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
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Received on Tue Nov 08 2011 - 15:00:02 PST
