On Tue, Nov 8, 2011 at 8:01 PM, Frank Barry <frank.james.barry.gmail.com>wrote:
I needed a /usr/bin/gcc-4.2 to get ./configure through the python step.
>
> Now my issue is that I can build without python ("$ ./configure
> -macAccelerate -nopython gnu") but not with.
>
Yes, this is the second time I've been told of this issue. I'm wary of
upgrading to Lion, myself, and am still using 10.6.8. Building Python on
the Mac is non-trivial, and must be done with the Xcode compilers (at least
according to my experience). Amber(Tools) Python programs should still
work without building Python with AmberTools, and it has actually been
removed in the upcoming version.
Note that needing -nopython is a Lion issue, nothing you're doing
specifically.
HTH,
Jason
Thanks,
> Frank
>
>
>
>
> On Tue, Nov 8, 2011 at 5:47 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > Hello,
> >
> > How did you get the configure script to recognize your MacPorts GCC 4.5
> > binaries? My suggestion is to do it via gcc_select, but the protocol for
> > doing that has changed recently. Do the following:
> >
> > sudo port install gcc_select
> > sudo port select gcc mp-gcc45
> >
> > Now, "gcc" should just be gcc 4.5. You can verify this via "gcc
> --version"
> > and "gfortran --version". Make sure these are the same.
> >
> > What appears to be happening here is that 32-bit libraries (NOT from the
> > version you're linking to) appear to be getting linked into your
> binaries,
> > which isn't what you want. (Although maybe you didn't build 64-bit
> copies
> > of your compilers? If you didn't do this intentionally, I'm pretty sure
> > that the default behavior is to build either universal or 64-bit
> binaries).
> >
> > HTH,
> > Jason
> >
> > On Tue, Nov 8, 2011 at 3:30 PM, Frank Barry <frank.james.barry.gmail.com
> >wrote:
> >
> >> I am having problems installing AmberTools1.5 on a new Mac.
> >>
> >> $ uname -a
> >> Darwin franks-mac-pro 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug 9
> >> 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64
> >>
> >> I am following the "amberonmac" blog instructions here
> >>
> >>
> http://amberonmac.blogspot.com/2011/04/building-ambertools-15-on-105x-or-106x.html
> >>
> >> I have the latest Xcode (4.2) and MacPorts (2.0.3).
> >>
> >> I run into "ld: symbol(s) not found for architecture x86_64" problems
> >> using my standard gcc (4.2.1) and gcc45 (4.5.3) from MacPorts, see
> >> full commands below.
> >>
> >> I found this related post http://archive.ambermd.org/201005/0652.html
> >> but I don't get as far as having a config.h generated.
> >> Any tips?
> >>
> >> Thanks in advance,
> >> Frank
> >>
> >>
> >>
> >> $ ./configure -macAccelerate gnu
> >> Obtaining the gnu suite version:
> >> gcc -v
> >> The version is 4.2.1
> >> Testing the gcc compiler:
> >> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> >> OK
> >> Validating the C++ compiler version:
> >> g++ -v
> >> The version is 4.2.1
> >> OK
> >> Testing the gfortran compiler:
> >> gfortran -O0 -o testp testp.f
> >> OK
> >> Testing mixed C/Fortran compilation:
> >> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
> >> testp.c
> >> gfortran -O0 -c -o testp.f.o testp.f
> >> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> >> testp.c.o testp.f.o -lgfortran -framework Accelerate
> >> ld: warning: ignoring file testp.f.o, file was built for i386 which is
> >> not the architecture being linked (x86_64)
> >> Undefined symbols for architecture x86_64:
> >> "_hello_", referenced from:
> >> _main in testp.c.o
> >> ld: symbol(s) not found for architecture x86_64
> >> collect2: ld returned 1 exit status
> >> ./configure: line 1397: ./testp: No such file or directory
> >> Error: Unable to compile mixed C/Fortran code.
> >> Please check your compiler settings and configure flags.
> >>
> >>
> >>
> >> ## And using MacPorts gcc 4.5.3
> >>
> >> $ ./configure-tmp gnu
> >>
> >> Obtaining the gnu suite version:
> >> gcc-mp-4.5 -v
> >> The version is 4.5.3
> >>
> >> Testing the gcc-mp-4.5 compiler:
> >> gcc-mp-4.5 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> >> testp.c
> >> OK
> >>
> >> Testing the gfortran compiler:
> >> gfortran -O0 -o testp testp.f
> >> OK
> >>
> >> Testing mixed C/Fortran compilation:
> >> gcc-mp-4.5 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o
> >> testp.c.o testp.c
> >> gfortran -O0 -c -o testp.f.o testp.f
> >> gcc-mp-4.5 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> >> testp.c.o testp.f.o -lgfortran
> >> ld: warning: ignoring file testp.f.o, file was built for i386 which is
> >> not the architecture being linked (x86_64)
> >> Undefined symbols for architecture x86_64:
> >> "_hello_", referenced from:
> >> _main in testp.c.o
> >> ld: symbol(s) not found for architecture x86_64
> >> collect2: ld returned 1 exit status
> >> ./configure-tmp: line 1399: ./testp: No such file or directory
> >> Error: Unable to compile mixed C/Fortran code.
> >> Please check your compiler settings and configure flags.
> >>
> >> _______________________________________________
> >> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 08 2011 - 20:30:03 PST
