Visualisation

What is Visualisation?

• Visualisation offers a "method for seeing the unseen"
• Its aim is to improve understanding by representing data in a way that the important features can be seen and intuatively understood by humans
• With the increasing size of simulation data, visualisation has become mandatory to exploit the high level of detail available in such large data sets

Why do we Need to Visualise?

"The purpose of computing is insight, not numbers" Richard Hamming (1962)

Why do we Need to Visualise?

"Computing, and in particular supercomputing, without visualisation, is like assembling a jigsaw puzzle in the dark" Richard Weinberg (1988)

Remote Visualisation

What is Remote Visualisation

• Remote visualisation is simply the method of running your visualisation workflow on a remote machine
• Creates an interactive remote desktop on an HPC system
• Remote machines can be any OS, you aren't restricted by your laptops OS

Old Style Remote Visualisation (X11 Forwarding)

• Version 11 of the X window system - X11
• X Server runs on the local machine
• X11 forwarding forwards the X11 packets from the remote machine to your local screen
• The server accepts requests for graphical output (windows) and sends back user input (from keyboard, mouse, or touch screen)
• X11 packets can be forwarded through SSH (secure shell)
• Any X11 programs started will then go through an encrypted channel
• Enabling X11 forwarding: ssh -X couXYZ@zeus.pawsey.org.au

X11 Forwarding Limitations

ssh -X couXYZ@zeus.pawsey.org.au
module load mesa 
glxgears

• Cannot be distributed easily on a cluster (user chooses the server)
• Runs on a single core and does not make use of the GPU
• Very slow compared to other modern remote visualisation techniques (eg. Virtual Network Computing - VNC)
• X11 forwarding will stop once your connection is broken
• Poses security hazard when used in untrusted environment

Web-based Remote Visualisation at Pawsey

Remote Visualisation Infrastructure at Pawsey

• Performed on Topaz
  • 20 nodes with 2x Intel Xeon Silver 4215 CPUs (8 cores in each CPU, 16 cores in total)
  • NVIDIA QUADRO RTX5000 GPU card (16GB DDR6 memory)
  • 192 GB RAM
  • 100Gbit Infiniband network connection
• Shares the same file systems with other Pawsey supercomputers
• /home - for storing user config files
• /scratch - for temporary storage of large research data and simulation output
• /group - for software and project files
• This avoids the need to copy simulation data across Magnus/Galaxy/Topaz

Why use Remote Visualisation

Hands on Session

Login Screen

• Open your preferred browser (e.g. Chrome, Firefox) and goto: remotevis.pawsey.org.au

Welcome Message

• Always note the latest news and instructions in the welcome message

Launch Session

• Click launch session to begin a remote visualisation session

If you see this error, try to connect again

Resize and Pin Topbar

• The resize button in the top bar will resize the virtual desktop to fit your browser window
• The pin button will toggle auto-hiding the top bar

Clipboard, Settings, Sharing

• The clipboard is for transferring text between the remote machine and your local computer
• Settings allows you to change quality and performance of the remote connection
• Sharing allows you to send your interactive session to another person

Copy Text to Remote Session

• Copy the text from your machine in the way you normally would
• Paste the text into the clipboard
• Click "Send To Remote"
• You can now paste the text into the remote machines applications

Copy Text Back to Local Machine

• Copy the text from the remote machine
• Click "Copy From Remote"
• The text will appear in the clipboard window
• You can now copy it from the clipboard and paste into your local machines applications

Bashrc Changes

vi .bashrc

if [ -f /etc/redhat-release ]; then
	if [ -f /etc/bashrc ]; then
	. /etc/bashrc
	fi
fi

vi .bash_profile

if [ -f /etc/redhat-release ]; then
	if [ -f ~/.bashrc ]; then
	. ~/.bashrc
	fi
fi

Running a Visualisation

• Right click on the desktop and click "xterm"
• Type the following commands into the xterm window

module load virtualgl

vglrun glxspheres64

Performance Comparison

• Type the following commands into the xterm window

module load virtualgl

vglrun glxgears

Comparison

• Note the difference in performance where gpu acceleration is used vs x11 fowarding

Terminate the Session

• Always terminate the session when you are done
• Otherwise the remote machine stays active even if you close your browser window

Visualising Using ParaView

ParaView

• Open-source, cross-platform data analysis and visualisation application
• Has a user-friendly interface built on top of the Visualisation ToolKit (VTK) library
• An extensible, modular architecture based on open standards
• Mainly used to analyse large datasets (petascale size) using distributed-memory computing resources
• Supports a wide range of data formats

Domain Specific Supported Data Types

ParaView Interface

ParaView Distributed Mode

Running ParaView in Distributed Mode

• Click connect to server button in the main toolbar
• A list of pawsey servers should be preconfigured
• Check the xterm window for a password prompt if one does not appear

Visualisation of Dam Break Simulation Using ParaView

• Column of water behind a membrane
• At t = 0s, membrane is removed, then:
• column of water collapses
• water impacts an obstacle
• creates a complicated flow structure
• 100 total timesteps

Visualisation of Dam Break Simulation Using ParaView

Visualising Using VMD

High-Performance
Molecular Visualisation Tool

• Molecular dynamics simulations
• Lattice cell simulations
• Quantum chemistry calculations
• Cyro-EM dencities, volume data
• User extensible custom scripting and plugin

VMD Interface

Molecular Simulation Visualisation Using VMD

Calcium carbonate is one of the most abundant minerals on Earth. It is a key component of seashells and corals, as well as scale. Better understanding its mechanisms of formation can have an impact in several regards, including the safeguard of marine life and reducing the maintenance costs in industrial plants.

Even at low concentrations (1 ion pair every 55,000 water molecules), calcium and carbonate ions in water do not remain isolated, but instead form small clusters composed of several molecules. Note how dynamic the structure of the cluster is and how often the atomic connectivity changes in the few nanoseconds represented in this movie.

Agglomeration and separation of calcium and carbonate ions (grey) in water, during atomistic simulations run on the Magnus supercomputer.