This worked perfectly, thanks Paul!
On Sat, 14 Aug 2010, Paul S. Nerenberg wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Aug 15 2010 - 14:00:03 PDT
