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

[Alexander Hansen]

On 9/8/13 8:27 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 ()

Using a "real" (FSF) gcc and g++ for the C|C++ compilers, and with 
optimizations at 0, I got the following:

(gdb) bt
#0  0x00007fff5fc1a176 in 
__dyld__ZN26ImageLoaderMachOCompressed20doBindFastLazySymbolEjRKN11ImageLoader11LinkContextEPFvvES5_ 
()
#1  0x00007fff5fc04017 in 
__dyld__ZN4dyld18fastBindLazySymbolEPP11ImageLoaderm ()
#2  0x00007fff89b658ee in dyld_stub_binder_ ()
#3  0x0000000100b38bf8 in int 
idx_vector::assign<octave_value>(octave_value const*, int, 
octave_value*) const::__func__ ()
#4  <signal handler called>
#5  0x00007fff8e44c212 in __pthread_kill ()
#6  0x00007fff86d96b54 in pthread_kill ()
#7  0x00007fff86ddadce in abort ()
#8  0x00007fff86dae9b9 in free ()
#9  0x00000001055e7c23 in Ffload ()
#10 0x00000001003db5cc in octave_builtin::do_multi_index_op 
(this=0x107052d90, nargout=1, address@hidden, lvalue_list=0x0) at 
ov-builtin.cc:131
#11 0x00000001003db27a in octave_builtin::subsref (this=0x107052d90, 
address@hidden, address@hidden, nargout=1, lvalue_list=0x0) 
at ov-builtin.cc:63
#12 0x00000001003db168 in octave_builtin::subsref (this=0x107052d90, 
address@hidden, address@hidden, nargout=1) at ov-builtin.cc:47
#13 0x00000001003dbdd5 in octave_builtin::subsref (this=0x107052d90, 
address@hidden, address@hidden) at ov-builtin.h:55
#14 0x0000000100484f0b in octave_value::subsref (this=0x7fff5fbfbd20, 
address@hidden, address@hidden, nargout=1) at ov.cc:1225
#15 0x0000000100484ff7 in octave_value::subsref (this=0x7fff5fbfbd20, 
address@hidden, address@hidden, nargout=1, lvalue_list=0x0) 
at ov.cc:1238
#16 0x00000001005203d2 in tree_index_expression::rvalue 
(this=0x10605a5b0, nargout=1, lvalue_list=0x0) at pt-idx.cc:413
#17 0x000000010051fb21 in tree_index_expression::rvalue 
(this=0x10605a5b0, nargout=1) at pt-idx.cc:284
#18 0x0000000100520668 in tree_index_expression::rvalue1 
(this=0x10605a5b0, nargout=1) at pt-idx.cc:425
#19 0x000000010050d9d4 in tree_simple_assignment::rvalue1 
(this=0x10605a720) at pt-assign.cc:210
#20 0x0000000100519b0e in tree_evaluator::visit_statement 
(this=0x100daa838, address@hidden) at pt-eval.cc:736
#21 0x0000000100538a5c in tree_statement::accept (this=0x106059fc0, 
address@hidden) at pt-stmt.cc:151
#22 0x0000000100519ccd in tree_evaluator::visit_statement_list 
(this=0x100daa838, address@hidden) at pt-eval.cc:772
#23 0x0000000100538de2 in tree_statement_list::accept (this=0x10604c7b0, 
address@hidden) at pt-stmt.cc:215
#24 0x00000001005195ad in tree_evaluator::visit_if_command_list 
(this=0x100daa838, address@hidden) at pt-eval.cc:573
#25 0x000000010053712a in tree_if_command_list::accept 
(this=0x10605a860, address@hidden) at pt-select.cc:83
#26 0x0000000100519497 in tree_evaluator::visit_if_command 
(this=0x100daa838, address@hidden) at pt-eval.cc:551
#27 0x00000001005373f4 in tree_if_command::accept (this=0x10605bf70, 
address@hidden) at pt-select.cc:108
#28 0x00000001005199fd in tree_evaluator::visit_statement 
(this=0x100daa838, address@hidden) at pt-eval.cc:706
#29 0x0000000100538a5c in tree_statement::accept (this=0x10605bfa0, 
address@hidden) at pt-stmt.cc:151
#30 0x0000000100519ccd in tree_evaluator::visit_statement_list 
(this=0x100daa838, address@hidden) at pt-eval.cc:772
#31 0x0000000100538de2 in tree_statement_list::accept (this=0x10604e4f0, 
address@hidden) at pt-stmt.cc:215
#32 0x000000010051a47c in tree_evaluator::visit_while_command 
(this=0x100daa838, address@hidden) at pt-eval.cc:1048
#33 0x0000000100523874 in tree_while_command::accept (this=0x106065a60, 
address@hidden) at pt-loop.cc:68
#34 0x00000001005199fd in tree_evaluator::visit_statement 
(this=0x100daa838, address@hidden) at pt-eval.cc:706
#35 0x0000000100538a5c in tree_statement::accept (this=0x106065aa0, 
address@hidden) at pt-stmt.cc:151
#36 0x0000000100519ccd in tree_evaluator::visit_statement_list 
(this=0x100daa838, address@hidden) at pt-eval.cc:772
#37 0x0000000100538de2 in tree_statement_list::accept (this=0x106065ac0, 
address@hidden) at pt-stmt.cc:215
#38 0x000000010051a335 in tree_evaluator::visit_unwind_protect_command 
(this=0x100daa838, address@hidden) at pt-eval.cc:1003
#39 0x000000010051b8da in tree_unwind_protect_command::accept 
