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)
Fix for HDFFV-7993 - h5repack fails with error "chunk size must be <= maximum dimension size for fixed-sized dimensions"
Description:
Fixed a failure when change the chunk size of a specified chunked dataset with unlimited max dims.
Also took care of converting to contiguous and compact from the dataset.
Test cases were added and tagged with jira#.
Merged from HDF5 trunk r22277.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), Windows (32-LE cmake), Cmake (jam)
Bring r22180, r22181 and r22214 from trunk to 1.8 branch:
Add new "metadata block size" command line option ('-M <x>' or
'--metadata_block_size=<x>') for h5repack.
[With release managers blessing]
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug)
(h5committest upcoming)
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-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)
HDFFV-5932 - h5repack breaks files with dimension scales
Description:
- Fixed h5repack to update values of references(object and region) of
attributes in h5repack for 1) references, 2) ARRAY of references,
3) VLEN of references, and 4) COMPOUND of references.
- Merged from HDF5 trunk 21393, 21382, 21386, 21389. (support Peter)
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)
Bring r20061 from trunk to 1.8 branch:
Bring changes from Coverity branch to trunk:
r19930:
Fix memory leaks involving VL attributes in h5repack and h5diff. The buffers in
copy_attr and diff_attr were not checked for the presence of a vlen before being
freed, and vlen storage was never reclaimed. Added checks and calls to
H5D_vlen_reclaim().
r19933:
Purpose: Fix memory leak in H5L_move_cb()
Description: H5L_move_cb copied the source link using H5O_msg_copy() but freed
it manually using H5MM_xfree(). Since H5O_link_copy allocates the link using
H5FL_MALLOC, this causes the link to be allocated from the free list but is
never put back on the free list when it is freed. This prevents the link free
list from shutting down properly. Modified H5L_move_cb() and H5L_move_dest_cb()
to free the link properly using H5O_msg_free().
r19973:
Fix resource leaks by freeing string created by HD5f2string
r19974:
Issue #345: Inialize buf variable to null
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(h5committested on Coverity branch)
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 r18650 from trunk to 1.8 branch:
Bring back various minor tweaks & cleanups from the revise_chunks
branch.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
(h5committested on trunk)
Bring r17980 from trunk to 1.8 branch:
Bring Coverity changes into the trunk: (also other minor cleanups)
r17955:
Fix Coverity item 24. Add missing error condition to
H5AC_ext_config_2_int_config.
r17956:
Fix Coverity item 24. Improve error checking in H5A_compact_build_table_cb.
r17957:
Fix Coverity item 150. Fix warning in H5A_compact_build_table_cb.
r17958:
Fix Coverity item 117. Fix error handling in H5B_shared_new.
r17959:
Fix Coverity item 209. Added an assertion for leaf->shared in
H5B2_cache_leaf_dest.
r17960:
Fix Coverity item 208. Added an assertion for internal->shared in
H5B2_cache_internal_dest.
r17961:
Fix Coverity item 89. Reworked the code to avoid array overrun in
H5C__autoadjust__ageout__insert_new_marker.
r17962:
Fix for coverity Resource_leak 195,203,204,205.
r17963:
Fix Coverity item 44. Prevented potential NULL dereference in H5D_btree_debug.
r17964:
Fix Coverity issues #197, 198 & 199: memory not being released. (Also
clean up other resource leaks in nearby and/or similar code).
r17965:
Fix Coverity issue #151: release resources on error
r17966:
Fix Coverity issue #187: Remove leftover code remnant from prior bugfix
which was causing resource leak of open files.
r17967:
Fixed Coverity issues # 193 & 194. Removed unnecessary memory allocation and
added comparison of length of path parameter to the size of the destination
buffer in h5import.h/h5import.c.
r17968:
Fix Coverity item 144. Fixed memory leak on error in H5D_chunk_copy.
r17969:
Fix for coverity Resource_leak #196.
r17970:
Coverity 167-173:
Initialized pointer of buffers.
In error handling, closed types and free memory.
Tested on:
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
(h5committested on trunk)
note : lots of weird warnings of the type
../../../../hdf5/tools/h5repack/h5repacktst.c:3919: warning: will never be executed
appear on the same code as 1.9 for the 1.8 branch
tested: linux
Bug fixes: change the options block size variable from int to hsize_t, to match the H5Pset_userblock call,
do not print print compression ratio when the requested filter is NONE
Tested: windows, linux
Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Tested on:
Mac OS X/32 10.5.5 (amazon)
No need for h5committest, just whitespace changes...
-t T, --threshold=T Threshold value for H5Pset_alignment
-a A, --alignment=A Alignment value for H5Pset_alignment
2) bug fix
the printing of the dataset name was not done for references (verbose mode)
tested: windows, linux
Add a userblock to an HDF5 file during the repack. The user gives
give a filename and userblock size as command line parameters to
h5repack and the contents of that file are stored in the
userblock for the HDF5 file created by h5repack.
