| Commit message (Collapse) | Author | Age | Files | Lines |
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file - src and test directories.
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header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email
addresses from library source code (still needs cleaned from other directories).
Misc. warning, style, and whitespace cleanup.
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* commit '145ef3ceee20c28a443bd11507c58858bea3f889':
more cleanup
change it back
pick up missing piece
fix unused related warnings
removed unused parameter
more fix and address comments
remove unsed var,function,macro, etc
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the message type until we've verified we understand the message type.
Reduce size of H5O_msg_class_g to *not* include space for
H5O_BOGUS_INVALID. Make bogus messages shareable. Add new bogus
message test with shareable messages to cover the formerly problematic
code. Re-run gen_bogus.c to add this test case and also to fix the
bogus_invalid messages that were no longer H5O_BOGUS_INVLAID due to a
new message class being added in a previous commit. Added comment to
remind developers to run gen_bogus.c when adding a new message class.
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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
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merge_hyperslab_updates
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merge_func_enter_vol
Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
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~DEROBINS/hdf5_der:develop to develop"
This reverts commit 4242753848c44ab3b5d226e66225eac2f64db314, reversing
changes made to b0e79fe6dd20ec7aa1b3e5f0f8b370639a4ef5bd.
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hdf5_1_10
* 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.
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improvements.
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and the tool and API wrappers will be coming in over the weekend.
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with revise_chunks changes, and remove unused "message locking" code.
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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
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Merge v3 metadata cache changes to trunk. Yay! :-)
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
Linux/32 2.6.x (jam) w/serial & parallel
(daily tested on branch)
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Clean up H5O interface, to align w/v3 metadata cache changes
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
Linux/32 2.6.* (jam) w/serial & parallel
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the arguments to be in a more logical order.
Tested on: h5committest
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Revert r25273, 25283 & 25439 (the hyperslab improvement changes). They
are buggy and it's taking me a long time to correct the problem. I'll check
in a revised form of the changes when I've got them straightened out.
Tested on:
Mac OSX 10.10.0 (amazon) w/gcc 4.9.x, C++, FORTRAN
Linux 2.6.x (jam) w/parallel
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Bring in Chao/Neil/my changes to optimize hyperslab selection operations
further, along with 3 new public API routines: H5Scombine_hyperslab(),
H5Sselect_select() and H5Scombine_select(), along with many minor cleanups to
the code and fixing a few compiler warnings.
Tested on:
Mac OSX/64 10.9.3 w/gcc 4.9.x and parallel w/OpenMPI
(h5commttest forthcoming)
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Switch propert list/class iteration from internal to external form of
iteration, cleaning up and simplifying the code a bit.
Bring other general improvements from plist_encode_decode branch back to
trunk.
Clean up many warnings.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/gcc 4.7, debug and C++ & FORTRAN
(too minor to require h5committest)
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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)
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Description:
When using the new object header format, it was possible for corruption to occur
if the first object header chunk changed size such that the lenght of the "chunk
0 size" field changed. This only occurred if there were messages that had not
been decoded. The original algorithm that changed the object header chunk size
marked all messages as dirty, causing those that had not been decoded to have
both the raw and native form invalidated. Changed the algorithm to avoid
marking messages dirty and added assertions to catch the case where messages
are dirtied without being decoded (or recently created) first.
Tested: jam, koala, ostrich (h5committest), durandal
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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
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Description:
An old patch was mistakenly committed in r21556. Replaced this fix with the
latest.
Tested: jam, koala, heiwa (h5committest)
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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
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H5O_move_msgs_forward() when writing attributes. h5committested.
Tests are checked into the performance suite.
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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
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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
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Bring r18720 from metadata journaling merging branch to trunk:
Bring changes from metadata journaling branch to 'merging' branch:
Rename H5[A]C_mark_pinned_or_protected_entry_dirty() to
H5[A]C_mark_entry_dirty() and get rid of H5[A]C_mark_pinned_entry_dirty().
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
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Add new internal object header routines to query the header chunk that
a message is in, and to lock/unlock a message into a chunk (so it doesn't get
moved into another chunk during allocation/free events).
Also, move dataspace message to beginning of object header messages
added to a dataset's object header, so it can be locked into chunk #0 (when
performing SWMR operations).
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
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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
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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
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Bring r18169 from 'merge_metadata_journaling' branch back to trunk:
Converge changes on metadata_journaling branch and trunk:
- Remove H5F_t* parameter from H5HL_unprotect()
- Remove H5F_t* parameter from H5HL_dirty()
- Remove H5F_t* parameter from H5O_unprotect()
- Bring changes to metadata caching routines back:
- H5AC_pin_protected_entry()
- H5AC_resize_pinned_entry()
- H5AC_unpin_entry()
- H5AC_mark_pinned_entry_dirty()
- H5AC_mark_pinned_or_protected_entry_dirty()
- Revise internal H5C routines to drop H5F_t* and/or H5C_t* as
parameter where possible
- Revise tests to follow internal routine changes
Also, drop file/cache pointer parameter from create/destroy flush
dependency internal cache calls.
