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
>
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Received on Mon Nov 21 2011 - 10:30:04 PST