(this=0x106068300, address@hidden) at pt-except.cc:99
#40 0x00000001005199fd in tree_evaluator::visit_statement 
(this=0x100daa838, address@hidden) at pt-eval.cc:706
#41 0x0000000100538a5c in tree_statement::accept (this=0x106068030, 
address@hidden) at pt-stmt.cc:151
#42 0x0000000100519ccd in tree_evaluator::visit_statement_list 
(this=0x100daa838, address@hidden) at pt-eval.cc:772
#43 0x0000000100538de2 in tree_statement_list::accept (this=0x106044e00, 
address@hidden) at pt-stmt.cc:215
#44 0x00000001005195ad in tree_evaluator::visit_if_command_list 
(this=0x100daa838, address@hidden) at pt-eval.cc:573
#45 0x000000010053712a in tree_if_command_list::accept 
(this=0x106044bb0, address@hidden) at pt-select.cc:83
#46 0x0000000100519497 in tree_evaluator::visit_if_command 
(this=0x100daa838, address@hidden) at pt-eval.cc:551
#47 0x00000001005373f4 in tree_if_command::accept (this=0x106071cf0, 
address@hidden) at pt-select.cc:108
#48 0x00000001005199fd in tree_evaluator::visit_statement 
(this=0x100daa838, address@hidden) at pt-eval.cc:706
#49 0x0000000100538a5c in tree_statement::accept (this=0x106071d20, 
address@hidden) at pt-stmt.cc:151
#50 0x0000000100519ccd in tree_evaluator::visit_statement_list 
(this=0x100daa838, address@hidden) at pt-eval.cc:772
#51 0x0000000100538de2 in tree_statement_list::accept (this=0x10613fbd0, 
address@hidden) at pt-stmt.cc:215
#52 0x0000000100478fcc in octave_user_function::do_multi_index_op 
(this=0x106071e20, nargout=1, address@hidden, lvalue_list=0x0) at 
ov-usr-fcn.cc:475
#53 0x0000000100478890 in octave_user_function::subsref 
(this=0x106071e20, address@hidden, address@hidden, nargout=1, 
lvalue_list=0x0) at ov-usr-fcn.cc:326
#54 0x000000010047877e in octave_user_function::subsref 
(this=0x106071e20, address@hidden, address@hidden, nargout=1) 
at ov-usr-fcn.cc:310
#55 0x000000010047c9fd in octave_user_function::subsref 
(this=0x106071e20, address@hidden, address@hidden) at 
ov-usr-fcn.h:299
#56 0x0000000100484f0b in octave_value::subsref (this=0x7fff5fbfced0, 
address@hidden, address@hidden, nargout=1) at ov.cc:1225
#57 0x0000000100484ff7 in octave_value::subsref (this=0x7fff5fbfced0, 
address@hidden, address@hidden, nargout=1, lvalue_list=0x0) 
at ov.cc:1238
#58 0x00000001005203d2 in tree_index_expression::rvalue 
(this=0x10737c390, nargout=1, lvalue_list=0x0) at pt-idx.cc:413
#59 0x000000010051fb21 in tree_index_expression::rvalue 
(this=0x10737c390, nargout=1) at pt-idx.cc:284
#60 0x0000000100520668 in tree_index_expression::rvalue1 
(this=0x10737c390, nargout=1) at pt-idx.cc:425
#61 0x000000010050d9d4 in tree_simple_assignment::rvalue1 
(this=0x10737cba0) at pt-assign.cc:210
#62 0x0000000100519b0e in tree_evaluator::visit_statement 
(this=0x100daa838, address@hidden) at pt-eval.cc:736
#63 0x0000000100538a5c in tree_statement::accept (this=0x10737b410, 
address@hidden) at pt-stmt.cc:151
#64 0x0000000100519ccd in tree_evaluator::visit_statement_list 
(this=0x100daa838, address@hidden) at pt-eval.cc:772
#65 0x0000000100538de2 in tree_statement_list::accept (this=0x107364c10, 
address@hidden) at pt-stmt.cc:215
#66 0x000000010047767b in octave_user_script::do_multi_index_op 
(this=0x10737c5c0, nargout=0, address@hidden) at ov-usr-fcn.cc:138
#67 0x00000001004853f0 in octave_value::do_multi_index_op 
(this=0x7fff5fbfd520, nargout=0, address@hidden) at ov.cc:1292
#68 0x000000010051d6d4 in tree_identifier::rvalue (this=0x107361280, 
nargout=0) at pt-id.cc:85
#69 0x000000010051d8ea in tree_identifier::rvalue1 (this=0x107361280, 
nargout=0) at pt-id.cc:106
#70 0x0000000100519b0e in tree_evaluator::visit_statement 
(this=0x100daa838, address@hidden) at pt-eval.cc:736
#71 0x0000000100538a5c in tree_statement::accept (this=0x1073612f0, 
address@hidden) at pt-stmt.cc:151
#72 0x0000000100519ccd in tree_evaluator::visit_statement_list 
(this=0x100daa838, address@hidden) at pt-eval.cc:772
#73 0x0000000100538de2 in tree_statement_list::accept (this=0x107361310, 
address@hidden) at pt-stmt.cc:215
#74 0x0000000100376e4b in main_loop () at toplev.cc:595
#75 0x000000010032a111 in octave_main (argc=6, argv=0x7fff5fbfd9f8, 
embedded=0) at octave.cc:943
#76 0x0000000100000f8c in main (argc=6, argv=0x7fff5fbfd9f8) at main.c:35


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