Convert internal chunk structures to use 'scaled' coordinates instead of
absolute coordinates.
Tested on:
Mac OSX/64 10.10.3 (amazon) w/parallel & serial
Linux 2.6.x/32 (jam) w/parallel & serial
Linux 2.6.x/64 (koala) w/serial
Description:
The test added failed in some machines because the data file contains infinity values that different machines print them differently as "inf", "INF", "Inf", ...
Solution:
Added a "ignorecase" option to TOOLTEST() to do caseless matching between generated output vs expected output. This solved most machines problem for now.
Tested: h5committest, emu by hand for both development and production modes.
But cmake built h5dump failed to read the data file. Using the same source to build h5dump by autotools produced a h5dump that can read the test data file. Don't know why cmake could not produce a correct binary.
The tool claimed it could handle 24bit images but there was no code to handle it.
(or might be there were but was removed by previous revisions.)
Also discovered that it does not accept multiple images nor -p for palette
as its user document and online help message indicated.
Solution:
Added code to verify dimension sizes are within 8 bit raster images limit and
added tests to verify the tools correctness.
Need to update user document tool.
Tested: h5committested.
Remove VPATH and related search path syntax checking.
Remove check for H5_LONE_COLON and checking for lone colon compiler confusion.
tools/h5dump/testh5dumpxml.sh.in
tools/h5dump/CMakeTestsXML.cmake
Remove test skipping for compilers that were formerly confused by lone colon.
Tested with h5committest.
Bring r26651 from autotools_rework branch to trunk:
Remove the VSNPRINTF_WORKS macro, it's working around bugs in old SGI
& HP compilers.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
Remove the VSNPRINTF_WORKS macro, it's working around bugs in old SGI
& HP compilers.
Tested on:
MacOSX/64 10.10.2 (amazon) w/serial & parallel
(h5committest not required on this branch)
- Adds 'F' suffixes for most float constants.
- A few constants MUST be of type double. These now receive the long
double L suffix and are then cast to double. I do this via a new
H5_DOUBLE() macro which was added to H5private.h.
Fixes: HDFFV-9148
Tested on: h5committest
branch.
Removed the configure option that allows selective disabling of individual
internal filters (fletcher32, shuffle, etc.).
This feature mucked up the code with a lot of #ifdefs, saved very little space,
and was not scalable to a general scheme for library size reduction. We've
decided to remove the feature while we investigate a more general scheme for
decreasing the library size.
Part of: HDFFV-9086
Tested on: h5committest
It should no longer be necessary to use --enable-using-memchecker
make check fails due to an issue with h5ls apparently unrelated to the merge
Tested: ummon
Cleans up time functions in the autotools input files. Removed deprecated
gettimeofday() time zone code and configure processing. Also removed
some unused time function configure checks and defines.
Fixes: HDFFV-9083 and HDFFV-9085
Tested on: 32-bit linux, serial and parallel (jam)
OS X (kite)
Solaris (emu)
- Remove Infering parallel compilers (C and Fortran) from configure.ac
- Remove restriction to build shared with parallel
- Cleanup parallel sections in configure.ac
- remove large file support checks
- MPE fixes.
tested with h5committest.
Developers will now have to run bin/reconfigure (deprecated, will be removed
soon) or autogen.sh after checking out code.
Part of: HDFFV-9120
Tested on: jam with Fortran and C++
Change AC_TRY_RUN TO AC_TRY_COMPILE
Changed all the instances of AC_TRY_RUN for the Fortran and C++ tests to use
AC_COMPILE_IFELSE and moved all the tests to new files in m4 directory:
aclocal_cxx.m4 (for C++ tests)
aclocal_fc.m4 (for Fortran tests)
tested: jam
Last changes had caused problems with Windows platform:
1. H5private.h in io_timer.h is not accessible in the distributed shared library of tools.
Need to move it to io_timer.c.
2. debug_start_stop_time() would not be available outside of h5perf. Some favor of compiler
does not like it. Screened it out for now.
3. mere "extern" is not good enough for Windows shared library. Must mark them as DLL. Need to mark them as
"H5TOOLS_DLL".
4. STANDALONE mode is broken. Screened out the code for now.
Tested; h5committest.
