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Installing Amber on Arch/Manjaro Linux

You will find below generic recommendations for installing Amber20 as well as specific instructions tailored for your Arch/Manjaro Linux system.

Generic installation instructions

About cmake:

Since Amber20, a new installation mechanism is provided that makes use of cmake. A decent version of cmake is needed, therefore it is highly recommended to download and install the cmake executable from the website.

About Python:

Many programs within Amber requires a decent version of Python. When configuring Amber, the run_cmake 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 run_cmake script install Python inside the Amber tree.

Building with cmake

We highly recommend that you refer to Chapter 2 of the Amber 2020 Reference Manual for detailed instructions on how to install Amber20.

Since Amber20, the build system has move to cmake. A script called run_cmake is available in the amber20_src/build directory. For most users, the options chosen in this script should be OK.

The installation of Amber is performed in two steps: cmake configuration, then building and install:

cd amber20_src/build
# optional: edit the run_cmake script to make any needed changes;
# most users should not need to do this
# Next, build and install the code:
make install

Arch/Manjaro Linux

You could install AmberTools and PMEMD packages from Arch User Repository (AUR). If you're new to the concept of Arch User Repository please take a look at this exhaustive description.

Here are links to the packages of interest:

Because of the licensing issues you should download AmberTools archive manually from AMBER site. If you want to install PMEMD as well please consider to purchase PMEMD module separately.

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 tarball from corresponding AUR page (or clone it with git), unpack and place necessary archive files in the directory where PKGBUILD resides: AmberTools20.tar.bz2 for AmberTools package; AmberTools20.tar.bz2 and Amber20.tar.bz2 for PMEMD package). Please be sure to provide all necessary dependencies before building packages (makepkg will complain about missing ones). Now you're ready to run makepkg utility!

    If you're facing some problems with building process feel free to ask in comments on package's page or write to the mailing list. Hint: it's always a good idea to try building in clean chroot. Use extra-x86_64-build script to build AmberTools and PMEMD and see if that helps.

  • Using AUR helper

    You can use any AUR helper which you like, however yay is highly recommended. Before commiting building and installation you should place necessary archive files in directory with PKGBUILD as described in previous section (for yay place files into ~/.cache/yay/{ambertools,pmemd} directories).

  • Additional info

    As of now packages from AUR doesn't ship tests and benchmarks so if you want to use them please unpack them from AmberTools tarball manually.

    AmberTools and PMEMD packages install convenient wrappers for sander and pmemd family of programs system-wide into /usr/bin so you don't need to do any special actions before using these programs: just run your favorite MD engines directly!

    To simplify user experience even more AmberTools provide special modulefile so you can use Environment Modules approach to prepare session for using AmberTools stuff. Install env-modules-tcl package from AUR, cd into /etc/modules/modulefiles and create symbolic link with ln -sf /opt/amber/share/modulefiles/ambertools .. Then you'll be able to prepare environment for AmberTools with simple module load ambertools! NB: old scheme with sourcing still present: if you wish you could add source /opt/amber/ line into your ~/.bashrc file.

    By default both AmberTools and PMEMD are compiled with MPI and CUDA support so these dependencies are for building time only (so-called makedeps in PKGBUILD language). However, if you want to use MPI and GPU versions of programs you should install OpenMPI compiled with GCC8 and/or CUDA packages from AUR and community repository, respectively.

    PLUMED metadynamics package is available for all MD engines — sander and pmemd (serial, MPI and CUDA versions) — out of the box. Please consider to install proper PLUMED packages: choose plumed package if you don't need MPI support and plumed-mpi package if you do.

    VMD is useful tool to visualize and analyze MD trajectories produced by AMBER MD engines. Refer to the vmd package page on AUR to install it.

    Another useful tool for working with trajectories and structures is PyMOL. It's also available in Arch community repository.

"How's that for maxed out?"

Last modified: May 26, 2020