Add "silent make" mode configure option.
Description:
Automake 1.11 has a new option available that allows for a
silent make mode. This functionality needs to be explicitly
enabled in configure.in via the use of the automake macro
AM_SILENT_RULES, which is what this commit is adding.
This introduces a new configure option:
--{en|dis}able-silent-rules
This option is on by default, and simplies compile and link
line outputs when building the library. Disabling this option
will print full "verbose" output (i.e., full compile and
linking lines for each target).
Tested:
This was tested on jam & h5committested
Fix HDFFV-4342 : GMQS: h5dump test fails when source directory is read-only
Description:
Updated h5dump test case script to prevent entire test failure upon
source code directory is read-only.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
Fixed issue HDFFV-5866 (BZ 2156). Changed scripts to run examples to use specific names for compiled executable files instead of a.out, which did not work on Cywin as it produces a.exe by default. Removed issue from known problems section of RELEASE.txt.
Tested with Cygwin 1.7.8 on Windows 7.
This line, and those below, will be ignored--
M release_docs/RELEASE.txt
M hl/c++/examples/run-hlc++-ex.sh.in
M hl/fortran/examples/run-hlfortran-ex.sh.in
M hl/examples/run-hlc-ex.sh.in
M c++/examples/run-c++-ex.sh.in
M fortran/examples/run-fortran-ex.sh.in
M examples/run-c-ex.sh.in
- Revise shared Fortran library disabling scenarios in configure
- Improve configure output summary
Description:
Shared Fortran libraries are not supported on Mac, but were being
disabled by configure in a way that also forced the C libraries
to be static-only. This has been fixed, so now only shared Fortran
is disabled while shared C can remain.
This prompted two additional changes:
1. While working on the check that addresses whether or not
shared Fortran libraries are allowed, removed old and no
longer needed check(s) that disable shared Fortran
libraries with HP, Intel 8, PGI, and Absoft compilers.
(Essentially, Mac is the only situation in which Fortran
shared are disabled by configure.)
2. Having two different states of libraries (i.e. shared C
library with static-only Fortran library) was not apparent
in the configure summary, which labeled all libraries as
either shared and/or static. I've added lines to both the
C++ and Fortran output sections to list shared/static-ness
of these libraries specifically.
Additionally, I've made sure that the new --enable-unsupported
configure option correctly overrides configure if it tries to
disable a shared library.
Tested:
jam, fred, & h5committest
Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for
--use-system-epsilon option
Description:
Merged from HDF5 1.8 branch r20369.
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)
Bug 2182 - h5ls and h5dump: update to use --enable-error-stack among tools, also update related descriptions
Description:
Decided to use --enable-error-stack long option name only to
display error stack messages from HDF5 lib among tools.
Updated to unify option name to '--enable-error-stack' for printing
HDF5 error stack messages for HDF5 tools. h5ls and h5dump for now.
For h5ls, this replaces "-e/--errors" option, which is deprecated.
For h5dump, remove -E from help page and RM , which was added by mistake
before release1.8.7.
Help page and RM got updated.
Updated test case.
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:
This is related to previous checkin r20294.
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), tejeda (mac32-LE), linew (solaris-BE)
Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the
different set of attributes (different number and names)
Description:
Previously h5diff compared attributes correctly only when two objects have
the same number of attributes and attribute names are identical.
This fix covers all other cases.
Also didn't display useful information about attribute difference.
This fixes both issues.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
Improve the previous fix for Bug 2216 - GMQS: h5diff - memory leak when
compares vlen string in dataset or attributes
Description:
Improve the fix along with the previous checkin r20266.
Add a new function to tool lib, h5tools_detect_vlen_data() which return
TRUE if include any kind of vlen data all at once, either VLEN-data or
VLEN-string and so on.
Also updated h5ls and h5dump code accordingly.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
Fixed Bug 1904 - h5ls : usage of '-a' option is not clear to display expected output
Description:
Fixed incorrect content and improved help page for -a option of h5ls.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), Cmake (jam)
Fix Bug 2120 - h5copy: improve to copy an object into same HDF file
Description:
Before the fix users can't copy an object (dataset or group) with
different name if input file (-i) and output file (-o) is same.
This feature would be useful to clone any object with different name and
reuse contents.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
Fixing Bug 2161 - GMQS: h5dump - only on Windows, skip displaying a data value every a certain lines in array type dataset
Description:
Fixed h5dump for skipping some values for long array type dataset on
Windows. This issue only occurred on Windows due to the different
return behavior from _vsnprintf() funtion.
Tested:
Windows, jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
Fixing Bug 2092 - h5dump does not display index for a dataset
Description:
h5dump skip displaying array indices every certain number when the
array type dataset is relatively big. The certain number varies
according to the size of each array.
This checkin fix the skipping array indices problem. This fix also
correct indentation of the dataset data output.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
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
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)
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!)
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)
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)
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)
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)
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
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.)
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
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.
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.
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)
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.
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
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
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
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)
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.
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.
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.
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.
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.
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
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)
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).
Tested:
jam, amani and heiwa
Change h5ls not to manipulate special characters in object name or attribute name for smart display.
Description:
Related to "But1784 h5ls has input and output issues with links that have '\' characters in them."
Tested:
jam, amani and linew
Description:
Previously, the chunk cache would, when looking for a chunk, alwaylook for the
chunk in the b-tree before checking the cache. Reworked the functions that
look up chunks to always check the cache first and avoid the b-tree lookup if
the chunk is in cache.
Tested: jam, linew, amani (h5committest)
PHDF5 changed to use "mpiexec", instead of mpirun, as the default MPI
applications startup command as defined in the MPI-2 definition, section
4.1. Note that only mpich related (using mpicc command) definitions are
changed to mpiexec. Other favors like hcc, AIX, champion, are not changed
since I don't have a way to verify them yet.
Tested:
jam and amani, using both current and new mpich.
Did not h5committested since this affects PHDF5 configure only.
Support follow symbolic links.
Description:
Add '--follow-symlinks' option to follow symbolic links (soft and external).
Update help page according to RM.
Remove some warning messages from compiler.
Tested:
jam, amani and linew
Fixed a bug (1855) in H5DSattach_scale, H5DSis_attached and H5DSdetach_scale
caused by using H5Tget_native_type function to determine the native
type for reading REFERENCE_LIST attribute. The bug was exposed on Mac PPC.
Platforms tested: juniper (Mac PPC), jam, amani, linew
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.
Tested:
jam, amani and linew
Description:
Previously, it was possible for a chunk to be flushed due to chunk operations in
the callback from H5B_iterate in H5D_chunk_prune_by_extent. Because flushing
the chunk can force it to be reallocated if it is filtered, this can change the
contents of the chunk b-tree in the middle of H5B_iterate. Because H5B_iterate
uses a locally cached copy of the b-tree, this causes subsequent operations
to be passed incorrect data. Rewrote H5D_chunk_prune_by_extent to avoid
H5B_iterate entirely.
Also fixed a bug in the dataset expand algorithm that could cause extra chunks
to be created.
Tested: jam, linew, smirom (h5committest)
Fixed a bug in the H5DSdetach_scale function when 0 bytes
were allocated after the last reference to a dim. scale
was removed from the list of references in a VL element of the
DIMENSION_LIST attribute; modified the function to comply
with the Spec: DIMENSION_LIST attribute is deleted now when no
dimension scales left attached.
Platforms tested: jam with electric fence, amani amd linew
