Bug 2182 - h5ls and h5dump: update to use --enable-error-stack among tools, also update related descriptions
Description:
Decided to use --enable-error-stack long option name only to
display error stack messages from HDF5 lib among tools.
Updated to unify option name to '--enable-error-stack' for printing
HDF5 error stack messages for HDF5 tools. h5ls and h5dump for now.
For h5ls, this replaces "-e/--errors" option, which is deprecated.
For h5dump, remove -E from help page and RM , which was added by mistake
before release1.8.7.
Help page and RM got updated.
Updated test case.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
Improve the previous fix for Bug 2216 - GMQS: h5diff - memory leak when
compares vlen string in dataset or attributes
Description:
Related to the previous checkin r20270 and r20266.
Improve h5tools_detect_vlen() code for better performance. H5Tdetect_class
already recusive on given type so don't need to be part of recusive call
again. Also improve error handlings in h5tools_detect_vlen and
h5tools_detect_vlen_str functions.
Also updated h5ls and h5dump code accordingly.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
Improve the previous fix for Bug 2216 - GMQS: h5diff - memory leak when
compares vlen string in dataset or attributes
Description:
Improve the fix along with the previous checkin r20266.
Add a new function to tool lib, h5tools_detect_vlen_data() which return
TRUE if include any kind of vlen data all at once, either VLEN-data or
VLEN-string and so on.
Also updated h5ls and h5dump code accordingly.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
Fixed Bug 1904 - h5ls : usage of '-a' option is not clear to display expected output
Description:
Fixed incorrect content and improved help page for -a option of h5ls.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), Cmake (jam)
htri_t H5Tdetect_vlen_str(hid_t tid) to h5tools. This needs to be called before any H5Aread/H5Dread and if TRUE, then call vlen_reclaim function after the corresponding h5tools_dump_xxx().
Tested: local linux and valgrind
Fixed Bug# 1979 Output from h5ls -rdlS on nested compound datatypes is
difficult to parse.
Description:
Update to add curly brackets for the nested compound members, when
S (--simple) option is used with -l (--label), so user can tell
which members blong to which compound type.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32)
Bug 1707 is that H5Eset_auto causes a seg fault when an application uses -DH5_USE_16_API with
the 1.8 library to compile.
I created a branch off the trunk called set_auto to continue working on the problem.
Tested on jam - backing out, simple.
through H5Eset_auto. I changed the union in the structure H5E_auto_t. Another change is to
make H5Eget_auto fail if H5Eset_auto is called to set the printing function. I'll write a
document for it.
Tested on heiwa, jam, and amani.
The property change in configure.in, config, and Makefile.am came from the merge of the 1.8
library change.
Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object
Description:
Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly.
Tested:
jam, amani, heiwa
Corrected use/name of source folder aliases.
Duplicated FindMPI.cmake so that non-c++ compiler is found first (recommemded commands did not work).
Tested: local linux with mpich
Merge r19290 & r19291 from 1.8 branch to trunk:
r19290:
Correct another error in metadata accumulator dirty region calculations
(this time with a corner case when freeing data in the file).
r19291:
Avoid getting object information for soft/external links if we aren't
going to traverse across the link itself.
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
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
Add --no-dangling-links option to h5ls.
Description:
Related to "Bug 1830 - Following an dangling external link in h5ls should set non-zero return code."
If --no-dangling-links option is specified and any dangling link is found, return exit code 1 (error).
Tested:
jam, amani and heiwa
Change h5ls not to manipulate special characters in object name or attribute name for smart display.
Description:
Related to "But1784 h5ls has input and output issues with links that have '\' characters in them."
Tested:
jam, amani and linew
Problem: some launching command like yod (and sometimes mpirun), do not pass
back the exit code of the executables back to the shell. It always returns 0
if it can launch the executable. This cause tests that expect non-zero exit
code to fail incorrectly.
Short term Solution:
Added the feature that if $RUNSERIAL_NOEXITCODE is defined, do not
test conditions that rely on non-zero exit code.
Tests:
dove-linux using RUNSERIAL=thgyod to see the failures and using
$RUNSERIAL_NOEXITCODE=yes to bypass the errors.
Also h5committested.
Fixed exit code (sometimes return code in Main) to follow the HDF5 standards.
Tested:
Tested in Dove-linux only since change is trivial and has passed in v1.8.
Support follow symbolic links.
Description:
Add '--follow-symlinks' option to follow symbolic links (soft and external).
Update help page according to RM.
Remove some warning messages from compiler.
Tested:
jam, amani and linew
Enable tools lib to be built as a dll on windows. Added two get/set functions for progname and d_status.
Also add windows import/export declarations to functions.
Updated error_mesg() and warn_mesg() to remove progname argument and use get functions
Tested:
Windows, linux
Improve configure's large-file support control.
