Domain decomposition in parallel computing

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Domain decomposition in parallel computing
COT 5405 Fall 2006

• Ashok Srinivasan
• www.cs.fsu.edu/asriniva
• Florida State University

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Outline

• Background
• Geometric partitioning
• Graph partitioning
• Static
• Dynamic
• Important points

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Background

• Tasks in a parallel computation need access to
  certain data
• Same datum may be needed by multiple tasks
• Example In matrix-vector multiplication, b2 is
  needed for the computation of all ci2, 1 lt i lt n
• If a process does not own a datum needed by its
  task, then it has to get it from a process that
  has it
• This communication is expensive
• Aims of domain decomposition
• Distribute the data in such a manner that the
  communication required is minimized
• Ensure that the computational loads on
  processes are balanced

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Domain decomposition example

• Finite difference computation
• New value of a node depends on old values of its
  neighbors

• We want to divide the nodes amongst the processes
  so that
• Communication is minimized
• Measure of partition quality
• Computational load is evenly balanced

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Geometric partitioning

• Partition a set of points
• Uses only coordinate information
• Balances the load
• The heuristic tries to ensure that communication
  costs are low
• Algorithms are typically fast, but partition not
  of high quality
• Examples
• Orthogonal recursive bisection
• Inertial
• Space filling curves

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Orthogonal recursive bisection

• Recursively bisect orthogonal to the longest
  dimension
• Assume communication is proportional to the
  surface area of the domain, and aligned with
  coordinate axes
• Recursive bisection
• Divide into two pieces, keeping load balanced
• Apply recursively, until desired number of
  partitions obtained

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Inertial

• ORB may not be effective if cuts along the x, y,
  or z directions are not good ones
• Inertial
• Recursively bisect orthogonal to the inertial axis

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Space filling curves

• Space filling curves
• A continuous curve that fills the space
• Order the points based on their relative position
  on the curve
• Choose a curve that preserves proximity
• Points that are close in space should be close in
  the ordering too
• Example
• Hilbert curve

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Hilbert curve

• Sources
• http//www.dcs.napier.ac.uk/andrew/hilbert.html
• http//www.fractalus.com/kerry/tutorials/hilbert/h
  ilbert-tutorial.html

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Domain decomposition with a space filling curve

• Order points based on their position on the curve
• Divide into P parts
• P is the number of processes
• Space filling curves can be used in adaptive
  computations too
• They can be extended to higher dimensions too

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Graph partitioning

• Model as graph partitioning
• Graph G (V, E)
• Each task is represented by a vertex
• A weight can be used to represent the
  computational effort
• An edge exists between tasks if one needs data
  owned by the other
• Weights can be associated with edges too
• Goal
• Partition vertices into P parts such that each
  partition has equal vertex weights
• Minimize the weights of edges cut
• Problem is NP hard
• Edge cut metric
• Judge the quality of the partitioning by the
  number of edges cut

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Static graph partitioning

• Combinatorial
• Levelized nested dissection
• Kernighan-Lin/Feduccia-Matheyses
• Spectral partitioning
• Multi-level methods

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Combinatorial partitioning

• Use only connectivity information
• Examples
• Levelized nested dissection
• Kernighan-Lin/Feduccia-Matheyses

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Levelized nested dissection (LND)

• Idea is similar to the geometric methods
• But cannot use coordinate information
• Instead of projecting vertices along the longest
  axis, order them based on distance from a vertex
  that may be one extreme of the longest dimension
  of a graph
• Pseudo-peripheral vertex
• Perform a breadth-first search, starting from an
  arbitrary vertex
• The vertex that is encountered last might be a
  good approximation to a peripheral vertex

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LND example Finding a pseudoperipheral vertex
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Initial vertex
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Pseudoperipheral vertex
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LND example Partitioning
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Partition
Initial vertex
Recursively bisect the subgraphs
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Kernighan-Lin/Fiduccia-Matheyses

• Refines an existing partition
• Kernighan-Lin
• Consider pairs of vertices from different
  partitions
• Choose a pair whose swapping will result in the
  best improvement in partition quality
• The best improvement may actually be a worsening
• Perform several passes
• Choose best partition among those encountered
• Fiduccia-Matheyses
• Similar but more efficient
• Boundary Kernighan-Lin
• Consider only boundary vertices to swap
• ... and many other variants

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Kernighan-Lin example
Swap these
Better partition Edge cut 3
Existing partition Edge cut 4
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Spectral method

