* Updated source file copyright headers to remove "Copyright by the Board of Trustees
of the University of Illinois", which is kept in the top-level COPYING file.
* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - files not in src or test.
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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
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.
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
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:
Purpose: Enhancement
Description: This example writes extendible dataset and doesn't use fill value.
On some systems (verebena, titan) unwritten data will be displayed as
garbage by h5_chunk_read.
Solution: Use H5Pset_fill_value to set 0 fill value.
Platforms tested: arabica, verbena, titan
Misc. update:
Purpose:
Bug fix
Description:
All examples used "FILE" string in the #define preprocessor
directive. That caused error on Windows platforms since
FILE is a structure returned by fopen calls.
Solution:
Changed "FILE" to "H5FILE_NAME"
Platforms tested:
Linux (eirene)
----------------------
./Makefile.in
Running `make distclean' will not fail if one of the
subdirectories has already been cleaned.
./config/BlankForm
./config/irix5.3
Cleaned it up more. Added better support/documentation for
systems that have more than one compiler.
./config/alpha-dec-osf4.0 [NEW]
Added a new config file as a result of testing on Jim Reus's
machine.
./test/chunk.c
Scaled down the testing range so we can actually run it
interactively.
./tools/h5import.c
Included <unistd.h> to get rid of warning for close().
./src/H5detect.c
Seg-faults on Linux for some reason when NDEBUG is defined, so
I just undef it at the top of the source.
./test/big.c
Added a fflush().
./tools/h5ls.c
The `-d' flag now works even when `-v' isn't specified.
./examples/h5_chunk_read.c
./examples/h5_compound.c
./examples/h5_extend_write.c
./examples/h5_group.c
./examples/h5_read.c
./examples/h5_write.c
Indented according to hdf5 standards.
Fixed compiler warnings
----------------------
./configure.in
./src/H5Fprivate.h
./src/H5Fsec2.c
We now detect and use lseek64() on systems that have it (e.g.,
Irix64) and are able to generate >2GB files on Irix XFS file
systems (and anything else that supports large files). This
change also removed some warning messages from the Irix `-64'
compiler.
> $ ls -l istore.h5
> -rw-r--r-- 1 matzke meshtv 8605436856 Feb 17 14:03 istore.h5
./configure.in
./src/H5Fprivate.h
./src/H5Fstdio.h
We now detect and use fseek64() on systems that have it (e.g.,
Irix64) and are able to generate >2GB files on Irix XFS file
systems (and anything else that supports large files). This
change also removed some warning messages from the Iris `-64'
compiler.
./src/H5E.c
./src/H5Epublic.h
Added the H5E_OVERFLOW error to signal file address overflow.
./src/H5Fpublic.h
./examples/h5_chunk_read.c
./examples/h5_compound.c
./examples/h5_extend_write.c
./examples/h5_group.c
./examples/h5_read.c
./examples/h5_write.c
./html/Datasets.html
./html/Files.html
./html/H5.api.html
./html/H5.intro.html
./html/H5.sample_code.html
./html/ph5example.c
./html/review1.html
./test/cmpd_dset.c
./test/dsets.c
./test/extend.c
./test/tfile.c
./test/th5p.c
./test/theap.c
./test/tohdr.c
./test/tstab.c
./testpar/phdf5.c
Renamed file access constants to follow the naming scheme.
Also changed the base names a little to be more accurate as to
what they do. The old names H5ACC_WRITE and H5ACC_OVERWRITE
will temporarily work.
H5ACC_DEFAULT --> H5F_ACC_RDONLY for H5Fopen()
H5ACC_DEFAULT --> H5F_ACC_EXCL for H5Fcreate()
H5ACC_WRITE --> H5F_ACC_RDWR
H5ACC_OVERWRITE --> H5F_ACC_TRUNC
Albert or Kim: The H5ACC_INDEPENDENT and H5ACC_COLLECTIVE
macros in H5Fpublic.h should be an enum typedef and have names
more like H5F_MPIO_INDEPENDENT and H5F_MPIO_COLLECTIVE. Also
change the access_mode argument of H5Cset_mpio().
H5Fcreate() and H5Fopen() are more strict now about which
flags are acceptable for the operation.
./src/H5Fprivate.h
./src/H5F.c
./src/H5C.c
Changed the file access template to make it more general. A
union contains a struct for each type of low-level driver and
the default template is initialized at run-time.
./src/H5Fpublic.h
./src/H5F.c
Added H5Fget_access_template() and cleaned up
H5Fget_create_template().
./src/H5C.c
The H5Cset_mpi() no longer trashes the file access template
when an error is detected. We check for errors and *then*
update the file access template.
Added H5C_close() so Albert and Kim have a place to release
the MPI communicator and info from the file access property
list.
Kim or Albert: I notice in H5Cset_mpi() you copy the MPI
communicator. Do you need to do something similar in
H5C_copy()?
./src/H5F.c
Added more error checking for the file creation and access
property lists because it used to be possible to make the
library dump core by swapping the creation and access property
list ID numbers of H5Fcreate().
./test/istore.c
./test/tfile.c
./test/th5p.c
./test/theap.c
./test/tohdr.c
./test/tstab.c
./testpar/testphdf5.c
One must pass H5C_DEFAULT as the file creation or access
property list in order to get the default property list. It
is no longer possible to pass zero or any other arbitrary bad
object ID.
./src/H5Fcore.c
./src/H5Ffamly.c
./src/H5Flow.c
./src/H5Fmpio.c
./src/H5Fsec2.c
./src/H5Fsplit.c
./src/H5Fstdio.c
./src/H5MF.c
The file access property list is passed to all H5F_low_...()
functions and to the drivers.
./src/H5Fcore.c
The block size can be set at run time on a per-file basis
instead of at compile time across all files. The "5000 items in
a group test" now takes 1.6 seconds.
./src/H5private.h
Removed inclusion of mpi.h and mpio.h since they're included
from H5public.h.
./src/H5Cpublic.h
./src/H5C.c
Added H5Cset_stdio(), H5Cset_sec2(), H5Cset_core(),
H5Cset_split(), and H5Cset_family() in addition to the
H5Cset_mpio() that Kim and Albert already wrote. We still
need the H5Cget_driver() and an H5Cget...() counterpart for
each of those functions. The split and family drivers still
need a little work but I'm checking this in anyway.
h5_write.c - stores INT array as INT32 little endian dataset in the HDF5 file.
h5_read.c - gets info about the dataset;
reads hyperslab from the dataset in the file into
2-dim slice of the 3 dimensional array.
h5_compund.c - creates compound dataset and writes it to the file;
reads subsets of the dataset.
h5_extend_write.c - writes extendable dataset.
h5_extend_read.c - gets info about the dataset;
reads dataset and one of the chunks.