New flags to handle this -u and -b
Tested : windows, linux
Following the new feature of h5repack to allow multiple filters for all datasets and the new function has_filters that checks if the repacked file has all the filters requested, I added a new function
has_filters_obj
that does the same for each dataset. The previous function that checked this only ckecked if the user input filters were in the output dataset. This new function does this but checks if the filters are exactly the same. Currently the behavior of h5repack is to delete all filters that are present in the input file (dataset) and replace them with the requested ones, so they must match exactly.
We might consider adding other logical operations, like keep the existing ones.
Additionally , the function also checks if the filter parameters match.
While doing this I noticed that for the shuffle filter , the values returned do not match and also the same for the N-bit and scale-offset
The new function that checks for the filter values fails then, and so I commented the h5repack tests that do this for the N-bit and scale-offset filter (previously for the same bug on the shuffle filter I added special code on the compare filter function but this is temporary until I find the issue)
tested: windows, linux, solaris
Minor tunings to output verbose messages:
1)when there is not a filter request do not print a message saying the filter was not apllied when the dataset was too small
2) avoid printing the message that has a list of objects to modify when there is none
Tested:linux
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.
Add "use the latest format" support for dataspace object header encode/
decode routines and clean up format a bit for the latest format (new to 1.8.x
releases)
Remove storing 'perm' parameter for array datatypes in memory and the file,
and add test to make certain that if any user applications are attempting to
store them, we get some reports back. (Should be unlikely, since the RefMan
says that the parameter is not implemented and is unsupported).
Carry those changes into the tests, etc.
Clean up a bunch more compiler warnings.
Tested on:
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/32 2.4 (heping) w/FORTRAN & C++
Linux/64 2.4 (mir) w/enable-1.6-compat
Code cleanup
Description:
Trim trailing whitespace in Makefile.am and C/C++ source files to make
diffing changes easier.
Platforms tested:
None necessary, whitespace only change
bug fix
Description:
h5repack was not dealing with family files
Solution:
use the toolslib function h5tools_open to open the file instead of H5Fopen in h5repack
Platforms tested:
linux
solaris
AIX
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/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
new feature
Description:
added a check that the chunk size must be smaller than pixels per block in SZIP request
prints a message and exits, if not met
Solution:
Platforms tested:
linux
aix
solaris
Misc. update:
bug fix
Description:
the option CHUNK:NONE (remove chunking ) was not setting the layout to contiguous
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
h5diff and h5repack changes
Description:
h5diff
introduced the following four modes of output:
Normal mode: print the number of differences found and where they occured
Report mode: print the above plus the differences
Verbose mode: print the above plus a list of objects and warnings
Quiet mode: do not print output (h5diff always returns an exit code of 1 when differences are found)
h5repack
added an extra parameter for SZIP filter (coding method)
the new syntax is
-f SZIP=<pixels per block,coding>
(pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN')
Example of use:
./h5repack -i file1 -o file2 -f SZIP=8,NN -v
updated usage messages, test scripts and files accordingly
Solution:
Platforms tested:
linux
AIX
solaris
Misc. update:
bug fix, new feature
Description:
fixed bug in the parse function:
cases where we have an already inserted name but there is a new name also
example:
-f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
dset1 is already inserted, but dset2 must also be (it was not)
added a CHECK_SZIP symbol to enable/disable checking of library related szip parameters
added the print of the filter name in verbose mode (confirms visually that the filter was applied )
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
h5repack changes
Description:
there were some requests to change some minor h5repack features
h5repack only made a warning about a non available filter in verbose mode ( -v )
without -v it kept silent, and users sometimes missed this warning
the request was that it should print this warning always. so, the new format, is e.g
./h5repack -i test_szip.h5 -o out.h5
Warning: dataset </dset_szip> cannot be read, SZIP filter is not available
due to this, and to avoid a lot of these messages in the shell test script, I modified
the script h5repack.sh so that it detects the presence of all filters in the environment
(previously it only detected SZIP)
the test files were also divided in more files , to make the script code easier to
follow
Solution:
Platforms tested:
linux
AIX (no szip)
solaris (no szip, no gzip )
Misc. update:
Purpose:
HDF5 now supports SZIP with no encoder.
Description:
SZIP can be configured to have both encoder and decoder or just to have the decoder. HDF5 can now query the configuration of any filter, and will throw errors if users try to write using a filter with encoding disabled.
Solution:
Added H5Zget_filter_info function, changed API for H5Pget_filter and H5P_get_filter_by_id. See SZIP RFC.
Platforms tested:
Copper (fortran, C++, parallel), Sleipnir (C++), Arabica (fortran, C++), Verbena (fortran, C++)
Misc. update:
bug fix
Description:
the routine for reading the options from a file had the "old" parse syntax
Solution:
Platforms tested:
linux
solaris
AIX
Misc. update:
new tests for h5repack
Description:
added more tests both to the test program and shell script that test
a variation of different filter converssions
Solution:
Platforms tested:
linux
Misc. update:
