| Commit message (Collapse) | Author | Age | Files | Lines |
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* Updated source file copyright headers to remove "Copyright by the Board of Trustees
of the University of Illinois", which is kept in the top-level COPYING file.
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* Straightforward conversion of sprintf to the safer snprintf
* Trickier conversion of sprintf to safer snprintf
This involved minor changes to private function signatures to take the size of the buffer.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* h5test.h testing macros get enclosed in do..while loops
* Adds missed macro in hl C++ code
* Fixes macro in Windows code
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* Fixes unused/unset variable warnings from aocc
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Fixed all clang-tidy bugprone-suspicious-string-compare warnings
This change was generated entirely by clang-tidy itself.
* Reformat code with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - src and test directories.
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Adds missing HD prefixes to API calls in src and test.
Adds some extra processing to bin/checkposix to keep the noise
levels down when running the script (not comprehensive).
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Removes redundant C library headers from hl library
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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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HDopen() calls.
Also fixed a minor const warning in the core VFD.
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according to MSDN. Partial fix for HDFFV-9630.
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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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modified: bittests.c
modified: cmpd_dset.c
modified: dsets.c
modified: dt_arith.c
modified: dtypes.c
modified: extend.c
modified: fillval.c
modified: filter_fail.c
modified: flush1.c
modified: gen_cross.c
modified: hyperslab.c
modified: istore.c
modified: links.c
modified: links_env.c
modified: objcopy.c
modified: plugin.c
modified: tcheck_version.c
modified: unlink.c
modified: unregister.c
Minor fixes to replace numeric exit codes with MACRO declarations. Not all codes found were boolean, and those cases were not changed.
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Bring warning cleanusp in r29990, 29993, 29997, 29999, 30004 from
revise_chunks branch to trunk.
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production.
(h5committest forthcoming)
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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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Clean up more compiler warnings, plus merge a few Coverity bug fixes from
the hdf5_1_8_coverity branch back to the trunk:
r20877:
Purpose: Fix coverity issue 1723
Description:
Modified test_generate in hl/test_image to close file "f" before exit, even if
an error occurs.
r20879:
Issue 63: change check of return of H5Tget_nmembers to <=0. No need to go
futher if call fails as well as empty.
r20881:
Coverity #659 in Run 46: I changed the Line 442 where it tries to check whether
FLAG_PRINTED is TRUE. But it had just been set to FALSE. I took out the
condition check in the print statement.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & Parallel
(too minor to require h5committest)
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project for
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
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a lack of sparse file support.
Minor change: tested on 64-bit Windows 7
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Minor change: tested on jam (test not skipped) and Mac OS-X Lion (test skipped
due to HFS not supporting sparse files).
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VFD is set).
This occurs due to the istore test creating very large files on systems which
do not have POSIX-like sparse file semantics. The large amount of I/O causes
the test to run for a very long period of time.
The fix was to copy the "big" test's sparse file check and only run the
largest sparse file test when POSIX-like sparse file semantics are found.
Tested on:
jam (nfs)
ostrich (nfs)
loyalty (ufs)
64-bit linux VM (ext4)
64-bit OS-X Lion (hfs, detected as not POSIX sparse)
64-bit Windows 7 (NTFS, detected as not POSIX sparse)
The OS-X failure to pass the sparse check is likely an error and will be
entered as a new bug.
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Description:
Added internal tesitng routines to traverse a file and verify that symbol table
information is *always* cached, whenever possible. Added this check to the end
of many tests to check all the test files, right before the call to h5_cleanup.
Tested: jam, amani, heiwa (h5committest)
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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
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Correct a minor error in file free space allocation which was affecting
the 'multi' VFD and preventing some tests from fully working with it.
Wholesale revisitation of all the places where tests were disabled
with various VFDs and remove or correct all these so that _only_ the tests
which _really_ can't work with particular VFDs are skipped during a
'make check-vfd' test.
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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Detect chunks that are >4GB before dataset gets created and return error
to application.
Tweak lots of internal variables that hold the chunk size/dimensions to
use an 'uint32_t', instead of a 'size_t', so that the integer size is constant.
Correct a number of our tests which were creating datasets with chunks
that were >4GB and add some specific tests for >4GB chunk size detection.
Minor whitespace & other code cleanups.
Tested on:
Mac OS X/32 10.5.2 (amazon)
Forthcoming testing on other platforms...
