This patch won't fix that error, it will fix the other one people were
getting.
This is really just a PATH issue. Look at your PATH variable
echo $PATH
and you will see that /usr/bin comes before /opt/local/bin (that's the only
possible explanation). Then you should look at your ~/.profile,
~/.bash_profile (if it exists), and your ~/.bashrc to see why this is
happening. Note the difference between prepending and appending to your
PATH.
Also, changing Xcode versions will NOT fix this issue.
HTH,
Jason
On Fri, Jun 8, 2012 at 9:59 AM, Jonathan Gough
<jonathan.d.gough.gmail.com>wrote:
> 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
> >
> _______________________________________________
> 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
Received on Fri Jun 08 2012 - 08:30:02 PDT
