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Installing Amber

These are "instructions for the impatient": shortcuts for getting Amber installed on popular operating systems. For more details, see Chapter 2 of the Amber 2018 Reference Manual, or visit Jason Swails' wiki.

Installing Amber on MacOS

Install XCode: Xcode contains Apple's development tools. You can download this from the Mac App store (just search for "xcode"). After installing XCode, you need to agree to the license. So run the following command in a terminal:

sudo xcodebuild -license
Then, read through the license (or type q to skip through it), and type "agree" when prompted. After this, you need to install the command-line tools. Running the following command in the terminal installs the command-line tools:
xcode-select --install

Install XQuartz: Starting with Mac OS X 10.8, Apple stopped including X11 with their OS. Instead, you have to download the XQuartz program. You can download it here.

Install gfortran: You will need to install a Fortran compiler, since Apple doesn't supply one. Get one for your MacOS version here.

Install Amber: Now you are ready to proceed with the installation instructions in the Amber manual. The configure command should be this:

./configure -macAccelerate clang

Notes about Mojave (OSX 10.14)

A few tweaks are needed for Mojave; there is an excellent post from Gustaf Olsson about using either Apple's clang compiler (plus an external fortran compiler, as described above), or the HomeBrew or Macports compilers.

Installing Amber on Ubuntu Linux and Windows 10

All of Amber will compile and run on Ubuntu Linux platforms (and Debian variants like lubuntu, Kubuntu and xubuntu, and the Windows 10 "subsystem for Linux"). The following command should get you the needed packages:

sudo apt-get install csh flex bison patch gcc gfortran g++ make \
     build-essential xorg-dev xutils-dev libbz2-dev zlib1g-dev \
     libboost-dev libboost-thread-dev libboost-system-dev

Note: Some or many of these may already be present on your system; the list above appears to work even for a "minimal install" of Ubuntu 18.04. Starting with AmberTools19, you don't need to install the boost libraries mentioned above, as these will come with the distribution.

Caution: depending on the graphics hardware (specifically, onboard intel chipsets) and associated drivers for your particular setup, installing the xorg-dev package on Ubuntu has been reported to sometimes also require a reinstall of the xserver (xserver-xorg) and associated machine-dependent 3D acceleration libraries. If you aren't ready to do this, then just configure AMBER with the -noX11 option.

If you want to install Amber in parallel, you can probably use the apt-get versions of MPI:

sudo apt-get install openmpi-bin libopenmpi-dev

Some users might prefer mpich to openmpi. In that case:

sudo apt-get install mpich libmpich-dev

If you have trouble with these, go to $AMBERHOME/AmberTools/src, and execute either ./configure_openmpi or ./configure_mpich2.

Caution: As of February, 2019, Amber won't compile with version 4 of openmpi. This release removes support from some older MPI calls that we still use. We are working on the problem.

Installing Amber on Fedora core Linux

Instructions are generally the same as above, except that yum is used as a package manager. The following command should get you the needed libraries:

sudo yum install gcc gcc-gfortran gcc-c++ flex tcsh zlib-devel \
     bzip2-devel libXt-devel libXext-devel libXdmcp-devel \
     tkinter openmpi openmpi-devel perl perl-ExtUtils-MakeMaker \
     patch bison boost-devel

The above should also work on CentOS and Red Hat Enterprise Linux systems as well.

Installing Amber on openSUSE Linux

Instructions are generally the same as above, except that zypper is used as a package manager. The following command should get you the needed libraries:

sudo zypper install gcc gcc-c++ gcc-fortran libtool \
     xorg-x11-devel xorg-x11-libXt-devel libbz2-devel \
     patch make flex glibc-devel-static boost-devel

"How's that for maxed out?"

Last modified: Feb 14, 2019