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Adaptive Mesh Applications: Sathish Vadhiyar

This document discusses adaptive mesh applications and the use of space-filling curves for partitioning and load balancing adaptive meshes. Adaptive mesh applications have irregular workloads that vary based on "interesting" regions, making it difficult to predict future workloads. Repartitioning is necessary to balance workloads as meshes are refined. Space-filling curves provide a way to map multi-dimensional meshes to one dimension while preserving locality, allowing for efficient partitioning and load balancing of adaptive meshes. Common space-filling curves discussed include Z-curves, Gray codes, and Hilbert curves.

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Atreya Dey
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34 views

Adaptive Mesh Applications: Sathish Vadhiyar

This document discusses adaptive mesh applications and the use of space-filling curves for partitioning and load balancing adaptive meshes. Adaptive mesh applications have irregular workloads that vary based on "interesting" regions, making it difficult to predict future workloads. Repartitioning is necessary to balance workloads as meshes are refined. Space-filling curves provide a way to map multi-dimensional meshes to one dimension while preserving locality, allowing for efficient partitioning and load balancing of adaptive meshes. Common space-filling curves discussed include Z-curves, Gray codes, and Hilbert curves.

Uploaded by

Atreya Dey
Copyright
© © All Rights Reserved
Available Formats
Download as PPT, PDF, TXT or read online on Scribd
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Adaptive Mesh Applications

Sathish Vadhiyar
Sources:
- Schloegel, Karypis, Kumar. Multilevel Diffusion Schemes for Repartitioning of
Adaptive Meshes. JPDC 1997 (Taken verbatim)

Adaptive Applications
Highly adaptive and irregular applications
Amount of work per task can vary drastically
throughout the execution similar to earlier
applications, but..
Has notions of interesting regions
Computations in the interesting regions of
the domain larger than for other regions
It is difficult to predict which regions will
become interesting

AMR Applications
An example of such applications is Parallel
Adaptive Mesh Refinement (AMR) for
multi-scale applications
Adaptive Mesh Mesh or grid size is not
fixed as in Laplace/Jacobi, but interesting
regions are refined to form finer level
grids/mesh
E.g.: to study crack growth through a
macroscopic structure under stress

AMR Applications Crack


propagation
Such a system is subject to the laws
of plasticity and elasticity and can be
solved using finite element method
Crack growth forces the geometry of
the domain to change
This in turn necessitates localized
remeshing

AMR Applications- Adaptivity


Adaptivity arises when advances crosses
from one subdomain to another
It is unknown in advance when or where the
crack growth will take place and which
subdomains will be affected
The computational complexity of a
subdomain can increase dramatically due to
greater levels of mesh refinement
Difficult to predict future workloads

Repartitioning
In adaptive meshes computation, areas
of the mesh are selectively refined or
derefined in order to accurately model
the dynamic computation
Hence, repartitioning and redistributing
the adapted mesh across processors is
necessary

Repartitioning
The challenge is to keep the
repartitioning cost to minimum limits
Similar problems to MD, GoL
The primary difference in AMR is that
loads can drastically change; cannot
predict; will have to wait for refinement,
then repartition

Structure of Parallel AMR

Repartitioning
2 methods for creating a new partitioning
from an already distributed mesh that has
become load imbalanced due to mesh
refinement and coarsening
Scratch-remap schemes create an
entirely new partition
Diffusive schemes attempt to tweak the
existing partition to achieve better load
balance, often minimizing migration costs

Graph Representation of Mesh


For irregular mesh applications, the
computations associated with a mesh can
be represented as a graph
Vertices represent the grid cells; vertex
weights represent the amount of
computations associated with the grid cells
Edges represent the communication
between the grid cells; edge weights
represent the amount of interactions

Graph Representation of Mesh


The objective is to partition across P
processors
Each partition has equal amount of vertex
weight
Total weight of the edges cut by the
partition is minimized

Scratch-map Method
Partitioning from scratch will result in
high vertex migration since as the
partitioning does not take the initial
location of the vertices into account
Hence a partitioning method should
incrementally construct a new partition
as simply a modification of the input
partition

