| Commit message (Collapse) | Author | Age | Files | Lines |
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Part of: HDFFV-9086
Tested on: jam (minor change)
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Removed the configure option that allows selective disabling of individual
internal filters (fletcher32, shuffle, etc.).
This feature mucked up the code with a lot of #ifdefs, saved very little
space and was not scalable to a general scheme for library size reduction.
We've decided to remove the feature while we investigate a more general
scheme for decreasing the library size.
Fixes: HDFFV-9086
Tested on: h5committest
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Merge changes that correspond to the 64-bit ID changes (without the actual
switch to 64-bit IDs) to the 1.8 release branch. (Plus a few minor cleanups
and alignments with the trunk that aren't on the branch)
Tested on:
Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN
(h5committested on branch already for a week)
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UD plugins.
Also warning session fixes.
Tested: CMake local linux
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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)
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Fix h5repacktst (test file generating binary) to address HDFFV-8016 h5repacktst failed in AIX 32bit mode
Description:
Segmentation fault occurred when h5repacktst try to generate a dataset when
system memory is limited to 256MB.
Add error handling to display apporiate message to exit and adjust the test
dataset according to the original size which didn't causing out of memory.
Tested: test was done by limit memory in csh.
jam (linux32-LE), ostrich (linuxppc64-BE)
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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)
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Bring r22220, r22221 & r22224 from trunk to 1.8 branch: improved h5repack metadata block size testing, and some code cleanups.
Tested on:
FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode
FreeBSD/64 8.2 (freedom) w/gcc4.6, w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (koala) w/Intel compilers, w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
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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)
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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
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Bring half of r21125 from trunk to 1.8 branch:
Correct char arrays that were too small for strings defined.
Tested on:
FreeBSD/32 8.2 (loyalty) w/debug
(h5committested on trunk)
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Fix for Bug1896 h5repack - changing layout to COMPACT does not work
Description:
Merged from hdf5 trunk (r19389)
Make h5repack be able to convert a layout to COMPACT for small size dataset as default. Also add verifying layout changes in our test script.
Tested:
jam, amani
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get/set functions for progname and d_status.
Also add windows import/export declarations to functions.
Updated windows - H5pubconf.h for packed bits function
Tested:
Windows, linux
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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)
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Fix for the bug1726 - NPOESS: h5repack loses attributes for datasets of
type H5T_REFERENCE.
Description:
Merged from hdf5 trunk rXXX
Tested:
jam
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Resolve windows build issue from previous checkin r18427
Description:
The previous checkin was for bug1814 - NPOESS: h5repack doesn't handle
references to the groups as an element of a dataset
Tested:
jam
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Fix for bug1814 - NPOESS: h5repack doesn't handle references to the groups
as an element of a dataset
Description:
Merged from hdf5 trunk r18425
handles object reference to named-datatype as well.
Add test cases.
Tested:
jam
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Trim trailing whitespace from source code files, with following command:
find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//'
Tested on:
None - eyeballed only
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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)
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Bring r17953 from trunk to 1.8 branch:
Bring Coverity changes into the trunk:
r17877:
Error 266: Uninitialized memspace set to -1. Changed malloc and free to HDmalloc and HDfree. Removed unused dtype var.
r17878:
Error 265: Uninitialized mem_space set to -1. Changed malloc and free to HDmalloc and HDfree.
Error 267: Uninitialized smspace set to -1. Changed malloc and free to HDmalloc and HDfree.
r17879:
Error 242: Uninitialized aid set to -1.
Error 243: Uninitialized sid set to -1.
Uninitialized tid set to -1 for consistency
r17880:
Error 242: reinitialized aid to -1 after close to be ready for reuse.
Error 243: reinitialized sid to -1 after close to be ready for reuse.
reinitialized tid to -1 for consistency after close to be ready for reuse.
r17881:
use valgrind to check there is a memory leak. The fix is to free ptrstr in line 5838 at xml_dump_group() of h5dump.c after it is used. run the valgrind after the fix, no memory leak for that part of the code.
r17882:
Fix Coverity items 256 and 269.
r17883:
Error 222-230: initialized hid_t vars to -1 after close to be ready for reuse.
Also added H5Tclose for tid in gent_bigdims
r17884:
Bug fix (Coverity run2, view 23, dead code)
(this is pair-program done by Albert, Elena and Larry).
Confirmed and fixed the deadcode in hyperslab read branch of function
diff_datasetid.
(Discovered other bad code that diff_datasetid() should be recoded.
