ovito

Overview

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

The latest Version installed on the CSF is version 3.13.0 (basic/community edition).

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  # no interactive use
module load apps/binapps/ovito/3.0.0-dev628
module load apps/binapps/ovito/3.13.0  

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).

Serial batch job submission

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

#!/bin/bash --login
#SBATCH -p serial         
#SBATCH -t 1-0 # Wallclock limit (days-hours). Required!

module purge
module load apps/binapps/ovito/3.13.0

# You MUST ensure you use the correct number of threads (1 for a serial job).
# $SLURM_NTASKS 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 $SLURM_NTASKS --script myviz.py
         #                                  #
         #                                  # Supply your python script name
         #
         # Prevent the GUI displaying in batch.

Submit the jobscript using:

sbatch 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 --login
#SBATCH -p multicore
#SBATCH -n 8         
#SBATCH -t 1-0 # Wallclock limit (days-hours). Required!

module purge
module load apps/binapps/ovito/3.13.0


# You MUST ensure you use the correct number of threads.
# $SLURM_NTASKS 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 $SLURM_NTASKS --script myviz.py
         #                                  #
         #                                  # Supply your python script name
         #
         # Prevent the GUI displaying in batch.

Interactive Use

Start an interactive session from the login node using the following command
srun-x11
See Interactive Jobs (srun, srun-x11) for further options.

Once interactive session has started load the Ovito module file

module purge
module load apps/binapps/ovito/3.13.0

# Start ovito
ovito

Further info

• Ovito user manual

Updates

None.