
Remember previous sub-hyperslab information and compare that with newly
generated sub-hyperslab to make certain they are the same.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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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
Description:
Hyperslab selections that had a selection offset and were applied to a
chunked dataset could get into an infinite loop or core dump if the same
selection was used multiple times, with different selection offsets.
Solution:
"Normalize" the selection with the selection offset, generate the
selections for the chunks overlapped and then "denormalize" the selection.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Bug fix
Description:
Fix problems with hyperslab operations with hyperslabs that have count == 0
or block == 0 values. (bugzilla #294)
Solution:
Detect zero sized selections and translate into appropriate action on the
current hyperslab, rather than go through the formality of generating span
trees with zero-sized spans, etc.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/parallel
Too minor to require h5committest
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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:
Allow I/O to occur on 0 element selections.
Platforms tested:
h5committest
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Bug fix
Description:
Allow buffer parameter to H5Dread & H5Dwrite to be NULL if there are no
elements to transfer.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
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Code cleanup & reorganization
Description:
Move further in the testing framework cleanup, eliminating all the
global variables (moving them into testframe.c as static variables) from the
testing framework code and moving it into the libh5test.a.
Platforms tested:
FreeBSD 4.9 (sleipnir) w & w/o thread-safety, c++ & parallel
h5committested
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Bug fix.
Description:
Using a selection offset with hyperslab selections in chunked datasets
was getting into an infinite loop and hanging the application.
Solution:
Apply the selection offset to the hyperslab selection properly.
Platforms tested:
FreeBSD 4.9 (sleipnir) w & w/o parallel
h5committest
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Bug fix
Description:
Single hyperslab selections (which were set with only one call to
H5Sselect_hyperslab) that had dimensions that could be "flattened" but were
interspersed with dimensions that could not be flattened were not correctly
handled, causing core dumps.
Solution:
Re-work "flattening" code to handle this case properly.
Platforms tested:
FreeBSD 4.9 (sleipnir) w/parallel
h5committest
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Bug fix
Description:
I/O on chunked datasets with a scalar dataspace for the memory dataspace
was not working correctly.
Solution:
Translate the scalar dataspace into a n-dimensional (where n is the number
of dimensions of the file's dataspace) dataspace of dimensions 1x1x1...
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest (modulo modi4 which is not working correctly)
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Bug fix
Description:
I/O on chunked datasets with point selections was not working correctly.
Solution:
Re-wrote some parts of raw data I/O routines that build the selections for
each chunk to correctly handle point selections.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Version update
Description:
Removed 1.4 compatibility code in the library.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Code cleanup
Description:
Reduce warnings when compiled with --enable_hdf5v1_4 compatibility switch.
Platforms tested:
FreeBSD 4.8 (sleipnir)
h5committest
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Bug fix
Description:
An earlier checkin changed some of the assumptions about single block
hyperslabs, causing them to fail in odd ways.
Solution:
Fix errors with single block hyperslabs by keying off of count==1 instead
of stride==1.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/parallel
h5committested
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Code cleanup & performance improvements
Description:
Optimize hyperslabs that are built to detect situations where "regular"
hyperslabs can be recovered from span tree descriptions.
Also, improve "same shape" routine to correctly work with all the different
combinations of selections.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
FreeBSD 4.8 (sleipnir) w/parallel
h5committested
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Code cleanup
Description:
Clean up older settings for strides of hyperslabs
Platforms tested:
h5committestted (although Fortran tests failed for some reason)
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Code cleanup
Description:
Clean up warnings exposed by compiling on O2K. Also, revert some of Bill
and my changes to the H5S_mpi_opt_types_g, etc. and settle them back into their
original location.
Platforms tested:
h5committested.
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Description: H5Sselect_hyperslab and H5Sselect_elements didn't check scalar
dataspaces.
Solution: put error detection in those functions.
Platforms tested: eirene(simple change).
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New feature/enhancement
Description:
Chunked datasets are handled poorly in several circumstances involving
certain selections and chunks that are too large for the chunk cache and/or
chunks with filters, causing the chunk to be read from disk multiple times.
Solution:
Rearrange raw data I/O infrastructure to handle chunked datasets in a much
more friendly way by creating a selection in memory and on disk for each chunk
in a chunked dataset and performing all of the I/O on that chunk at one time.
There are still some scalability (the current code attempts to
create a selection for all the chunks in the dataset, instead of just the
chunks that are accessed, requiring portions of the istore.c and fillval.c
tests to be commented out) and performance issues, but checking this in will
allow the changes to be tested by a much wider audience while I address the
remaining issues.
Platforms tested:
h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
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Update
Description:
Updated the Copyright statement
Platforms tested:
Linux (This change is only in the comments, so I just check that the
modules still compile)
Misc. update:
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New feature
Description:
Add support for scalar dataspaces in parallel I/O.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Also, FreeBSD 4.7 (sleipnir) serial & parallel
Misc. update:
Update release_docs/RELEASE for bug fixes, new features, etc.
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Bug fix
Description:
I/O using "none" selections in parallel wasn't working correctly. Also,
add serial "none" selection test.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
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Code cleanup
Description:
Add a bit more debugging information to one failure mode.
Platforms tested:
FreeBSD 4.6 (sleipnir)
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