Skip to main content

amber

About

"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

Amber is developed in an active collaboration of David Case at Rutgers University, Tom Cheatham at the University of Utah, Tom Darden at NIEHS, Ken Merz at Florida, Carlos Simmerling at SUNY-Stony Brook, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals. Amber was originally developed under the leadership of Peter Kollman, and Version 9 is dedicated to his memory.

Version and Availability

Softenv Keys for amber on oliver
Machine Version Softenv Key
oliver 10.0 +amber-10-intel-11.1-mvapich-1.1
oliver 11.0 +amber-11-at1.5-intel-11.1-mvapich-1.1
oliver 11.0 +amber-11-intel-11.1-mvapich-1.1
▶ Display Softenv Keys for amber all clusters
Machine Version Softenv Key
eric 10.0 +amber-10-intel-11.1-mvapich-1.1
eric 11.0 +amber-11-at1.5-intel-11.1-mvapich-1.1
eric 11.0 +amber-11-intel-11.1-mvapich-1.1
qb 10.0 +amber-10-intel-11.1-mvapich-1.1
qb 11.0 +amber-11-at1.5-intel-11.1-mvapich-1.1
qb 11.0 +amber-11-intel-11.1-mvapich-1.1
qb 12.0 +amber-12-intel-11.1-openmpi-1.3.4
oliver 10.0 +amber-10-intel-11.1-mvapich-1.1
oliver 11.0 +amber-11-at1.5-intel-11.1-mvapich-1.1
oliver 11.0 +amber-11-intel-11.1-mvapich-1.1
louie 10.0 +amber-10-intel-11.1-mvapich-1.1
louie 11.0 +amber-11-at1.5-intel-11.1-mvapich-1.1
louie 11.0 +amber-11-intel-11.1-mvapich-1.1
poseidon 10.0 +amber-10-intel-11.1-mvapich-1.1
poseidon 11.0 +amber-11-at1.5-intel-11.1-mvapich-1.1
poseidon 11.0 +amber-11-intel-11.1-mvapich-1.1
poseidon 12.0 +amber-12-intel-11.1-openmpi-1.3.4
painter 10.0 +amber-10-intel-11.1-mvapich-1.1
painter 11.0 +amber-11-at1.5-intel-11.1-mvapich-1.1
painter 11.0 +amber-11-intel-11.1-mvapich-1.1
philip 11.0 +amber-11-intel-11.1-mpich-1.2.7p1
pandora 10 +amber-10
supermike2 12.0 +amber-12-Intel-13.0.0-openmpi-1.6.2-CUDA-4.2.9
▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.

Softenv

SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

Using the softenv command, a user may view the list of available packages. Currently, it can not be ensured that the packages shown are actually available or working on the particular machine. Every attempt is made to present an identical environment on all of the LONI clusters, but sometimes this is not the case.

Example,

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
....
Listing of Available Packages

See Packages Available via SoftEnv on LSU HPC and LONI.

For a more accurate, up to date list, use the softenv command.

Caveats

Currently there are some caveats to using this tool.

  1. packages might be out of sync between what is listed and what is actually available
  2. resoft and soft utilities are not; to update the environment for now, log out and login after modifying the ~/.soft file.
Availability

softenv is available on all LSU HPC and LONI clusters to all users in both interactive login sessions (i.e., just logging into the machine) and the batch environment created by the PBS job scheduler on Linux clusters and by loadleveler on AIX clusters..

Packages Availability

This information can be viewed using the softenv command:

% softenv
Managing Environment with SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft

Amber 11 is compiled with AmberTools 1.4 and 1.5 (at1.5 in soft key)

Usage

Make sure softenv keys are matched up with corresponding versions of the compiler and MPI library. For instance:

+amber-11-intel-11.1-mvapich-1.1
+mvapich-1.1-intel-11.1

Amber is normally run via a PBS job script.

▶ Open Example?

Note: the usual executable name used is sander (serial) or sander.MPI (parallel).

#!/bin/bash
#PBS -A my_allocation_code
#PBS -q checkpt
#PBS -l nodes=X:ppn=4
#PBS -l walltime=HH:MM:SS
#PBS -j oe
#PBS -N NAME

cd $PBS_O_WORKDIR
export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`
mpirun -np $NPROCS -machinefile $PBS_NODEFILE sander.MPI -O \
   -i my.in -o  my.out -c my.inpcrd -p my.prmtop -r my.rst

Resources

  • The Amber Home Page has a variety of on-line resources available, including manuals and tutorials.

Last modified: March 07 2013 12:30:04.