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
Avoid getting object information for soft/external links if we aren't
going to traverse across the link itself.
Tested on:
Linux/64 2.6 (chicago) w/debug & production
(h5committest coming up)
Bring r19252 & 19253 from trunk to 1.8 branch:
Bring Coverity changes from branch to trunk:
r19161:
Fixed the part for matching the subset info with dataset
r19189:
BZ1646: h5dump does not check number of dimensions for subsetting parameters against the dataset
Changed subset_t structure from holding hsize_t pointers to holding new subset_d pointers, which hold the original hsize_t pointer + len. this len is then checked against dataset ndims in the handle_dataset function of h5dump.
Changed all references to use new data structure.
Added tests for each subset parameter.
r19190:
Added new h5dump ddl files
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(h5committested on Coverity branch)
Bring r19153 from trunk to 1.8 branch:
Bring changes on Coverity branch back to trunk:
r19040:
Fixed coverity #440 - NULL check after dereference. We moved the NULL check up
into the IF block and changed it to assertion.
r19041:
Maintenance: Addressed Coverity issues 441 and 449 by initializing proper
variables
r19042:
In function H5O_chunk_protect (H5Ochunk.c):
- Initialize H5O_chunk_proxy_t pointers chk_proxy and ret_value.
- Free chk_proxy on error.
r19043:
Addressed coverity issues 442 - 448 by initializing pointers to NULL.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(Too minor to require h5committest)
Add --no-dangling-links option to h5ls.
Description:
Related to "Bug 1830 - Following an dangling external link in h5ls should set non-zero return code."
If --no-dangling-links option is specified and any dangling link is found, return exit code 1 (error).
Merged from hdf5 trunk r19051
Tested:
jam, amani, heiwa
Introduced a new feature in the tools library regarding command line parsing
In the definition of arguments, an "*" means that the switch can or can not have an optional argument. This "*" is put in the code regarding the letter definition, and it is transparent to the user (e.g b* instead of the previous b: ), where ":" notes a required argument after the letter (and no ":" or "*" notes no argument, mandatory)
Used for the h5dump binary option -b
It can be now
1) -b (defaults to NATIVE)
2) - b NATIVE
3) - b FILE
4) -b LE
5) -b BE
Note: the keyword NATIVE replaces MEMORY
This feature (-b with no argument) was tested with the sequence of h5dump to binary (NATIVE) then h5import to generate an HDF5 file from the binary file and h5diff to compare the 2 HDF5 files
Tested: windows, linux
Description: Improved external link traversal of h5dump. h5dump will now
properly avoid all cycles, even those spanning multiple files. Improvement
to the output of committed datatypes. Committed datatypes are now checked
for uniqueness (like other objects). Tests added for these cases.
Tested: kagiso, linew, smirom (h5committest)
Description:
As part of our Windows cleanup, we try to remove windows-specific tweaks in the source code. There are many instances where Windows code is introduces via ifdef's. We re-evaluate whether they are still required, and found that many of them are not. Others we change to "feature"-specific code, rather than Windows-specific.
Tested:
VS2005 on WinXP
VS.NET on WinXP
h5committest (kagisopp, smirom, linew)
Add H5Lvisit_by_name() API routine to library.
Eliminated all (five!) other group traversal routines and changed them
all to use the new API routine.
Cleaned up output of h5ls & h5stat:
- Issue error when requesting recursive traversal of a file
with the "group info" flag, but no group given
- Print info about root group in all(?) appropriate situations
- Don't print "verbose" information about root group until the
root group is in the list of objects to display
(mostly because h5ls & h5stat had a different twist on traversing the
groups in a file that the other utilities)
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Change H5Oget_info -> H5Oget_info_by_name and re-add H5Oget_info in a
simpler form for querying a particular object, to align with other new API
routines.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Change H5Literate -> H5Literate_by_name and add simpler form of
H5Literate, to bring this routine into alignment with the other new API
routines.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Make H5Dopen versioned and change all internal usage to use H5Dopen2
Add simple regression test for H5Dopen1
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Move H5Giterate() and H5G_iterate_t to deprecated symbols section,
replacing them with H5Literate and H5L_iterate_t respectively.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
AIX/32 5.3 (copper)
Solaris/32 5.10 (linew)
Mac OS X/32 10.4.10 (amazon)
Make h5dump more gracious and informative about objects it doesn't
understand.