• Based on the observation that a Fiedler vector of
  a graph contains connectivity information
• Laplacian of a graph L
• lii di (degree of vertex i)
• lij -1 if edge i,j exists, otherwise 0
• Smallest eigenvalue of L is 0 with eigenvector
  all 1
• All other eigenvalues are positive for a
  connected graph
• Fiedler vector
• Eigenvector corresponding to the second smallest
  eigenvalue

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Fiedler vector

• Consider a partitioning of V into A and B
• Let yi 1 if vi e A, and yi -1 if vi e B
• For load balance, Si yi 0
• Also Seij e E (yi-yj)2 4 x number of edges
  across partitions
• Also, yTLy Si di yi2 2 Seij e E yiyj
• Seij e E (yi-yj)2

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Optimization problem

• The optimal partition is obtain by solving
• Minimize yTLy
• Constraints
• yi e -1,1
• Si yi 0
• This is NP hard
• Relaxed problem
• Minimize yTLy
• Constraints
• Si yi 0
• Add a constraint on a norm of y, example, y2
  n0.5
• Note
• (1, 1, ..., 1)T is an eigenvector with eigenvalue
  0
• For a connected graph, all other eigenvalues are
  positive and orthogonal to this eigenvector,
  which implies Si yi 0
• The objective function is minimized by a Fiedler
  vector

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Spectral algorithm

• Find a Fiedler vector of the Laplacian of the
  graph
• Note that the Fiedler value (the second smallest
  eigenvalue) yields a lower bound on the
  communication cost, when the load is balanced
• From the Fiedler vector, bisect the graph
• Let all vertices with components in the Fiedler
  vector greater than the median be in one
  component, and the rest in the other
• Recursively apply this to each partition
• Note Finding the Fiedler vector of a large graph
  can be time consuming

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Multilevel methods

• Idea
• It takes time to partition a large graph
• So partition a small graph instead!
• Three phases
• Graph coarsening
• Combine vertices to create a smaller graph
• Example Find a suitable matching
• Apply this recursively until a suitably small
  graph is obtained
• Partitioning
• Use spectral or another partitioning algorithm to
  partition the small graph
• Multilevel refinement
• Uncoarsen the graph to get a partitioning of the
  original graph
• At each level, perform some graph refinement

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Multilevel example(without refinement)
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Multilevel example(without refinement)
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Multilevel example(without refinement)
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Multilevel example(without refinement)
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Multilevel example(without refinement)
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Dynamic partitioning

• We have an initial partitioning
• Now, the graph changes
• Determine a good partition, fast
• Also minimize the number of vertices that need
  to be moved
• Examples
• PLUM
• Jostle
• Diffusion

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PLUM

• Partition based on the initial mesh
• Vertex and edge weights alone changed
• Map partitions to processors
• Use more partitions than processors
• Ensures finer granularity
• Compute a similarity matrix based on data already
  on a process
• Measures savings on data redistribution cost for
  each (process, partition) pair
• Choose assignment of partitions to processors
• Example Maximum weight matching
• Duplicate each processor of partitions/P times
• Alternative Greedy approximation algorithm
• Assign in order of maximum similarity value
• http//citeseer.nj.nec.com/oliker98plum.html

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JOSTLE

• Use Hu and Blakes scheme for load balancing
• Solve Lx b using Conjugate Gradient
• L Laplacian of processor graph, bi Weight on
  process Pi Average weight
• Move max(xi-xj, 0) weight between Pi and Pj
• Leads to balanced load
• Equivalent to Pi sending xi load to each neighbor
  j, and each neighbor Pj sending xj to Pi
• Net loss in load for Pi di xi - Sneighborj xj
  L(i)x bi
• where L(i) is row i of L, and di is degree of i
• New load for Pi weight on Pi - bi average
  weight
• Leads to minimum L2 norm of load moved
• Using max(xi-xj, 0)
• Select vertices to move, based on relative gain
• http//citeseer.nj.nec.com/walshaw97parallel.html

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Diffusion

• Involves only communication with neighbors
• A simple scheme
• Processor Pi repeatedly sends a wi weight to each
  neighbor
• wi weight on Pi
• wk (I a L) wk-1 , wk weight vector at
  iteration k
• Simple criteria exist for choosing a to ensure
  convergence
• Example a 0.5/(maxi di),
• More sophisticated schemes exist

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Important points

• Goals of domain decomposition
• Balance the load
• Minimize communication
• Space filling curves
• Graph partitioning model
• Spectral method
• Relax NP hard integer optimization to floating
  point, and then discretize to get approximate
  integer solution
• Multilevel methods
• Three phases
• Dynamic partitioning additional requirements
• Use old solution to find new one fast
• Minimize number of vertices moved