Avogadro2

Overview

Avogadro2 is a free and open source molecular editor and visualization tool.

Version 1.102.1 of Avogadro2 is installed on the CSF. Following the Slurm (and O/S) upgrade, any earlier versions no longer work.

Restrictions on use

There are no restrictions on access Avogadro2 on the CSF. It is licensed under the BSD 3-Clause “New” or “Revised” License and all usage must adhere to this license.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load apps/singularity/avogadro2/1.102.1

Running the application

Please do not run Avogadro on the login node. Jobs should be submitted to the compute nodes via an interactive session using srun. For example:

# From the login node, start a 2-core 1-hour interactive session on the AMD nodes:
module load apps/singularity/avogadro2/1.102.1
srun -p interactive -c 2 -t 0-1 avogadro2

# To run on a GPU node:
module load apps/singularity/avogadro2/1.102.1
srun -p gpuA -G 1 -c 2 -t 0-1 avogadro2

Further info

• Avogadro Documentation

Updates

None.