AMBER-pcluster

Category

Chemistry

Program On

pcluster

Version

8,10

Author / Distributor

See http://ambermd.org , this website contains the reference(s) to use when citing Amber in the literature.

Description

Amber is a package of molecular simulation programs.

Pcluster currently has Amber 8 and Amber 10 installed. Amber 8 is the default version, which is on users’ path and by default the AMBERHOME variable is set to /usr/local/amber8.

In order to run Amber 10, users need to invoke the commands with the full path and define AMBERHOME in the script, as described below.

Running Program

Amber 8

Important Note sander is a single processor executable. A parallel version of this program is called psander.

Example of a shell script to run sander on the batch queue:

To run a serial job (serial.sh)

#!/bin/csh
cd working_directory
/usr/bin/time sander -i ...

To run a parallel job (multi.sh):

#!/bin/csh
cd working_directory
/usr/bin/time psander -i ...

Amber 10

Important Note sander is a single processor executable. A parallel version of this program is called sander.MPI.

Example of a shell script to run sander on the batch queue:

To run a serial job (serial.sh)

#!/bin/bash
cd working_directory
export AMBERHOME=/usr/local/amber10
/usr/local/amber10/bin/sander -i ...

To run a parallel job (multi.sh):

#!/bin/bash
cd working_directory
export AMBERHOME=/usr/local/amber10
poe /usr/local/amber10/bin/sander.MPI -i ...

For Amber 8 and Amber 10

To submit a 10 hour long serial job to the batch queue:

ugsub T1-i1-t1-10h serial.sh

To submit a 10 hour long 4-processor parallel job to the batch queue:

ugsub T4-i4-t1-10h multi.sh

or use the following command to ensure that all 4 processors assigned are on the same node:

ambersub 4 10 multi.sh

Type llqueue at your pcluster login prompt to get more information about the batch queuenames.

Note When a parallel job is submitted with ugsub as shown above, it is not guaranteed that all processors assigned to the job will be on the same node. If you want to ensure that all processors (up to 8) assigned to the job are on the same node (to use shared memory communication), please submit your job with ambersub instead of ugsub. Type ambersub at a pcluster command prompt to see its usage.

Documentation

User guide and documents available in /usr/local/amber8/doc/ (Amber8) and /usr/local/amber10/doc/ (Amber10)

More information at http://ambermd.org/

Installation

Amber8 is installed in /usr/local/amber8 and it is on users' default path.

Amber10 is installed in /usr/local/amber10 and it is not on users' default path.

Compiled with the IBM compilers, using MPI for the parallel versions.

AmberTools 1.2 was compiled with XLF 9.1 and gcc 3.3.2 and it is installed in /usr/local/amber10

System

Unix (AIX)