including the merge of `hdffv/hdf5/develop`, back to the branch that Vailin and
I share.
Now I need to put this branch on a fork with a less confusing name than
vchoi_fork!
* 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.
Clean up warnings (from 2774 -> 1560, with my standard debug build)
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Bring object/dataset/group/named datatype features from revise_chunks
branch to trunk. Also CMake support for h5format_convert and a bunch of
misc. cleanups.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
Discovered when I temporarily #defined HDfree() to a more complicated
function while investigating something.
Tested on a local linux VM. This is a very minor change.
Bring changes from Coverity branch back to trunk:
r20914:
Use HDstrncpy and HDstrncat! --gh
20915:
Use HDstrncpy and HDstrncat! --gh
Tested on:
Mac OSX/64 10.9.3 (amazon) w/gcc 4.9.0, C++, FORTRAN & parallel
(too minor to require h5committest)
Brought changes from Coverity branch back to trunk, and cleaned up misc.
other warnings & formatting issues:
r20833:
Fixed Coverity 667 and 668 with real integer overflow tests this time.
r20834:
Use HDstrncpy and HDstrncat. --gh
r20835:
Change to use strncpy - use base_len + 1 for line 156, use HDstrlen(path) + 1 for line 159
r20836:
Fixed coverity 585 by casting output of fgetc() to a char.
r20837:
Changed sprintf calls to snprintf with size 1 less than the allocated buffer to address coverity issue #967.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(too minor to require h5committest)
Bring r24479 from 1.8 branch to trunk:
Fix ph5diff worker command handling so it can correctly respond to
situations where there's no work to perform. Also, a few minor code cleanups.
Tested on:
Mac OSX/64 10.9.0 (amazon) w/parallel
(too minor to require h5committest)
HDFFV-5919 - GMQS: h5diff - The number of object difference is not consistent between dataset and group/type when attribute(s) have differences
Description:
Object differences are not consistent between dataset and group/datatype when their attribute(s) have differences. This is because attribute(s) differences is not accumulated to group or datatype object’s difference, but accumulated to dataset difference.
To fix, do not accumulate attribute difference to dataset difference. This is referred to h5diff’s default behavior and also past report from users that users were confused by the accumulated behavior. (also can’t figure out only for dataset difference , also hard to spot dataset difference when it has lots of attributes or differences)
This also lead to fix inconsistent format indicating difference between dataset and group/datatype object.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
Purpose:
HDFFV-8003 - ph5diff (parallel h5diff): daily test failure on ember intermittently during non comparable test file comparison
HDFFV-7755 - parallel h5diff : hanging on koala intermittently during non comparable test file comparison
Description:
non-comparable test intermittently hung on koala and ember, but not on jam. it didn't occur until -np reaches 4 or bigger. it occurred once out of many repeated attempts of the same test.
There was a incorrectly (mistakenly?) duplicated code in MPI section which caused such hang in a certain condition. The test used more processes than other tests, which increased chance to trigger more undone processes, and such process could enter the incorrect code section and wait for wrong pair of send. it explains why it occurred intermittently according to machine condition and using a certain feature.
Removed incorrect code which blocked correct code.
Tested: some manually repeated test performed
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE)
Fix for HDFFV-7998-h5diff: incorrect behavior and output for comparing symbolic dangling links without following-symlinks option
Description:
Fix not to check and display dangling link status without --follow-symlinks option.
Berfor the fix, when comparing symbolic link to symbolic link without follow-symlinks option, h5diff followed to check if those links are dangling or not. It caused to display output incorrectly (dangling link instead of symbolic link).
The fix also improved performance when comparing lots of symbolic links without the --follow-symlinks option.
Test cases were added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
Fix for HDFFV-7644 GMQS: h5diff - incorrect behaviors when comparing HDF5 files with different type of objects (dataset, group, type) as common objects
Description:
Fixed failure for comparing same named object with different object types in comparing groups. (common object comparison)
Prior to the fix, h5diff resulted in error. After the fix, h5diff detects such case as non-comparable and display messages accordingly.
Test cases were added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
Fix for HDFFV-7837 - h5diff: incorrect behavior with exclude-path option when unique object exist only in one file
Description:
If unique objects exists only in one file and try to exclude
the unique objects with --exclude-path option, h5diff missed
excluding some objects.
Fixed to exclude objects correctly in such case.
Test cases were added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
Fix for HDFFV-7835 h5diff: incorrect result for comparing the two same type symlinks as dangling links.
Description:
When two symbolic dangling links are compared with --follow-symlinks option,
the result should be same. It works for comparing two files, but didn't work
for comparing two objects.
Test cases were added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
