A
daptive mesh refinement, developed
by Marsha Berger and her colleagues
in the 1980s for gas dynamical simu-
lations,
1
is a type of multiscale algo-
rithm that achieves high spatial resolution in lo-
calized regions of dynamic, multidimensional
numerical simulations. Greg Bryan’s excellent ar-
ticle
2
in the March/April 1999 issue of Computing
in Science & Engineering describes our cosmolog-
ical AMR algorithm and how we have applied it to
star, galaxy, and galaxy cluster formation. Basi-
cally, the algorithm allows us to place very high
resolution grids precisely where we need them—
where stars and galaxies condense out of diffuse
gas. In our applications, AMR allows us to achieve
a local mesh refinement, relative to the global
coarse grid, of more than a factor of 10
6
. Such res-
olution would be totally impossible to achieve
with a global, uniform fine grid. Thus, AMR al-
lows us to simulate multiscale phenomena that are
out of reach with fixed grid methods.
The AMR algorithm accomplishes this by
producing a deep, dynamic hierarchy of increas-
ingly refined grid patches. The data structures
for storing AMR data are complex, hierarchical,
dynamic, and in general quite large. For exam-
ple, the simulation of an X-ray galaxy cluster
shown in Figure 1 used a grid hierarchy seven
levels deep containing over 300 grid patches.
Existing visualization, animation, and data-
management tools developed for simple mesh
data structures cannot handle AMR data sets.
Consequently, in the past several years we have
been working at the National Center for Super-
computing Applications to overcome this deficit.
Here we describe our progress in four main ar-
eas: portable file formats, desktop visualization
tools, virtual-reality navigation and animation
techniques, and Web-based workbenches for han-
dling and exploring AMR data. Although we have
applied our work specifically to cosmology, we be-
lieve our solutions have broader applicability.
AMR data structures
Within an evolving AMR simulation, the data is
organized in a grid hierarchy data structure—
think of a tree of arbitrary structure and depth
(see Figure 2). The AMR algorithm generates
this tree recursively and adaptively. Every node
and leaf of the tree is associated with a 3D grid
patch (hereafter, simply a grid); these have vari-
ous sizes, shapes, and spatial resolutions.
DIVING DEEP : DATA -MANAGEMENT
AND V ISUALIZATION S TRATEGIES
FOR A DAPTIVE MESH R EFINEMENT
S IMULATIONS
The authors’ cosmological applications illustrate problems and solutions in storing,
handling, visualizing, virtually navigating, and remote-serving data produced by large-
scale adaptive mesh refinement simulations.
MICHAEL L. NORMAN, JOHN SHALF , STUART LEVY,
AND GREG DAUES
National Center for Supercomputing Applications
1521-9615/99/$10.00 © 1999 IEEE
M ASSIVE D ATA
V ISUALIZATION
36 COMPUTING IN S CIENCE & E NGINEERING