AMBER Archive (2009)

Subject: Re: [AMBER] Installation on MacOSX

From: David Watson (dewatson_at_olemiss.edu)
Date: Mon Dec 14 2009 - 14:01:52 CST

On Dec 14, 2009, at 12:59 PM, Freedman, Tanya wrote:

> Hi,
> I have used amber before, but I'm a beginner when it comes to installing this type of package. I haven't yet been able to find very simple, step-by-step guidelines for getting Amber installed and running on MacOSX. Can anyone give me these instructions in the simplest, most cookbook terms possible?
> Thanks for your help!
>

1) Get XCode 3 from Apple or install an older version from your OS installation media
    http://developer.apple.com/technology/tools.html

2) Get a fortran compiler and install it. I would recommend gfortran for price, intel fortran for speed.
    gfortran: http://hpc.sourceforge.net/
    or intel: http://www.programmers.com/PPI_US/PartnerCenter/partners.aspx?name=intel (you may find it at other vendors)
    or absoft: http://www.absoft.com/

3) unpack your amber tarball and learn how to use "sudo" from the command-line, as you will likely want to install Amber to /usr/local/amber or some such directory where you will need root permissions.

4) Download the latest and greatest AmberTools (you may want to wait a week or two) and install that package using the installation instructions. You don't need to use MKL or intel fortran for these, and it's probably best to avoid them if at all possible. Make sure that you export AMBERHOME appropriately (read the instructions!) in your .bash_profile, then log out and back into a Terminal session.

5) Follow the instructions to build Amber in serial, but go ahead and use MKL if you have the intel compilers.
You will have to edit your .bash_profile to export MKL_HOME. Also, make note of
    http://dev-archive.ambermd.org/200807/0009.html#start
as that note is your best friend.

6) If you want to use all cores on a modern system, then you will want to get a working installation of mpi.
I would recommend mpich2, but you are going to have to download the source and compile it to support your fortran compiler. Install this to /opt/mpich2, then set up your .bash_profile to export MPI_HOME=/opt/mpich2 before you attempt to install parallel. Please read the Installer guide and User guide for mpich2 if you run into problems with this one. And before you attempt to compile amber parallel, be sure that you can run
    /opt/mpich2/bin/mpirun -np 2 hostname
without errors (e.g. you will see your computer's name printed on two separate lines.)

7) If you've gotten to this point, you may want to compile pmemd, but this requires mojo and I'm not going to explain it in anymore detail unless you get to this point and write me back personally.

Some important notes:
a) You will want to be familiar with the bash shell, so pick up a book on that if you aren't a console guru.
b) Your choice of fortran compiler can make simulations go faster, but newer intel compilers with MKL can cause weird problems on a few of the tests.
c) At no point in time should you fail to read the instructions. Memorize them, recite them in prayer to your deity (if applicable), and if you are persistent, you will be rewarded.

I hope that's enough to get you pointed in the right direction.
I have configuration files available upon request for compiling 64 bit versions of sander (serial and parallel) and pmemd with intel fortran.
I can't provide support for them, should you wish to use them, because you will likely have a different MKL path than I do.

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