parcellfun test issue on Mac OS 10.8, was Re: problems installing openmpi_ext

[Alexander Hansen]

(thought I'd change the subject)

On 9/8/13 7:54 AM, Alexander Hansen wrote:
> On 9/8/13 6:33 AM, Benjamin Abbott wrote:
> > On Sep 8, 2013, at 8:42 AM, Francis Poulin <address@hidden> wrote:
> >
> > > Hello,
> > >
> > > Thanks to both of you for looking into this.  I am happy to try this
> > > in the debugger but I admit that I've never used it before and I'm
> > > having problems getting started.
> > >
> > > First, you don't mean to use the debugger in octave I bather?  I
> > > tried starting
> > >
> > > octave --debug
> > >
> > > and that give a lot of output, none of which seemed at all useful.
> > >
> > > Second ,you suggest running octave in a debugger and show 'run-octave
> > > -g'.  I did not know you could run octave in a debugger and am not
> > > sure exactly how to do that.  If you could get me started I'm happy
> > > to share the output.
> > >
> > > Thanks again,
> > > Francis
> >
> > Run octave in the gnu debugger, start octave, execute the
> > parcell_example script, when octave crashes run a back trace. The
> > commands are ...
> >
> > run-octave -g
> > run
> > parcell_example
> > bt
> >
> > The copy the output from bt into your reply.
> >
> > Ben
>
> Let me elaborate on how to do this via Fink:
>
> 1)  "run-octave" doesn't get installed under the default Octave build
> and install operation, which is more or less what we do, and Fink by
> default deletes the Octave build directory to save space, so it's
> probably not present.
>
> "fink -k rebuild octave" will do another build but not delete the build
> directory. (The default location is /sw/src/fink.build/octave-3.6.4-5/)
>
> 2)  When you do that rebuild, You might want to edit the CFLAGS and
> CXXFLAGS settings in
> /sw/fink/10.7/stable/main/finkinfo/sci/octave-3.6.4.info to include the
> "-g" flag, e.g
>
>   export CFLAGS='-O3 -MD -g'
>
> to generate debug symbols (I'll probably turn that on for everybody the
> next time I put out a new revision).
>
> 3)  However, I found when I tried this kind of operation last that
> Apple's clang didn't seem to generate the full debugging information, or
> possibly that the gdb debugger as provided by Xcode 4.x didn't know what
> to do with it.  Some additional things to try would be
>
> a) Install Fink's gdb package, which is newer than what Xcode has
> b) Switch the compilers in the "SetCC" and "SetCXX" lines of
> octave-3.6.4.info to be gcc-fsf-4.8 and g++-fsf-4.8, respectively.
>
> I've got a build going right now to do any or all of these.

Here's what I'm seeing right now, with the -g option turned on, using 
clang as the C|C++ compiler, and using the gdb from the Xcode 4.6 
Command Line Tools:

octave:2> parcellfun_example
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Elapsed time is 19.6002 seconds.
parcellfun: child process 72538 created
parcellfun: child process 72539 created
parcellfun: 0/200 jobs donepanic: Trace/BPT trap: 5 -- stopping myself...
panic: Trace/BPT trap: 5 -- stopping myself...
Reading symbols for shared libraries . done


Program received signal EXC_SOFTWARE, Software generated exception.
<signal handler called>
(gdb)
(gdb) bt
#0  <signal handler called>
#1  0x00007fff8e44c280 in read$NOCANCEL ()
#2  0x00007fff86e027b0 in _sread ()
#3  0x00007fff86e01d2f in __srefill1 ()
#4  0x00007fff86dff3e3 in __fread ()
#5  0x00007fff86dff2eb in fread ()
#6  0x00000001027d6f9b in std::istream::read ()


--
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/