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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 2019 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

See also Gustaf Olsson's blog post for a detailed exposition of OSX installation options.

Installing Amber on Windows 10

Amber's Windows support is pretty minimal. All of Amber should compile and run on the Windows 10 "subsystem for Linux". Follow the instructions for Ubuntu, below. This is essentially like running Linux on a Windows machine; further, this option may not work for the GPU-enabled codes.

Amber will mostly work on cygwin, but that option is no longer officially supported (unless/until we get a volunteer willing to take this on....)

Installing Amber on Linux

All of Amber will compile and run on Linux platforms. Depending on your Linux flavor, the procedure to install the minimal set of needed packages may vary. Below are the recommended commands to process for different Linux platforms in order to get all the necessary packages required for an Amber installation.

About Python: Many programs within Amber requires a decent version of Python. When configuring Amber, the configure script will check your installation and will most probably recommend to download and install a compatible Python from Continuum IO (via miniconda). It is highly recommended to follow this suggestion and let the configure script install Python inside the Amber tree.

CentOS 7

The following command should get you all the necessary packages to get Amber to compile:

yum -y install tcsh make \
               gcc gcc-gfortran gcc-c++ \
               which flex bison patch bc \
               libXt-devel libXext-devel \
               perl util-linux wget bzip2 \
               bzip2-devel zlib-devel

If you want to install Amber in parallel, you can use OpenMPI through:

yum -y install openmpi openmpi-devel environment-module

then, in your terminal, access the MPI compilers using:

module load mpi/openmpi-x86_64

CentOS 6

Installation of Amber on a CentOS 6 Linux node is a little tricky since the default GNU compiler is now too old to compile the source code. The recommended procedure is to install a more recent version using the Developer Toolset software collection (devtoolset).

yum -y install tcsh make \
               which flex bison patch bc \
               libXt-devel libXext-devel \
               perl util-linux wget bzip2 \
               bzip2-devel zlib-devel

# update to a newer gcc
yum -y install centos-release-scl
yum -y install devtoolset-8

then, in your terminal, access the newer GNU compiler using:

source /opt/rh/devtoolset-8/enable

Debian

The following command should get you all the necessary packages to get Amber to compile:

apt -y install tcsh make \
               gcc gfortran g++ \
               flex bison patch \
               libbz2-dev libzip-dev xorg-dev wget

If you want to install Amber in parallel, you can use OpenMPI through:

apt -y install openmpi-bin libopenmpi-dev

Fedora

The following command should enable the compilation of Amber on Fedora systems:

dnf -y install tcsh make \
               gcc gcc-gfortran gcc-c++ \
               which flex bison patch bc \
               libXt-devel libXext-devel \
               perl util-linux wget bzip2 \
               bzip2-devel zlib-devel

If you want to install Amber in parallel, you can use OpenMPI through:

dnf -y install openmpi openmpi-devel environment-modules

Then:

module load mpi/openmpi-x86_64

OpenSuse 15.0

The following command should install all necessary packages to compile Amber on OpenSuse 15.0:

zypper -n install tcsh \
                  gcc gcc-fortran gcc-c++ \
                  which patch make libtool flex bison wget bc \
                  gzip bzip2 xorg-x11-devel

If you want to install Amber in parallel, you can use OpenMPI through:

zypper -n install openmpi3 openmpi3-devel

OpenSuse 15.1

The following command should install all necessary packages to compile Amber on OpenSuse 15.1:

zypper -n install tcsh \
                  gcc gcc-fortran gcc-c++ \
                  which patch make libtool flex bison wget bc \
                  gzip bzip2 xorg-x11-devel

If you want to install Amber in parallel, you can use OpenMPI through:

zypper -n install openmpi3 openmpi3-devel

Caveat: Compilation of Amber can failed with recent miniconda installation. If you encounter an error like:

[...]compiler_compat/ld: /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to initialize decompress status for section .debug_aranges
Then apply the following patch:
/bin/rm $AMBERHOME/miniconda/compiler_compat/ld
ln -s /usr/bin/ld $AMBERHOME/miniconda/compiler_compat/ld

Ubuntu 18.04

The following command should install all necessary packages to compile Amber on Ubuntu 18.04:

apt -y install software-properties-common
add-apt-repository universe
apt -y update
apt -y install tcsh make \
               gcc gfortran \
               flex bison patch \
               bc xorg-dev libbz2-dev wget

If you want to install Amber in parallel, you can use OpenMPI through:

apt -y install openmpi-bin libopenmpi-dev

Ubuntu 16.04

The following command should install all necessary packages to compile Amber on Ubuntu 16.04:

apt -y install tcsh make \
               gcc gfortran \
               flex bison patch \
               bc xorg-dev libbz2-dev wget

If you want to install Amber in parallel, you can use OpenMPI through:

apt-get -y install openmpi-bin libopenmpi-dev

Arch Linux

AmberTools and AMBER packages may be installed via Arch User Repository (AUR). Here are links to available packages:

  • ambertools — AmberTools package (without PMEMD module)
  • pmemd — PMEMD package
  • pmemd-cuda — PMEMD package (with CUDA support)

Because of the licensing issues you should download AmberTools archive manually from AMBER site and/or purchase PMEMD module.

You can install these packages in two ways: manual and with AUR helper.

  • Manual installation

    For this type of installation you should download the whole archive from corresponding AUR page, unpack it and place necessary files in the directory where PKGBUILD resides (AmberTools19.tar.bz2 for AmberTools package; AmberTools19.tar.bz2 and Amber18.tar.bz2 for pmemd and pmemd-cuda packages).

  • Using AUR helper

    You can use any AUR helper which you like. Before commiting building and installation you should place necessary files in directory with PKGBUILD (as described in previous section).

  • Additional info

    PLUMED package is available for all MD modules: sander and pmemd (serial, MPI and CUDA versions). sander and sander.MPI modules work with PLUMED out-of-the-box, but PMEMD modules should be patched against PLUMED. However, if you install these packages from AUR the process of interfacing PLUMED with PMEMD is very simple. You should only install plumed-patches package from AUR before installation of PMEMD. This also requires you to install proper PLUMED version. Choose plumed package if you don't need MPI support and plumed-mpi package if you need it. Installation script will auto-detect the presence of PLUMED and corresponding patch and will enable support for PLUMED.

"How's that for maxed out?"

Last modified: Oct 7, 2019