DynamO

Overview

DynamO is a free and open-source event-driven particle simulator, used a molecular dynamics package to study model fluids or as a granular dynamics package to investigate solid particle processes.

Version 1.5.0 (stable branch) is installed on the CSF. It was compiled with the GCC 4.8.2 compiler and Boost 1.5.1 libraries.

Please note that the DynamO visualizer (Coil) is not available on the CSF. All work should be run in batch.

Restrictions on use

There are no restrictions on accessing this software on the CSF. If you publish results calculated by using this software, please use the citation as detailed at the dynamo publications page.

Set up procedure

To access the software you must first load one of the following modulefiles:

• Latest development branch (as of 2014-09-18) – the git master branch

  module load apps/gcc/dynamo/140918-master

• The stable 1.5.0 branch (circa 2011)

  module load apps/gcc/dynamo/1.5.0

File formats changed between these versions so please use the version appropriate to any existing files.

This modulefile will load the required GCC and BOOST modulefiles automatically.

Running the application

Please do not run DynamO on the login node. Jobs should be submitted to the compute nodes via batch.

Several DynamO executables are available, the main ones being dynamod and dynarun. The dynarun application can be run with multiple threads (see below for an example jobscript).

Serial batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

dynarun --out-data-file out.xml.bz2 -o config.out.xml.bz2 --engine 1 config-files
  #
  # The 'engine' can be 1, 2 or 3

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission

Some DynamO operations can use multiple threads. You must add the -N numthreads option if supported and specifty the Parallel Environment in the jobscript. For example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings
#$ -pe smp.pe 8     # Use 8 cores (in this example)

# $NSLOTS is automatically replaced by the number of cores from above
dynarun -N $NSLOTS --out-data-file out.xml.bz2 -o config.out.xml.bz2 --engine 1 config-files
  #
  # The 'engine' can be 1, 2 or 3

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• DynamO website (documentation available)

Updates

None.