Oi. No luck.
copied bugfix.8 to $amberhome directory.
did ./patch_amber.py --apply bugfix.8
(not sure where the directory is to move the file to though)
and I still get the gcc 4.2.1 error.
I am now kicking myself for being impatient and downgrading xtools... also
laughing because there is nothing else i can do...
./configure gnu
Checking for updates...
AmberTools12 is up to date
Amber12 is up to date
Searching for python2... Found python2.7: /opt/local/bin/python2.7
Obtaining the gnu suite version:
gcc -v
The version is 4.2.1
ERROR: RISM and PBSA FFT solver require version 4.3 or higher of the GNU
compiler.
Please re-run configure with the '-nofftw3' flag to use this
compiler:
./configure -nofftw3 gnu
Configure failed due to the errors above!
On Fri, Jun 8, 2012 at 9:25 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, Jun 8, 2012 at 8:51 AM, Jonathan Gough
> <jonathan.d.gough.gmail.com>wrote:
>
> > i'm now downloading the app store version of xcode. do you think i need
> to
> > uninstall and reinstall macports again?
> >
>
> No, you should be fine. If you apply the fix I posted, it should work
> regardless.
>
> As was mentioned elsewhere, some ports "remember" which Xcode was used to
> build them, but in this case, if GCC does remember, the bug will not be an
> issue. If it doesn't, the patch should fix things, anyway.
>
> HTH,
> Jason
>
>
> >
> > On Fri, Jun 8, 2012 at 8:05 AM, Jonathan Gough
> > <jonathan.d.gough.gmail.com>wrote:
> >
> > > thats too funny...
> > >
> > > i have
> > >
> > > which gcc
> > > /usr/bin/gcc
> > >
> > > # MacPorts Installer addition on 2011-12-17_at_20:09:57: adding an
> > > appropriate PATH variable for use with MacPorts.
> > > export PATH=/opt/local/bin:/opt/local/sbin:$PATH
> > > # Finished adapting your PATH environment variable for use with
> MacPorts.
> > > export AMBERHOME=/Users/jonathangough/amber12
> > >
> > > On Fri, Jun 8, 2012 at 8:01 AM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> > >
> > >> On Fri, Jun 8, 2012 at 7:56 AM, Jonathan Gough
> > >> <jonathan.d.gough.gmail.com>wrote:
> > >>
> > >> > I did a FULL uninstall of Xcode and macports (including wiping
> > >> /opt/local).
> > >> > Used the shell script to clear out xcode, deleted the app files.
> > >> macports
> > >> > I followed all the instructions including removing all other files.
> (
> > >> > http://guide.macports.org/#installing.macports.uninstalling)
> > >> >
> > >> > Installed 4.3.1 and the lion macports pkg.
> > >> >
> > >> > installed all the ports needed for amber (sudo port install gcc44
> > gcc46
> > >> > gcc_select mpich2 +gcc44 python27 py27-numpy python_select molden
> > +gcc44
> > >> > grace gnuplot bkchem chemtool netpbm pymol)
> > >> >
> > >> > ./configure gnu
> > >> >
> > >> >
> > >> > gives me the following error.
> > >> >
> > >> > he version is 4.2.1
> > >> >
> > >> > ERROR: RISM and PBSA FFT solver require version 4.3 or higher of the
> > GNU
> > >> > compiler.
> > >> >
> > >> > Please re-run configure with the '-nofftw3' flag to use this
> > >> > compiler:
> > >> >
> > >> > ./configure -nofftw3 gnu
> > >> >
> > >> > Configure failed due to the errors above!
> > >> >
> > >> > i did the switch to mp-gcc46
> > >> >
> > >> > port select --list gcc
> > >> >
> > >> > Available versions for gcc:
> > >> >
> > >> > gcc42
> > >> >
> > >> > llvm-gcc42
> > >> >
> > >> > mp-gcc44
> > >> >
> > >> > mp-gcc45
> > >> >
> > >> > mp-gcc46 (active)
> > >> >
> > >> > none
> > >> >
> > >> > but gcc -v gives me
> > >> >
> > >> > gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build
> > >> 2336.9.00)
> > >> >
> > >> > any thoughts on how to proceed next?
> > >> >
> > >>
> > >> Type "which gcc" and make sure your PATH is set up correctly. In your
> > >> ~/.bash_profile or ~/.profile you should see lines like this:
> > >>
> > >> # MacPorts Installer addition on 2012-04-22_at_18:23:26: adding an
> > >> appropriate PATH variable for use with MacPorts.
> > >> export PATH=/opt/local/bin:/opt/local/sbin:$PATH
> > >> # Finished adapting your PATH environment variable for use with
> > MacPorts.
> > >>
> > >> For me it's in my ~/.profile.
> > >>
> > >> On the bright side (downside since you went through all this
> already?),
> > I
> > >> just got a fix working for Xcode 4.3.2 that solves the issues on my
> > >> machine
> > >> (literally just now within the last 10 minutes).
> > >>
> > >> Since there were so many threads reporting the issue (i.e., more than
> 1
> > >> :))
> > >> I'm going to announce separately.
> > >>
> > >> All the best,
> > >> Jason
> > >>
> > >> --
> > >> Jason M. Swails
> > >> Quantum Theory Project,
> > >> University of Florida
> > >> Ph.D. Candidate
> > >> 352-392-4032
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jun 08 2012 - 07:00:03 PDT
