Visualization

From Alliance Doc
Jump to navigation Jump to search
Other languages:

External documentation for popular visualization packages[edit]

ParaView[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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[edit]

Prerequisites[edit]

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[edit]

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 SWR (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[edit]

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[edit]

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[edit]

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[edit]

  • "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[edit]

Full- or half-day workshops[edit]

Webinars and other short presentations[edit]

Tips and tricks[edit]

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[edit]

WestGrid[edit]

SciNet, HPC at the University of Toronto[edit]

SHARCNET[edit]

Visualization gallery[edit]

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[edit]

You can contact us via email.

Message Passing Interface

Retrieved from "https://docs.alliancecan.ca/mediawiki/index.php?title=Visualization&oldid=9582"