AMBER-Installer

This repository provides a Bash script to install AmberTools and PMEMD for Linux with various build configurations (CPU/GPU and MPI/Non-MPI). The script also manages the Miniforge/Conda environment setup, ensuring a smooth and automated installation process.

Features

• 🔹 Single-Flag Build Selection: Allows you to specify exactly one of the following mutually exclusive build configurations:

  • -cpu: Build the serial (non-MPI) CPU version.
  • -gpu: Build the serial GPU version.
  • -mpi_cpu: Build the parallel (MPI-enabled) CPU version.
  • -mpi_gpu: Build the parallel GPU version (MPI + CUDA).

• 🔹 AMBER Package Selection: Choose which components to build: AmberTools or PMEMD with minimal dependencies (no Python, Perl, or GUI).

• 🔹 Custom Installation Directory: Set your preferred install location via -path_install <path> (default: $HOME/amber25).

• 🔹 CPU Core Control: Use -nproc <n> to specify the number of CPU threads for compilation (default: all cores).

• 🔹 Automated Environment Setup: Automatically installs Miniforge3 if not already present. If ./miniforge3 directory exists, the script will use the existing Miniforge installation.

• 🔹 Conda Environment: The script creates and activates a conda environment from env.yml (e.g., amber-installer) before building.

• 🔹 Patch for QUICK CMakeLists: Automatically applies a patch to avoid issues with mpi.h in QUICK.

Requirements

• Files:

  • env.yml (Conda environment specification)

  • ambertools25.tar.bz2 and/or pmemd24.tar.bz2 must be in the current directory (amber-installer folder).

    Note: Please download ambertools25.tar.bz2 and pmemd24.tar.bz2 from https://ambermd.org/

• Internet Connection: Needed for downloading Miniforge3 if it's not already present.

• Unix-like Environment: The script is designed for Linux.

Usage

1. Clone this repository (or download the script and required files):

   git clone https://github.com/manbaritone/amber-installer.git
   cd amber-installer

2. Ensure env.yml is present and that ambertools25.tar.bz2 and/or pmemd24.tar.bz2 are in the same directory as the script.
3. Run the script with the desired build option:

   bash amber25-installer.sh [OPTIONS]

   Example for AMBER25

   bash amber25-installer.sh -ambertools -gpu -path_install /opt/amber25

   bash amber25-installer.sh -pmemd -mpi_cpu -path_install /opt/amber25

   Options

   • -cpu: Build with serial CPU version.

   • -gpu: Build with serial GPU version.

   • -mpi_cpu: Build with parallel (MPI) CPU version.

   • -mpi_gpu: Build with parallel (MPI) GPU version.

   • -ambertools: Build AmberTools25.

   • -pmemd: Build PMEMD24.

   • -path_install <path>: Specify the installation prefix (default: ~/amber25).

   • -nproc <n>: Specify number of CPU cores for compilation (default: all cores).

   • -h: Display the help message.

     Note: Only one of the four build options (-cpu, -gpu, -mpi_cpu, or -mpi_gpu) can be specified at a time.

Running Amber and AmberTools

Once you have successfully installed AmberTools and/or PMEMD using the installer script, you can run Amber programs by activating the conda environment and using the installed executables.

Activate the Conda Environment

After installation, an environment named amber-installer was created. To activate it, run:

source amber-installer/miniforge3/bin/activate
conda activate amber-installer
source path/to/amber_installation_folder/amber.sh

License

This project is licensed under the MIT License. See the LICENSE file for details.