HDFFV-8145 h5diff slowness with version >= 1.8.7
Description:
Improved speed when comparing HDF5 files with lots of attributes. Much slower performance was identified with release version from 1.8.7 to 1.8.10 compared to 1.8.6.
Merged from HDF5 trunk r22933.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), cmake (jam)
HDFFV-8012 - h5repack changes max dims and cause failure if only "-f none" is used without changing layout for chunked dataset when a chunk dim is bigger than a dataset dim
Description:
"h5repack -f <obj>:NONE <file.h5> out.h5" command failed if source file contains chunked dataset and a chunk dim is bigger than a dataset dim.
Another issue is that the command changed max dims if chunk dim is smaller than the dataset dim.
These issue occurred when dataset size is smaller than 64k (compact size limit)
Fixed them.
Merged from HDF5 trunk r22805
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
HDFFV-8143 Provide a routine(s) for telling the user why the library broke collective data access
Description:
Added H5Pget_mpio_no_collective_cause() function that retrive reasons why the collective I/O was broken during Read/Write IO access.
Reasons to break collective I/O:
- SET_INDEPENDENT
- DATATYPE_CONVERSION
- DATA_TRANSFORMS
- MPIPOSIX
- NOT_SIMPLE_OR_SCALAR_DATASPACES (NULL Space)
- POINT_SELECTIONS
- NOT_CONTIGUOUS_OR_CHUNKED_DATASET (Compact or External-Storage)
- FILTERS
Merged from HDF5 trunk r22735, r22741 , 22743, 22744, 22763.
Tested:
jam-pp (linux32-LE), koala-pp (linux64-LE), wallaby-pp
Update RELEASE.txt
Description:
Merge changes from 1.8.9's known issues and platforms tested
section of the RELEASE.txt up to the 1.8 branch in preparation
for the 1.8.10 release.
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.
Merged from HDF5 trunk r22751.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
Convert configure.in to configure.ac.
Align TESTS usage with autotools convention.
Update all references from configure.in to configure.ac
Tested: h5committest
Address HDFFV-7942 - h5diff: incorrect result for comparing attribute data with different type size in same class
Description:
When comparing attribute data values with same type class but different size, the result was incorrect. It was due to the size difference and got truncated.
Fixed to match up the smaller type size to big type size like what dataset does.
Merged from HDF5 trunk r22684 and r22691.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), Windows (32-LE cmake), cmake (jam)
HDFFV-8107 testh5diff will fail if build/test in HDF5 source tree
Description:
This is sub-task for "HDFFV-8105 testh5diff.sh uses the wrong operator (-a) in an if statement."
From the HDFFV-8105's update, h5diff test failed if build&test is performed in HDF5 source tree because 'cp' try to copy test files to self dir.
It's addressed by skipping if cp's src dir and dest dir is same.
Also this applied for all other tools under src/tools dir.
No change to the CMakeLists.txt files because CMake cautions/demands that in-source builds be avoided.
Merged from HDF5 trunk r22617.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), some manual tests as well
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.
Merged from HDF5 trunk r22618.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), some manually repeated test performed in parallel
Description:
The test command in COPY_TESTFILES_TO_TESTDIR used the wrong operator -a which
means and. It is not sufficient to test mere existence as $tstfile could have
been a directory or other non-file things. If the file is not readable, the
$CP command would fail but its return code was not checked.
Solution:
Get rid of the test command and go ahead to $CP it and then check its returned
code and report errors if detected.
Tested; committested.
