This looks like a compiler error. Try starting from a clean tree (make
clean) and start over.
Also, what gcc/gfortran versions are you using?
All the best,
Jason
On Mon, Nov 21, 2011 at 1:25 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> cheers I am not quite there yet
>
> I get this new error during compilation
>
> amber11/bin/nab -o matgen matgen.o
> Undefined symbols for architecture x86_64:
> "__gfortran_os_error", referenced from:
> _cstr2fstr_ in libsff.a(amber_rism_interface.o)
> _rism_writesolvdistf_ in libsff.a(amber_rism_interface.o)
> _unorient_ in libsff.a(amber_rism_interface.o)
> _orient_ in libsff.a(amber_rism_interface.o)
> _rism_thermo_ in libsff.a(amber_rism_interface.o)
> _rism_force_ in libsff.a(amber_rism_interface.o)
> ___rism3d_opendx_MOD_readdxheader_unit in librism.a(rism3d_opendx.o)
> ...
> "__gfortran_runtime_error_at", referenced from:
> ___rism3d_c_MOD_rism3d_destroy in librism.a(rism3d_c.o)
> ___solvent_accessibility_MOD_sa_driver in libpbsa.a(sa_driver.o)
> ___rism3d_closure_c_MOD_rism3d_closure_destroy in
> librism.a(rism3d_closure_c.o)
> ___safemem_MOD_safemem_realloc_1d_integer in librism.a(safemem.o)
> ___safemem_MOD_safemem_realloc_2d_integer in librism.a(safemem.o)
> ___safemem_MOD_safemem_realloc_1d_logical in librism.a(safemem.o)
> ___safemem_MOD_safemem_realloc_1d_real in librism.a(safemem.o)
> ...
> ld: symbol(s) not found for architecture x86_64
> collect2: ld returned 1 exit status
> cc failed!
> make[1]: *** [matgen] Error 1
> make: *** [serial] Error 2
>
>
> On Mon, Nov 21, 2011 at 5:07 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > On Mon, Nov 21, 2011 at 10:16 AM, Gustavo Seabra
> > <gustavo.seabra.gmail.com>wrote:
> >
> >> Hi Jason,
> >>
> >> What will happen to the Python-based tools that are currently part of
> >> AmberTools?
> >>
> >
> > They will just use the system Python.
> >
> >
> >>
> >> Gustavo Seabra
> >> Professor Adjunto
> >> Departamento de Química Fundamental
> >> Universidade Federal de Pernambuco
> >> Fone: +55-81-2126-7417
> >>
> >>
> >> On Mon, Nov 21, 2011 at 12:04 PM, Jason Swails <jason.swails.gmail.com
> >> >wrote:
> >>
> >> > Hello,
> >> >
> >> > Python does not build on OS X Lion. Try configuring with the
> -nopython
> >> > flag. We won't be distributing Python with Amber/AmberTools in the
> >> future.
> >> >
> >> > HTH,
> >> > Jason
> >> >
> >> > On Mon, Nov 21, 2011 at 9:47 AM, Jorgen Simonsen <jorgen589.gmail.com
> >> > >wrote:
> >> >
> >> > > Hi all
> >> > >
> >> > > I am trying to install AmberTools in Lion Os with the following
> version
> >> > >
> >> > > uname -v
> >> > >
> >> > > Darwin Kernel Version 11.2.0: Tue Aug 9 20:54:00 PDT 2011;
> >> > > root:xnu-1699.24.8~1/RELEASE_X86_64
> >> > >
> >> > > I use the configure script with the following parameters as
> specified
> >> > >
> >> > > ./configure -macAccelerate gnu
> >> > >
> >> > > and get the following error
> >> > >
> >> > > /usr/bin/libtool: can't locate file for: -lSystemStubs
> >> > > /usr/bin/libtool: file: -lSystemStubs is not an object file (not
> >> > > allowed in a library)
> >> > > make[1]: *** [Python.framework/Versions/2.6/Python] Error 1
> >> > > make: *** [python] Error 2
> >> > >
> >> > > my version of python is 2.7.2 and gcc is 4.2.1
> >> > >
> >> > > >From the python2.6_config.log file I get the flooding warning
> >> > >
> >> > > configure: WARNING:
> >> > >
> >> > > By default, distutils will build C++ extension modules with "c++".
> >> > > If this is not intended, then set CXX on the configure command
> line.
> >> > >
> >> > > How to fix this - thanks
> >> > >
> >> > > _______________________________________________
> >> > > 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
> >> >
> >> _______________________________________________
> >> 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
> >
>
> _______________________________________________
> 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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AMBER.ambermd.org
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Received on Mon Nov 21 2011 - 11:30:06 PST