Description:
Modified configure to now attempt to add defines necessary for
supporting largefiles on all systems, instead of solely on linux. This
is in response to user requests to enable largefile support on Solaris
by default, as well as to give extra control on AIX (instead of just
jamming the necessary flag into the config files).
The old --enable-linux-lfs flag has been removed in favor of the
--enable-largefile flag (enabled by default), which can be used on all
platforms.
On systems where large files cannot be supported in this manner,
configure will report as such.
Tested:
h5committest
AIX (NCSA's blue_print machine)
duty, liberty, and linew.
size of nested compound type are calculated by using H5T_cmp_offset. The old way had a bug
in it (see bug #1850).
Tested on jam. I tested the same change for 1.8 on amani, linew, and jam.
Fix for Bug 1793 - h5ls on a non-existent file gives 0 return code
Description:
After the fix, h5ls returns 1 (EXIT_FAILURE) if non-existent file is given.
Tested:
jam, amani, linew
Autotool Upgrade / Libtool Bug Fix
Description:
Updated autotools referenced in bin/reconfigure as follows:
Autoconf 2.64 --> Autoconf 2.65
Automake 1.11 --> Automake 1.11.1
Libtool 2.2.6a --> Libtool 2.2.6b-mcg
The referenced libtool version is a custom version of 2.2.6b. It
has been tweaked to fix a bug in libtool that occurs
when using PGI 10.0 compilers. A check incorrectly categorizes
the C++ compiler as version 1.0 instead of 10.0, and the link
line is subsequently set up incorrectly and fails to compile.
A patch has been made available and will be included in the next
release of libtool, but in the meantime I've applied the patch to a custom
installation as indicated above. This bin/reconfigure now references
the custom installation, and the resulting configure script will correctly
categorize the PGI 10.0 C++ compiler.
Ran bin/reconfigure to regenerate configure and makefiles.
Tested:
jam and amani with PGI 10.0 compilers.
h5committest
The mixed use of RUNTEST (original) and RUNTESTS (new) caused
confusion. E.g., the timings in test/ was still using the old
$RUNTEST. It made more sense to use $RUNTEST which is used
by the dejagnu feature of automake. So, I changed all
$RUNTEST or $RUNTESTS to $RUNEXEC.
config/commence.am & config/conclude.am are the two files
that got changes. Also fixed an error in test/Makefile.am.
The rest are changed by bin/reconfigure.
Tested: h5committested.
Comment says Error exit code is -1 but actual code use 1.
Changed it to EXIT_FAILURE (1) and exit(0) to exit(EXIT_SUCCESS) for
better coding.
Tested: jam.
CFLAGS overhaul
Description:
Modified the way configure handles CFLAGS.
(note: all changes also apply to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS).
1. The configure process will now always preserve a user's CFLAGS
environment variable setup. Any additional flags necessary for compilation
added at configure time will be passed into the Makefiles as AM_CFLAGS,
which is an automake construct to be used in addition to CFLAGS.
This will allow a user to have the final say, as CFLAGS will always appear
later in the compile line than AM_CFLAGS. Additionally, setting CFLAGS
during make will no longer completely erase all flags set by configure,
since they're maintained in AM_CFLAGS.
2. Additionally, where possible, flags previously being assigned directly
into CFLAGS (and thus propagating into h5cc) have now been redirected into
H5_CFLAGS, so they're used ONLY for compiling hdf5, and not embedded into
the h5cc wrapper script as well.
*Note that H5_CFLAGS ultimately is assigned into AM_CFLAGS for use in the
Makefiles. Complete description of changes and build process will be
included in a Configure Document that Elena and I are working on.
3. Removed unsupported config files. This includes:
config/dec-osf*
config/hpux11.00
config/irix5.x
config/powerpc-ibm-aix4.x
config/rs6000-ibm-aix5.x
config/unicos*
4. Modified configure summary to display additional values. Specifically,
appropriate AM_* variables are being shown, as well as H5_FCFLAGS and
H5_CXXFLAGS, which were for some reason not already present.
Tested:
- H5committest
- Tested on all THG / NCSA machines, using several combinations of the more
prominent configure options (c++, fortran, szip, threadsafe, parallel,
et cetera). (Thanks to Quincey for rysnc testing setup!)
- With regards to new automated testing, anything *necessary* for
compilation will be caught by the daily tests as it stands now. (i.e.,
if LDFLAGS is not properly set when szip is used, linking will fail).
Additionally, with regards to which flags get into h5cc, if any
*necessary* flags have been improperly removed, then daily tests should
fail during make installcheck. Additional machine-specific desired
behaviors and/or checks may have to be set up separately within the
daily tests, so this is something to work on.
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.
