h5diff issues "unable to read attribute" error message when comparing
two files
Description:
h5diff did not handle attributes of variable length strings
correctly. It created the wrong memory type if one but not both
compared attributes are of the variable strings type. It ended in
H5Aread() failure.
Solution:
We decided to treat the case when one type is variable length string
and the other is not as incomparable. That bypassed the above error.
We still need to figure out the proper way, if possible, to compare
variable string with non-variable string types.
Tested: h5committested plus tested in Swallow (OS X 10.8).
HDFFV-7643 - h5diff - incorrect exit-code returns for extra attribute exist
Description:
h5diff: Fixed to return correct exit code 1 when detect unique
attribute. Prior to this fix, h5diff returned exit code 0 indicating
two files are identical.
Merged from HDF5 trunk r23304.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE), emu (solaris-BE), Windows (32-LE cmake), cmake (jam)
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)
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)
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#.
This merged from HDF5 trunk r22319.
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#.
Merged from HDF5 trunk 22176.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), 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#.
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)
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)
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)
HDFFV-7770 - h5diff segmentation fault on JPSS files
Description:
Fixed segfault over non-comparable attribute with different dimention or
rank, along with '-c' option to display details.
Merged from HDF5 trunk r21658.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows, Cmake
HDFFV-7693 - h5diff produces different behavior between versions: 1.8.3 and 1.8.6
Description:
There were two issues on this.
One was not displaying all the comparable objects if non-comparable
object/attribute exist and compared before comparables ones. This issue
occurred after 1.8.4 release. This is the issue from user.
The other issue was not displaying all the comparable attributes,
if non-comparable object/attribute exist and compared ahead. This issue
were exist even before 1.8.4 release. So it's possible some attribute
comparison may have not displayed correctly in the past, if non-comparable
data were exist in common object.
Fixed h5diff to display all the comparable object and attribute regardless
of non-comparables.
Merged from HDF5 trunk r21396 and r21397.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam, Windows)
Merged from HDF5 trunk r21237.
Add test cases for HDFFV-7656 - "--delta=something" considers two NaN of the same type are different.
The fix was added (r21105) before but test cases were incorrectly added and missing for cmake script.
Tested:
jam (linux32-LE), koala (linux64-LE), tejeda (mac32-LE), cmake (jam)
Merged from HDF5 trunk r21105
Fixed two bugs:
- h5repack: h5repack failed to copy dataset if the layout is changed from c
hunked with unlimited dims to contiguous. (PC -- 2011/07/15)
- h5diff: "--delta" option considers two NaN of the same type are different
, which is wrong based on http://www.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Diff. (PC -- 2011/07/15)
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
Work for HDFFV-7600 - GMQS: h5diff - argument options -d, -p and --use-system-epsilon should be mutually exclusive.
Description:
Merge from HDF5 trunk r21072.
Fixed h5diff to display instructive error message and exit with 1
when mutually exclusive options (-d, -p and --use-system-epsilon)
are used together.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
- HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects
Description:
Merged from HDF5 trunk r20676.
Fixed:
1) adding h5tools_is_obj_same() function to check if two given IDs or paths point to the same object. This function can be very useful for other tools and applications.
2) using h5tools_is_obj_same() at h5diff() and diff() in h5diff.c. If two paths point to the same object, there is no need to check the details of the object since we know there is no difference. The fix will increase the performance by skipping the content comparison. It also fixed the problem of reporting difference for some cases of comparing the same file, e.g. empty files or files with incomparable objects the same file.
Test update:
Updat prvious test cases (171, 172, 530) affected by this fix, so they
still perfrom originally intended testing without bypassing.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for
--use-system-epsilon option
Description:
Fixed h5diff for --use-system-epsilon option: the calculation changed
from ( |a - b| / b ) to ( |a - b| ). This was decided for better
performance and was corrected only in HDF5 trunk, so 1.8 got updated.
Also comments for equal_XXX() function were updated correctly.
Also help page and RM got updated correctly.
Also add test cases for testing the differences w/wo the option.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the
different set of attributes (different number and names)
Description:
Merged from HDF5 trunk r20334.
This is related to previous checkin r20299.
Add help page update for verbose option level feature, which displays
useful information about attribute difference with -v1, --verbose=1 -v2
or --verbose=2 option.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the
different set of attributes (different number and names)
Description:
Merged from HDF5 trunk r20294
Previously h5diff compared attributes correctly only when two objects have
the same number of attributes and attribute names are identical.
Also didn't display useful information about attribute difference.
This fix covers all other cases.
This fixes both issues.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE)
Bug 2089 - GMQS: h5diff segfault on a compound dataset with fixed length +
vlen string type order
Description:
Merged from HDF5 trunk r19892.
This is fix for the segfault when h5diff compares a compound dataset with
combination of fixed length string types and vlen string types in certain
orders. Optimized vlariable length string handling codes. The fix is
referred from h5dump handling vlen strings.
For testing, several compound datasets were added with various combinations.
Previous failed cases:
- Vlen string, Fixed length string, Vlen string, Fixed length string
- Fixed length string, Fixed length string, Vlen string, Vlen string
- Fixed length string, Vlen string, Fixed length string, Vlen string
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), linew (solaris-BE)
Fixed h5diff to handle variable-length strings in a compound dataset
correctly. Also variable-length string array in a compound dataset.
Bug #1989.
Description:
Garbage values were displayed when h5diff compared variable-length
strings (or string array) in a compound type dataset.
Merged from hdf5 trunk r19712.
Tested:
jam (linux32-LE), heiwa (linuxppc64-BE)
Update help page for exclude-path feature.
