Amber12

Description

From the Amber homepage: 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.

The Amber software suite is divided into two parts: AmberTools13, a collection of freely available programs mostly under the GPL license, and Amber12, which is centered around the sander and pmemd simulation programs, and which continues to be licensed as before, under a more restrictive license.

Version

  • Amber12 u21 & AmberTools13 u26

Authorized Users

  • Members of the Amber12 research group

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Amber12 requires the following module file to run:

  • apps/amber/12

Running Amber12 on CIRCE

The Amber12 user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting a Job

You must create a submit script (for example, “amber-test.sh”) like the following:

#!/bin/bash
#
#SBATCH --nodes=2 
#SBATCH --ntasks-per-node=4 
#SBATCH --job-name=amber-test
#SBATCH --output=amber.%j.output
#SBATCH --time=01:00:00

#### SLURM task using 2 Nodes with 4 Processors per Node for Amber test to run for 1 hour.

module purge
module load apps/amber/12

mpirun -np $SLURM_NTASKS -ppn $SLURM_NTASKS_PER_NODE sander.MPI -ng <# groups> -groupfile 

 
The above script can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. Scripts are provided as examples only. You will need to make modifications before the script can be used. Your executables, tools, and options will vary. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Next, make sure that you are in your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./amber-test.sh
  • You can view the status of your job with the “squeue -u <username>” command
    • Please note that you should alter the number of nodes, and number of processors per node requested to appropriately balance your CPU and node count. For example, for a job requiring a CPU count of 20, the following lines would properly balance your CPU/Node count via SLURM:
-N 2 --ntasks-per-node=10 (2 nodes, 10 cpus per node)
-N 4 --ntasks-per-node=5 (4 nodes, 5 cpus per node)
-N 5 --ntasks-per-node=4 (5 nodes, 4 cpus per node)

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Amber12 to the IT Help Desk: rc-help@usf.edu