Visualisation applications available on the remote visualisation servers

Visualisation applications available on the remote visualisation servers

The main visualisation applications available on the remote visualisation servers will be discussed below. In addition, the software available via the module system on the Linux cluster can also be used on the remote visualisation servers (use module avail to get a list of available software packages).

Please tell us if you are interested in using other (e.g. more specialized) visualisation applications.

The following table lists the visualisation applications available on the remote visualisation servers. Due to the OS update to SUSE 11 some old software packages are no longer available.

Desktop-Icon R Desktop Icon

Name

Version

Usage with VirtualGL ("direct mode")

Usage with TurboVNC
("raw mode")

w/o reservation

w/ reservation

Amira

5.2

$ rv run_amira.sh

Desktop-Icon Amira Desktop Icon

AVS/Express

7.2

rv run_avs.sh

Desktop-Icon AVS/Express Desktop Icon

Blender

2.48

rv run_blender.sh

Desktop-Icon Blender Desktop Icon

Maestro

9.0

rv run_maestro.sh

Desktop-Icon VMD Desktop Icon

Paraview

2.6

rv run_paraview.sh

Desktop-Icon Paraview Desktop Icon

PyMOL

0.99

rv run_pymol.sh

Desktop-Icon PyMOL Desktop Icon

R

2.8.0

rv run_R.sh

Vapor

2.0.0

rv run_vapor.sh

Desktop-Icon Vapor Desktop Icon

VisIt

1.11.1

rv run_visit.sh

Desktop-Icon VisIt Desktop Icon

VMD

1.8.9

rv run_vmd.sh

Desktop-Icon VMD Desktop Icon

Amira

Amira (Screenshot)

Amira is a commercial visualisation application. Unfortunately at the moment it is not possible to use more than one graphics card or more than one CPU core with Amira. The latest version installed on the remote visualisation server is Amira 5.2.

Documentation: Please refer to the online help.

(On rvs1, Amira 4.1.2 is also still available. With an active reservation, start it with

qsub -q <your queue> /usr/local/qscripts/RUN.amira-4.1.2

Without active reservation type

rvrun -d <duration in hours> amira-4.1.2

AVS/Express

AVS/Express screenshot

AVS/Express is versatile data visualization tool for both non-programmers and experienced developers. The software offers rapid data analysis and rich visualization techniques combined with an intuitive, graphical application development environment.

AVS/Express offers many features, such as:

  • Develop and deploy on Windows, Linux, Macintosh, Sun, HP, SGI and Alpha systems.
  • Object-oriented visual editor for quickly creating powerful visualizations and applications.
  • More than 850 visualization objects with full 3D lighting, motion and flow structures.
  • Support on 64-bit platforms--scales to very large data and very complex systems.

Documentation: Can be found through the built-in help function. The program also comes pre-loaded with many demo files (look for "Examples" and drag one to the workspace in the lower half of the start-up screen).

Blender (3d animation software)

Blender screenshot

Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License. Blender 2.48 is the latest version that is installed on the remote visualisation servers.

Blender can be used for modeling, UV unwrapping, texturing, rigging, water simulations, skinning, animating, rendering, particle and other simulations, non-linear editing, compositing, and creating interactive 3D applications. Blender is available for several operating systems, including Microsoft Windows, Mac OS X, Linux, IRIX, Solaris, NetBSD, FreeBSD, OpenBSD with unofficial ports for BeOS, SkyOS, AmigaOS, MorphOS and Pocket PC. Blender has a robust feature set similar in scope and depth to other high-end 3D software such as Softimage/XSI, Cinema 4D, 3ds Max, Lightwave and Maya. These features include advanced simulation tools such as rigid body, fluid, cloth and softbody dynamics, modifier based modeling tools, powerful character animation tools, a node based material and compositing system and Python for embedded scripting. Among its capabilities are:

  • Support for a variety of geometric primitives, including polygon meshes, fast subdivision surface modeling, Bezier curves, NURBS surfaces, metaballs, digital sculpting, and outline fonts.
  • Versatile internal rendering capabilities and integration with YafRay, a Free Software ray tracer.
  • Keyframed animation tools including inverse kinematics, armature (skeletal), hook, curve and lattice-based deformations, shape keys (morphing), non-linear animation, constraints, vertex weighting, soft body dynamics including mesh collision detection, LBM fluid dynamics, Bullet rigid body dynamics, particle based hair, and a particle system with collision detection.
  • Modifiers to apply non-destructive effects.
  • Python scripting for tool creation and prototyping, game logic, importing and exporting from other formats such as OBJ, FBX, DXF, COLLADA, task automation and custom tools.
  • Basic non-linear video/audio editing and compositing capabilities.
  • A fully integrated node based compositor within the rendering pipeline.