Move timing measurement routines used by h5perf and h5perf_serial to tools/lib
so that they can be used by other tools too.
tools/lib/io_timer.c
tools/lib/io_timer.h
tools/perform/io_timer.c
tools/perform/io_timer.h
renamed perform/io_timer.[ch] to lib/io_timer.[ch]
tools/lib/Makefile.am
tools/lib/Makefile.in
tools/lib/CMakeLists.txt
tools/perform/Makefile.in
tools/perform/Makefile.am
tools/perform/CMakeLists.txt
MANIFEST
updated due to the move.
Tested; h5committest and jam (serial)
tools/perform/sio_timer.h:
tools/perform/pio_timer.c:
tools/perform/io_timer.h:
tools/perform/io_timer.c:
Renamed pio_timer.[ch] as io_timer.[ch];
merged content of sio_timer.[ch] into io_timer.[ch] so that both h5perf and h5perf_serial
call the combined io_timer.[ch].
Moved the debug printing code segment in set_time() in [sp]io_timer.c to as debug_start_stop_time() in [sp]io_perf.c where it belongs.
Screened out set_timer_type() and get_timer_type() which were not used by any code.
tools/perform/Makefile.am:
tools/perform/Makefile.in:
tools/perform/CMakeLists.txt
Adjusted to use io_timer.c for both h5perf and h5perf_serial.
tools/perform/pio_perf.c:
tools/perform/sio_perf.c:
tools/perform/pio_perf.h:
tools/perform/sio_perf.h:
Renamed [sp]io_time_destory() to same io_time_destroy();
Moved the debug printing code segment in set_time() in [sp]io_timer.c to as debug_start_stop_time() in [sp]io_perf.c where it belongs.
tools/perform/pio_engine.c:
tools/perform/sio_engine.c:
Removed #include io_timer.h since it was already #include by [sp]io_perf.h.
MANIFEST:
Updated the merge of [sp]io_timer.[ch] into io_timer.[ch].
Tested: h5committest and jam in extra.
Benchpar.c is retired/deleted. If it is ever needed, it can be retrieved from the SVN repository
or even previous version of HDF5 source code.
Tested: jam parallel make passed.
Previously, ph5diff may hang in a test in Linux 32 platform(HDFFV-587).
No solution was available and a patch to bypass the test is implemented.
Since the company is changing domain name soon, the patch would not be valid any more.
Tests were done (repeat 100 mpiexec -np 6 ./ph5diff -v h5diff_hyper1.h5 h5diff_hyper2.h5)
and the previous hanging problem did not occur. It is likely the newer versions of
mpich no longer have this problem. Therefore, it is decide to remove this patch
to make the test script cleaner, if nothing else.
Tested: ran build and test in Jam (linux 32) and the repeat 100 command mentioned above.
All passed.
Discovered when I temporarily #defined HDfree() to a more complicated
function while investigating something.
Tested on a local linux VM. This is a very minor change.
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)
Bring changes from Coverity branch back to trunk:
r20914:
Use HDstrncpy and HDstrncat! --gh
20915:
Use HDstrncpy and HDstrncat! --gh
Tested on:
Mac OSX/64 10.9.3 (amazon) w/gcc 4.9.0, C++, FORTRAN & parallel
(too minor to require h5committest)
Bring changes from hdf5_1_8_coverity branch back to trunk:
r20878:
Issue 76: Check if H5Tget_nmembers(type) fails and simply return(FALSE). Also move printf to after check.
r20880:
Issue 192: Create ret_val var set to -1. Add out label for failures to jump to, return ret_val at bottom.
r20882:
Fixes for coverity:
1) bug #1679: remove dead code in test/mf.c
2) bug #1680: remove dead code in tools/lib/h5diff_dset.c
r20883:
Fix coverity issue 585
Description:
Changed variable "c" in processStrData in h5import.c to an int, to match fgetc
return value, and removed call to feof, instead checking if c == EOF.
Tested on:
MacOSX/64 10.9.3 (amazon) w/C++, FORTRAN & parallel
(too minor to require h5committest)
ib files. The fix also removed dependencies on libhdf5, etc. when the --disable-sharedlib-rpath co
nfigure option was invoked.
