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
Add bug fixes for Tools.
Description:
Added list:
1726 - NPOESS: h5repack loses attributes for datasets of type H5T_REFERENCE
1814 - NPOESS: h5repack doesn't handle references to the groups as an
element of a dataset
1817 - h5copy fail to copy dangling link by specifying link path directly
1793 - h5ls on a non-existent file gives 0 return code
Tested:
no, just text update.
Fix memory leaks
Description
Added a routine to free memory which addresses a memory leak
when variable length strings are used as fill values.
Tested:
h5committest and valgrind (on jam/amani) to confirm freed memory.
Added notes about
+ PropList::PropList(id) pclass id/plist id
+ new DataSet::getInMemDataSize
+ CommonFG::getLinkval and CommonFG::getComment take default values
+ bugzilla 1061
+ read/write methods of DataSet and Attribute
Improve configure's large-file support control.
Description:
Modified configure to now attempt to add defines necessary for
supporting largefiles on all systems, instead of solely on linux. This
is in response to user requests to enable largefile support on Solaris
by default, as well as to give extra control on AIX (instead of just
jamming the necessary flag into the config files).
The old --enable-linux-lfs flag has been removed in favor of the
--enable-largefile flag (enabled by default), which can be used on all
platforms.
On systems where large files cannot be supported in this manner,
configure will report as such.
Tested:
h5committest
AIX (NCSA's blue_print machine)
duty, liberty, and linew.
Autotool Upgrade / Libtool Bug Fix
Description:
Updated autotools referenced in bin/reconfigure as follows:
Autoconf 2.64 --> Autoconf 2.65
Automake 1.11 --> Automake 1.11.1
Libtool 2.2.6a --> Libtool 2.2.6b-mcg
The referenced libtool version is a custom version of 2.2.6b. It
has been tweaked to fix a bug in libtool that occurs
when using PGI 10.0 compilers. A check incorrectly categorizes
the C++ compiler as version 1.0 instead of 10.0, and the link
line is subsequently set up incorrectly and fails to compile.
A patch has been made available and will be included in the next
release of libtool, but in the meantime I've applied the patch to a custom
installation as indicated above. This bin/reconfigure now references
the custom installation, and the resulting configure script will correctly
categorize the PGI 10.0 C++ compiler.
Ran bin/reconfigure to regenerate configure and makefiles.
Tested:
jam and amani with PGI 10.0 compilers.
h5committest
Description:
Attempting to copy an object with NULL references (all bytes zero) with the
H5O_COPY_EXPAND_REFERENCE_FLAG flag set would cause a failure or an assertion
(depending on whether it was in debug mode). Changed copy routine to detect
NULL references (object and region) and avoid attempting to expand the reference
in this case.
Tested: jam, linew, amani (h5committest)
Description:
Modified algorithm for extending a dataset with early allocation so it only
deals with the new chunks. Formerly, it would loop over all chunks, checking
to see if each existed in cache and on disk, causing major performance issues
with large numbers of chunks.
Tested: jam, linew, amani (h5committest)
Description:
The core file driver previously matched files only based on the name used to
open them, even when a backing store is used. This caused problems in the
failing test when it traversed an external link to itself, and did not recognize
that it was the same file. Similar tests in links.c were skipped when the core
file driver was used. The failure was previously masked by inappropriate file
flushes caused by external link traversal. Added code to the core file driver
to keep track of low level file information of the backings store to allow for
accurate recognition of duplicate files. Also re-enabled all links.c tests for
the core file driver.
Tested: Fedora (core and sec2 drivers; no time for full commit test, will
monitor daily tests)
Description:
Support for expanding external links was not implemented in H5Ocopy, even though
a flag existed for H5Pset_copy_object to enable this. This patch implements
this feature.
Tested: jam, amani, linew (h5committest); Fedora
Description:
Previously, the library would reopen the source file when traversing an external
link if unable to find the target file otherwise. This has been corrected.
Also moved the call to H5F_flush from H5F_try_close to H5F_dest, so the file is
only flushed when the last identifier for the file is closed. This prevernts
situations where the library could attempt to flush a file with protected
metadata.
Tested: jam, amani, linew (h5committest); Fedora
bugzilla 1754: h5diff: support comparing through links.
Description:
Fix incorrect (or hanging) behavior in parallel mode when specifying
invalid combination of command options.
(ex: -v and -q , --no-dangling-links without --follow-links)
Add relate test case
Update h5diffgentest.c due to add test files this and previous time
Note:
svn #18266 (prior to this)
svn #18164 (original check-in)
Tested:
h5committest (jam, amani and linew)
bugzilla 1754: h5diff: support comparing through links.
(original check-in svn revision #18164)
Description:
fix the hang issue in parallel mode when compare external-link.
add --no-dangling-links option.
add test cases (#450-#459) relate to the new option.
improve test script to check exit code.
update --help relate to the new options.
correct some indentations.
Tested:
h5committest (jam, amani and linew)
Description:
In certain cases, removal of an object in a v1 b-tree would cause the leftmost
key in the right neighbor to be overwritten. While this did not pose a problem
for group b-trees, with chunked datasets it would overwrite the offset value
of the neighbor's leftmost child, causing corruption. Reworked the code to
differentiate between b-trees whose children are fundamentally associated with
their left key and those who are associated with their right key.
Tested: jam, linew, amani (h5committest)
