Bring r22171 from trunk to 1.8 branch:
Bring "merge committed datatypes during H5Ocopy" feature from branch to
trunk. (Also has some minor bugfixes with it)
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug
(h5committest coming up)
STDIO VFD fixes (HDFFV-7917). Mainly Windows correctness issues (propagated from the SEC2 VFD and the old Windows VFD) and issues where large files are accessed.
Tested on:
64-bit Mac OS-X
64-bit Windows 7
jam
koala
ostrich
Merge fix for HDFFV-944 (r22149) from trunk to hdf5_1_8.
(Also reran bin/reconfigure which updated trace information
for the two new MPI functions for getting/setting atomicity
in src/H5Fmpi.c)
Tested:
h5committest
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#.
Merged from HDF5 trunk 22176.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
Purpose: Fix HDFFV-7762
Description:
When copying an object with attribute creation order tracked, the attribute
creation order was not copied correctly to the destination file, causing an
error if the creation order was also indexed (due to attempting to insert
duplicate keys) or incorrect creation orders otherwise. Fixed to copy the
creation order correctly.
Also fixed the attribute character set not being copied, and fixed an issue
where an attribute opened with H5Aopen (or similar, but not by_idx), from an
object using the latest format but without creation order being tracked, would
always report the creation order as 0 (and marked as valid).
Tested: jam, koala, ostrich (h5committest), durandal
when it fails to allocate memory. I didn't add any test to the test suite since there is no good way to test it. But I tested and verified the error stack by hand.
Tested on jam - this is a merge from the trunk.
The parser mistaked "-" as substraction. I fixed it and also fixed another problem
with some special cases like 100-x and 2/x. This is a merge from the trunk.
Tested on jam, koala, and ostrich.
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#.
Merged from HDF5 trunk r22114.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
Purpose: Fix rare corruption bug (HDFFV-7879)
Description:
When using the new object header format, it was possible for corruption to occur
if the first object header chunk changed size such that the lenght of the "chunk
0 size" field changed. This only occurred if there were messages that had not
been decoded. The original algorithm that changed the object header chunk size
marked all messages as dirty, causing those that had not been decoded to have
both the raw and native form invalidated. Changed the algorithm to avoid
marking messages dirty and added assertions to catch the case where messages
are dirtied without being decoded (or recently created) first.
Tested: jam, koala, ostrich (h5committest), durandal
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#.
Merged from HDF5 trunk r22038.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
Bring r22053 from trunk to 1.8 branch:
Correct corner case for creating a contiguous dataset with a zero-sized
dataspace, when the allocation time is set to early.
Also clean up a few compiler warnings in the dataspace code.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug & parallel
Task for HDFFV-7862 - Select data by chunk direction to improve performance in h5repack
Description:
h5repack sometimes became very slow when handling big chunked datasets in
certain cases. (when chunk boundary doesn't match with a hyperslab boundary.)
The main issue was from figuring out a hypeslab without considering chunk
boundary to read from and write to such datasets.
The update was made to figure out a better hyperslab unit with considering
chunk boundary to improve performance for such cases prior to the update.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows
Merge 1.8 and h5dump/tools and tests based on tools library from trunk.
Reduced warnings.
HDFFV-7949:
Remove duplicated functions in h5ls
Tested: local linux,h5committest
Fix for HDFFV-7836 h5diff: displays error stack message for comparing the two dangling symlink with follow-symlinks option
Description:
While ago, to improve performance, skipping same object checking
(h5tools_is_obj_same()) was added.
However the checking function doesn't understand about the dangling link and
caused the issue.
Since handling dangling link code section already implemented, move the
checking function after handling dangling-links to address the problem.
Test was 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-7840 h5repack: memory leak over one of the h5diff test file
Description:
Turned out that there were two causes of memory leaks.
1. for handling variable length string in attribute.
2. for handling compound type with non-reference members.
The first issue is fixed in copy_attr() which is updated to use h5tools_detect_vlen to take care of vlen string as well as vlen data.
The second is fixed in copy_refs_attr() of compound handling code.
Merged from HDF5 trunk r21869.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
Fix for HDFFV-7838 h5ls: segfault for handling region reference in attribute with -v option
Description:
Segfault occurred when h5ls access region reference data in an attribute.
This didn't occurred when -v option was used.
The cause was "h5tool_format_t info;" struct variable members were accessed
without proper values were assigned (was NULL), so printf failed later in the code.
Merged from HDF5 trunk r21865.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), , cmake-Windows (32-LE)
