| Commit message (Collapse) | Author | Age | Files | Lines |
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Merged r24993 from the trunk.
Adds core VFD write tracking functionality. When enabled, the core VFD
will track dirty regions of the file and only write out the changed
regions. The new H5Pget/set_core_write_tracking() API call controls this
feature. A new "core_paged" VFD target was added to the check-vfd target
in test/Makefile.am that runs all tests with the new write tracking
functionality.
Tested on:
32-bit LE linux (jam)
64-bit LE linux (koala)
64-bit BE linux (ostrich)
Each platform was tested with HDF5_DRIVER set to "core" and "core_paged".
Jam was also tested with the standard sec2 driver.
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Bring r23219 from trunk to 1.8 branch:
Bring reviewed changes from Coverity branch back to trunk (QK & JK):
r20457:
Coverity issue 691: return of H5duo could be negative. Fixed by using
STDOUT_FILENO and redesign parse_command_line and main to cleanup file
allocations. The output_file var is null when using stdout. In cleanup do not
close output_file if NULL.
r20510:
Initialize ufid = -1 and predicate HDclose call on ufid != -1
r20511:
Purpose: Fix coverity issue 1715
Description: Free "file" and nested data on failure in H5FD_core_open.
r20512:
Initialize ifid = -1 and predicate HDclose call on ifid != -1
r20514:
Initialize h5fid = -1 and predicate HDclose call on h5fid != -1
r20516:
Added else branch to the if (ret_value < 0) check.
r20522:
Addressed coverity issues 930-933, 850, 836, 835, 1307. All minor
potential buffer overwrite bugs, or coverity errors. Fixed by replacing
strcpy and sprintf with strncpy and snprintf.
r20523:
fixed coverity issues 68, 1120, 1116i
r20524:
Check H5Z_SZIP->encoder_present < 1 assuming 0 represents absence.
r20601:
Purpose: Fix coverity issues 1703-1705
Description: Modified the cleanup code in test_free in accum.c to reset
allocated buffers to NULL after they are freed, and modified the error cleanup
code to check if these buffers are NULL before freeing them. Also fixed some
unrelated warnings in accum.c.
r20602:
Use HDsnprintf and HDstrncat
r20603:
Purpose: Fix coverity issues 808-809
Description: Modified test_core in vfd.c to check the returns from malloc, and
keep track of whether points and check are allocated by setting them to NULL
when they are not. Added code to free points and check on error if they are
not NULL. Also fixed unrelated warnings in vfd.c.
r20604:
Use HDstrncpy.
r20605:
Use HDstrncpy and HDstrncat.
r20606:
Purpose: Fix coverity issue 807
Description: Modified long_compact in stab.c to keep track of whether objname is
allocated by setting it to NULL when it is not. Added code to free objname on
error if it is not NULL.
r20607:
Changed string function calls to use versions that specify the string length
to fix coverity issues 832 and 839.
Tested on:
Mac OSX/64 10.8.2 (amazon)
(Too minor to require h5committest)
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adding cast
Tested: local linux
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H5_HAVE_WIN32_API and H5_HAVE_VISUAL_STUDIO defines only need to be set on windows. Autotools configure is not affected.
Trunk passed for a week and cmake branch has been in place > 3 weeks.
Tested: local linux
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whole MULTI file saved in the
super block. We took it out in v1.8 library because it's meaningless
for the MULTI file. v1.8 library saves the EOA for the metadata file,
instead. But this caused some backward compatibility problem.
v1.8 library couldn't open the file created with v1.6 library. I
fixed the problem by checking the EOA value to detect the file
created with v1.6 library.
Tested on jam, koala, and linew.
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Bring r20551 from trunk to 1.8 branch:
Correct 'FILE **' back to 'FILE *' for H5Fget_vfd_handle call.
Tested on:
FreeBSD/32 6.3 (duty) w/debug
(h5committest performed on trunk)
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to fail on some platforms.
