Updating autotools
Description:
Installed new autotools and used them to reconfigure HDF5.
- Automake upgraded to 1.11
- Autoconf upgraded to 2.64
- bin/reconfigure script edited to use new versions (on jam), and
run to generate new configure script and Makefile.in's.
- configure.in script edited to add "_cv_" to all AC_CACHE_VAL strings
(in order to comply with new autoconf standard).
Tested:
Tested on machines jam, smirom, liberty, linew.
Tested w/ features c++, fortran, parallel.
Tested w/ compilers gcc, pgcc, icc.
Further testing via Daily Tests should catch any other outliers. Upon
passing DT's, I'll propogate the new tools into 1.8, hdf4, et cetera.
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
Fix BZ #1583
Description:
The --enable-static-exec flag was broken. Configure was adding the
-all-static linker flag to an environment variable which was subsequently
never used. (looks like it was used in 1.6 Makefile.ins, but never
moved to 1.8's Makefile.ams when we added automake support).
To fix, I've added this environment varibale to the link lines of all the
tools. Now, when --enable-static-exec is invoked, it will correctly
generate statically linked executables in the installed bin directory.
Tested:
I've tested manually to ensure that the generated execs are static when
the flag is used and dynamic when not. I've also tested when szip is
used, as this was a use case mentioned in the bug report.
Also: ran full tests with make check on jam and smirom for good measure.
ISSUE: h5ltread_dataset_string_f causes library assertion with g95.
SOLUTION: convert the fortran string buffer to a C buffer with HD5f2cstring, and pass this string to the C function
TEST: added a test call in the fortran test lite program
DOCS: added the note in RELEASE.txt "- Lite: the h5ltread_dataset_string_f and h5ltget_attribute_string_f functions had memory problems with the g95 fortran compiler. (PVN - 5/13/2009) 1522
Bring r16846 from revise_chunks branch back to trunk:
Fix broken (for how long?) H5_ASSIGN_OVERFLOW macro to actually detect
overflows during assignments, along with several errors it [now] detected.
Cleaned up a fix minor warnings and/or pieces of code also.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
(h5committest not needed - multi-platform test performed on branch)
- Updated bin/reconfigure to use latest version of automake (1.10.2).
Re-generated Makefile.in's by running bin/reconfigure.
- Added libtool version numbers to c++, fortran, hl, hl c++, and hl fortran
libraries.
Tested:
jam, liberty, smirom
ISSUE2: the scale index input/output parameter value passed to H5DSiterate_scales was not always incremented (it returns the scale index current iteration).
SOLUTION FOR ISSUE2: modified the cycle in H5DSiterate_scales so that the scale index is always incremented
TEST: added some test cases with calls to invalid indices and H5DSiterate_scales with return scale indices and visitor data
tested: windows, linux
ISSUE: When some functions are called with an invalid dimension index (for example, greater than the rank of the dataset) the function does not immediately fail, rather asserts down the code.
SOLUTION: added this check for H5DSdetach_scale, H5DSset_label, H5DSget_label (the other functions have this check) . H5DSiterate_scales also added a check for an invalid dimension scale index
TEST: added some test cases with calls to invalid indices
DOCS: Nothing added
ISSUE: Purify (Windows Visual Studio 6) complains of a memory leak in H5DSdetach_scale call regarding a H5Aread call (stack is H5A_read, H5T_convert, H5T_conv_vlen, H5T_vlen_seq_mem_write, H5MM_malloc).
SOLUTION: When a scale is detached from a dataset, the variable length structure length field is decreased in one entry. The associated pointer must be reallocated with the new length.
DOCS AND TEST: Nothing added
tested: windows with purify, linux
1. #1487 (B1) DS memory leaks ISSUE 1: On a "go to" error condition, previously allocated buffers were not freed. NOTE: these are "potential" memory leaks because typically the error conditions do not occur, so the potential memory leaks also do NOT occur. ISSUE 2: A function used to read dimension scales realistic data (topography of the North Atlantic, latitude and longitude) was being called without the data buffer being freed. SOLUTION FOR ISSUE 1: added "free" calls for the allocated buffers on the error sections. SOLUTION FOR ISSUE 2: added a "free" call after the read_data function, after using the buffer (on a H5Dwrite and H5Screate_simple). The read_data function reads both data and dimensions from the ASCII data files. DOCS: no docs added. Done for 1.9 and 1.8 STATUS: Closed bug
tested: h5committest
Bug Fix
Description:
Fixing BZ #1381. The --includedir=DIR configure option, which is used
to specify the installation location of C header files, did not work
correctly as the path was hard-coded in config/commence.am. I'm presuming
this is because an older version of automake didn't know where to put
c header files. In any case, removing this line now defaults the includedir
to the same directory that it is currently hard-coded to, and also fixes
the configure flag to allow customization of this value.
Tested:
jam, liberty
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)
the way h5ls prints types, it starts searching for NATIVE types first. One solution would be h5ls not to detect these native types, using for example the same print datatype function that h5dump does, that would make the output look the same on all platforms ("32-bit little-endian integer" would be printed instead). Drawback, this "native" information would not be available. Other solution is to have not one but 2 expected outputs and make the shell script detect the endianess and compare with one output or other
tested: h5committest
Description:
- Remove need to set LD_LIBRARY_PATH when using shared szip library.
- Libtool 2.2.6a is now used to generate libraries.
- 'make check install' dependency bug is fixed, and should no longer
break the build.
- removed hard coding of shell in config/commence.am, as this causes
problems on Solaris with the new version of libtool.
- RELEASE.txt with appropriate changes.
Tested:
- kagiso, smirom, linew (merged from 1.8, pretty quick tests)
The custom rules for installing h5cc, h5fc, and the fortran modules in fortran
and in hl/fortran don't use $(DESTDIR). Added it to all those rules.
Tested: kagiso both serial and parallel with fortran and cxx enabled.
Tested by:
make install
make DESTDIR=/tmp/acheng install
diff -r /tmp/acheng/.../hdf5 hdf5
Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $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...
Description:
The daily test failure caused by the C++ API was fixed, so put
the packet table test back.
Platforms tested:
SunOS 5.10 (linew)
Linux 2.6 (kagiso)
FreeBSD (duty)
the file didn't have the data. It happened because each handle had its own
object structure, and the empty one overwrote the data with fill value. This is
fixed by making some attribute information like the data be shared in the
attribute structure.
Tested on smirom, kagiso, and linew.
