Description:
Applied the typo fixes from user's report.
The previous pull request couldn't be merged because it was too old,
and it was too complicated for me to resolve conflicts.
Platform tested:
Linux/64 (jelly) - very minor
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
Complete revamp of package initialization/shutdown mechanism in the library.
Each package now has a single init/term routine.
This new way should avoid packages being re-initialized during library
shutdown and is also be _much_ more proactive about giving feedback for
resource leaks internal to the library.
Introduces a new "module" header file for packages in the library
(e.g src/H5Fmodule.h) which sets up some necessary package configuration macros
for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly
modified version of this header, src/H5FDdrvr_module.h)
Also cleaned up a bunch of resources leaks all across the library and tests,
along with addressing many warnings, as I encountered them.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
Linux/64 3.10.x (kituo) w/serial & parallel
Linux/64 2.6.x (ostrich) w/serial
Description:
When copying an object with attribute creation order tracked, the attribute
creation order was not copied correctly to the destination file, causing an
error if the creation order was also indexed (due to attempting to insert
duplicate keys) or incorrect creation orders otherwise. Fixed to copy the
creation order correctly.
Also fixed the attribute character set not being copied, and fixed an issue
where an attribute opened with H5Aopen (or similar, but not by_idx), from an
object using the latest format but without creation order being tracked, would
always report the creation order as 0 (and marked as valid).
Tested: jam, koala, ostrich (h5committest), durandal
Bring "merge committed datatypes during H5Ocopy" feature from branch to
trunk. (Also has some minor bugfixes with it)
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug
(h5committest coming up)
Refactor function name macros and simplify the FUNC_ENTER macros, to clear
away the cruft and prepare for further cleanups.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
Description:
H5Ocopy could get confused when copying a named datatype containing an
attribute which used that named datatype as its datatype. This happened
because H5Ocopy would recurse into the attribute's datatype before the object
the attribute was in was fully copied (i.e. before the "post-copy" pass).
Modified H5Ocopy to avoid recursing before the post-copy step in this case.
Required many changes, including to how non-committed shared messages are
copied.
Tested: jam, koala, heiwa (h5committest); durandal
Bring Coverity changes back to trunk:
r20340:
Address coverity issue 248. Set freed pointer to NULL if realloc fails, then check for NULL before attempting to close array of handles stored in memory addressed by pointer.
r20341:
Added initialization udata.path = NULL; udata.visited = NULL; to prevent unintialized use after done: label.
Do C-style initialization AFTER all variable definitions.
r20342:
Fix valgrind error in H5DUMP-XML-tall.h5
r20343:
Addressed Coverity issue 591 - check the return value of H5S_SELECT_ITER_RELEASE.
r20344:
Added initialization udata.path = NULL; to prevent uninitialized used after done: label
r20347:
Purpose: Fix memory leak in overhead.c
Description: Fixed leak in test() in overhead.c where array "had" was never
freed.
r20348:
Addressed Coverity issue 705 - added prototype for resize_configs_are_equal to cache_common.h.
r20392:
Purpose: Fix coverity issues 1677 and 1678
Description: Added return value checking for 4 funciton calls in
H5tools_get_symlink_info().
r20394:
Purpose: Fix coverity issues 1674 and 1675
Description: Modified H5Epush2() and H5E_printf_stack() to keep track of whether
va_start() has been called, and to call va_end() at the end if so.
r20395:
Should be H5MM_calloc(count * sizeof(void*)). Fixed --gh
r20396:
Should be H5MM_calloc(count * sizeof(void*)). Fixed. --gh
Tested on:
Mac OSX/32 10.6.7 (amazon) w/debug & production
(h5committested on branch)
Bring changes from Coverity branch to trunk:
r19975:
Fixed potential mem leak at H5O_attr_open_by_name
r19980:
Fix coverity issue 792.
Free tmp_env_prefix in H5Lexternal.c line 365 if it is not NULL but its contents are 0 when it goes out of scope.
r20039:
Eliminate warnings about nested extern and implicit declarations of parallel_print and address Coverity defects 712-781 by #including h5tools_utils.h in h5diff_array.c, h5diff_attr.c, h5diff_dset.c and h5diff_util.c.
r20046:
Purpose: Address TOCTOU warnings in h5jam and h5unjam
Description: Coverity is afraid that the state of the input file could change
between the call to stat() and the call to open(). This is called a time-of-
check time-of-use (TOCTOU) vulnerability. Modified stat calls to fstat which
uses an open file pointer so it (hopefully) won't complain any more.
r20047:
Addressed coverity issues 135-137, 462-464. Local pointers that needed to be freed in case of error were moved out of a switch statement in src/H5Tnative.c, set to NULL, and checked before freeing.
Tested on:
Mac OS X/32 10.6.6 (amazon) w/debug & production
(h5committested on Coverity branch)
Bring changes on Coverity branch back to trunk:
r19040:
Fixed coverity #440 - NULL check after dereference. We moved the NULL check up
into the IF block and changed it to assertion.
r19041:
Maintenance: Addressed Coverity issues 441 and 449 by initializing proper
variables
r19042:
In function H5O_chunk_protect (H5Ochunk.c):
- Initialize H5O_chunk_proxy_t pointers chk_proxy and ret_value.
- Free chk_proxy on error.
r19043:
Addressed coverity issues 442 - 448 by initializing pointers to NULL.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(Too minor to require h5committest)
is shared now. The only situation that requires copying the data is when the metadata cache
evicts and reloads this attribute. The attribute structure will be different in that
situation.
Tested on jam.