Notations
Let B(q) be the set of vertices with
partition q
Weight of any partition q can be defined as:
Average partition weight:
A graph is imbalanced if it is partitioned,
and:

Terms
A partition is over-balanced if its weight
is greater than the average partition
weight times (1+ )
If less, under-balanced
The graph is balanced when no partition
is over-balanced
Repartitioning existing partition used
as an input to form a new partition

Terms
A vertex is clean if its current partition
is its initial partition; else dirty
Border vertex adjacent vertex in
another partition; those partitions are
neighbor partitions
TotalV sum of the sizes of the vertices
which change partitions; i.e., sum of the
sizes of the dirty vertices

3 Objectives
Maintain balance between partitions
Minimize edge cuts
Minimize TotalV

Different Schemes
Repartitioning from scratch
Cut-and-paste repartitioning: excess
vertices in an overbalanced partition
are simply swapped into one or more
underbalanced partitions in order to
bring these partitions up to balance
The method can optimize TOTALV, but
can have a negative effect on the edgecut

Different Schemes
Another method is analogous to diffusion
Concept is for vertices to move from
overbalanced to neighboring
underbalanced partitions

Example

(Assuming edge and vertex weights as equal to 1)

Example (contd..)

Analysis of the 3 schemes


Thus, cut-and-paste repartitioning
minimizes TotalV, while completely
ignoring edge-cut
Partitioning the graph from the scratch
minimizes edge-cut, while resulting in
high TotalV
Diffusion attempts to keep both TotalV
and edge-cut low

Space Filling Curves for Partitioning and Load Balancing

Space Filling Curves


The underlying idea is to map a
multidimensional space to one dimension
where the partitioning is trivial
There are many different ways
But a mapping for partitioning algorithms
should preserve the proximity information
present in the multidimensional space to
minimize communication costs

Space Filling Curve


Space filling curves are quick to run, can be
implemented in parallel, and produce good load
balancing with locality
A space-filling curve is formed over grid/mesh
cells by using the centroid of the cells to
represent them
The SFC produces a linear ordering of the cells
such that cells that are close together in a
linear ordering are also close together in the
higher dimensional space

Space Filling Curve


The curve is then broken into segments based
on the weights of the cells (weights computed
using size and number of particles)
The segments are distributed to processors;
thus cells that are close together in space are
assigned to the same processor
This reduces overall amount of communication
that occur, i.e., increases locality

SFC representation
One method is to define recursively
curve for a 2^k x 2^k grid composed of
four 2^(k-1) x 2^(k-1) curves
Another method is using bit interleaving
the position of a grid point along the curve
can be specified by interleaving bits of
the coordinates of the point
The interleaving function is a
characteristic of the curve

Z-curve or Morton ordering


The curve for a 2^k x 2^k grid composed of four
2^(k-1) x 2^(k-1) curves, one in each quadrant of
the 2^k x 2^k grid
Order in which the curves are connected is the
same as the order for 2x2 grid

Graycode Curve
Uses same interleaving function as Zcurve
But visits points in the graycode order
Graycode two successive values differ
in only one bit
The one-bit gray code is (0,1)

Graycode Curve
The gray code list for n bits can be
generated recursively using n-1 bits
By reflecting the list (reversing the list)
[1,0]
Concatenating original with the reflected
[0,1,1,0]
Prefixing entries in the original list with 0,
and prefixing entries in the reflected list
with 1 [00,01,11,10]

Graycode Curve
3-bit gray code:
000,001,011,010,110,111,101,100

Hilbert Curve
Hilbert curve is a smooth curve
that avoids the sudden jumps in Zcurve and graycode curve
Curve composed of four curves of
previous resolution in four
quadrants
Curve in the lower left quadrant
rotated clockwise by 90 degree,
and curve in lower right quadrant
rotated anticlockwise by 90 degree

SFCs for AMR


All these curve based partitioning
techniques can also be applied for
adaptive mesh by forming hierarchical
SFCs

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