| Commit message (Collapse) | Author | Age | Files | Lines |
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Description:
When using the scale-offset filter with floating point data or fill values, big
endian machines would save some metadata in the wrong byte order. This caused
such datasets to yield incorrect data when read on little endian machines.
Fixed the scale-offset filter to always save this metadata in the right byte order (i.e. little endian).
Tested: jam, amani, heiwa (h5committedt); fedora, linew
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corrected.
Tested: local linux
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Tested: local linux
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Bug 2089 - GMQS: h5diff segfault on a compound dataset with fixed length +
vlen string type order
Description:
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), tejeda (mac32-LE), linew (solaris-BE)
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Add "--enable-unsupported" configure flag.
Description
The "--enable-unsupported" configure flag allows a user to
prevent configure from failing due to the use of incompatible
options, such as c++ with parallel.
Specifying --enable-unsupported will bypass all of configure's
checks for incompatible and unsupported combinations of flags.
There are no guarantees that the library will be configured
in any sort of working condition, but that's the risk of
using the --enable-unsupported flag.
I've changed all default error messages related to unsupported
option combinations to indicate that using --enable-unsupported
will allow configure to complete without error.
Tested:
by hand on jam, tested all unsupported configure option
combinations with and without the new flag, making sure
the flag allows configure to finish without error.
(h5committest wouldn't do any good here; it won't test
the new option, and since we're enabling unsupported
combinations, failures are likely to occur in build or
tests with --enable-unsupported turned on anyways.
That's why they're unsupported!)
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Add additional error checking to catch erroneous user input.
Description:
Attempting to retrieve a links's name by index in the case
where the link is external and the file that the object is
located in doesn't exist was causing a segmentation fault
(in production) and an assertion failure (in debug).
The segfault wasn't occuring until the metadata accumulator
attempted a write, so I've added error checking higher in
the pipeline in H5O_protect (where there was previously just
an assert) to catch this. I've also added additional asserts
in the H5F layer where there were none.
Additionally, I added another case to the links.c test to
test that this fails gracefully instead of segfaulting or
asserting out.
Tested:
h5committest and gandalf (mac os x)
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Improve h5diff performance.
Description:
The following changes for improving h5diff performance:
1) use HDmemcmp() before comparing each elements
(memcmp() is very fast at both linew and jam)
2) replace the expensive H5Tequals() calls
3) retrieve datatype information at dataset level not each element level
for compound datasets
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
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Fixed Bug# 1979 Output from h5ls -rdlS on nested compound datatypes is
difficult to parse.
Description:
Update to add curly brackets for the nested compound members, when
S (--simple) option is used with -l (--label), so user can tell
which members blong to which compound type.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32)
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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.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (Mac32)
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Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.
Description:
Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed.
Tested:
jam, amani, heiwa
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Backout the previous changes (r19598):
(Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.)
Description:
Some failure occurred on talwit, so backout the changes and will put it back
after the fix.
(Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. This is expected to be failed.
Merged from hdf5 trunk r19598.)
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Fix for bug# 2040 - h5copy should fail gracefully for expected failure copying to non-exist nested group without -p option.
Description:
Fixed h5copy to fail gracefully when copying object to non-exist group without -p option. Expected to be failed.
Tested:
jam, amani, heiwa
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compilers; set default to -O for all
unknown versions of the C Intel compilers.
Modified apple config file to display Intel compiler information.
Updated RELEASE.txt notes accordingly.
Platfroms tested: jam, amani and dubna (Mac 64-bit) with Intel C, Fortran and C++ compilers.
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unresolved issues - r19441 and 19467.
Bug 1707 is that H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with
the 1.8 library to compile.
I created a branch off the trunk called set_auto to continue working on the problem.
Tested on jam - backing out, simple.
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Description:
Library versions 1.6.3 and earlier contain a bug which causes them to be unable
to perform certain operations on a group if that group's symbol table
information is not cached in the parent group's symbol table. Versions 1.8.0
to 1.8.5 did not cache this information. Modified library to cache this
information.