Tested on:
Mac OS X/32 10.4.10 (amazon)
No need for h5committest - very minor
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
fixed 2 initializations of char* with HDstrdup and HDcalloc
info->prefix = HDcalloc(1, 1);
fname = HDstrdup(argv[opt_ind]);
some were exposed by compiler warnings
h5dump bug 701. Symptom: The creation of a hardlink pointing to the root group "/" causes h5dump to display it as a link pointing to itself.
Cure: the root group was not being inserted in the table that keeps track of object names and links.
Added a test for this in the test generation program, the creation of a hardlink to the root
Anti-feature
Description:
Revert changes to H5G_stat_t struct, to make it compatible with the 1.6.x
branch again. The information that was added to the H5G_stat_t struct will
be reported through other API routines.
Platforms tested:
FreeBSD 4.11 (sleipnir) w/C++
Linux 2.4/64 (mir) w/C++ & Fortran
Solaris 2.9 (shanti)
Code cleanup
Description:
Check in some of the code cleanups from working on the external link
support. (This doesn't include any of the external link features)
Platforms tested:
FreeBSD 4.11 (sleipnir)
Mac OSX.4 (amazon)
Linux 2.4
Bug fix
Description:
Correct use of H5Gget_objinfo() which recent compact group checkins
exposed: we were attempting to follow dangling soft links.
Solution:
Don't follow links for H5Gget_objinfo() when initializing object tables
for h5dump.
Platforms tested:
Solaris 2.8 w/64-bit enabled
Linux 2.4
FreeBSD 4.11 (sleipnir)
Code cleanup (sorta)
Description:
Adjust H5G_stat_t to prepare for eventual "external link" information.
This also puts the information for regular objects and soft links into more
obviously separate places.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4
Code cleanup & speedup
Description:
Refactor h5dump & related code to be considerably cleaner & faster for
files with large #'s of objects.
Platforms tested:
FreeBS 4.11 (sleipnir)
Linux 2.4
Bug fix
Description:
ph5diff had been hanging in Tflops. Found out that vsnprintf ph5diff
uses was a local coded that did not limit printing according to the size
argument. That resulted in buffer overflow and other problems.
Solution:
Added some sort of size checking in the home-grown vsnprintf and
had ph5diff checked for error return of vsnprintf. Leon also
revamped the ph5diff manager's way of handling communications with
the workers. That eliminated all but the last case of hanging.
Platforms tested:
Tflops.
Misc. update:
Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Bug fix/code cleanup
Description:
Add tests to determine that very long (64K+) object names are working.
Fixed a couple of bugs in h5dump where they weren't...
Platforms tested:
FreeBSD 4.11 (sleipnir)
Solaris 2.9 (shanti)
Purpose:
bug fix, new test file
Description:
h5dump was not properly displaying array indices > 3D
Solution:
added the same algorythm and data structure that h5diff uses to calculate the array index
from a element number position
Platforms tested:
linux
solaris
Misc. update:
bug fix
Description:
Currently h5dump test on windows won't separate error form standard output; which shows at function error_message.
A #ifdef WIN32 macro at this file make stderr to be the same as stdout on windows.
Solution:
Separate standard error from standard output.
Platforms tested:
windows xp VS 6.0(by xuan bai), no needs to test on other platforms
Misc. update:
Bug Fix
Description:
There was a problem with having a lot of groups nested together. We
could only handle 1024 characters at most, but, in a parallel program
especially, it could occur that there were lots and lots of groups
and would be more than 1024.
Solution:
I made the "objname" part of the obj_t structure a pointer instead of
a fixed size. Added code to allocate/deallocate the memory we need
for it. Had to fix how the "prefix" was being handled in the h5dump
program. It was also set to only 1024 characters in length. I made it
dynamic.
Added a test case...Go me!
Platforms tested:
Linux, Solaris
Purpose:
fixing the format of dumper output for windows test
Description:
New dumptest includes the feature that an error of the output will be put into stderr in linux
On windows, that stderr will not be redirected into the output file and the comparsion between the expected file and the dumper output is not correct.
Solution:
change fprintf(stderr .....) at h5tool_util.c into fprintf(stdout ......) so that it fits the comparison.
Platforms tested:
windows 2000
New Modules
Description:
Separated the "generic" functions out of the h5tools module into
their own separate module to make things a bit nicer to deal with.
Platforms tested:
Linux
