my gcc -v is
Using built-in specs.
Target: i686-apple-darwin11
Configured with:
/private/var/tmp/llvmgcc42/llvmgcc42-2335.15~25/src/configure
--disable-checking --enable-werror
--prefix=/Developer/usr/llvm-gcc-4.2 --mandir=/share/man
--enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm-
--program-transform-name=/^[cg][^.-]*$/s/$/-4.2/
--with-slibdir=/usr/lib --build=i686-apple-darwin11
--enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2335.15~25/dst-llvmCore/Developer/usr/local
--program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11
--target=i686-apple-darwin11
--with-gxx-include-dir=/usr/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)
gfortran -v is
Using built-in specs.
Target: x86_64-apple-darwin11
Configured with: ../gcc-4.4.6/configure --prefix=/opt/local
--build=x86_64-apple-darwin11
--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
--disable-multilib --enable-fully-dynamic-string
Thread model: posix
gcc version 4.4.6 (GCC)
I still get the same error 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 8:09 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 21 2011 - 12:00:03 PST
