Running Amber on Microsoft Windows

All of Amber (except for pmemd and the X-windows parts) will compile and run on Windows using the Cygwin development tools: see http://www.cygwin.com. The cygwin package provides a way to make Microsoft Windows machines resemble a Linux/Unix environment; if you are unfamiliar with the Linux/Unix environment, you will need to learn at least the basics of that in order to use Amber on Windows.

Note that Cygwin provides a POSIX-compatible environment for Windows. Effective use of this environment requires a basic familiarity with the principles of Linux or Unix operating systems. Building the Windows version is thus somewhat more complex (not simpler) than building under other operating systems. The Windows version has primarily been used in serial (single-cpu) mode; it will work with the LAM libraries supplied with Amber10, or with MPICH2 libraries. For long-running jobs, Windows can have an annoying habit of giving lots (or all) of the CPU time to an interactive process, so that background processes suffer.

The bottom line is that the Windows version is functional, but the primary development and target operating system is Unix or Linux.

Detailed instructions for installing AmberTools version 1.3 on Windows

  1. Download AmberTools itself from http://ambermd.org. Save the file somewhere, e.g. on the desktop. Don't do anything right now with this file.

  2. Go to http://www.cygwin.com, and click on "install cygwin now". You might want to save the file (called "setup.exe") on your desktop, since you will need to run this program again later on.

  3. Run the setup.exe program. The first time, just accept all of the defaults. This will make an icon called "cygwin" on your desktop. If you double-click on that, you will get a text terminal (white text with a black background.) This is where you will type commands. [If you click on the top window bar, and select "properties", you can change the color scheme or the font size -- I'm old enough to certainly appreciate a larger font!]

  4. Run setup.exe again; accept all the defaults until you get to the list of programs. There is a button in the upper right corner, called "view" that cycles between various views of the optional packages. Click this once and it should say "all", and you will have a giant list (in alphabetical order) of all possible packages. For most of these, the status column will say "skip". If you go to some package and click on the little arrows next to it, the "skip" label will change to a version number. [Clicking again and again on the arrows cycles between all the possibilities -- play with this a bit unitl you see how it works -- it's only intuitive after you've experimented a bit.]

    Choose the following programs to install:

    gcc4, gcc4-fortran, make, m4, flex, diffutils, tcsh, util-linux

    then press "next" at the bottom to complete the installation.

  5. Now under the C:\ directory, you will find a directory called \cygwin\home\name, where "name" is your name. This is called your home directory, and it is the default location when you click on the "cygwin" icon. Drag AmberTools-1.3.tar.bz2 from the desktop to your home directory.

  6. Start cygwin, and type the following command:

    tar xvfj AmberTools-1.3.tar.bz2

    This will extract the files from the tar file. If you type "ls" (equivalent to the dos "dir" command), you should see two files: the AmberTools file, and a new directory called "amber11". You can explore now, for example with commands like the following:

    cd amber11 (moves you "into" the amber11 directory)
    ls (lists the files and directories)
    cd src (moves you down further into the src directory).

  7. Once you are in the amber11/src directory, type the following:

    ./configure -cygwin -noX11 gnu

    [Aside: you can type "./configure --help" to see more options.] Assuming(!) that this works, then type:

    export AMBERHOME=/home/name/amber11 (where name is your name!)
    make -f Makefile_at

    At this point the screen will fill up with compilation messages, for several minutes. The end you should see the message:

    "Completed installation of AmberTools ver. 1.3"

  8. You can test the installation by doing the following:

    cd ../test
    make -f Makefile_at test

    This will run a series of tests, most of which should say PASS.

Note 1: it looks like sleap is not running correctly on Windows; we'll post a bug-fix if/when we can track this down.

Note 2: Cygwin has just undergone a major change (as of 12/23/09); right now the xleap installation is not working, hence the "-noX11" flag in the instructions above. Since all this used to work with the older cygwin, we will try to post updated instructions here soon.