Alliance Doc

Visualization

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External documentation for popular visualization packages

ParaView

ParaView is a general-purpose 3D scientific visualization tool. It is open source and compiles on all popular platforms (Linux, Windows, Mac), understands a large number of input file formats, provides multiple rendering modes, supports Python scripting, and can scale up to tens of thousands of processors for rendering of very large datasets.

VisIt

Similar to ParaView, VisIt is an open-source, general-purpose 3D scientific data analysis and visualization tool that scales from interactive analysis on laptops to very large HPC projects on tens of thousands of processors.

VMD

VMD is an open-source molecular visualization program for displaying, animating, and analyzing large biomolecular systems in 3D. It supports scripting in Tcl and Python and runs on a variety of platforms (MacOS X, Linux, Windows). It reads many molecular data formats using an extensible plugin system and supports a number of different molecular representations.

VTK

The Visualization Toolkit (VTK) is an open-source package for 3D computer graphics, image processing, and visualization. The toolkit includes a C++ class library as well as several interfaces for interpreted languages such as Tcl/Tk, Java, and Python. VTK was the basis for many excellent visualization packages including ParaView and VisIt.

Visualization on new Compute Canada systems

This section will be updated as the new systems come online starting with Cedar (SFU) and Graham (Waterloo) in April-May 2017.

Running client-server ParaView and client-server VisIt in a cloud VM

Prerequisites

You can launch a new cloud virtual machine (VM) as described in the Cloud Quick Start Guide. Once you log into the VM, you'll need to install some additional packages to be able to compile ParaView or VisIt. For example, on a CentOS VM you can type: 

[~]$ sudo yum install xauth wget gcc gcc-c++ ncurses-devel python-devel libxcb-devel
[~]$ sudo yum install patch imake libxml2-python mesa-libGL mesa-libGL-devel
[~]$ sudo yum install mesa-libGLU mesa-libGLU-devel bzip2 bzip2-libs libXt-devel zlib-devel flex byacc
[~]$ sudo ln -s /usr/include/GL/glx.h /usr/local/include/GL/glx.h

If you have your own private-public SSH key pair (as opposed to the cloud key), you may want to copy the public key to the VM to simplify logins, by issuing the following command on your laptop: 

[~]$ cat ~/.ssh/id_rsa.pub | ssh -i ~/.ssh/cloudwestkey.pem centos@206.12.97.3 'cat >>.ssh/authorized_keys'

Upcoming visualization events

  • winter semester visualization webinars in January and March - topics and dates TBA
  • winter semester full-day VisIt visualization workshops at UofCalgary (date TBA), UofAlberta (date TBA), and SFU (2017-Feb-01)

Compute Canada visualization presentation materials

Full- or half-day workshops

Webinars and other short presentations

Tips and tricks

This section will describe visualization workflows not included into the workshop/webinar slides above. It is meant to be user-editable, so please feel free to add your cool visualization scripts and workflows here so that everyone can benefit from them.

Regional visualization pages

WestGrid

SciNet, HPC at the University of Toronto

SHARCNET

Visualization gallery

You can find a gallery of visualizations based on models run on Compute Canada systems in the visualization gallery. There you can click on individual thumbnails to get more details on each visualization.

How to get visualization help

You can contact us via email.

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