Hi Jason,
I got amber 12 and ambertools 13 compiled on OSX 10.8.4 by doing the following:
1. sudo port uninstall gcc47
2. sudo port install gcc47
3. sudo port select gcc mp-gcc47
4. sudo port uninstall netcdf
5. sudo port uninstall mpich
6. sudo port install openmpi
7. ensure the pathing to Macport openmpi is correct
8. ./configure -macAccelerate gnu
9. make -j 4 install
10. ./configure -macAccelerate -mpi gnu
11. make -j 4 install
The reason for switching to openmpi instead of mpich was that pmemd.MPI binary was not working correctly even though it could be compiled.
Thank you for all the help !!
On 11 Jul, 2013, at 8:53 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> On Jul 11, 2013, at 2:01 AM, "Wang Chern Hoe (Dr)" <WangCH.ntu.edu.sg> wrote:
>
>>
>> server:amber12 user$ port installed | grep netcdf
>> netcdf .4.2.1.1_2+dap+netcdf4 (active)
>
> Try deactivating your NetCDF port when you install Amber. What's happening is that the installation process is trying to use the NetCDF library you built with macports (which does not have the Fortran symbols) instead of the one built by Amber.
>
> Use the command
>
> sudo port deactivate netcdf
>
> Then run make again. Afterward, you can reactivate NetCDF if you need it.
>
> sudo port activate netcdf
>
> HTH,
> Jason
>
>
> --
> 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
CONFIDENTIALITY:This email is intended solely for the person(s) named and may be confidential and/or privileged.If you are not the intended recipient,please delete it,notify us and do not copy,use,or disclose its content.
Towards A Sustainable Earth:Print Only When Necessary.Thank you.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 11 2013 - 08:30:03 PDT
