ParaView

VDI nodes

Two large memory graham remote desktop machines for pre/post-processing

  • access to all files (don’t have to transfer data back and forth)

  • full details on docs.alliancecan.ca

Accessing

Connect via VNC (TigerVNC viewer recommended) to gra-vdi.alliancecan.ca

Windows and OS X

Download latest version from TigerVNC website

  • releases (at top) -> binaries are available from bintray (end of changes list)

Linux

Install with your package manager

  • Debian and Ubuntu: sudo apt-get install tigervnc-viewer

  • Fedora: sudo yum install tigervnc

Software

  • Compute Canada stack is the same as is on cluster

  • Nix stack lets you install and customize your own packages

  • Limited number of local-only packages: module load clumod

JuypterHub

Spawn a JupyterHub desktop on a compute node and connect to it via a browser

  • access to all files (don’t have to transfer data back and forth)

  • full details on docs.alliancecan.ca

Accessing

Go to https://jupyterhub.<cluster>.alliancecan.ca (https://jupyter.scinet.utoronto.ca for niagara) in your browser. Sign in with your alliance username and password. Enter you reservation details and click start

  • reservation: None unless taking part in a course (not this one) with a reservations,

  • account: ending in gpu if using a GPU (including hardware OpenGL) and cpu otherwise,

  • time: 3hrs or less (runs in the interactive queue) for faster start,

  • cores: enough cores so memory/core is 12G or less (regular memory queue) for faster start,

  • memory: at least 8GB for a desktop session (see cores note about keeping memory/core 12G or less),

  • oversubscription: select if possible (shares CPUs with other users) for faster start,

  • gpu configuration: GPU type cluster has most of for faster start, and

  • user interface: JupyterLab (Jupter Notebook is the older version before the renaming).

Once JupyterLab starts, click the Desktop icon in the launcher window. This will open a desktop session in now browser tab.

The desktop session is persistent. Closing the tab just closes the tab. It does not end the session. Clicking the Desktop icon again will just reopen the existing one. To close it pick Log out in the menu bar along the top of the Desktop. The same is true of the entire JupyterLab session. To end it, pick Log out unde the File menu in the menu bar along the top.

Issue workarounds

If the browser fails to connect to the desktop, trying waiting around thirty seconds and then refresh the failed connection page (press the F5 key).

If you see … relocation error: …/rebind.so … in your terminal, you have run into an issue caused by the JupyterHub desktop websockify LD_PRELOAD. Disable this by running

$ unset LD_PRELOAD

If you see warning messages about ipykernel when loading modules, you have run into issues caused by JupyterHub pre-loading the ipython-kernel. Unload this by running

$ module --force unload ipython-kernel python

Software

Personal computer

Available for Windows, OS X, and Linux

Windows and OS X

Download latest version from ParaView website

  • older version may if newer fails on older OS or graphics card

Linux

Install with your package manager (can also download as above)

  • Debian and Ubuntu: sudo apt-get install paraview

  • Fedora: sudo yum install paraview

VDI/JupyterHub

Enable the Compute Canada stack on VDI (this is already done on JupyterHub)

$ module load CcEnv StdEnv

and then (for both) load the paraview module

$ module load paraview

or just install it in your personal Nix environment (the install only needs to be done once)

$ module load nix
$ nix-env -iA nixpkgs.paraview

Tutorial

Working through the ParaView tutorial is one of the quickest and easiest ways to get up-to-speed on ParaView.

  • basic usage (what we will be going over)

  • batch python scripting

  • visualizing large models

$ cp -r /home/tyson/ParaView .

Basis of visualization

  • map raw data to visual data

  • spacial and temporal data

  • topology and types of grids

User interface

  • menu bar

  • tool bars

  • pipeline browser

  • properties panel

  • view

Basic interface

  • creating a source

  • interacting with a 3d view

  • modifying visualization paramaters (filter, display, view)

  • undo and redo (regular vs camera)

Loading data

  • opening file (selecting which variables to load)

  • representation and field coloring

  • scaling

Filters

  • selecting filters (toolbar, menu, and search)

  • applying a filter (contours, slices)

Multiview

  • creating a multiple views

  • linking cameras

  • re-arranging the views

Vector visualization

  • streamlines

  • tubes and glyphs

  • surface LIC

Volume rendering

  • Enabling

  • Transfer function

Plotting

  • histogram plot

  • plot over a line in space

  • plot over a curve

  • plot over time

Selections

  • Query and view based selections

  • Data vs spatial selections

  • Selection labels

  • Extract selection and spreadsheet