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

[Ben Abbott]

On Sep 8, 2013, at 11:27 AM, Alexander Hansen wrote:

> (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 ()

Alex,

Sorry for the late response.  I'm able to run the parcellfun_example using 
3.6.4 from Macports.  My variants are +atlas+docs+fltk+gcc47+x11.

        
https://trac.macports.org/browser/trunk/dports/math/octave-devel/Portfile

Perhaps duplicating the configure options used by macports will clear things up 
for you?

Ben