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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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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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Check in changes from Elena and I to get pgcc compiler working again.
Primarily (all?) changes to move from using 'hsize_t' as array index to using
something else ('size_t') mostly.
Tested on:
Linux/32 2.4 kagiso w/pgcc
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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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Clean up more warnings...
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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"make check-vfd" will now run all tests in the test directory with different
file drivers (at least, all of those tests that use the testing framework's
FAPL). Tests that fail will be skipped.
This is not a perfect fix, but is better than nothing.
Along with this change, check-vfd should be added to the Daily Tests.
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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/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:
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Bug fix (sorta)
Description:
Change reading of "missing" chunks from datasets with undefined fill
values to not overwrite the application buffer with random garbage from
memory. Note that this is almost the same, since whatever garbage the
application had in those locations will still be there...
Platforms tested:
FreeBSD 4.10 (sleipnir)
IRIX64 6.5 (modi4)
h5committested
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Code cleanup
Description:
Clean up lots of warnings based on those reported from the SGI compilers
as well as gcc.
Platforms tested:
SGI O3900, IRIX64 6.5 (Cheryl's SGI machine)
FreeBSD 4.9 (sleipnir) w/ & w/o parallel
h5committest
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Bug fix & code cleanup
Description:
Allowing the library to call malloc with a size of 0 bytes causes problems
for some users, so we check for allocations of 0 bytes and disallow them now.
Cleaned up some code which could call malloc with 0 size.
Changed some code calling HDmalloc directly to call H5MM_malloc(), which
allows us to check for 0 sized allocations.
Platforms tested:
FreeBSD 4.9 (sleipnir)
too minor to require h5committest
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Bug fix
Description:
Make --disable-hsizet work properly again by fixing a couple of tests and
correcting the definition of SSIZET_MAX.
Platforms tested:
FreeBSD 4.9 (sleipnir)
h5committest not used, as it doesn't test this configuration.
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Code cleanup
Description:
Remove redundant "Testing" from test output.
Platforms tested:
h5committestted (although Fortran tests failed for some reason)
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Purpose: Maintenance and bug fixes and test of latest szip library..
Description: Recently Quincey enabled MEDIUM test for istore. That caused
daily tests to fail on verbena. It looks like that test
creates a pretty big file, and afs write fails. Test passes
when run in /tmp.
Solution: Disable MEDIUM test and filed bug report to investigate the problem
little bit more carefully.
Platforms tested: verbena, arabica, arabica-64 (since I also tested newest szip)
Misc. update:
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Code cleanup
Description:
Uncomment tests that we previously commented out with my "Uncomment tests!"
note.
Platforms tested:
h5committested
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New feature/enhancement
Description:
Chunked datasets are handled poorly in several circumstances involving
certain selections and chunks that are too large for the chunk cache and/or
chunks with filters, causing the chunk to be read from disk multiple times.
Solution:
Rearrange raw data I/O infrastructure to handle chunked datasets in a much
more friendly way by creating a selection in memory and on disk for each chunk
in a chunked dataset and performing all of the I/O on that chunk at one time.
There are still some scalability (the current code attempts to
create a selection for all the chunks in the dataset, instead of just the
chunks that are accessed, requiring portions of the istore.c and fillval.c
tests to be commented out) and performance issues, but checking this in will
allow the changes to be tested by a much wider audience while I address the
remaining issues.
Platforms tested:
h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
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Code cleanup
Description:
Clean up miscellaneous warnings which have crept into the code.
Fix "_POSIX_C_SOURCE not defined" warning on FreeBSD.
Adjust gcc compiler flags to be more concise for production mode.
Refactor the H5O code so that there is a stronger boundary between code
in the H5O package and code in the library which just calls H5O routines.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel and gcc 2.95.4 & gcc 3.2.2
Misc. update:
Update MANIFEST if you add or remove any file.
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Bug Fix
Description:
Metadata cache in parallel I/O can cause hangs in applications which
perform independent I/O on chunked datasets, because the metadata cache
can attempt to flush out dirty metadata from only a single process, instead
of collectively from all processes.
Solution:
Pass a dataset transfer property list down from every API function which
could possibly trigger metadata I/O.
Then, split the metadata cache into two sets of entries to allow dirty
metadata to be set aside when a hash table collision occurs during
independent I/O.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
FreeBSD 4.7 (sleipnir) serial & parallel
Misc. update:
Updated release_docs/RELEASE
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