Amber Installation [EN]

Owned by Chompoonut Rugnim
Last updated: Sept 23, 2021 by Viwan Jarerattanachat
2 min read

Software website : http://ambermd.org/Installation.php

Amber20 for CPU Installation

This is for running Amber20 on compute and memory node(s).

  1. Obtain Amber20 at http://ambermd.org and download source codes

  2. Upload and extract amber source codes at your project home director

    cd /tarafs/data/project/projxxxx #change projxxxx to your project ID tar xvfj AmberTools20.tar.bz2 tar xvfj Amber20.tar.bz2

  3. Set the AMBERHOME home directory environment variable

    cd amber20_src export AMBERHOME=$PWD

  4. Load modules and prepare for AMBER20 installation

    module purge module load bzip2/1.0.8-GCCcore-8.3.0 module load GCC/8.3.0 module load XZ/5.2.4-GCCcore-8.3.0

  5. Go to the amber directory and execute the compilation script

  6. Install and test

  7. After the installation is successful, you can compile parallel (MPI) versions of Amber20 by load OpenMPI module

  8. Then, recompilation with MPI

Amber20 for GPU Installation

This is for running Amber20 on GPU node. After finishing the Amber20 for CPU installation, please follow the following steps to install Amber20 on GPU.

  1. Go to the AMBERHOME home directory environment variable

  2. Load modules and prepare for AMBER20 installation

  3. Go to the amber directory and execute the compilation script for the installation with cuda

  4. Testing

  5. After the installation is successful, you can compile parallel (MPI) versions with cuda

  6. Then, recompilation with MPI for GPU

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