* 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.
and replace it with new url for COPYING file.
Fix 2 lines in java error test expected output file where messages
include line numbers changed by reducing the copyright header by 2
lines.
Comment added to address HDFFV-8270. The sample ontput in the
file's comments are not up-to-date with the scripts in the file
that remove output unique to certain systems when running test
scripts. This output doesn't match expected output files for
the tests, causing them to fail. Ther output_filter.sh file
removes such output. Currently we don't have access to these
systems to update the comments.
testflushrefresh.sh.in:
flushrefresh and other SWMR tests have been failing
occasionally but regularly since bringing them to the develop
branch. The logs and debugging point to unexpected deletion of
signal files as the point of failure, and John Mainzer suggests
that two such tests running simultaneously in the same directory
may lead to the operating system deleting the other test's
signal file. Running the flushrefresh test in its own directory
seems to solve the problem.
Added code to update version strings in
config/cmake/scripts/HDF5config.cmake.
release:
Added options to create CMake tar.gz and zip files containing the
HDF5 source and scripts to build and test HDF5 with cmake and ctest
by running a single command. These were previously assembled
manually.
Added a call to h5vers to set the version being released where it
occurs in files. In particular, the sub-release version string
"currently under development" was not being removed from
cpp_doc_config or HDF5config.cmake.
HDF5 develop branch. Most of the changes are for the switch from
subversion to it repositories. This copy is not used for THG daily
tests, but is available for testing on remote machines.
* commit '5aee5213190f145b5a734f5dc76a67c82f7d6b82':
emoved .gitattributes and .gitignore, as the manual migration did not create them. Corrected bbrelease script to create new release version with revision hash.
Translate svn commands to git commands for chkmanifest and bbrelease scripts with source in git repository. Removed the -p option from the command to run autogen.sh. It interfered with running chkmanifest on a machine with the correct autotools versions but without access to /usr/hdf/bin/AUTOTOOLS. The autogen.sh script says the option is for HDF group use only and is likely to be removed. The same effect can be achieved by adding /usr/hdf/bin/AUTOTOOLS to the beginning of PATH.
Removed the -p option from the command to run autogen.sh. It interfered with running chkmanifest on a machine with the correct autotools versions but without access to /usr/hdf/bin/AUTOTOOLS. The autogen.sh script says the option is for HDF group use only and is likely to be removed. The same effect can be achieved by adding /usr/hdf/bin/AUTOTOOLS to the beginning of PATH.
with running chkmanifest on a machine with the correct autotools
versions but without access to /usr/hdf/bin/AUTOTOOLS. The autogen.sh
script says the option is for HDF group use only and is likely to be
removed. The same effect can be achieved by adding
/usr/hdf/bin/AUTOTOOLS to the beginning of PATH.
Svn revisions reverted: 29341, 29326
Branch features/h5check_version was created for further development.
Files changed
test/tcheck_version.c
test/testcheck_version.sh.in
src/H5public.h
src/H5.c
config/lt_vers.am
bin/h5vers
Tested with h5committest.new
bin/h5vers:
Changed to copy the shared lib version from lt_vers.am to H5public.h
(Thanks to Larry who made the changes.)
config/lt_vers.am:
cosmetic change, nothing material.
src/H5public.h:
Changed by bin/h5vers.
src/H5.c:
Changed H5check_version() to use shared library version for compatibility
checking.
test/tcheck_version.c:
test/testcheck_version.sh.in:
Changed to use shared library version numbers instead of the HDF5 library
version numbers for testing.
Tested: tested in Jam (C only), platypus and osx1010dev (enable fortran and C++).
The current implementation for Mac OSX platform is a kludge that sometimes left behind mounted volumes.
Temporary screen out the checking of installtion_check step (so that daily test may pass).
Tested: by hand running cmakehdf5 in platypus and osx1010test.
installation.
Tried to find out what went wrong but all output files were deleted already.
Added a verbose option to display all cmake process output in order to see what
might have gone wrong. Default is on.
Using --disable-verbose will turn it off.
Tested: osx1010dev, osx1010test, playtypus.
This was giving a lot of users headaches and the parser code rarely
changes. There is now a new script (bin/genparser) which can be
run as needed.
Tested on: Ubuntu 15.10 (x86_64 Linux 4.2.0)
gcc 5.2.1, flex 2.5.39, bison 3.0.2
r27860-27883
r27892-27916
Tested on: - h5committest
- jam (parallel) fails with an existing, unrelated MPI config error
- platypus fails with due to an existing, unrelated cmakehdf5 error
where it does not recognize --enable-fortran2003.
Removes .pl extension from Perl scripts. This may be returned in the future,
but it's best to keep the script names unchanged while we merge with the
trunk.
Tested on: h5committest
The only remaining code consists of a few floating-point tests
that rely on pre-generated and checked-in VMS files. These have
been left alone, even though they will not be possible to
recreate, since testing VMS float behavior is still important.
Tested on: h5committest
Tested w/ h5committest
NOTES: - The manifest may still be messed up.
- Cmake fails since the dual binary work needs to be merged with
this repo's CMake externals.
The configure summary (libhdf5.settings) was missing from the configure output.
