Re: [AMBER] Amber 12 on OSX 10.8.4

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 11 Jul 2013 00:44:22 -0400

What is the result of the following command:

port installed | grep netcdf

?


On Wed, Jul 10, 2013 at 10:09 PM, Wang Chern Hoe (Dr) <WangCH.ntu.edu.sg>wrote:

> Hi Jason,
>
> I followed your instructions on your wiki, and still got a similar error
> message.
>
> Undefined symbols for architecture x86_64:
> "___netcdf_MOD_nf90_close", referenced from:
> ___trajenemod_MOD_trajene in trajene.o
> ___bintraj_MOD_close_binary_files in bintraj.o
> ___binrestart_MOD_read_nc_restart in binrestart.o
> ___binrestart_MOD_check_nc_restart in binrestart.o
> ___binrestart_MOD_read_nc_restart_box in binrestart.o
> ___binrestart_MOD_write_nc_restart in binrestart.o
> ___ncsu_umbrella_MOD_umbrella_save in ncsu-umbrella.o
> .
>
> ld: symbol(s) not found for architecture x86_64
> collect2: error: ld returned 1 exit status
> make[2]: *** [sander.MPI] Error 1
> make[1]: *** [parallel] Error 2
>
>
>
>
>
> On 11 Jul, 2013, at 7:41 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
> >
> >
> > On Jul 10, 2013, at 7:17 PM, "Wang Chern Hoe (Dr)" <WangCH.ntu.edu.sg>
> wrote:
> >
> >> Hi,
> >>
> >> I got this error message while compiling using this configure setting:
> >>
> >> ./configure -macAccelerate -mpi gnu
> >> make install
> >>
> >> ncsu-umbrella.F90:9.42:
> >>
> >> use netcdf, only : nf90_double, nf90_float
> >> 1
> >> Fatal Error: Wrong module version '10' (expected '4') for file
> 'netcdf.mod' opened at (1)
> >> make[2]: *** [ncsu-umbrella.o] Error 1
> >> make[1]: *** [parallel] Error 2
> >> make: *** [install] Error 2
> >
> > This indicates that a different compiler was used to build the NetCDF
> module as you are currently using to build Amber. There is a link to my
> wiki on the Amber website with instructions for setting up a Mac to work
> with Amber.
> >
> > When everything is set up correctly, use the command "make uninstall" to
> clean out the old files and then recompile.
> >
> > HTH,
> > Jason
> >
> >>
> >> Can someone help me please ? I really do not wish to use the -nobintraj
> option.
> >>
> >>
> >> Thanks
> >>
> >> _______________________________________________
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> >> 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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Received on Wed Jul 10 2013 - 22:00:02 PDT
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