AMBER

Category(ies): Computational Chemistry

Version: 8

Author / Distributor: See http://amber.scripps.edu

Description:

Amber is a package of molecular simulation programs.

altix: not available on altix

inQuiry: not available at inQuiry

pcluster: Running Program | Documentation | Installation | System

Running Program:

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 ...

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

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

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

pcluster> ugsub T4-i4-t1-10h 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/
More information at http://amber.scripps.edu/

Installation:

Compiled with the IBM compilers, using MPI for the parallel versions.
Installed in /usr/local/amber8/

System: Unix (AIX)

rcluster,IOB: not available on rcluster, IOB