Documentation: Can be found on the Wiki docs. The page also includes tutorials and demo files.

Ensight

Ensight screenshot

Ensight is a commercial visualisation application especially suited for CFD data. Ensight runs in parallel on multiple CPU cores, but can only handle one GPU.

EnSight's distributed architecture handles scientific and engineering analysis models containing up to billions of nodes while optimizing memory use.

Features unique to EnSight Gold include:

  • SMP parallel processing support for more than 2 processors.
  • Output to POV-Ray ray-tracing program for photorealistic images.
  • Collaboration between remote users.

Documentation: The manuals are available here and there are is also a general tutorial and a CFD tutorial.

Hint: If ensight hangs when reading a file, removing ~/.ensight8 may help.

ParaView

Paraview screenshot

Paraview is a open-source visualisation application that is able to utilize multiple CPU cores and multiple graphics cards. It has a client-server architecture to facilitate remote visualization of datasets, and generates level of detail (LOD) models to maintain interactive framerates for large datasets. ParaView 2.6 is installed on the remote visualisation server, We just compiled ParaView 3.4.0 and it will be available soon - we're working on it!.

Please note: At the moment volume rendering does not work reliably in the parallel version. However, it works in the serial version.

ParaView provides many tools for scientific visualization but the most commonly-used are

  • isocontouring: finding curves or surfaces in space where a function takes on a single value,
  • clipping: removing some spatial region from a dataset,
  • volume rendering: drawing a scalar function defined over a volumetric region of space with some translucent appearance so that the interior of the dataset can be observed,
  • cutting: intersecting a dataset with another (usually lower-dimensional) curve or surface,
  • thresholding: removing some region of a dataset based on the value of a function defined over space,
  • Subsetting: removing data to reduce its size with minimal impact on its visual appearance (this is most commonly used for structured grids), and
  • picking: selecting a single point or cell in order to inspect function values associated with it.

Although it was initially intended mainly for use with unstructured grids, ParaView can represent data in structured grids.

Documentation: Besides the online help there is a ParaView wiki and a ParaView FAQ page.

Please note: A number of empty windows will pop up when ParaView renders in parallel. Please do not close these windows! Just leave them in the background. ParaView will crash if one of the windows is closed.

Please note: Using more CPU cores will speed up numerical operations on the data and e.g. operations like isosurface extraction. However, the parallelization overhead may reduce the rendering speed. Therefore — depending on the data size and how the data is visualized — the serial version may even be faster than the parallel version.

Please note: Due to paraviews client-server concept, there is no reasonable configuration for two graphics cards. If you reserve two GPUs and run Paraview, only one GPU will be used. If you reserve three or more GPUs, all of them will be used, unless you specify the "-onegpu" option when starting RUN.paraview or vnc-paraview.sh. This may be useful, because:

Please note: Volume rendering works in the serial version and also in the parallel version, if not more than one GPU is used. When more GPUs are used, Paraview crashes. This problem is under investigation...

PyMOL (molecular visualization system)

PyMOL screenshot

PyMOL is a (user-sponsored) molecular visualization system on an open-source foundation. PyMOL 0.99rc6 is the latest version that is installed on the remote visualisation servers.

It is well suited to producing high quality 3D images of small molecules and biological macromolecules such as proteins. According to the author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.

PyMOL is one of few open source visualization tools available for use in structural biology (another one being VMD, which is also available on the remote visualisation servers). The Py portion of the software's name refers to the fact that it extends, and is extensible by the Python programming language.

If you use PyMOL to create images or movies for your publications, please use the following citation:
DeLano, W.L. The PyMOL Molecular Graphics System. (2008) DeLano Scientific LLC, Palo Alto, CA, USA. http://www.pymol.org

Documentation: Can be found on the PyMOL wiki. The page also offers several tutorials. Demo files are included in PyMOL (click on Wizard->Demo).

R

R screenshot

R is a free software environment for statistical computing and graphics. R comes with a huge number of libraries for every purpose imaginable. It has very powerful functions and easy-to-learn syntax. With a few lines of code you can import, manipulate and interactively visualise your data, and easily create publication-ready images.

R provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, and others) and graphical techniques. R is designed around a true computer language, and it allows users to add additional functionality by defining new functions. Much of R's system is itself written in the language, which makes it easy for users to follow the algorithmic choices made. For computationally-intensive tasks, C, C++ and Fortran code can be linked and called at run time. Advanced users can write C code to manipulate R objects directly.

R is also highly extensible through the use of user-submitted packages for specific functions or specific areas of study. Due to its S heritage, R has stronger object-oriented programming facilities than most statistical computing languages. Extending R is also eased by its permissive lexical scoping rules.

Another of R's strengths is its graphical facilities, which produce publication-quality graphs which can include mathematical symbols. R has its own LaTeX-like documentation format, which is used to supply comprehensive documentation, both on-line in a number of formats and in hard copy.

R has its roots in statistics, but its extensibility, ease-of-use and powerful graphics makes it ideal for users looking for alternatives to applications like IDL or MATLAB (which are both also available on the visualisation servers via the module system - type 'module avail' at the prompt to see what software is installed; follow this link for more information).

To get a quick overview of the abilities of R, use the following commands on the remote visualisation server:

rvs1:> rvrun -d 1 R
> library(rgl)
> demo(rgl)

Documentation: The R home page offers links to Manuals, FAQs, Books and a Newsletter. There is also an R Wiki.

Vapor

Vapor screenshot

Vapor is the Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers (VAPOR). The software is based on wavelet transformation, which makes it extremely fast and responsive in day-to-day visualisation applications. It provides (quoting from the vapor website):

  • A visual data discovery environment tailored towards the specialized needs of the geosciences CFD community.
  • A desktop solution capable of handling terascale size data sets.
  • Advanced interactive 3D visualization tightly coupled with quantitative data analysis.
  • Support for multi-variate, time-varying data.
  • Close coupling with RSI's powerful interpretive data language, IDL.
  • Support for 3D visualization of WRF-ARW datasets.

If you use Vapor to create images for your publications, the developers ask you to cite them as follows:

For journal articles, proceedings, etc.:

Clyne, J., Mininni, P., Norton, A., and Rast, M. "Interactive desktop analysis of high resolution simulations: application to turbulent plume dynamics and current sheet formation", New Journal of Physics 9 (2007) 301.
Clyne, J. and Rast, M. "A prototype discovery environment for analyzing and visualizing terascale turbulent fluid flow simulations", in proceedings of Visualization and Data Analysis 2005, pp. 284-294, January 2005.

For presentations, posters, etc:

Imagery produced by VAPOR (www.vapor.ucar.edu), a product of the National Center for Atmospheric Research.

Alternatively, in both cases you can cite the URL:

www.vapor.ucar.edu

VisIt

VisIt screenshot

VisIt is an open-source visualisation application that is able to utilize multiple CPU cores. VisIt 1.11.1 is the latest version that is installed on the remote visualisation servers (VisIt 1.6.1 is still available on rvs1).

VisIt is an open source interactive parallel visualization and graphical analysis tool for viewing scientific data. It can be used to visualize scalar and vector fields defined on 2D and 3D structured and unstructured meshes. VisIt was designed to handle very large data set sizes in the terascale range and yet can also handle small data sets in the kilobyte range

Features of VisIt include:

  • Rich feature set for scalar, vector, and tensor field visualization. VisIt handles 2D and 3D data equally well. VisIt also has the ability to animate data, allowing users to see the time evolution of their data.
  • Provides qualitative and quantitative visualization and analysis. VisIt provides support for derived fields, which allow new fields to be calculated using existing fields. For example, if a dataset contains a velocity field, it is possible to define a new field that is the velocity magnitude. It also supports a generalized query interface, which allows you to query derived quantities such as volume or surface area.
  • Supports multiple mesh types. VisIt provides support for a wide range of computational meshes, including two- and three-dimensional point, rectilinear, curvilinear, and unstructured meshes. In addition, VisIt supports structured AMR meshes and CSG meshes.
  • Powerful, full-featured graphical user interface. VisIt's graphical user interface allows novice users to quickly get started visualizing their data, as well as allowing power users access to advanced features. It automatically creates time-based animations from data sets that contain multiple time steps. In addition, it also has a keyframe animation capability that allows users to create sophisticated animations. VisIt allows users to pan, zoom, and rotate objects interactively using the mouse. It also gives users the ability to interactively size and position geometric objects such as planes and spheres.
  • Parallel and distributed architecture. VisIt employs a distributed and parallel architecture in order to handle extremely large data sets interactively. VisIt's rendering and data processing capabilities are split into viewer and engine components that may be distributed across multiple machines:
    • Viewer is responsible for rendering and is typically run on a local desktop or visualization server so that it can leverage the extremely powerful graphics cards.
    • Engine is responsible for the bulk of the data processing and input/output. The engine can be run serially on a single processor or in parallel on (up to) thousands of processors.
  • Interfaces with C++, Python, and Java. The C++ and Java interfaces make it possible to provide alternate user interfaces for VisIt or allow existing C++ or Java applications to add visualization support. The Python scripting interface gives users the ability to batch process data using a scripting language. This feature can be used to create extremely sophisticated animations or implement regression suite.
  • Extensible with dynamically loaded plug-ins. VisIt achieves extensibility through the use of dynamically loaded plugins. All of VisIt's plots, operators, and database readers are implemented as plugins and are loaded at run-time from the plugin directory. New plugins can be added simply by installing them in this directory. VisIt comes with a graphical plugin creation tool, which greatly simplifies the process of creating new plugins.