Commit metadata tagging framework.
Description:
This check-in contains a new framework whose goal is to apply
a tag value to each new entry in the metadata cache as it is created.
This tag value is such that it relates each piece of metadata to the
HDF5 object that it belongs to (dataset, group, et cetera).
This changeset includes the framework that applies the tags as
well as a suite of tests to verify correct tag application, though does
not yet make use of the tag values to flush/evict individual objects.
Please refer to the "flush/evict individual objects" RFC for further
discussion of these changes.
Tested:
jam, amani, linew (h5committest)
liberty, abe, blue print
Remove the size parameter from H5[A]C_unprotect() and the
H5[A]C__SIZE_CHANGED_FLAG, switching all clients & tests over to using
H5[A]C_resize_entry appropriately.
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/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) 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-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Increment reference count on object header when "fake" object header
chunk proxy is returned from H5O_chunk_protect(). Also, clean up the
interface to H5O_chunk_unprotect by removing the unnecessary 'oh' parameter.
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/default API=1.8.x,
w/C++ & FORTRAN, w/threadsafe, in debug mode
Linux/64-amd64 2.6 (amani) 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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Bring r18542 from metadata journaling "merging" branch to trunk:
Bring new object header pin/unpin & protect/unprotect routines and
split-out object header chunk proxy changes from metadata_journaling branch to
"merging" branch, along with some other minor tweaks to clean up compiler
warnings, etc.
Also: clean up chunk protect/unprotect calls when allocating or freeing
space in a chunk, optimize metadata accumulator code to avoid some re-reading
of information from the file, refactor H5O_pin/H5O_unpin from way they are done
on the merging branch back to way they were previously done on trunk, other
minor code cleanups, etc.
Tested on
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/64-amd64 2.6 (amani) 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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.3 (amazon) in debug mode
Mac OS X/32 10.6.3 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Bring r18030 from merge_metadata_journaling branch to trunk:
Bring "brush clearing" changes (whitespace & style issues, mostly) from
metadata_journaling branch to the "merging" branch, to converge the trunk and
the metadata_journaling branch.
Also, some other minor cleanups along the way.
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/default API=1.8.x,
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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Bring "brush clearing" changes (whitespace & style issues, mostly) from
metadata_journaling branch to the "merging" branch, to converge the trunk and
the metadata_journaling 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 (jam) w/PGI compilers, w/default API=1.8.x,
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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Finish refactoring v2 B-trees so that they can have client callback
context provided to the encode/decode callbacks.
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/default API=1.8.x,
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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Remove old shim H5B2 routines from refactoring, rename new routines to
old routine names and switch all users of the H5B2 interface back to the old
routine names now that the switch to using the more current open -> <operation>
-> pattern is used for all the H5B2 code. This is the final change before
adding a context to the H5B2 client encode/decode callbacks.
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/default API=1.8.x,
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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Switch a bunch of misc. places in interfaces that were already
converted to use the refactored v2 B-tree routines to use the refactored v2
B-tree routines.
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/default API=1.8.x,
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 debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
#1585). I changed it to undefined and let the caller functions decide the location
of the datatype. For H5Tdecode, it should mark the datatype as in memory. For other
callers like H5Dopen or H5Aopen, they should makr it as on disk.
Tested it on jam, smirom, linew.
Clean up (i.e. remove) more internal calls to H5E_clear_stack(), along with
some other minor code cleanups.
Tested on:
Mac OS X/32 10.5.6 (amazon)
(too minor to require h5committest)
file handles.
Description:
An attribute's "oloc" field which specifies the file it resides in was located
in the attribute's "shared" structure. So when an attribute was opened multiple
times all of the handles for that attribute pointed to the same file id, even if
different file id's were used to open the different handles for the attribute.
The "oloc" has been moved to the top level H5A_t struct.
Tested: jam, smirom (h5committest)
Description: When attempting to copy an object with a message shared in its own
object header, the library attempts to protect the same object header twice.
Previously, it was possible for the object header to be protected with write
access in one or both of these protects, which would be illegal. The library
should now always protect with read only access in this case. The conditions
for fixing incorrect datatype versions have been made weaker to support this
change. The version will only be corrected if the object header the datatype
is in is modified.
Tested: jam, smirom (h5committest)
Description: Fixes a possible datatype id leak that could occur during compound
datatype conversion, or more precisely, when unregistering those conversions.
Datatype ids normally registered by the library are no longer visible to the
application via H5Fget_obj_ids and H5Fget_obj_count.
Tested: kagiso, linew, smirom (h5committest)
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...
datatype versions are encountered.
Description: The library now recognizes some problems with datatype versions in
H5O_decode_helper(), and, if not performing strict format checks, automatically
corrects them. Framework added for other message decode routines to
automatically correct file errors. Datatype version information added to
h5debug.
Tested: kagiso, smirom, linew (h5committest)
the file didn't have the data. It happened because each handle had its own
object structure, and the empty one overwrote the data with fill value. This is
fixed by making some attribute information like the data be shared in the
attribute structure.
Tested on smirom, kagiso, and linew.
Add H5Aexists and H5Aexists_by_name API routines, to match H5Lexists.
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
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Refactor H5HF_size() size statistics code for fractal heap to conform to
how the rest of the fractal heap routines work.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.10 (amazon)
Rename H5A_get_version() to H5A_set_version() and actually set the
attributes version in the routine.
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Fix bug where the version of an attribute would change after it was
created, causing the amount of space used to encode it to change.
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
Various code cleanups and refactor recent changes for h5stat to fit
into the existing library data structures better.
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
