got it.
I did
port select --list gcc
sudo port select gcc mp-gcc46
Selecting 'mp-gcc46' for 'gcc' succeeded. 'mp-gcc46' is now active.
which gcc
/opt/local/bin/gcc
whew.... Thanks Jason
On Fri, Jun 8, 2012 at 11:34 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Try it in a new shell. Something must be borked.
>
> Unless... do:
>
> ls /opt/local/bin/gcc
>
> Is there anything there?
>
>
> On Fri, Jun 8, 2012 at 11:28 AM, Jonathan Gough
> <jonathan.d.gough.gmail.com>wrote:
>
> > this is what I get.
> >
> > echo $PATH
> >
> >
> /opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
> >
> > I think /opt/local/bin is first. or am i reading it backwards?
> >
> > On Fri, Jun 8, 2012 at 11:06 AM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > 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
> > >
> > _______________________________________________
> > 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
Received on Fri Jun 08 2012 - 09:00:04 PDT
