That helps Jason, thanks!
Using gcc_select gets me further, however I note something funny here
possibly related to my previous linking efforts.
$ sudo port select gcc mp-gcc44
Selecting 'mp-gcc44' for 'gcc' succeeded. 'mp-gcc44' is now active.
$ gcc -v
gcc-mp-4.4: error trying to exec
'/opt/local/bin/i686-apple-darwin11-llvm-gcc-4.2': execvp: No such
file or directory
$ gfortran --version
GNU Fortran (GCC) 4.4.6
Copyright (C) 2010 Free Software Foundation, Inc.
...
$ gcc
gcc-mp-4.4: error trying to exec
'/opt/local/bin/i686-apple-darwin11-llvm-gcc-4.2': execvp: No such
file or directory
This may be related to my use of:
$ sudo ln -s llvm-gcc-4.2 /usr/bin/gcc-4.2
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.
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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Received on Tue Nov 08 2011 - 17:30:02 PST