The problem was that the test was a clone of the SEC2 test. The SEC2 test accepts a file descriptor (int) via a void pointer from H5Fget_vfd_handle() whereas the STDIO test needs to accept a FILE pointer. Storing the FILE pointer in an integer failed on some systems. The STDIO test now stores the file handle in FILE pointer and checks it for NULL instead of < 0.
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Trim trailing whitespace from source code files, with following command:
find . \( -name "*.[ch]" -or -name "*.cpp" -or -name "*.f90" \) -print |xargs -n 1 sed -i "" 's/[[:blank:]]*$//'
Tested on:
None - eyeballed only
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Bring r17980 from trunk to 1.8 branch:
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/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
(h5committested on trunk)
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The file failed to compiled in AIX which flags syntax error.
Fixed by making the statements more explicitly compare with NULL
and added a missing trailing semi-colon.
Tested:
Tested in AIX (Up at LLNL) only. The changes are trivial and should
be portable to all platform.s
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refactored tests that were discovered to copy data files to avoid writing to data files checked into svn to use the new function.
Tested on amani, jam, and linew with h5committest and on jam with a read only mount of source files on pegdub.
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created with v1.6 library could
be deleted by cleanup routine. I corrected it in this checkin.
Tested on jam - simple change.
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original family files under the library
source directory. Since the test opens the files with write mode, it's safer to make copies of
the original files. I added the copying step in test_family_compat in vfd.c. I changed the
Makefile.am to clean up the copied files. I created a new family_v16_00000.h5 with v1.6 library.
Tested on jam - supposed to be simple change.
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necessary as Quincey pointed out.
I took it out and used the driver address instead.
Tested on jam - simple change.
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is opened and closed with
v1.8 library, v1.8 library writes the driver info block in the superblock. But v1.6
doesn't write it. This caused the data after the superblock to be overwritten. The
solution is to use a flag to indicate when the original file doesn't have the driver
info, v1.8 library doesn't write it either.
Tested on jam. I have some trouble to access smirom and linew using h5committest.
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Bring r15800 back from trunk:
- File free space branch changes through r15794
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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Skip one of the tests in flush2.c since it looks like VMS system
flsuhes the file anyway (like on Winodws with DLLs)
Renamed files family*.h5 that are used in backward compatibility
testing to have only one '.' in a file name, otherwise VMS system
becomes confused and test fails.
Cleaned up the only test (Fortran multi-file test) that is failing on
VMS (C counterpart passesa).
Added new script to facilitate the build process on VMS
Updated MANIFEST
PLatforms tested: VMS server, kagiso and linew (minor changes)
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Changed H5Acreate2 -> H5Acreate_by_name, to be more consistent with
other new API routines.
Re-added simpler form of H5Acreate2, which creates attributes directly
on an object.
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
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Enable the backward compatibility file format test for the family VFD
in all situations.
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
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Add H5Dcreate to API versioned routines, replacing internal usage with
H5Dcreate2
Fix thread-safe error stack initialization for API versioned error
stack printing routines.
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
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Make H5Dopen versioned and change all internal usage to use H5Dopen2
Add simple regression test for H5Dopen1
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
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Put H5Acreate() under API versioning, with all internal usage shifted
to H5Acreate2().
Add regression tests for H5Acreate1().
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
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Move H5Gget_objinfo() to deprecated symbols section and retarget
internal usage to H5Lget_info()/H5Oget_info().
Misc. other code cleanups...
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
AIX/32 5.3 (copper)
Solaris/32 2.10 (linew)
Mac OS X/32 10.4.10 (amazon)
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Remove all plain calls to H5Gopen() from source, replacing them with
either H5Gopen2().
Add test for H5Gopen1().
Reformatted several pieces of code, to clean them up.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
Mac OS X/32 10.4.10 (amazon)
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will
check if fseeko is available. Using it instead of fseek can support
big files because the offset is of type off_t not long int. Also
added the test for STDIO in big.c.
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but file system doesn't, added a
condition check of writing aligned data. Skip the test for direct VFD if it's this situation.