Bug 1693 is entered for this.)
r17906:
Fix Coverity item 260.
r17907:
262: Initialized hid_t's dtype, dtype_tmp and file to -1. Initialized H5T_t * dt to NULL.
r17908:
Fix Coverity item 261.
r17909:
Fix Coverity item 248.
r17910:
Revise fix for Coverity item 248.
r17911:
Resolved coverity issues #s 263, 162, 163, 164. All issues in dsets.c. Initialized fid and did hid_t's. filter_corrupt function was returning in the middle of an if statement, bypassing free calls. Updated error handling to free buffers and hid_t's appropriately.
r17912:
(done by Larry and Albert)
Cleanup Coverity view warnings (#231-241) about
using uninitialized variables. Initialized all
of them.
r17913:
Resolved issue 251 and 264. Initialized tid2 to -1 and initialized buffers that were freed in case of an error.
r17914:
Resolved coverity issues 66, 220, and 221:
66: Negative Return assignment ignored
220,221: Initialized hid_t's.
r17915:
Fix Coverity item 247.
r17916:
Fix Coverity item 246.
r17917:
Fix Coverity item 245.
r17918:
Fix Coverity item 244.
r17919:
Coverity Issue #84: Moved asserts in H5T_cmp to the top of the function, and converted them to HDassert. Coverity complaining about using potentially NULL pointer without checking it. Want to see if Coverity will accept Assertions as acceptable checking before using the value.
Tested on:
FreeBSD/32 6.3 (duty) w/debug
(h5committested on trunk)
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Bring r17553 from trunk to 1.8 branch:
Bring general fixes/improvements from file_free_space branch back to
trunk.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Bring r17313 from trunk to 1.8 branch:
Bring back various minor code cleanups from the file free space branch
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (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/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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bug fix: h5repack was not applying a requested contiguous layout for a dataset with filters
added a test to the C program test (not to the script), that verifies the layout and filters
tested: linux
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Description:
h5repack previously would not take named datatypes into consideration when copying
datasets and attributes. This would cause extra anonymous datatypes in the target file
at best, and cause errors halfway through the repacking at worst. h5repack should now
always handle named datatypes correctly. Named datatypes are also now converted to the
native type when -n is given.
Tested: jam, linew, smirom (h5committest)
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fix compiler error on a missing "static" declaration
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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
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#1402 (B1) h5repack does not preserve creation order indexing.
ISSUE : h5repack does not handle group creation order flags.
ACTION: call H5P(g)(s)et_link_creation_order functions when handling groups, add new groups with these flags to the test generation program, and verify results in the test program.
TEST: in the test program, function that compares property lists, added code to verify groups
DOCS: Added the note to RELEASE.txt: "h5repack now handles group creation order. PVN - 2009/4/2 - 1402".
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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
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Bring r16560 back from trunk.
Tested on:
Mac OS X/32 10.5.6 (amazon) debug & production
(Following up with tests on more platforms)
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replacing all instances with long long.
Tested:
h5comittest
fedora 10 x64
XP32, VNET
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return 2 instead of -1 on error status
Tested: windows, linux
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Add a default user block size of 1024 when none is given
add a failure condition of writing user block
Tested: windows, linux
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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...
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Together they allow a call to H5Pset_alignment to be made
-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
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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
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Summary: when using h5diff to compare the results of h5repack (or other tools that copy one HDF5 file to another), a new option is needed to allow h5diff to make an "absolute" comparison of the 2 files. This is the "contents" mode explained in the usage below.
If this mode is present, objects in both files must match (must be exactly the same). If this does not happen, the tool returns an error code of 1 (instead of the success code of 0)
Changes to the h5repack test script: the call to h5diff was changed to include -c (maintaining the previous -q).
tested: windows, linux
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scale-offset filter adding
changed the logic of the filter compare function to first compare filter type, then filter client data values (separate here in each individual case, since some filters return private filter values. Todo: handle the nbit and scale-offest cases)
tested: windows, linux
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match for each individual dataset
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
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filters
usage is to repeat the -f option
tested: windows, linux, solaris
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Changed H5Acreate2 -> H5Acreate_by_name, to be more consistent with
other new API routines.
Re-added simpler form of H5Acreate2, which creates attributes directly
on an object.
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
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Make H5Tarray_create() and H5Tget_array_dims() versioned, and drop the
"perm" parameter from the '2' versions.
Shift internal library usage to '2' versions.
Add simple regression tests for '1' versions.
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
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Add H5Dcreate to API versioned routines, replacing internal usage with
H5Dcreate2
Fix thread-safe error stack initialization for API versioned error
stack printing 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
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Put H5Acreate() under API versioning, with all internal usage shifted
to H5Acreate2().
Add regression tests for H5Acreate1().
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
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Add regression test for h5repack with userblock
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 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Add API versioning to H5Tcommit()
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 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Move H5Gunlink to deprecated symbol section, replacing internal calls
with H5Ldelete.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
Mac OS X/32 10.4.10 (amazon)
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Move H5Glink2 to deprecated routines section.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
Mac OS X/32 10.4.10 (amazon)
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