.. hightlight:: rst

AMBER Roll

AMBER Molecular Dynamics

Contents

• AMBER Roll
  • Introduction
  • Downloads
  • Building the roll
  • Installing
  • What is installed
  • Building GaMD version of roll

Introduction

This roll installs AMBER tools. There are 4 flavors compiled for each compiler (gnu, intel):

serial,
mpi
cuda
cuda mpi

Downloads

Amber is a licensed software. Get licensed files for AMBAER and AmberTools from amber roll and put source files in src/amber. Download GaMD patches (provided by developer Yinglong Miao):

amber14_GaMD_patch_confidential.txt
amber14-gamd-updates-20160104.tgz

Building the roll

Dependencies

• The mpi roll must be installed on the build/install host. depends on mpi libraries.
• The cuda roll must be installed on build/install host . In the absence of cuda, edit src/amber/Makefile targets to remove cuda-specific compilation.
• The roll sources assumes that modulefiles provided by intel, cuda and mpi rolls are available.

The roll uses openmpi compiled with gnu compiler for eth fabric. To make a roll use the following command:

# make ROLLCOMPILER='gnu' ROLLMPI='openmpi'  ROLLNETWORK='eth' 2>&1 | tee build.log

or simply

# make  2>&1 | tee build.log

A successful build will create the file amberGaMD-*.disk1.iso.

Installing

To install, execute these instructions on a Rocks frontend:

# rocks add roll amberGaMD*.iso
# rocks enable roll amberGaMD
# (cd /export/rocks/install; rocks create distro)
# rocks run roll amberGaMD > add-amberGaMD.sh
# bash add-amberGaMD.sh

Rebuild the compute nodes or

# rocks run host compute "yum clean all; yum install amberGaMD-gnu-eth amberGaMD-module-gnu-eth"

What is installed

The roll installs GaMD patched amber14 (AmberTools15) and environment module files in:

/opt/amberGaMD/gnu - compiled with GNU
/opt/modulefiles/applications/amberGaMD<VERSION> - environment modules

Building GaMD version of roll

For Sep 2015 workshop buid amberGaMD roll based on a received patch for amber14 source Create the following changes to the amber roll source:

modified:   src/amber-modules/amber.module.in
modified:   src/amber-modules/version.mk
modified:   src/amber/Makefile
modified:   src/amber/version.mk
modified:   version.mk

replace in graphs/default: amber.xml with amberGaMD.xml
replace in nodes: amber-common.xml.in with amberGaMD-common.xml.in

add a GaMD patch/distro to src/amber/ (patch received via email from author, source )