* 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.
More warning cleanups, bringing the build down to 25 unique types of
warnings, with 550 warnings in 122 files (down from 28, 770, and 134).
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial & parallel
(h5committest forthcoming)
Clean up many mismatches between malloc/free and H5MM_malloc/H5MM_xfree
in the library and tests (and use of H5free_memory and H5Dvlen_reclaim). Also
make H5Ocopy use a private version of H5Lexists, which doesn't internally
throw (and suppress) errors when an object (or the path to it) isn't found in
the destination.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
Fix tests accordingly and fix misuse of hbool_t in various places
Fix initialization of H5Pgcpl/ocpl structs in property decoding routines
Tested on:
Linux/32 (jam)
Linux/64 (platypus)
Linux/PPC64 (ostrich)
MacOSX/64 10.11
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
The only remaining code consists of a few floating-point tests
that rely on pre-generated and checked-in VMS files. These have
been left alone, even though they will not be possible to
recreate, since testing VMS float behavior is still important.
Tested on: h5committest
Merge 64-bit ID changes from branch to trunk. (Plus a few minor cleanups
that aren't on the branch)
Tested on:
Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN
(h5committested on branch already for a week)
functions that return library-allocated memory. The test and tool
code were modified to use this new function where it's appropriate.
Fixes HDFFV-7710, HDFFV-8519, and HDFFV-8551
Tested on:
64-bit Windows 7 w/ VS2012
32-bit LE linux w/ parallel and fortran (jam)
32-bit LE linux w/ fortran and C++ (jam)
Prep work for adding a memory free function, part of HDFFV-8551.
Tested on:
32-bit LE linux (jam)
* with C++, Fortran
* with thread safety on
These are minor changes (almost entirely renaming foo functions
to HDfoo) that don't change functionality. This should not
require a full commit test.
Clean up warnings, enable new compiler warning flag(s) and bring back
changes from Coverity branch:
r20813:
Remove the dead code as listed for coverity bug #1722. h5committested.
r20814:
Issue 69: Check return value and throw error if negative return. Also free datatype id on error
r20815:
Use HDstrncpy. --gh
r20816:
Replaced one last HDstrcat call with HDstrncat to resolve coverity issue 832.
r20817:
Use HDstrncpy and HDstrncat. --gh
r20818:
Purpose: Fix valgrind issues with h5jam
Description:
Modified h5jam to free strings strdup'd in parse_command_line before exit. Note
that they may still not be freed in case of error, due to the widespread use of
exit().
r20819:
Issue 80: change loop to use int as loop index.
r20820:
Maintenance: Fixed the bug found by coverity CID 788
There were two problems with this function:
1) it tried to unnecessary free NULL pointer
2) it tried to allocate c_name buffer that is done by H5Pget_class_name
Tested on:
Mac OSX 10.8.4 (amazon) w/gcc 4.8.1, C++ & FORTRAN
(too minor to require h5committest)
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)
Further patches for Jira 7638, to ensure that H5D/Aget_type will
be attached to the correct top file. (This change to the library should
reverted when Jira 7638 is finally finished)
Tested on:
FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode
FreeBSD/64 8.2 (freedom) w/gcc4.6, 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 (koala) 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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Mac OS X/32 10.6.8 (amazon) in debug mode
Mac OS X/32 10.6.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Check in ugly version of fix for Jira #7638. I'm going to leave the issue
open in Jira and when the library has been refactored to use shared file
pointers (instead of top file pointers) for file operations, I'll uncomment
the check in src/H5Oshared.c
Tested on:
Mac OS X/32 10.6.8 (amazon) w/debug
(too small for h5committest)
data, overflowing values are retained. When conversion happens, the values become -1. The conversion function puts -1
when overflow happens. I added two new dataset transfer property to control whether to fill 0xff in the destination
data or convert to the destination data when overflow happens. The two new functions are H5Pset(get)_enum_conv_overflow. I also added test cases in enum.c and dtypes.c.
Tested on jam, koala, and heiwa.
