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Amber MD

From Ambermd.org:

Amber is a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community; see our history page and our contributors page for more information.

The term “Amber” refers to two things. First, it is a set of molecular mechanical force fields for the simulation of biomolecules; these force fields are in the public domain, and are used in a variety of simulation programs. Second, it is a package of molecular simulation programs which includes source code and demos.

Amber is distributed in two parts: AmberTools and Amber.

For more information: https://ambermd.org/index.php

This software page is a work in progress - it is not yet available for use.

Running Amber MD on Comet

Amber - Serial

Amber - Parallel / MPI

Amber - CUDA

Amber - Interactive Desktop GUI

Building Amber MD on Comet

Important!

This section is intended for RSE HPC staff, or users who are interested in how the software is configured. If you only need to use the software, stop reading here.

Amber appears to have few dependencies at first, but as you configure the source it looks for a lot of additional libraries. At least the following build tools are required:

GCC
Nvidia CUDA SDK
flex
bison
m4
python3
build-essential
autoconf
cmake
git

In addition these libraries are needed:

libopenmpi-dev
liblapack-dev
libblas-dev
libarpack2-dev
libucpp-dev
libnlopt-dev
libz-dev
libbz2-dev
libapbs-dev
libfftw3-mpi-dev
libfftw3-dev
libprotobuf-dev
xorg-dev
libxext-dev
libxt-dev
libx11-dev
libice-dev
libsm-dev
libgomp1

Build script:

Note that you must download the files ambertools25.tar.bz2 and pmemd24.tar.bz2 from https://ambermd.org/GetAmber.php - these are behind a download form - and they should be placed in the same directory as the build script.

#!/bin/bash

echo "Loading modules..."
module load apptainer

echo ""
echo "Building container..."
export APPTAINER_TMPDIR=/scratch

# You must supply a copy of AMBERMD tar files 
# in this SOURCE_DIR
SOURCE_DIR=`pwd`

AM24="pmemd24.tar.bz2"
AM25="ambertools25.tar.bz2"

echo ""
echo "Checking source files..."
if [ -s "$SOURCE_DIR/$AM24" ]
then
	echo "- Found - $SOURCE_DIR/$AM24"
else
	echo "- WARNING - $SOURCE_DIR/$AM24 is MISSING"
	echo ""
	echo "Press return to continue or Control+C to exit and fix"
	read	
fi

if [ -s "$SOURCE_DIR/$AM25" ]
then
    echo "- Found - $SOURCE_DIR/$AM25"
else
    echo "- WARNING - $SOURCE_DIR/$AM25 is MISSING"
    echo ""
    echo "Press return to continue or Control+C to exit and fix"
    read
fi

apptainer build --bind $SOURCE_DIR:/mnt ambermd.24.25.sif ambermd.def 2>&1 | tee ambermd.log

Container Definition:

Bootstrap: docker
From: nvidia/cuda:12.8.1-cudnn-devel-ubuntu24.04

####################################################################
#
# Amber MD container
# ==================
# This is a runtime environment for the Ambder MD tools.
# Please see: 
#	https://hpc.researchcomputing.ncl.ac.uk/dokuwiki/dokuwiki/doku.php?id=advanced:software:ambermd
#
####################################################################

%post
    # Prevent interactive prompts
    export DEBIAN_FRONTEND=noninteractive

####################################################################
#
# Basic system packages
#
####################################################################

    # Update & install only necessary packages
    apt-get update
	# Base stuff everything will need
	apt-get install -y apt-utils wget build-essential aptitude gcc g++ gfortran cmake automake autoconf vim less git

	# These are specifically needed by Amber MD
	apt-get install -y \
		libopenmpi-dev \
		python3 \
		flex \
		bison \
		m4 \
		liblapack-dev \
		libblas-dev \
		libarpack2-dev \
		libucpp-dev \
		libnlopt-dev \
		libz-dev \
		libbz2-dev \
		libapbs-dev \
		libfftw3-mpi-dev \
		libfftw3-dev \
		libprotobuf-dev \
		xorg-dev \
		libxext-dev \
		libxt-dev \
		libx11-dev \
		libice-dev \
		libsm-dev \
		libgomp1 \
		devscripts \
		debhelper \
		fakeroot

