Desmond

Description

From the Desmond web site: DesmondDesmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters, general-purpose supercomputers, and GPUs. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.

Version

2016.2

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

Desmond requires the following module file to run:

apps/desmond/2016.2

See Modules for more information.

Running Desmond on CIRCE

The Desmond 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.

If, for example, you have a Dalton input file named dalton.in, and a molecule file named dalton.mol, you would set up a submit script like this:

The script below (for testing, name it “dalton-test.sh”) 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.

#!/bin/bash
#
#SBATCH --comment=dalton-test
#SBATCH --ntasks=8
#SBATCH --job-name=dalton-test
#SBATCH --output=output.%j.dalton-test
#SBATCH --time=01:00:00

#### SLURM 8 processor Dalton test to run for 1 hour.

module purge
module load apps/dalton/2.0

mpirun dalton dalton.in dalton.mol

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./dalton-test.sh

You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

Dalton Home Page
- http://dirac.chem.sdu.dk/daltonprogram.org
Dalton User's Guide
- http://daltonprogram.org/www/resources/dalton2013manual.pdf
- /opt/apps/dalton/2.0/dalton20manual.pdf

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

Dalton Known Tests
- /opt/apps/dalton/2.0/tests

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

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