On Tue, May 4, 2010 at 5:26 AM, Alan <alanwilter.gmail.com> wrote:
> Hi Jason!
>
> On Tue, May 4, 2010 at 01:09, Jason Swails <jason.swails.gmail.com> wrote:
>
> >
> > Something that may make compilation go along better, and is probably a
> > better option if you plan on building other software packages, create a
> > link
> > to gcc-4 and g++-4 named gcc and g++, respectively, in /sw/bin, and make
> > sure that is in your path before /usr/bin (so "gcc" and "g++" invokes the
> > fink gcc-4 and g++-4 rather than the xcode tools version supplied in
> > /usr/bin)
> >
> > You can do this with the commands:
> > cd /sw/bin
> > ln -s gcc-4 gcc
> > ln -s g++-4 g++
> >
> > And in your .bashrc file put
> >
> > export PATH=/sw/bin\:$PATH
> >
> > This should prevent any user from having to modify the config.h file to
> get
> > the right compilers invoked. It should also fix mpicc and mpif90/mpif77,
> > since those are really only wrappers calling gcc and gfortran, anyway. I
> > say this here because both methods result in a successfully built Amber11
> I
> > would imagine, but this method will probably be a more universal fix for
> > other packages users may want to install (i.e. an older version of Amber,
> > another MD package, or any other package someone wishes to build from
> > source).
>
>
> You're absolutely right here. I just want to remember why once discussing
> at
> Fink list they decided to make gcc-4 instead of having Fink gcc overriding
> Apple's gcc in the way you said... Need to check that again with them.
>
I'd imagine it'd have something to do with the fact that FINK actually
downloads source code, modifies what needs to be modified to get it to work
on Mac OS X, and then compiles the programs (rather than having a repository
of binaries that it just downloads and puts in the right place). In this
case, they probably modify what they need to fit the Xcode tools versions of
the gnu compilers. They probably run into some issues if they use different
versions of the compilers occasionally.
Even so, when problems are encountered using FINK, I would probably just
temporarily remove/change the priority of which gcc/g++ is used (by removing
the links or changing PATH or something) so FINK finds the gcc/g++ it wants.
This is a guess based on my experience with MacPorts (which does the same
thing, and after creating symbolic links to gcc/g++/cpp with their version,
I've had trouble building some other softwares with it, though I haven't
tried going back to the old compilers).
All the best,
Jason
>
>
> > > 2) AT 1.4 and Amber11 with Intel Compilers (v. 11.1.088)
> > >
> > > 2.1) With Amber's OMPI 1.4.1 script:
> > > Apart some issues with tests in serial, the paralles versions of
> > ptraj.MPI,
> > > nab, sander.MPI, sander.LES.MPI and pmemd.MPI all failed to run with
> > > something like:
> >
> > I do not get these errors with MacPorts GCC 4.4 installed alongside
> either
> > OpenMPI 1.4.1 (compiled from source with a simple ./configure; make; make
> > install) or MPICH2 1.2.1 (built the same way).
>
>
> Just to be clear, the errors I get are with Intel Compilers and OMPI. With
> Fink GCC 4.4 all fine with Fink OMPI 1.3.3. I didn't test with Amber's OMPI
> 1.4.1 script and Fink GCC but I would be confident that should work fine.
>
> Thanks and all the best,
>
> Alan
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue May 04 2010 - 06:30:04 PDT
