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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.

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

Versions and Availability

▶ Display Softenv Keys for amber on 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
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.

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

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

The command softenv will provide a list of available packages. The listing will look something like:

$ 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
... some stuff deleted ...
Managing 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

The command soft can be used to manipulate the environment from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user to pay attention to possible order dependencies. That is, best results require the user to remove keywords in the reverse order in which they were added. It is handy to test out individual keys, but can lead to trouble if changing multiple keys. Changing the .soft file and issuing the resoft is the recommended way of dealing with multiple changes.

▶ Display Module Names for amber on all clusters.
Machine Version Module
▶ Module FAQ?

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

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Modules

Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- some stuff deleted ---
velvet/1.2.10/INTEL-14.0.2
vmatch/2.2.2

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- some stuff deleted ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

add/load mod1 mod2 ... modn . . . Add modules
rm/unload mod1 mod2 ... modn  . . Remove modules
switch/swap mod . . . . . . . . . Switch or swap one module for another
display/show  . . . . . . . . . . List modules loaded in the environment
avail . . . . . . . . . . . . . . List available module names
whatis mod1 mod2 ... modn . . . . Describe listed modules

The -h option to module will list all available commands.

Module is currently available only on SuperMIC.

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: November 11 2014 16:26:11.