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from configuration to run-time
detection in H5FD_direct_open in H5FDdirect.c.
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copyright notice.
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.
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The problem
came from the EOA for the whole MULTI file. It's taken out because it's
meaningless for MULTI file. Instead, each individual file has its EOA.
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depending
the setting of backing store through H5Pset_core_fapl and file open
flag. Added test cases in vfd.c.
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systems like copper and sleipnir
doesn't require alignment for Direct I/O. If this's true, write or read data just like sec2
does.
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made the test more complete by writing
two data sets. One is aligned, and the other isn't.
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size is set through
H5Pset_fapl_direct. It's been added to H5FD_direct_read in the previous checkin. Still, a test is
needed at later checkin.
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H5Pset_fapl_direct be a structure and passed
through driver info functions in H5FD_direct_open, H5FD_direct_read, and H5FD_direct_write. The
external change is to add a new API function H5Pget_fapl_direct to query 3 control values, the
memory boundary, file system block size, and the maximal buffer size for copying data.
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H5Pset_fapl_direct to control
memory boundary, file block size, and maximal copy buffer size; second in H5FD_direct_write and
H5FD_direct_read, the library checks whether data buffer is aligned. If it is, then write and
read the data directly instead of making a copy buffer.
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Altix (cobalt). There's a configure
option --enable-direct-vfd/--disable-direct-vfd to enable/disable Direct I/O support. The default
is enabled. There's a small test in test/vfd.c. Another way to test it is to set environment
variable HDF5_DRIVER to "direct" and run "make check" in the test/ directory. There'll be some
further improvement in the following checkin including allowing user to provide memory boundary
value, file block size, and copying buffer size.
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Fix file handle destroy routine to not attempt to flush out partially
initialized file handles (when opening a file fails).
Tested on: (until they finished testing, this time... :-)
FreeBSD/32 4.11 (sleipnir) w/threadsafe
Linux/64 2.4 (mir) w/1.6 compat
Linux/32 2.4 (heping) w/FORTRAN & C++
Mac OSX/32 10.4.8 (amazon)
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New feature
Description:
Check in baseline for compact group revisions, which radically revises the
source code for managing groups and object headers.
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
This initiates the "unstable" phase of the 1.7.x branch, leading up
to the 1.8.0 release. Please test this code, but do _NOT_ keep files created
with it - the format will change again before the release and you will not
be able to read your old files!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!!
Solution:
There's too many changes to really describe them all, but some of them
include:
- Stop abusing the H5G_entry_t structure and split it into two separate
structures for non-symbol table node use within the library: H5O_loc_t
for object locations in a file and H5G_name_t to store the path to
an opened object. H5G_entry_t is now only used for storing symbol
table entries on disk.
- Retire H5G_namei() in favor of a more general mechanism for traversing
group paths and issuing callbacks on objects located. This gets us out
of the business of hacking H5G_namei() for new features, generally.
- Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t
- Lots more...
Platforms tested:
h5committested and maybe another dozen configurations.... :-)
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Avoid bug for family file driver backward compatibility with 1.6.
Description:
Because there is no srcdir on windows, string pathname should be
initialized as NULL before using strcat.
Solution:
Changed the code as above.
Platforms tested:
too minor to test.
Misc. update:
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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
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Bug fix & code cleanup
Description:
Don't unmount child files from a parent file if the parent file is
being held open by an object.
Also, moved the mounting routines into their own source file and the
superblock routines into their own file also.
Solution:
Moved the code for unmounting child files down in the H5F_close routine
and also add checks to the file and group mounting code to unmount child
files when the last object holding open a file closes.
Platforms tested:
FreeBSD 4.11 (sleipnir)
h5committest
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Renamed file_handle.c as vfd.c since its tests have evloved from
merely file handles tests to other basic features of VFD's.
Did some minor cosmetic changes in vfd.c.
Updated Makefile.am with the new name.
Makefile.in is regenerated.
Platforms tested:
In heping only since the changes are trivial.
Misc. update:
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