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.
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
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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
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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
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project description |
more visualization examples
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2004 INCITE Project
Quantum Monte Carlo Study of Photoprotection via
Carotenoids in Photosynthetic Centers
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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
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project description |
more visualization examples
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2004 INCITE Project
Fluid Turbulence and Mixing at High Reynolds Number
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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
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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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