Analytics: Visualization

Visualization of data is the transformation of data - experimental data or simulation results - into images. Visualizing data is an invaluable tool for data exploration because it provides multiple views of the data (e.g., isosurfaces, volume rendering, streamlines) and facilitates searching for features or regions of interest. In addition, when presented as a series of images representing a change in time, parameter values, etc., data visualization provides a medium for sharing and communicating results.

This page describes NERSC facilities (hardware and software) for visualization and graphics, how to get started, and how the Analytics Team can work with NERSC users. Each section contains links to more detailed information. Examples of collaborations between NERSC users and the Analytics Team are listed under Case Studies.

J. B. Bell, et al., Numerical simulation of a laboratory-scale turbulent V-flame, Proc. Natl. Acad. Sci., 102(29), 10006-10011, 2005.

Visualization Resources

Hardware. Though all NERSC machines have some graphics or visualization software available, DaVinci, the primary analytics and visualization machine, is well suited to data intensive tasks due to its SMP architecture. DaVinci has 32 64-bit Intel Itanium-2 processors running at 1.4 GHz, 192 GB of RAM, and 24 TB of disk space. DaVinci is an SGI Altix 350 server running the SGI ProPack 4 64-bit Linux operating system based on SUSE Linux Enterprise Server 9 (SLES9).

Software. Many graphics and visualization applications have been installed on NERSC machines. Click on one of the links below for more information.

• Graphics Libraries at NERSC
• Graphics/visualization applications by platform:   all   Bassi   Davinci   Jacquard
• Descriptions of visualization and graphics applications and links to documentation

Getting Started

If you know what application you want to use, check for its availability on the platform you are planning to use by clicking on one of the links above. On the linked pages, next to each software application, are links to on-line documentation provided by NERSC, the Visualization Group, or the vendor. Start by reading the NERSC documentation to get a quick overview. The NERSC documentation provides links to more detailed documentation, and in some cases, training presentations and examples produced using the application. Refer to the vendor documentation for the most up-to-date and detailed reference material.

To have the output from a graphics or visualization application being run on one of the NERSC platforms displayed on your workstation, you need to tell the application how to route the output. The secure method for doing this is to specify the -X option when you connect using ssh:

% ssh -X davinci.nersc.gov -l your_user_name

The -X option tells ssh to route all Xlib command back to your workstation. An alternative method is described on the Visualization Group's Web site.

NERSC uses the modules approach to managing the user environment for accessing different software versions on all machines. See the modules page for more information on how to use the modules package.

Tutorials

As mentioned in the Getting Started section above, on-line documentation, including tutorials and training presentations, are available by following the links on the Graphics Libraries at NERSC or Visualization Applications and Graphics Libraries pages.

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How Tos

         Accelerating Remote X Performance on DaVinci Using NX   NEW
         AVS/Express and VisIt Training - presented at the NUG Meeting, June 2006
         How to Route Graphics Output through SSH
         How to Set up a Remote Desktop on DaVinci Using NX (recommended) or Using VNC
         How to Write an AVS/Express Module
         Making MPEG Movies at NERSC
         Remote License Services at NERSC
         Running a Remote VisIt Compute Engine on DaVinci
         Using EnSight SOS mode

Visualization Services

The NERSC Analytics Team includes members of the Berkeley Lab Visualization Group, whose mission is to assist researchers in achieving their scientific goals more quickly through creative and inspired visualization of their data. The Visualization Group provides the expertise to help users focus on visualizing their data without having to invest the significant amount of time required to learn about visualization tools and techniques. The Case Studies section below gives some examples of collaborations between NERSC users and members of the Visualization Group. In addition, Analytics Team/Visualization Group members work with users to develop data readers to facilitate importing simulation or experimental data into visualization applications.

Case Studies

The following examples shows how different visualization techniques (e.g., isosurface and volume rendering) can be effectively combined to explore and present simulation results. Each image is linked to a Web page with more examples.

2006 INCITE Project Particle-in-Cell Simulation of Laser Wakefield Particle Acceleration
		Experiments with laser wakefield accelerators (LWFA) have demonstrated accelerating gradients thousands of times greater than those obtained in conventional particle accelerators. LWFAs use the electric field of a plasma wave - the wakefield - driven by the radiation pressure of an intense laser. The simulations proposed in this study will interpret recent experiments and assist in the planning of the next generation of particle accelerators and ultrafast applications in chemistry and biology. This image shows a horizontal slice through the electric field; the electrons are colored by the magnitude of the momentum. Visualization applications used: AVS/Express, VisIt          project description | more visualization examples
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2005 INCITE Project Magneto-Rotational Instability and Turbulent Angular Momentum Transport
		In space, gases and other matter often form swirling disks around attracting central objects such as newly formed stars. The presence of magnetic fields can cause the disks to become unstable and develop turbulence, causing the disk material to fall onto the central object. This project will carry out large-scale simulations to test theories on how turbulence can develop in such a scenario. These simulations may provide insights into magnetically caused instabilities being studied on a smaller scale in laboratory experiments. In this image volume rendering has been used to visualize the time evolution of hydrodynamic entropy. The color scale is from blue (low) to orange (high). Visualization applications used: AVS/Express, VisIt
		project description | more visualization examples
2004 INCITE Project Quantum Monte Carlo Study of Photoprotection via Carotenoids in Photosynthetic Centers
		The goal of this project is to increase understanding of the complex processes that occur during photosynthesis. Photosynthesis, which is an efficient energy transfer system, is an example of fundamental electron chemistry. The QMC method was used to solve the Schrodinger equation and produced datasets of walkers for the electron density of carotenoid molecules. Each walker is a snapshot of the configuration of the 3N electronic coordinates, where N is the number of electrons. The image to the left shows a ball-and-stick model of spheroidene. An isosurface of the electron density is shown in yellow; walkers are colored in shades of green, rose, and teal. Visualization application used: AVS/Express
		project description | more visualization examples
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2004 INCITE Project Fluid Turbulence and Mixing at High Reynolds Number
		Turbulence is a phenomenon that is not well understood and is extremely difficult to model. Being able to improve the simulation of turbulence will lead to a better understanding of the effect of turbulent flow in areas such as astrophycis, combustion and propulsion, dispersion of contaminants, meteorology, and oceanography. This image uses volume rendering to display the sheet-like structures present in the flow field (middle of the image). False color and terrain height mapping are used to show high-density features (bottom of the image). Visualization applications used: AVS/Express, EnSight          project description | more visualization examples

Research

Members of the Visualization Group work with NERSC users as well as collaborators at LBNL and other national labs and universities to develop tools that

• improve the performance and capabilities of visualization applications,
• integrate scientific data management and visualization applications to find and display interesting regions and features in and to improve visual data analysis performance on large, complex datasets.

These tools are then made available to NERSC users. Visit the Visualization Group's Web site to read more about the research that group members are involved in. Several members of the Visualization Group are part of the DOE SciDAC Visualization and Analytics Center for Enabling Technologies (VACET).

More Information

More examples of visualizations from a wide variety of scientific applications are available on the Berkeley Lab Visualization Group Web site. Links to the group's publications and presentations also are available.

Contact the NERSC Analytics Team (consult@nersc.gov) if you have questions about visualization applications or techniques, or would like help visualizing your data or simulation output.

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