Tested: jam, amani, heiwa (h5committest)
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application uses -DH5_USE_16_API with the 1.8 library to compile. The cause is from the mismatch of H5Eprint1 and H5Eprint2 set
through H5Eset_auto. I changed the union in the structure H5E_auto_t. Another change is to
make H5Eget_auto fail if H5Eset_auto is called to set the printing function. I'll write a
document for it.
Tested on heiwa, jam, and amani.
The property change in configure.in, config, and Makefile.am came from the merge of the 1.8
library change.
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Also added section on CPack.
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Add --exclude-path option
Description:
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 and heiwa
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Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object
Description:
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, heiwa
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Fix for Bug1896 h5repack - changing layout to COMPACT does not work
Description:
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, heiwa
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file pointer
Description:
The fractal heap header structure keeps a pointer to the file associated with
it. However, it is possible for that file pointer to be closed while the
header is still in cache (through the shared file pointer). Previously, the
header's file pointer was not updated and subsequently pointed to an invalid
file structure. Modified fractal heap code to update the file pointer every
time the header is accessed.
Tested: jam, linew, amani (h5committest)
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Add windows threads support to HDF5.
Description:
Added calls to the windows threads library to the H5TS layer, and wrapped
most calls to either pthreads or windows threads library with portable
H5TS-style defines. Modified tests to use portable function definitions
as well.
This can be configured via CMake with the HDF5_ENABLE_THREADSAFE
option, and should work on windows vista and later operating systems.
Tested:
h5committest, plus threadsafe with pthreads on jam and amani,
and tested on a Windows Vista VM with threadsafe using windows threads.
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couldn't close (bug 1260). The fix releases all resources and closes
the dataset but returns a failure.
Tested with h5committest - jam, heiwa, amani.
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be set. This is to avoid
H5Eclose_stack clearing the default stack. Please see bug 1799.
Tested on jam - simple change.
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I added a new byte order
H5T_ORDER_MIXED specifically for compound types and its derived types. They report mixed
orders if they have members of different orders.
There is no change to configure.in, config, and Makefile.am in the top directory. They have
some property changes when I merged the code from 1.8.
Tested on jam. I tested the same change for 1.8 with h5committest.
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types with some restictions:
1. For enum type, members shouldn't be defined yet.
2. H5T_ORDER_NONE only works for reference and fixed-length
string.
3. For opaque type, the order will be ignored.
4. For compound type, all restrictions above apply to the
members.
I'll change H5Tget_order and do another commit.
There is no change to configure.in, config, and Makefile.am. There is some property change for
these files when I did a merge from 1.8.
Tested on jam. But I tested the 1.8 on heiwa, and amani.
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should return htri_t not
herr_t. To minimize the change of the library's behavior, in the function
H5Z_prelude_callback of H5Z.c, if the return value of can_apply is FALSE and
the filter is MANDATE, this function returns a FAILURE. If the return value is FALSE
but the filter is OPTIONAL, this function returns a SUCCEED. During the IO, the filter
will fail and return a size of zero. But the pipeline will skip this filter.
Tested the same change for 1.8 on jam, linew, and amani. Tested on jam with szip.
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HDF4-to-HDF5 tools. The tools became
a part of the h4h5tools distribution long time ago, but the INSTALL file
was not updated in the development branch and slipped into 1.8 releases and current trunk.
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Description:
In certain circumstances, the direct I/O driver did not perform correctly when
data was unaligned. The driver has been patched to fix this. Also added some
potential performance improvements for the unaligned case, and strengthened the
test for whether the data needs to be aligned.
Tested: cobalt
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Tested: Local Linux
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Description:
A bug introduced in 1.8.5 causes local heap data blocks to be mis-aligned when
sizeof_offsets + 2*sizeof_lengths is not a multiple of 8. In this case, the
address of the data block as stored in the heap prefix is aligned but the actual
data block is not. This causes files created with these sizes to be corrupted,
and prevents uncorrupted files with these sizes to be unreadable. Modified
local heap code to account for alignment.
Tested: jam, amani, linew (h5committest)
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Changed the use of mpirun to mpiexec which is the MPI-2 official standard.
INSTALL_parallel:
Also bring in previous update of Red Storm support.
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