Hi John,
My response might sound somewhat like a broken record, but I would
recommend building with the "real" gnu compilers (which can be
obtained/built in a fairly straightforward manner by MacPorts or
fink...or even from scratch) rather than a hodge-podge of Xcode and a
pre-compiled gfortran. If you search back in the list archive,
several people have posted information about doing this, but I will
include my abbreviated instructions (adapted from
http://amberonmac.blogspot.com/2010/04/step-by-step-ambertools-14-installation.html)
that seem to work well on a variety of 10.5 and 10.6 machines:
(1) download and install the latest Xcode (3.2.x) -- sounds like
you've already done this
(2) download and install the latest version of MacPorts (1.9.x)
(3) use MacPorts to install gcc 4.4.4 (sudo port install gcc44)
(4) use MacPorts to install gcc_select (sudo port install gcc_select)
(5) use gcc_select to make gcc 4.4.4 your default compilers (sudo
gcc_select mp-gcc44)
(6) download AmberTools and unpack it into a directory *other than* /
usr/local (e.g., /Users/your_username/amber11) -- this avoids all of
the permission/ownership issues of trying to build in /usr/local
(7) set your $AMBERHOME environment variable to the appropriate
directory (this depends on what shell you're using, but usually can be
done in the .profile file in your home directory)
(8) configure AmberTools as "usual" (./configure -macAccelerate gnu)
Best,
Paul
On Aug 14, 2010, at 10:04 PM, John McGuigan wrote:
> Hello fellow AMBER users,
>
> I'm having trouble compiling just AmberTools-1.4 (amber11) on a OS X
> 10.6.4 machine. When I run ./configure gnu it seems to go okay, but
> after
> running make it goes for a while and stops with this error:
>
> /usr/local/apps/amber11/bin/nab -o matgen matgen.o
> Undefined symbols:
> "_rfftwnd_f77_destroy_plan_", referenced from:
> ___rism3d_c_MOD_reallocbox in libnab.a(rism3d_c.o)
> ___rism3d_c_MOD_reallocbox in libnab.a(rism3d_c.o)
> ___rism3d_c_MOD_rism3d_destroy in libnab.a(rism3d_c.o)
> ___rism3d_c_MOD_rism3d_destroy in libnab.a(rism3d_c.o)
> "_rfftwnd_f77_one_real_to_complex_", referenced from:
> ___rism_fft_MOD_rlft3i in libnab.a(rism_fft.o)
> "_rfftw3d_f77_create_plan_", referenced from:
> ___rism_fft_MOD_fftw_make_plans in libnab.a(rism_fft.o)
> ___rism_fft_MOD_fftw_make_plans in libnab.a(rism_fft.o)
> "_rfftwnd_f77_one_complex_to_real_", referenced from:
> ___rism_fft_MOD_rlft3i in libnab.a(rism_fft.o)
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> cc failed!
> make[1]: *** [matgen] Error 1
> make: *** [serial] Error 2
>
> I see earlier on in the compiling process specifically for fftw,
> ranlib
> complains that:
>
> /usr/bin/ranlib: file: libnab.a(fftwf77.o) has no symbols
> /usr/bin/ranlib: file: libnab.a(rfftwf77.o) has no symbols
> rm -rf /usr/local/apps/amber11/lib/temp
> ranlib libnab.a
> ranlib: file: libnab.a(fftwf77.o) has no symbols
> ranlib: file: libnab.a(rfftwf77.o) has no symbols
>
> I presume that these are connected but I don't know how to compile
> fftwf77.o or rfftwf77.o with (debugging?) symbols.
>
> I'm using the version of GCC that came with Xcode for 10.6 and
> gfortran
> (and g77) from http://hpc.sourceforge.net/
>
> Any help in this matter would be greatly appreciated.
>
> Thanks,
>
> John McGuigan
>
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> AMBER.ambermd.org
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Received on Sun Aug 15 2010 - 00:00:05 PDT