Correct several problems with compound datatypes that don't have any
fields added:
- Change assertion to error report when a file is encountered which has this
situation.
- Added check to attribute creation to avoid creating attributes with a
datatype like this (datasets and named datatypes already have the check)
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, w/threadsafe, in production mode
Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
Clean up a few compiler warnings and style issues in/near recent changes.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(too minor to require h5committest)
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.
Close out various resource leaks and usages of uninitialized memory that
were flagged by valgrind. [There's still some more valgrind warnings, but
it's better now... :-/ ]
Also clean up warnings and code formatting.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & valgrind
(h5committest forthcoming)
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.
Bring revisions from Coverity branch back to trunk:
r19044:
Coverity #449 - Line 1560 called function H5O_chunk_protect for 2 pointers to allocate. But when there's failure on the second one, the first wasn't freed
(H5O_chunk_unprotect). We fixed it by freeing the pointers when an error happens.
r19045:
Fixed coverity issue # 319. Free sec_node in done if it is not NULL.
r19046:
Add intended but missing assignments to initialize pointers to NULL (coverity issue fixes).
r19049:
Hdf5_1_8_coverity branch was recreated from hdf5_1_8 branch in revision 18839 without fix for Coverity issue #84 having been propagated to the hdf5_1_8 branch. This revision adds the fix again.
r19060:
added parentheses to see if they will keep subversion from getting confused
r19061:
Fix coverity item 139. Fixed incorrect condition for freeing buffer on error.
Fix coverity items 20 and 21. Removed unused NTESTS facility from dtypes.c.
Cleanup in H5Shyper.c.
r19062:
Fix coverity item 450. Check to see if chk_proxy has been allocated before
attempting to free it.
Fix coverity item 454. Check to see if allocation of buf failed in
H5D_fill_refill_vl.
Fix coverity items 455-457. Initilize hid_t's to -1, check their value before
attempting to close them, and check if the close failed.
r19063:
New fix to address coverity issue #84. Check that pointers in H5Z_xform_find_type are not NULL before passing them to H5T_cmp.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(Too minor to require h5committest)
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 Coverity fixes from 1/22/10 session to trunk:
r18137:
219: Initialized hid_t to -1 and added close to error block.
189-191: Initialized line to NULL and added free line, and close fp to error block.
r18138:
19: Moved code block for printing that the number of enums is empty to the error block. (Would never have been executed otherwise)
r18139:
Fix coverity item 58. Moved code related to displaying the parent of a repeated
group to the else(isRoot) section, as the root group has no parent.
r18140:
218: Initialized ret_value variable to -1. Because of throw Exception in default case of switch, the coverity problem would not have executed anyway. Good pratice is to initialize variables.
r18141:
Fix coverity item 92. Added code to H5E_register_class to free cls in case of
an error.
r18142:
Fix coverity item 91. Added code to H5E_create_msg to free msg in case of an
error.
r18143:
fixed issue 14,
took away "if" and used #ifndef_xxx.
r18144:
Fix coverity item 110. Added code to H5Eget_minor to free msg_str in case of
an error.
r18145:
fixed coverity #18 removed "aligned", it is always NULL.
r18146:
Fix coverity item 109. Added code to H5Eget_major to free msg_str in case of
an error.
r18147:
Fixed coverity #81 and #82, Check for bad pointer(s), but can't issue error, just leave
r18148:
Fix coverity item 97. Added code to H5FD_fapl_open to free copied_driver_info
in case of an error.
r18149:
Fix coverity item 96. Added code to H5FD_dxpl_open to free copied_driver_info
in case of an error.
r18150:
Fix Coverity issue #29: Protected cache_ptr dereferences with "if(pass)"
block
r18151:
Fix coverity item 93. Added code to H5FL_fac_init to free factory and new_node
in case of an error.
r18152:
Fix coverity items 98 and 99. Added code free allocated space in case of
error.
r18155:
124: Freed head pointer before jumping to done. There was no error handling block and normal exit used same path out.
