Visualization

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.

• ParaView official documentation
• ParaView gallery
• ParaView wiki
• ParaView Python scripting

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.

• VisIt manuals
• VisIt gallery
• VisIt user community wiki
• VisIt tutorials along with sample datasets

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.

• VMD User's Guide

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.

• VTK tutorials

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@vm.ip.address 'cat >>.ssh/authorized_keys'

Compiling ParaView with OSMesa

Back on the VM, compile cmake::

wget https://cmake.org/files/v3.7/cmake-3.7.0.tar.gz
unpack and cd there
./bootstrap
make
sudo make install

Next, compile llvm:

cd
wget http://releases.llvm.org/3.9.1/llvm-3.9.1.src.tar.xz
unpack and cd there
mkdir -p build && cd build
cmake \
 -DCMAKE_BUILD_TYPE=Release \
 -DLLVM_BUILD_LLVM_DYLIB=ON \
 -DLLVM_ENABLE_RTTI=ON \
 -DLLVM_INSTALL_UTILS=ON \
 -DLLVM_TARGETS_TO_BUILD:STRING=X86 \
 ..
make
sudo make install

Next, compile Mesa with OSMesa:

cd
wget ftp://ftp.freedesktop.org/pub/mesa/mesa-17.0.0.tar.gz
unpack and cd there
./configure \
 --enable-opengl --disable-gles1 --disable-gles2 \
 --disable-va --disable-xvmc --disable-vdpau \
 --enable-shared-glapi \
 --disable-texture-float \
 --enable-gallium-llvm --enable-llvm-shared-libs \
 --with-gallium-drivers=swrast,swr \
 --disable-dri \
 --disable-egl --disable-gbm \
 --disable-glx \
 --disable-osmesa --enable-gallium-osmesa
make
sudo make install

Next, compile ParaView server:

cd
wget http://www.paraview.org/files/v5.2/ParaView-v5.2.0.tar.gz
unpack and cd there
mkdir -p build && cd build
cmake \
     -DCMAKE_BUILD_TYPE=Release \
     -DCMAKE_INSTALL_PREFIX=/home/centos/paraview \
     -DPARAVIEW_USE_MPI=OFF \
     -DPARAVIEW_ENABLE_PYTHON=ON \
     -DPARAVIEW_BUILD_QT_GUI=OFF \
     -DVTK_OPENGL_HAS_OSMESA=ON \
     -DVTK_USE_OFFSCREEN=ON \
     -DVTK_USE_X=OFF \
     ..
make
make install

Running ParaView in client-server mode

Now you are ready to start ParaView server on the VM:

./paraview/bin/pvserver --mesa-swr-avx2

Back on your laptop, organize an SSH tunnel from the local port 11111 to the VM's port 11111:

ssh centos@vm.ip.address -L 11111:localhost:11111

Finally, start the ParaView client on your laptop and connect to localhost:11111. If successful, you should be able to open files on the remote VM. During rendering in the console you should see the message "SWR detected AVX2".

Compiling VisIt with Mesa

VisIt can be built via a single script:

wget http://portal.nersc.gov/project/visit/releases/2.12.1/build_visit2_12_1
chmod u+x build_visit2_12_1
./build_visit2_12_1 --prefix /home/centos/visit --mesa --system-python \
   --hdf4 --hdf5 --netcdf --silo --szip --xdmf --zlib

This might take a couple of hours. Once finished, you can test the installation with:

~/visit/bin/visit -cli -nowin

This should start a VisIt Python shell.

Running VisIt in client-server mode

Start VisIt on your laptop and in Options -> Host profiles... edit the nickname, host name, path to VisIt installation, your username on the VM, enable tunneling through ssh. Don't forget to save settings with Options -> Save Settings. Then opening a file (File -> Open file... -> Host = cloud west) you should see the VM's filesystem. Load a file and try to visualize it.

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

• VisIt workshop slides from HPCS'2016 in Edmonton by Marcelo Ponce and Alex Razoumov
• ParaView workshop slides from February 2016 by Alex Razoumov
• Gnuplot, xmgrace, remote visualization tools (X-forwarding and VNC), python's matplotlib slides by Marcelo Ponce (SciNet/UofT) from Ontario HPC Summer School 2016
• Brief overview of ParaView & VisIt slides by Marcelo Ponce (SciNet/UofT) from Ontario HPC Summer School 2016

Webinars and other short presentations

• VisIt scripting from November 2016 by Alex Razoumov
• Batch visualization webinar slides from March 2015 by Alex Razoumov
• CPU-based rendering with OSPRay from September 2016 by Alex Razoumov
• Gephi webinar notes from March 2016 by Alex Razoumov
• 3D graphs with NetworkX, VTK, and ParaView slides from May 2016 by Alex Razoumov
• Remote Graphics on SciNet's GPC system (Client-Server and VNC) slides by Ramses van Zon (SciNet/UofT) from October 2015 SciNet User Group Meeting
• VisIt Basics, slides by Marcelo Ponce (SciNet/UofT) from February 2016 SciNet User Group Meeting
• Intro to Complex Networks Visualization, with Python, slides by Marcelo Ponce (SciNet/UofT)
• Introduction to GUI Programming with Tkinter, from Sept.2014 by Erik Spence (SciNet/UofT)

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

• visualization quickstart guide
• remote visualization
• batch rendering

SciNet, HPC at the University of Toronto

• visualization software
• VNC
• visualization nodes
• further resources and viz-tech talks
• using ParaView

SHARCNET

• Overview
• Running pre-/post-processing graphical applications
• Supported software (see visualization section at bottom)

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.

Message Passing Interface