I'm assuming you recompiled? Perhaps try to remove the whole amber11
directory, untar the archive again, and retry.
Good luck!
Jason
On Thu, Jul 8, 2010 at 8:41 AM, Jorgen Simonsen <jorgen589.gmail.com> wrote:
> hmmm strange I keep on getting the error
>
> Users/greisen/amber11/bin/nab -c matextract.nab
> /Users/greisen/amber11/bin/nab -o matextract matextract.o
> /Users/greisen/amber11/bin/nab -c matgen.nab
> /Users/greisen/amber11/bin/nab -o matgen matgen.o
> Undefined symbols:
> "_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_real_to_complex_", referenced from:
> ___rism_fft_MOD_rlft3i in libnab.a(rism_fft.o)
> "_rfftwnd_f77_one_complex_to_real_", referenced from:
> ___rism_fft_MOD_rlft3i in libnab.a(rism_fft.o)
> "_rfftwnd_f77_destroy_plan_", referenced from:
> ___rism3d_c_MOD_rism3d_destroy in libnab.a(rism3d_c.o)
> ___rism3d_c_MOD_rism3d_destroy in libnab.a(rism3d_c.o)
> ___rism3d_c_MOD_reallocbox in libnab.a(rism3d_c.o)
> ___rism3d_c_MOD_reallocbox in libnab.a(rism3d_c.o)
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> cc failed!
>
> I run these
> make clean
>
> sudo port install gcc44
> sudo port install gcc_select
> sudo gcc_select mp-gcc44
>
>
>
> I have updated the gcc as suggested
>
> gfortran -v
> Using built-in specs.
> Target: i386-apple-darwin9
> Configured with: ../gcc-4.4.4/configure --prefix=/opt/local
> --build=i386-apple-darwin9
> --enable-languages=c,c++,objc,obj-c++,java,fortran
> --libdir=/opt/local/lib/gcc44 --includedir=/opt/local/include/gcc44
> --infodir=/opt/local/share/info --mandir=/opt/local/share/man
> --with-local-prefix=/opt/local --with-system-zlib --disable-nls
> --program-suffix=-mp-4.4
> --with-gxx-include-dir=/opt/local/include/gcc44/c++/ --with-gmp=/opt/local
> --with-mpfr=/opt/local --enable-stage1-checking
> Thread model: posix
> gcc version 4.4.4 (GCC)
>
> Using built-in specs.
> Target: i386-apple-darwin9
> Configured with: ../gcc-4.4.4/configure --prefix=/opt/local
> --build=i386-apple-darwin9
> --enable-languages=c,c++,objc,obj-c++,java,fortran
> --libdir=/opt/local/lib/gcc44 --includedir=/opt/local/include/gcc44
> --infodir=/opt/local/share/info --mandir=/opt/local/share/man
> --with-local-prefix=/opt/local --with-system-zlib --disable-nls
> --program-suffix=-mp-4.4
> --with-gxx-include-dir=/opt/local/include/gcc44/c++/ --with-gmp=/opt/local
> --with-mpfr=/opt/local --enable-stage1-checking
> Thread model: posix
> gcc version 4.4.4 (GCC)
>
>
>
>
>
> On Thu, Jul 8, 2010 at 1:14 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > Hello,
> >
> > You should be using the same version of gcc and gfortran. I think your
> > version of gcc is too old, anyway. Try installing gcc-4.4 from macports
> or
> > fink, and use those compilers instead. amberonmac.blogspot.com has
> > instructions for how to do this.
> >
> > Good luck!
> > Jason
> >
> > On Thu, Jul 8, 2010 at 6:42 AM, Jorgen Simonsen <jorgen589.gmail.com>
> > wrote:
> >
> > > Hi
> > >
> > > I have followed the instructions on that homepage but I still get the
> > same
> > > error
> > >
> > > My gcc is gcc version 4.0.1 (Apple Inc. build 5493) and gfortran is gcc
> > > version 4.2.3
> > >
> > > thanks in advance
> > >
> > > On Thu, Jul 8, 2010 at 2:58 AM, Jason Swails <jason.swails.gmail.com>
> > > wrote:
> > >
> > > > Hello,
> > > >
> > > > What version of gcc and gfortran are you using? Did you read and
> > follow
> > > > the
> > > > instructions for installing on amber on macs at
> > > > http://amberonmac.blogspot.com/ ? If you follow those instructions
> > and
> > > > make
> > > > sure you have the proper compilers (you should update with macports
> if
> > > all
> > > > you have is the version apple includes from xcode tools).
> > > >
> > > > Good luck!
> > > > Jason
> > > >
> > > > On Wed, Jul 7, 2010 at 7:21 PM, Jorgen Simonsen <jorgen589.gmail.com
> >
> > > > wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > > I am trying to compile ambertools on Mac OS leopard but i get this
> > > error
> > > > >
> > > > > ld warning: for symbol _blk_green_ tentative definition of size
> 74096
> > > > from
> > > > > /Users/amber11/lib/libnab.a(pb_force.o) is is smaller than the real
> > > > > definition of size 74088 from
> /Users/amber11/lib/libnab.a(pb_init.o)
> > > > >
> > > > > Undefined symbols:
> > > > > "_rfftw3d_f77_create_plan_", referenced from:
> > > > > ___rism_fft__fftw_make_plans in libnab.a(rism_fft.o)
> > > > > ___rism_fft__fftw_make_plans in libnab.a(rism_fft.o)
> > > > > "_rfftwnd_f77_one_real_to_complex_", referenced from:
> > > > > ___rism_fft__rlft3i in libnab.a(rism_fft.o)
> > > > > "_rfftwnd_f77_one_complex_to_real_", referenced from:
> > > > > ___rism_fft__rlft3i in libnab.a(rism_fft.o)
> > > > > "_rfftwnd_f77_destroy_plan_", referenced from:
> > > > > ___rism3d_c__rism3d_destroy in libnab.a(rism3d_c.o)
> > > > > ___rism3d_c__rism3d_destroy in libnab.a(rism3d_c.o)
> > > > > ___rism3d_c__reallocbox in libnab.a(rism3d_c.o)
> > > > > ___rism3d_c__reallocbox in libnab.a(rism3d_c.o)
> > > > > ld: symbol(s) not found
> > > > > collect2: ld returned 1 exit status
> > > > > cc failed!
> > > > > make[1]: *** [matgen] Error 1
> > > > > make: *** [serial] Error 2
> > > > >
> > > > > Any help appreciated thanks in advance
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Graduate Student
> > > > 352-392-4032
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 08 2010 - 06:00:05 PDT