Description:
Merged from hdf5 trunk (r19491).
Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19406)
Tested:
jam, linew
Fix for group comparison with exclude-path case. Use relative path.
Description:
Merge from hdf5 trunk (r19443)
Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19407)
Tested:
jam, amani
Add extra test cases for Bug1975 h5diff - support recursive comparison on group when specified as an object
Description:
Merged from hdf5 trunk (r19409)
Additional tests for combination of group recursive and --follow-symlinks
with multi-linked external links with several files (same name/strucure).
Tested:
jam, amani, heiwa
Add --exclude-path option
Description:
Merged from hdf5 trunk (r19406).
Specified path to an object will be excluded from comparing the two files or two groups. If group is specified all the member objects will be excluded.
Related to "1890: h5diff excluding object for file comparison via command line"
Tested:
jam, amani
Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object
Description:
Merged from hdf5 trunk (r19400).
Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly.
Tested:
jam, amani
Rename '--follow-links' to '--follow-symlinks'
Description:
The '--follow-links' option is to follow symbolic links (soft and external).
Make the name more intuitive and specific to the feature.
Merged from hdf5 trunk r18873.
Tested:
jam
Work for bugzilla 1754: h5diff: support comparing through links.
Description:
merged from hdf5 trunk (18164, 18165, 18166, 18167, 18170, 18266, 18273)
Tested:
h5committest (jam, amani and linew)
Additional fix relted to the fix of bug1672.
Description:
The fix of bug1672 caused some changes of output which required modifying
some test cases. After some discussion, restoring the changes of the test
cases was decided. After many experiments for the solution, this fix was
made so the code which improved performance can stay.
Tested on Jam.
Fix Bug1672 - Display garbage value on LE machine for BE data.
Description:
Casuing by calling diff_dataset twice when -r or no option was given.
Change to call it once which fix the problem.
It also improves the performance. (diffing time in half)
According further test, it also occurred on BE machine as well and it
seems occruing only with the BE data attached to Bugzilla.
Don't know how the file was created. Anyway this fix will prevent
from diffing with garbage values in similiar potential case.
Tested on:
linux32 (jam) , linux64 (almani), solaris (linew)
" Use "--use-system-epsilon" for system EPSILON
" Use "-p" or "-d" for whatever user's choice of epsilon
" Use "-p 0" or "-d 0" for strict equality (same as default)
1. #1501 (B1) tools bug if dataset is larger than H5TOOLS_BUFSIZE limit.
ISSUE : the tools use the following formula to read by hyperslabs: hyperslab_size[i] = MIN( dim_size[i], H5TOOLS_BUFSIZE / datum_size) where H5TOOLS_BUFSIZE is a constant defined of 1024K. This is OK as long as the datum_size does not exceed 1024K, otherwise we have a hyperslab size of 0 (since 1024K/(greater than 1024K) = 0). This affects h5dump. h5repack, h5diff
SOLUTION: add a check for a 0 size and define as 1 if so.
TEST FOR H5DUMP: Defined a case in the h5dump test generator program of such a type (an array type of doubles with a large array dimension, that was the case the user reported). Since the written file commited in svn would be around 1024K, opted for not writing the data (the part of the code where the hyperslab is defined is executed, since h5dump always reads the files). Defined a macro WRITE_ARRAY to enable such writing if needed. Added a run on the h5dump shell script. Added 2 new files to svn: tools/testfiles/tarray8.ddl, tools/testfiles/tarray8.h5. NOTE: while doing this I thought of adding this dataset case to an existing file, but that would add the large array output to those files (the ddls). The issue is that the file list is increasing.
TEST FOR H5DIFF: for h5diff the check for reading by hyperslabs is H5TOOLS_MALLOCSIZE (128 * H5TOOLS_BUFSIZE) or 128 Mb. This makes it not possible to add such a file to svn, so used the same method as h5dump (only write the dataset if WRITE_ARRAY is defined). As opposed to h5dump, the hyperslab code is NOT executed when the dataset is empty (dataset is not read). Added the new dataset to existing files and shell run (tools/h5diff/testfiles/h5diff_dset1.h5 and tools/h5diff/testfiles/h5diff_dset2.h5 and output in tools/h5diff/testfiles/h5diff_80.txt).
TEST FOR H5REPACK: similar issue as h5diff with the difference that the hyperslab code is run. Added a run to the shell script (with a filter, otherwise the code uses H5Ocopy).
FURTHER ISSUES: the type in question ("double") has a different output cross platforms (e.g on liberty some garbage number is printed at some array locations)
SOLUTION: defined an "int" type for this test. However the printing of such an array has a bogus output at least in one platform (FreeBsd), so eliminated the test run altogether and filed a bug report on this
Bug fix: for compound types, the not comparable test for members was not done
Solution: for compound types, recursively apply that check
Two new cases are added
1) the compound type has a different number of members. Message printed is
<obj1> has X members <obj2> has Y members
Where X and Y are the number of members of each compound type being compared
2) the compound type has not comparable types (for example a double and an int at the same index)
In this case the message
Comparison not possible: object1 is of class1 and object2 is of class2
Is replaced with
Comparison not possible: object1 has a class1 and object2 has a class2
Modified the test generator program to have these 2 cases
Added a shell run for these 2 cases
Tested: h5committest
bug fix
a new line was not inserted at the end of output, causing diff to complain between linux and frebsd
tested: linux (freebsd tested on the trunk)
#1368 (E1) h5diff: implement "not comparable" messages. Implemented RFC. The new option is <-c, --compare List objects that are not comparable>
added some test cases
tested: windows, linux
