- 1 External documentation for popular visualization packages
- 2 Visualization on new Compute Canada systems
- 3 Upcoming visualization events
- 4 Compute Canada visualization presentation materials
- 5 Tips and tricks
- 6 Regional visualization pages
- 7 Visualization gallery
- 8 How to get visualization help
External documentation for popular visualization packages
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.
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 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.
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
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 firstname.lastname@example.org 'cat >>.ssh/authorized_keys'
Compiling ParaView with OSMesa
Since the VM does not have access to a GPU (most Cloud West VMs don't), we need to compile ParaView with OSMesa support so that it can do offscreen (software) rendering. The default configuration of OSMesa will enable OpenSWR (Intel's software rasterization library to run OpenGL). What you'll end up with is a ParaView server that uses OSMesa for offscreen CPU-based rendering without X but with both llvmpipe (oder and slower) and SWR (newer and faster) drivers built. We recommend using SWR.
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 with SWR rendering:
Back on your laptop, organize an SSH tunnel from the local port 11111 to the VM's port 11111:
ssh email@example.com -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 with offscreen rendering support can be built with 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 may 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 connection nickname (let's call it Cloud West), the VM host name, path to VisIt installation (/home/centos/visit) and your username on the VM, and 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. Data processing and rendering should be done on the VM, while the result and the GUI controls will be displayed on your laptop.
Upcoming visualization events
- "Using ParaViewWeb for 3D visualization and data analysis in a web browser" visualization webinar in March
- winter semester full-day VisIt visualization workshops at UofCalgary (date TBA), UofAlberta (2017-Feb-28), 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
- Running pre-/post-processing graphical applications
- Supported software (see visualization section at bottom)
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.