.. 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 Amarolab and save copy in nbcr.ucsd@gmail.com account Download the appropriate amber source files into the src/amber. Download the benchmark suite in src/amber-test:

# cd src/amber-test; wget http://ambermd.org/Amber14_Benchmark_Suite.tar.bz2

Building the roll

Dependencies

• The mpi roll must be installed on the build/install host. depends on mpi libraries.
• The intel roll must be installed on the build/install host. In the absence of intel compiler the roll should be buld with ROLLCOMPILEr='gnu'.
• 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 intel and gnu compilers for eth fabric. To make a roll use the following command:

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

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

Installing

To install, execute these instructions on a Rocks frontend:

# rocks add roll *.iso
# rocks enable roll amber
# (cd /export/rocks/install; rocks create distro)
# rocks run roll amber | bash

What is installed

Tthe roll installs amber and environment module files in:

/opt/amber/gnu - compiled with GNU
/opt/amber/intel - compiled with Intel compilers
/opt/modulefiles/applications/amber<VERSION> - environment modules
/root/rolltests/amber.t  - roll installation test
/opt/amber/benchmark/Amber14_Benchmark_Suite.tar.bz2 - benchmark suit distro

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 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 patch to src/amber/ (patch received via email from author, source )

See diffs for the above files in GaMD-diffs file at the top of the roll. After creating changes build amberGaMD roll

Testing

A test script amber.t can be run to verify proper installation of the roll binaries and module files. To run the test scripts execute the following command(s):

# /root/rolltests/amber.t

A benchmark suit distro (from Amber site) contains a shell script run_bench_CPU+GPU.sh and required input to run suite of tests. Untar, adjust cpu and gpu counts in the script for a specific host.