Added instead configure variable hardcode_into_lib=no. This removes rpath from lib files on Linux
and solaris machines.
Tested with h5committest on jam, koala, ostrich and platypus (cmake), and with configure option --disable-sharedlib-rpath on emu, platypus and quail.
h5diff issues "unable to read attribute" error message when comparing two files
Description:
h5diff did not handle attributes of variable length strings correctly. It created the wrong memory type if one but not both compared attributes are of the variable strings type. It ended in H5Aread() failure.
Solution:
We decided to treat the case when one type is variable length string and the other is not as incomparable. That bypassed the above error. We still need to figure out the proper way, if possible, to compare variable string with non-variable string types.
Tested: h5committested plus tested in Swallow (OS X 10.8).
h5diff segfaults with user's files
Solution:
Added a variable to indicate if real data are in the buffer and will call H5Dvlen_reclaim()
only when real data are in the buffer.
Tested: with the user provided data files and no more segmentaion fault.
Also h5committ tested.
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)
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)
Remove all traces of MPI-POSIX VFD and GPFS detection/code.
Remove remaining traces of stream VFD.
Remove testpar/t_posix_compliant test (it's not actually verifying anything).
Clean up H5D__mpio_opt_possible() further.
Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).
A few other small code cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
KitWare recommendations: Change CMake commands to lower case.
Bump up CMake minimum versions.
Split test file into separate file for h5repack test.
Tested: local linux
KitWare recommendations: Change CMake commands to lower case.
Bump up CMake minimum versions.
Split test file into separate file for h5repack test.
Tested: local linux
Brought changes from Coverity branch back to trunk, and cleaned up misc.
other warnings & formatting issues:
r20833:
Fixed Coverity 667 and 668 with real integer overflow tests this time.
r20834:
Use HDstrncpy and HDstrncat. --gh
r20835:
Change to use strncpy - use base_len + 1 for line 156, use HDstrlen(path) + 1 for line 159
r20836:
Fixed coverity 585 by casting output of fgetc() to a char.
r20837:
Changed sprintf calls to snprintf with size 1 less than the allocated buffer to address coverity issue #967.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel
(too minor to require h5committest)
Rename GCC_DIAG_OFF/ON macros to H5_GCC_DIAG_OFF/ON and move from
src/H5private.h to src/H5public.h. Wrap typedef of hsize_t and hssize_t
in DIAG_OFF(long-long) macros.
Clean up a bunch of "macro '-' is unused" warnings.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/gcc 4.8.2, C++, FORTRAN, parallel
(too minor to require h5committest)
Revert some earlier usage of strncpy, which was incorrect.
Bring Coverity changes from branch back to trunk:
r20821:
Use HDstrncpy. --gh
(Fixed already, with strdup)
r20822:
(Not merged, incorrect use of HDstrncpy())
r20823:
(Not merged, incorrect use of HDstrncpy())
r20824:
Maintenance: Bug fix: addressed CID 666.
Value stored at *expression_len should be used in the call to
HD5packFstring to avoid overflow (and unnecessary arithmetic
calculation and casting)
r20825:
Issue 642: Added check for error and handler with print to stderr and exit.
r20826:
Undo revision 20818, as that issue has already been fixed in the 1.8 branch
and trunk (but not coverity branch)
r20827:
(Not merged, incorrect use of HDstrncpy())
r20828:
Use HDstrncpy. --gh
(Corrected use of strncpy())
r20829:
Check return of H5Lget_val(print_udata->fid, path, targbuf,
linfo->u.val_size + 1, H5P_DEFAULT) and if error set trgbuf[0] to 0.
Check if H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL,
&filename, &objname) was successful and allow print. Otherwise filename
and objname are not created. (init those to NULL)
r20830:
resolved coverity issues 939, 940, 941, 944, and 947.
all were complaints about use of sprintf, and in all cases, the
buffers used were large enough for all eventualities.
Resolved issue by replacing calls to sprintf with calls
to snprintf.
r20831:
Maintenance: Addressed CID 852
Replaced sprintf with snprintf
r20832:
Purpose: Fix valgrind issues with hl/examples/ex_image2
Description:
Modified hl/examples/ex_image2 to free global "gbuf" before exit.
