Ovito

Overview

Ovito is a Scientific visualization and analysis software for atomistic simulation data.

Version 2.9.0 is installed on the CSF.

Restrictions on use

There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v3 license and all usage must adhere to that license.

Please cite your usage of the software according to the instructions at the Ovito how-to-cite page.

Set up procedure

To access the software you must first load the modulefile:

module load apps/binapps/ovito/2.9.0

Running the application

Please do not run Ovito on the login node. Jobs should be submitted to the compute nodes via batch (to process python scripts that generate visualization) or should be run interactively on a back-end compute node via the qrsh command. Note that remote use of the GUI will be very slow. We recommend you only run the application in batch and write python scripts to do the processing.

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

# You MUST ensure you use the correct number of threads (1 for a serial job).
# $NSLOTS will be replaced automatically with the correct number.

# You MUST also unset the following to prevent a QXcbConnection error occuring:
unset DISPLAY

# Now run ovito without the GUI to process your python script
ovito --nogui --nthreads $NSLOTS --script myviz.py
         #                                  #
         #                                  # Supply your python script name
         #
         # Prevent the GUI displaying in batch.

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel 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
#$ -pe smp.pe 8     # Number of cores to use (2-24 permitted)

# You MUST ensure you use the correct number of threads.
# $NSLOTS will be replaced automatically with the correct number from above.

# You MUST also unset the following to prevent a QXcbConnection error occuring:
unset DISPLAY

ovito --nogui --nthreads $NSLOTS --script myviz.py
         #                                  #
         #                                  # Supply your python script name
         #
         # Prevent the GUI displaying in batch.

Interactive Use on a compute node

If using the GUI, this should be done interactively by first scheduling an interactive session on a compute node:

# From the login node
qrsh -l inter -l short

# Wait for a login to a compute node to occur, then
module load apps/binapps/ovito/2.9.0
ovito --nthreads 1

It is not uncommon for the GUI to be too slow to be usable when running remote graphics in this manner.

Further info

• Ovito user manual

Updates

None.