Ovito on GPU Nodes

When rendering visualizations of large systems in our group, we often use Ovito, running on an Intel Mac in our office space. This seems a little strange, given that we have large amounts of high-performance computing resources at our disposal. Here’s a quick demo of how we can set up Ovito to run on a remote system. More generally, this is a demo of how to install any tricky-to-compile software, whether it be due to permission errors, missing dependencies, or out-of-date distributions.

If you just want to get Ovito running, skip to “Using an Ovito image”.

Building a New Image

First, we pull and build a sandboxed Apptainer image of a distribution that makes compilation easy. Here, I use Debian 12. In our remote system with Apptainer, we run the following to pull the latest Debian image from Docker.

apptainer build --fakeroot --sandbox ovito-test/ docker://debian

After this builds, we can connect to the image using fakeroot:

apptainer shell --fakeroot --writable ovito-test/

Once inside, we can start to compile Ovito (or another software) in this compatibility layer where we have more flexibility. For Ovito, copy the .tar.xz archive from the Ovito website to the clusters, and then extract using tar. In this case, we’ll also need to install xz-utils to extract the Ovito image.

apt install xz-utils
tar xJfv ovito-basic-3.11.3-x86_64.tar.xz 

We will also have to install a few XCB system libraries (below is an accumulation from Ovito’s documentation and my own testing, all are probably not necessary). I have found that compiling in ThinLinc avoids some of these issues.

apt install libxcb1 libx11-xcb1 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \
         libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 \
         libxcb-sync1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb-cursor0 \
         libfontconfig1 libfreetype6 libopengl0 libglx0 libx11-6
apt-get install libegl1-mesa libegl1 libglib2.0-0

Ovito is now compiled, with all of its dependencies! Congrats.

Using an Ovito Image

I’ve created a working version of this Ovito implementation and left it in /depot/prism/data/knykiel/ovito-test. The following commands will get you up and running quickly if you don’t care to set up your own Apptainer image.

1. Login with ThinLinc at https://desktop.gilbreth.rcac.purdue.edu:300/ to obtain a persistent remote graphical desktop session, and open up a terminal.

2. Submit an interactive job - it’ll be faster, and you won’t waste front-end resources:

sinteractive -A strachan-k -N1 -n32 --gpus-per-node=1 --time 04:00:00

3. Start a shell in the Ovito image on depot:

cd /depot/prism/data/knykiel
apptainer shell --fakeroot --writable /depot/prism/data/knykiel/ovito-test/

4. Run Ovito:

./ovito-basic-3.11.3-x86_64/bin/ovito