and replace it with new url for COPYING file.
Fix 2 lines in java error test expected output file where messages
include line numbers changed by reducing the copyright header by 2
lines.
More warning cleaups: down to 770 warnings (from ~940) in 134 files (from
148), with 28 unique kinds of warnings (from 31).
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial & parallel
(h5committest forthcoming)
H5S recursive functions where an aliased pointer was
incorrectly set too early.
Tested on: Ubuntu 15.04 (Linux 3.19 x86_64) w/ gcc 4.9.2
serial and parallel (w/ MPICH 3.1.4)
changes will be merged more carefully so we can more easily
identify any errors that arise.
Tested on: Ubuntu 15.04 (Linux 3.19 x86_64) w/ gcc 4.9.2
serial and parallel (w/ MPICH 3.1.4)
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
Revert changes to pass file pointer to selection serialize/deserialize
routines. Also patch back in some changes that were merged out in the
previous merge w/trunk.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial
(h5committest not required on this branch)
numbers of elements selected, incorrect "slice" through limited dimensions,
incorrect number of printf substitutions.
Patch source selection space extent with bounds of selection if extent is
unknown before returning via H5Pget_virtual_srcspace.
Write updated VDS dataspace to file when it changes due to unlimited selections.
Other minor fixes/cleanup.
Tested: ummon
Revise dataspace encode/decode routines to make them work better with
future virtual dataset feature.
Tested on:
Mac OSX/64 10.10.2 (amazon) w/serial
(h5committest forthcoming)
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
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)
view objects. The addition of view objects in the fastforward project
is expected to be brough into the trunk sometimes in the future, which
is why we need to make this change.
Tested Manually on Jam and Ostrich.
Tested with h5commitest - Koala with intel compilers failed, but nothing had to do with those changes.
error on Koala: error while loading shared libraries: libirng.so
Changes resulting from Klocwork static analysis tool, from Mark Miller
@ LLNL (miller86@llnl.gov).
Tested on:
Mac OS X/64 10.7.4 (amazon) w/debug, C++ & FORTRAN, using gcc 4.7.x
(too minor to require h5committest)
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)
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
Bring "shape same" changes from LBL branch to trunk. These changes
allow shapes that are the same, but projected into dataspaces with different
ranks to be detected correctly, and also contains code to project a dataspace
into greater/lesser number of dimensions, so the I/O can proceed in a faster
way.
These changes also contain several bug fixes and _lots_ of code
cleanups to the MPI datatype creation code.
Many other misc. code cleanup are included as well...
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 debug 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 r18672 from metadata journaling "merging" branch to trunk:
Mostly changes to move to only using one 'user data' parameter for
calls to H5AC_protect(), along with some minor reformatting code cleanups.
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
Bring Coverity fixes back from branch to trunk:
r18336:
Fix coverity issues 275, 276, 277, 323, 432, 433, and 434
r18337:
Fix Coverity issue #106: release free space section node on error
r18338:
Fixed Coverity #94 - In H5P_register, new_class wasn't closed when there's an
error after it's created.
r18339:
Fix Coverity #185 - In test_conv_str_1, BUF wasn't freed when there's an error
in this function.
r18340:
Correct error in r18337 that wasn't releasing indirect fractal heap block
early enough.
r18341:
Close nodes if any failed in the middle of allocating new nodes. Coverity 140
and 141
r18342:
Correct [another] problem w/r18337.
r18343:
Fix coverity items 185, 20, and 21.
r18344:
Fix Coverity 213 - In H5FD_family_close, the double pointer file->memb was
dereferenced without NULL checking
(We believe).
r18345:
Fix Coverity issue # 210; removed NULL check after pointer dereferenced in
H5HFdblock.c. Also assigned NULL to pointer in H5Pint.c to fix segmentation
fault.
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,
in production mode
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)
Bring revision 16278 back from revise_chunks branch:
Update layout information in DCPL to unify all information in one
underlying property and switch to using H5O_layout_t for storing it, which
simplifies things considerably.
Also, fix many compiler warnings.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(Original patch tested on many machines)
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
Correct the prototype for H5Sselect_elements() to take an 'hsize_t *' for
the coordinates, instead of 'hsize_t **'.
Tested on:
Mac OS X/32 10.5.1 (amazon)
- Extracted common code from H5D_select_read/H5D_select_write into single
routine (H5D_select_io) and made H5D_select_read/H5D_select_write
"gateway" routines, passing I/O buffer to operate on in "op" struct.
- Create optimized pathway in H5D_select_io for I/O operations on single
elements.
- Make "get linear offset of first element" callback for each type of
selection (used in "optimized pathway", above)
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
- Remember # of elements in file selection, instead of querying more than
once
- Handle building chunk map for single element as special case
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
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
Description: Removed PABLO from the source
Solution:
Platforms tested: arabica with 64-bit, copper with parallel,
heping with GNU C and C++ and PGI fortran (but
I disabled hl, there is some weird problem only
on heping: F9XMODFLAG is not
propagated to the Makefile files
Misc. update:
Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
Code cleanup
Description:
Clean up almost all warnings from Windows builds.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
Code cleanup & minor optimization
Description:
Re-work the way interface initialization routines are specified in the
library to avoid the overhead of checking for them in routines where there is
no interface initialization routine. This cleans up warnings with gcc 3.4,
reduces the library binary size a bit (about 2-3%) and should speedup the
library's execution slightly.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/gcc34
h5committest
Code cleanup & optimization
Description:
Remove old structures that used a union to store information about the
dataspace extent and just store the information directly in the dataspace
extent itself.
Remove ifdef'd references to permutation ordering in dataspaces. We'll
definitely need more than this code if/when we implement this feature.
Change allocation of dataspace information from calloc() to malloc().
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
Code optimization
Description:
Revised dataspace selections to use a more "object oriented" mechanism
to set the function pointers for each selection and selection iterator. This
reduces the amount and number of times that dataspace selection info has to
be copied.
Additionally, change hyperslab selection information to be dynamically
allocated instead of an inline struct.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.10 (sleipnir) w/parallel
Too minor to require h5committest
Code optimization
Description:
Expand the use of macros to inline trivial function pointer lookup and
calls to reduce the overall number of functions invoked during normal operation
of the library.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir) w/parallel
Too minor to require h5committest
Code optimization
Description:
Move the element size for the selection into the selection iterator instead
of always passing it as a parameter.
Also, eleminate another 64-bit multiply for "all" selections.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
Code optimization
Description:
Stop straddling the line and always use elements instead of bytes to
determine how how I/O to perform on a selection.
Platforms tested:
Solaris 2.7 (arabica)
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
Code cleanup
Description:
Clean up compiler warnings, especially the 'FUNC' variable not used which
comes out in production mode.
Solution:
Had to add a new FUNC_ENTER_NOAPI_NOINIT_NOFUNC macro for those non-API
functions which don't need the 'FUNC' variable defined. (This will be _so_
much easier when C99 is standard on all our supposed platforms, since it has a
__FUNC__ macro... )
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor for h5committest (although there were lots of files changed, the
change was minor in each one)