Documentation: Can be found on the VisIt documentation page. Additional information can be found in the VisIt users wiki.

VisIt was compiled at LRZ to be run in parallel with a default number of 4 processor cores to ease the handling of large data files and time consuming analysis. When you open a moderately sized data file, please limit visit to one or two processor cores. If you have a large data file and have to perform many time consuming calculations, you can tell VisIt to use more than just one processor core. In any case, you have to select rvs1.hlrb2.lrz-muenchen.de instead of localhost in the top-most drop down menue of the File->Open dialogue 'Host' (see the following image)!

Visit screenshot: File->Open Dialogue box

After you have selected a file, you will be asked how many processes should be started ('Num procs'). The default number of processor cores assigned to visit is 4. Please note that using more processor cores might even slow VisIt down! For example, the ENZO module distributes the data by grid patch, so there won't be any speed-up for data files containing only one grid patch!
Press 'OK' to start loading the data (see the following image).

Visit screenshot: Select number of cores

VisIt will now load the data and start the parallel compute engine. This may take a few seconds and you will see the following message window:

Visit screenshot: Starting parallel engine

Now, VisIt should behave just like when you run it with only one core.

Please note: The parallelization is controlled by the visit file import modules, which distribute the data over the cpu cores, using different strategies. The ENZO module distributes data grid patch by grid patch. Therefore there won't be any parallel speedup for data files containing only one grid patch!

VMD (Visual Molecular Dynamics)

VMD screenshot

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code. VMD 1.8.6 is the latest version that is installed on the remote visualisation servers.

VMD is an extremely powerful tool to analyse, visualise and create publication-ready images and movies of just about any molecular system. It has built-in support to download structures from the protein data bank (PDB - will not work for HLRB-II users on rvs1 due to firewall settings!).

If you use VMD to create images or movies to be used in your publications, the developers ask you to cite the use of VMD. Follow this link for details.

VMD is developed and maintained by people from the same university that also develop NAMD, a powerful and extremely scalable code for molecular dynamics simulations. NAMD is available on HLRB-2 and the Linux-Cluster via the module system ("module load namd"). VMD can be used to connect to a NAMD simulation to perform interactive molecular dynamics (IMD). For details, please read the documentation on the NAMD and VMD home page.

Documentation: Can be found on the VMD home page. The page also includes tutorials and demo files.

Maestro (Versatile molecular modelling)

maestro

Maestro is the unified interface for molecular modelling environment for all Schrödinger software and desmond. Impressive rendering capabilities, a powerful selection of analysis tools, and an easy-to-use design combine to make Maestro a versatile modeling environment for all researchers. Maestro version 9.0 is the latest version that is installed on the LRZ platforms.

Maestro has built-in support to download structures from the protein data bank.

Please cite the Maestro modules in all published work.

Schrödinger is proud to make Maestro available to academic users at no charge. Please click here for additional details.

Documentation: Can be found on the Schrödinger home page.

XTerm with OpenGL for user applications

XTerm with OpenGL (screenshot)

Some users have purchased their own license for specialised applications or written their own code to analyse and visualise their data.

For those users, we provide a terminal window (XTerm) with hardware accelerated OpenGL enabled. Any application started from within the context of this terminal will have access to the previously reserved number of graphics cards.

Start it by clicking on the desktop icon if you're using TurboVNC (remote desktop). From the Linux command line on the remote visualisation server, start it by typing either 'qsub' (in case you have an active reservation) or 'rvrun' (in case you don't have an active reservation):

rvs1:> qsub -q <your queue> opengl-xterm

or

rvrun -d <duration in hours> opengl-xterm