Tested on:
Mac OSX/64 10.9.1 (amaon) w/C++, FORTRAN & Threadsafety
(too minor to require h5committest)
Bring r24479 from 1.8 branch to trunk:
Fix ph5diff worker command handling so it can correctly respond to
situations where there's no work to perform. Also, a few minor code cleanups.
Tested on:
Mac OSX/64 10.9.0 (amazon) w/parallel
(too minor to require h5committest)
The h5dump tests only looked at headers and never the data. Data reads would fail with invalid number of params (7 expected 20).
Regenerated file and replacement ddls updated.
New h5dump test will be added to read the data.
behind by "make distclean" (see below); modified appropriate Makefile.am files and ran
bin/reconfigure to create Makefile.in to fix the problem.
Here is the list of the files "make disclean" doesn't remove:
tools/h5dump/testfiles
tools/h5repack/testfiles/h5diff_attr1.h5
tools/h5repack/testfiles/tfamily00000.h5
tools/h5repack/testfiles/tfamily00010.h5
tools/h5repack/testfiles/tfamily00002.h5
tools/h5repack/testfiles/tfamily00004.h5
tools/h5repack/testfiles/tfamily00006.h5
tools/h5repack/testfiles/tfamily00008.h5
tools/h5repack/testfiles/tfamily00001.h5
tools/h5repack/testfiles/tfamily00003.h5
tools/h5repack/testfiles/tfamily00005.h5
tools/h5repack/testfiles/tfamily00007.h5
tools/h5repack/testfiles/tfamily00009.h5
tools/h5jam/testfiles/h5jam-ub-nohdf5.txt.err-sav
tools/h5jam/testfiles/h5jam-help.txt.err-sav
tools/h5jam/testfiles/h5unjam-help.txt.err-sav
tools/h5jam/testfiles/h5jam-ub-nohdf5.txt.out-sav
tools/h5jam/testfiles/h5jam-help.txt.out-sav
tools/h5jam/testfiles/h5unjam-help.txt.out-sav
hl/fortran/test/dsetf5.h5
c++/test/tattr_multi.h5
c++/test/tattr_scalar.h5
c++/test/tfattrs.h5
c++/test/tattr_basic.h5
c++/test/tattr_compound.h5
c++/test/tattr_dtype.h5
Tested on jam and emu in place and using srcdir with the svn stat command.
This fix doesn't address two problems:
tool/h5dump/testfiles directory is not removed by "make distclean" and it should be
tools/misc/testfiles directory is removed by "make distclean" and it shouldn't be
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)
A) Fix for HDFFV-1238:
--Add 3 new options to allow users in setting threshold for small groups/datasets/attributes (tools/h5stat/h5stat.c)
--Generate new test file for testing the new options (tools/h5stat/h5stat_gentest.c)
--Add tests for the new options (tools/h5stat/testh5stat.sh.in)
--Update expected output files (tools/h5stat/testfiles/*.ddl)
B) Fix a bug in determining maximum dimension size for 1-D dataset in dataset_stats() (tools/h5stat/h5stat.c)
tools/h5diff/testh5diff.sh is run in every "make check", even after it
has passed in the previous run.
The error was in the previous change made to Makefile.am
when testh5diff.sh.in was created. The mistake was in the
SCRIPT_DEPEND=h5diff$(EXEEXT) $(H5PDIFF) $(srcdir)/testh5diff.sh
$(srcdir)/testh5diff.sh no longer existed. It is now generated in the
current built directory from $(srcdir)/testh5diff.sh.in (which configure
takes care of).
I updated the dependance to
SCRIPT_DEPEND=h5diff$(EXEEXT) $(H5PDIFF) testh5diff.sh
and that fixes the error.
Reviewed: HDF5-149
Tested: h5committested.
Found and removed two more "//" comments.
Tested: in Koala by
$ env CFLAGS="-ansi" ../hdf5/bin/buildhdf5 -fortran -cxx -config # enable fortran and cxx, configure only
$ make AM_CFLAGS=-ansi # compile all source file by setting HDF5 build CFLAGS as "-ansi" only