	# Python 3 modules needed by Amber MD
	apt-get install -y \
		python3-pip \
		python3-numpy \
		python3-tk \
		python3-scipy \
		python3-matplotlib

    # Clean up APT cache to save space
    apt-get clean

	# Clean out Python pip cache
	pip3 cache purge 

#################################################################################
#
# This is all the custom stuff needed to build the various bioinformatics tools
#
#################################################################################

	# This flag needs to be set to indicate which CPU architecture we
	# are optimising for.
	AMD_ARCH=1

	if [ "$AMD_ARCH" = "1" ]
	then
		# Compiling on AMD Epyc
		export BASE_CFLAGS="-O3 -march=native -pipe"
		export BASE_CFLAGS_ALT="-O3 -march=native -pipe"
		export MAKE_JOBS=8
	else
		# Compiling on generic system
		export BASE_CFLAGS="-O"
		export BASE_CFLAGS_ALT="-O"
		export MAKE_JOBS=8
	fi
	
	export CFLAGS="$BASE_CFLAGS"
	export CPPFLAGS=""
	export CXXFLAGS="$CFLAGS"
	export LD_LIBRARY_PATH=/opt/lib:$LD_LIBRARY_PATH
	export PATH=/opt/bin:$PATH

	echo ""
	echo "Post-OS-install setup for Bio apps container"
	echo "============================================"

	# A download place for external libraries
	mkdir -p /src/zipped
	
	# Where installations go
	mkdir -p /opt/pmemd24

	echo ""
	echo "1. Install Amber MD 24"
	echo "======================"
	cd /src
	if [ -s /mnt/pmemd24.tar.bz2 ]
	then
		tar -jxf /mnt/pmemd24.tar.bz2
		cd /src/pmemd24_src/build
		cmake /src/pmemd24_src \
			-DCMAKE_INSTALL_PREFIX=/opt/pmemd24 \
			-DCOMPILER=GNU  \
			-DMPI=TRUE \
			-DCUDA=TRUE \
			-DINSTALL_TESTS=TRUE \
			-DDOWNLOAD_MINICONDA=FALSE \
			-DBUILD_PYTHON=TRUE \
			-DBUILD_PERL=TRUE \
			-DBUILD_GUI=TRUE \
			-DPMEMD_ONLY=TRUE \
			-DCHECK_UPDATES=FALSE
		make -j$MAKE_JOBS
		make install
	else
		echo "Amber MD 24 source file not found"
		exit 1
	fi

	echo ""
    echo "2. Install Amber MD 25"
    echo "======================"
    cd /src
    if [ -s /mnt/ambertools25.tar.bz2 ]
    then
        tar -jxf /mnt/ambertools25.tar.bz2
		cd /src/ambertools25_src
		cmake /src/ambertools25_src \
			-DCMAKE_INSTALL_PREFIX=/opt/ambertools25 \
			-DCOMPILER=GNU  \
			-DMPI=TRUE \
			-DCUDA=TRUE \
			-DINSTALL_TESTS=TRUE \
			-DDOWNLOAD_MINICONDA=TRUE
		make -j$MAKE_JOBS
		make install
	else
        echo "Amber MD 25 source file not found"
        exit 1
    fi

	# Remove all src packages
	echo ""
	echo "Cleaning up downloaded src tree"
	echo "=================================="
	cd
	rm -rf /src
	
	echo ""
	echo "All done"

%environment
	export PATH=/opt/bin:$PATH
	export LD_LIBRARY_PATH=/opt/lib:$LD_LIBRARY_PATH
	export CFLAGS="-O3 -march=native -pipe"
	export CXXFLAGS="$CFLAGS"
	export MANPATH=/opt/man

%runscript

Run Script:

#!/bin/bash

module load apptainer

IMAGE_NAME=/nobackup/shared/containers/ambermd.24.25.sif

container.run() {
    # Run a command inside the container...
    # automatically bind the /scratch and /nobackup dirs
    # pass through any additional parameters given on the command line
    apptainer exec --nv --bind /scratch:/scratch --bind /nobackup:/nobackup ${IMAGE_NAME} $@
}

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