Re: [AMBER] Amber 12 on OSX 10.8.4

From: Wang Chern Hoe (Dr) <"Wang>
Date: Thu, 11 Jul 2013 10:09:00 +0800

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
>>
>> _______________________________________________
>> 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 Wed Jul 10 2013 - 19:30:03 PDT
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