Solution:
Append the configure summary to the configure logfile if configure succeeds.
Tested:
hand ran cmakehdf5 in jam and inspected the logfile.
configure.ac
hl/src/H5LTparse.c
hl/src/H5LTparse.h
Address HDFFV-9010: configure issue with gcc 4.9.2 "-l ".
Change default to disable_shared on CYGWIN.
release_docs/INSTALL_Cygwin.txt
release_docs/RELEASE.txt
Update for changed default and no CYGWIN szip binary.
c++/src/cpp_doc_config
bin/h5vers
AddressHDFFV-9010: Add cpp_doc_config to h5vers
Tested with h5committest, on CYGWIN.
That broke the testings as some testfiles have zlib compressed datasets.
Added options control to enable the linking of zlib external libarary by
default and turn off the szip library linking as szip library may not be
avaiable. This matches the established settings.
Tested: run cmakehdf5 by hand in jam and platypus.
Also tested in wren but it failed in the testing stage.
Also tried "cmakehdf5 --script" in jam. It failed.
columns that are output by svn stat.
Previously, the script assumed that they would all be blank for newly-
added files. This is not always true when merging.
Part of: HDFFV-8895
Tested on: jam (bin/chkmanifest only)
calls that use a FUNC_ENTER macro that does not include parentheses.
This does not affect any source code at this time.
Part of: HDFFV-9141
Tested on: jam (bin/trace behavior only)
Updates the bin/chkmanifest script so that it parses the output
of svn commands instead of hacking at the .svn/entries file. This
will make the script more future-proof and allows it to work with
current Subversion repositories.
Tested on: jam (bin/chkmanifest only)
bin/genltanalyze script, which has been deleted. Also removed the
generated hl/src/H5LTparse.c/h and H5LTanalyze.c files.
Part of: HDFFV-9120
Tested on: Local Ubuntu VM
- Modified autogen.sh to run libtoolize.
NOTE: OS-X often uses glibtoolize. This will be fixed soon.
- Addational helpful output added to autogen.sh.
Part of HDFFV-9120
Tested on: 64-bit Linux VM
Fix cmakehdf5 so that it can figure out where the source directory is.
It expects cmakehdf5 itself resides at $srcdir/bin/cmamkehdf5.
Tested: Jam by invoking cmakehdf4 with different paths.
different language API's and testings. See "cmakehdf5 --help" for details.
Tested: jam using different combinations of option and verified correctness
by inspeacting libhdf5.settings output.
Merge 64-bit ID changes from branch to trunk. (Plus a few minor cleanups
that aren't on the branch)
Tested on:
Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN
(h5committested on branch already for a week)
The temporary directory used by zip is the same as the rest but it has to be different.
Changed tar2zip to use a different (ztmpdir) name.
Tested: by hand running "bin/release ... gzip zip md5".
Need to unify Windows release process (zip file) and Unix release process (bin/release-> tarfile)
Solution:
Added a new option (zip) to generate Windows zip file from the release tarball.
Tested: by hand running "bin/release ... gzip zip" to verify zip file looks right.
Allen and Dana then confirmed the zip file can be used to build and test HDF5
library without error.
Remove all traces of MPI-POSIX VFD and GPFS detection/code.
Remove remaining traces of stream VFD.
Remove testpar/t_posix_compliant test (it's not actually verifying anything).
Clean up H5D__mpio_opt_possible() further.
Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).
A few other small code cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
Changed to use the quick steps described in INSTALL_CMake.txt.
Previous version is available by --old.
Added a help page to explain how to use.
Added a fix to figure out the current HDF5 version and use that to find the
correct file for install. (Still need to figure out the platform name.)
Tested: Jam and Koala
The h5dump tests only looked at headers and never the data. Data reads would fail with invalid number of params (7 expected 20).
Regenerated file and replacement ddls updated.
New h5dump test will be added to read the data.
Clean up warnings, switch library code to use Standard C/POSIX wrapper
macros, remove internal calls to API routines, update checkapi and checkposix
scripts.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
Big-Endian Linux/64 (ostrich)
Bring changes from Coverity branch to the trunk:
r20612:
Changed string functions to versions with string length to fix coverity issues
922, 942 and 943.
r20614:
Use HDsnprintf. --gh
r20675:
Fix for coverity #1714 due to the fix for #810.
Use HDfree() instead of H5MM_xfree().
r20678:
Repaired coverity issue #598 -- failure to check return value from a
call to fstat(), or to tidy up in the event of failure.
r20679:
Use HDstrncpy. --gh
r20681:
Use HDstrncat and HDstrncpy. --gh
Tested on:
Mac OSX/64 10.8.2 (amazon) w/Debug, etc.
(too minor to require h5committest)
Description:
Adds 2 new API functions, H5Dscatter and H5Dgather. H5Dscatter retrieves data
from a specified callback function and scatters it into a selection, defined by
a supplied dataspace, within a supplied memory buffer. H5Dgather gathers data
from a selection within a supplied memory buffer and passes it in a contiguous
form to a supplied callback function. Added tests for these functions
Tested: jam, ostrich, koala (h5committest); ummon