Also, other minor changes to speedup the 'cache' test.
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 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
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Bring r18076-18096 from hdf5_1_8_coverity branch to trunk:
r18076:
Correct Coverity issue #1 by removing dead code
r18077:
Fix coverity item 142. When an error occurred while copying a linked list in
H5S_point_copy, the library would not free the partially allocated list. Added
code to free the list in this case.
r18078:
Correct Coverity issue #2 by removing impossible to reach code.
r18079:
Correct #3 by removing impossible to reach code.
r18080:
Correct Coverity issue #4 by removing impossible to reach code.
r18081:
fix coverity 26 , check (dblik->parent) before calls H5HF_man_iblock_detach().
r18082:
Fixed coverity issues 321 and 316.
321: freed sm_buf in error handling to remove resource leak.
Also set sm_buf to NULL after other instances in which
it is freed to prevent double free.
316: initialized nmembs to 0.
r18083:
Correct Coverity issue #6 by removing debugging knob from error reporting code.
r18084:
Fix coverity item 269 + others. When a error occurred in a function using the
h5tools error framework, the "past_catch" variable would not be set to true
because that statement was before the label that goto jumped to. This could
cause a failure in the cleanup section to go back to the start of the section,
freeing variables twice, etc.
Moved the label infront of past_catch=TRUE.
r18085:
fixed coverity #27, check if (heap) before use heap->obj....
r18086:
fixed coverity #28, check curr_span not null before use it at if(curr_span &&
(io_bytes_left==0 || curr_seq>=maxseq))
r18087:
Correct Coverity issue #7 by cleaning up correctly on error
r18088:
Correct Coverity #8 by removing unchanged variable checking code.
r18089:
Correct Coverity issue #9 - remove impossible to reach code.
r18090:
Correct Coverity issue #11 by removing impossible to reach code. Also clean
up some minor style issues.
r18091:
Fix coverity items 314 and 318. Changed the improper assertion of the return
value of a library function to a check, and a return(void) on failure.
r18092:
Fix coverity item 70. Changed the improper assertion of the return value of a
library function to a check, and a return(void) on failure.
r18093:
Correct Coverity issue #12 by removing dead code.
r18094:
Correct Coverity issue #16 by removing debugging code.
r18095:
Fixed coverity issue # 271.
Removed redundant checking and freeing of sm_buf1 and sm_buf2.
r18096:
Correct Coverity issue #17 by refactoring test to remove dead code.
Also, removed previous "coverity" statements in comments, we'll review
those issues again and see if we can figure them out, now that we have more
experience with Coverity.
Tested on:
Mac OS X/32 10.6.2 (amazon)
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Bring r18035 from merge_metadata_journaling branch to trunk:
More "brush clearing" convergence between metadata_journaling branch
and the 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/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
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More "brush clearing" convergence between metadata_journaling branch
and the trunk.
Tested on:
Mac OS X/32 10.6.2 (amazon) debug & prod
(h5committest not required on this branch)
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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
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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
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Description:
Some files apparently exist in the wild which have corrupt symbol table messages
on the root group. These files can be opened by 1.6 (which uses the cached
information in the superblock) but not by 1.8. This patch fixes 1.8 and 1.9 so
they can now open these files, and will correct them if necessary. Also fix
some potential (rare) problems with array datatype versions.
Tested: jam (parallel; h5committest not working on linew or smirom)
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Description:
When an attribute was created with a datatype or dataspace that was shared in
the same object header that the attribute was in, the attribute could not be
deleted. Changes made to ensure that the attribute can be deleted both when the
attribute is in the object header and when it is shared in the heap. Object
header message decode routines now take an "open_oh" parameter to enable them to
avoid opening the same object header twice.
Tested: jam, smirom (h5committest)
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Rename H5O_msg_read_real -> H5O_msg_read_oh, to be more consistent with
other routines in library.
Move H5O_msg_read_oh and H5O_msg_exists_oh from package to private
header file, so other routines in library can use them.
Tested on:
FreeBSD/32 6.3 (duty)
Too minor to require h5committest
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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)
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Bring file free space branch changes through r15795 into trunk, which
includes a fair bit of code cleanup & rearrangement along with a couple of
bug fixes also.
Tested on:
Mac OS X/32 10.5.5 (amazon) in debug mode
Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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
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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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