120-123: Freed list of lists in error handling block.
r18156:
Fix coverity issues 179, 180, 181, 182, 183, 184, 186, 320, 407. These were resource leak issues where allocated memory was not freed, generally in the case of tests that failed.
Tested on:
Mac OS X/32 10.6.2 (amazon) debug & production
Bring Coverity changes into the trunk: (also other minor cleanups)
r17955:
Fix Coverity item 24. Add missing error condition to
H5AC_ext_config_2_int_config.
r17956:
Fix Coverity item 24. Improve error checking in H5A_compact_build_table_cb.
r17957:
Fix Coverity item 150. Fix warning in H5A_compact_build_table_cb.
r17958:
Fix Coverity item 117. Fix error handling in H5B_shared_new.
r17959:
Fix Coverity item 209. Added an assertion for leaf->shared in
H5B2_cache_leaf_dest.
r17960:
Fix Coverity item 208. Added an assertion for internal->shared in
H5B2_cache_internal_dest.
r17961:
Fix Coverity item 89. Reworked the code to avoid array overrun in
H5C__autoadjust__ageout__insert_new_marker.
r17962:
Fix for coverity Resource_leak 195,203,204,205.
r17963:
Fix Coverity item 44. Prevented potential NULL dereference in H5D_btree_debug.
r17964:
Fix Coverity issues #197, 198 & 199: memory not being released. (Also
clean up other resource leaks in nearby and/or similar code).
r17965:
Fix Coverity issue #151: release resources on error
r17966:
Fix Coverity issue #187: Remove leftover code remnant from prior bugfix
which was causing resource leak of open files.
r17967:
Fixed Coverity issues # 193 & 194. Removed unnecessary memory allocation and
added comparison of length of path parameter to the size of the destination
buffer in h5import.h/h5import.c.
r17968:
Fix Coverity item 144. Fixed memory leak on error in H5D_chunk_copy.
r17969:
Fix for coverity Resource_leak #196.
r17970:
Coverity 167-173:
Initialized pointer of buffers.
In error handling, closed types and free memory.
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
compound type, it says it's a VL type. We want to tell user a VL string is a string. But
internally we treat it as a VL type. I added a flag as a parameter of H5T_detect_class.
It tells whether the caller is the public function H5Tdetect_class. I also added a
detection for VL string in the private function for the compound case (or array or nested
VL type).
Tested on jam and amani - I tested the same change for 1.8 with h5committest.
Description:
Calling H5Tcommit_anon on a file with read only access would cause an
assertion failure. Added a check to H5T_commit to return a failure in
this case. Removed redundant check in H5T_commit_named.
Tested: Fedora 11 (very minor change)
Description:
Calling H5Tcommit1 or H5Tcommit2 on a file with read only access would cause an
assertion failure. Added a check to H5T_commit_named to return a failure in
this case. Also a minor fix in the link_filters test.
Tested: Fedora 11 (very minor change)
Bring r17266 from 1.8 branch to trunk:
Clean up various compiler warnings from IRIX64 build
Tested on:
Mac OS X/32 (amazon) debug & production
(yes, I know it's not an IRIX64 system :-)
Too minor to require h5committest
Description:
When using H5T_copy on committed datatypes that are already open, H5T_copy would
properly use the already existing shared struct, but would still deep copy all
of the fields in that struct. This would cause memory leaks, and in the case of
a compound containing a vlen (or reference), the change in size would cause the
size of the resulting type to be set to an incorrect value. Changed H5T_copy to
properly avoid deep copies when using a reopened shared struct.
Tested: jam, linew, smirom (h5committest), purify on jam
Remove another call to H5E_clear_stack() from within the library.
Clean up lots of compiler warnings.
Tested on:
Mac OS X/32 10.5.6 (amazon)
(followup on other platforms forthcoming)
Description: H5Tset_order will now properly reject H5T_ORDER_NONE for most
datatypes. Previously this could cause major problems as the file could not be
flushed.
Tested: jam, smirom (h5committest)
