Re: problems installing openmpi_ext

[Alexander Hansen]

On 9/6/13 6:09 PM, Alexander Hansen wrote:
> On 9/6/13 2:00 PM, Alexander Hansen wrote:
> > On 9/4/13 2:56 AM, c. wrote:
> > > On 3 Sep 2013, at 20:03, Francis Poulin <address@hidden> wrote:
> > >
> > > > Hello,
> > > >
> > > > I took your advice.  I removed octave and then reinstalled it along
> > > > with octave-dev (on fink).  After, I installed the packages using
> > > > -forge and loaded general.
> > > >
> > > > When I try running the example it seems to have a different problem,
> > > > see below.  Unfortunately, I can't figure out what the problem is.
> > > >
> > > > Any advice would be greatly appreciated.
> > > >
> > > > Thanks,
> > > > Francis
> > >
> > > It is usually not recommended to mix installation methods, so if you
> > > installed Octave via Fink,
> > > you should also install forge packages via Fink when available.
> > >
> > > You should probably also remove the file
> > >
> > >    ~/.octave_packages
> > >
> > > and the folder
> > >
> > >    ~/octave
> > >
> > > before reinstalling the packages to avoid conflicts.
> > >
> > > just for your reference here is the output I get from
> > > parcellfun_example on my mac:
> > >
> > > > > parcellfun_example
> > > Elapsed time is 11.9283 seconds.
> > > parcellfun: child process 34820 created
> > > parcellfun: child process 34821 created
> > > parcellfun: 200/200 jobs done
> > > parcellfun: waiting for child process 34820 to close
> > > parcellfun: waiting for child process 34821 to close
> > > Elapsed time is 8.0128 seconds.
> > >
> > > c.
> >
> >
> > Fink's build process for the general package is pretty much identical to
> > just installing it manually, and it appears to produce the same failure.
> > :-(
> >
> > My assumption is that some of the options that I'm using to build Octave
> > aren't the best.  Here's what Fink uses (at least for the variant that
> > uses untuned LAPACK):
> >
> > octave:2> octave_config_info.config_opts
> > ans = '--prefix=/sw' '--with-lapack=-L/sw/lib/lapack/3.4.2 -lreflapack'
> > '--with-blas=-L/sw/lib/lapack/3.4.2 -lrefblas' '--with-framework-carbon'
> > '--with-x' '--x-libraries=/usr/X11/lib' '--x-includes=/usr/X11/include'
> > '--with-magick=GraphicsMagick'
> > '--with-qhull-includedir=/sw/include/libqhull'
> > '--host=x86_64-apple-darwin' '--build=x86_64-apple-darwin'
> > '--infodir=/sw/share/info' '--mandir=/sw/share/man'
> > '--libexecdir=/sw/lib' '--enable-shared' '--enable-dl'
> > '--disable-static' '--disable-docs' '--enable-dependency-tracking'
> > 'build_alias=x86_64-apple-darwin' 'host_alias=x86_64-apple-darwin'
> > 'CC=flag-sort -r gcc' 'CFLAGS=-O3 -MD' 'LDFLAGS=-Wl,-dead_strip_dylibs
> > -L/sw/lib' 'CPPFLAGS=-I/sw/include' 'CXX=flag-sort -r g++' 'CXXFLAGS=-O3
> > -MD -I/usr/X11/include' 'F77=/sw/bin/gfortran-fsf-4.8' 'FFLAGS=-O3'
>
> I should have added that "flag-sort" is a script that sorts the flags
> fed to the compiler, and that "g++" and "gcc" are Apple's clang++ and
> clang in this case.

Following up:

I tried rebuilding Octave (followed by rebuilding general) changing -O3 
to -O0 in the CFLAGS and CXXFLAGS, as well as switching the C and C++ 
compilers to our FSF gcc-4.8, but I'm still getting the malloc() error 
that Francis reported

octave:1> parcellfun_example
Elapsed time is 9.4712 seconds.
parcellfun: child process 46393 created
parcellfun: child process 46394 created
parcellfun: 0/200 jobs doneoctave(46386,0x7fff7479d180) malloc: *** 
error for object 0x10c7f07e0: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
panic: Abort trap: 6 -- stopping myself...

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