efficient parallelization for amr mhd multiphysics calculations
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Efficient Parallelization for AMR MHD Multiphysics Calculations. Implementation in AstroBEAR. Outline. Motivation Better memory management Sweep updates Distributed tree Improved parallelization Level threading Dynamic load balancing. Outline. Motivation – HPC

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efficient parallelization for amr mhd multiphysics calculations

Efficient Parallelization for AMR MHD Multiphysics Calculations

Implementation in AstroBEAR

outline
Outline
  • Motivation
  • Better memory management
  • Sweep updates
  • Distributed tree
  • Improved parallelization
  • Level threading
  • Dynamic load balancing
outline1
Outline
  • Motivation – HPC
    • Better memory management
      • Sweep updates
      • Distributed tree
    • Improved parallelization
      • Level threading
      • Dynamic load balancing
sweep method for unsplit stencils
Sweep Method for Unsplit Stencils
  • At the end of an update we need new values for the fluid quantities Q at time step n+1
sweep method for unsplit stencils1
Sweep Method for Unsplit Stencils
  • At the end of an update we need new values for the fluid quantities Q at time step n+1
  • The new values for Q will depend on the EMF’s calculated at the cell corners
sweep method for unsplit stencils2
Sweep Method for Unsplit Stencils
  • At the end of an update we need new values for the fluid quantities Q at time step n+1
  • The new values for Q will depend on the EMF’s calculated at the cell corners
  • As well as the x and y fluxes at the cell faces
sweep method for unsplit stencils3
Sweep Method for Unsplit Stencils
  • At the end of an update we need new values for the fluid quantities Q at time step n+1
  • The new values for Q will depend on the EMF’s calculated at the cell corners
  • As well as the x and y fluxes at the cell faces
  • The EMF’s themselves also depend on the fluxes at the faces adjacent to each corner.
sweep method for unsplit stencils4
Sweep Method for Unsplit Stencils
  • At the end of an update we need new values for the fluid quantities Q at time step n+1
  • The new values for Q will depend on the EMF’s calculated at the cell corners
  • As well as the x and y fluxes at the cell faces
  • The EMF’s themselves also depend on the fluxes at the faces adjacent to each corner.
  • Each calculation extends the stencil until we are left with the range of initial values Q at time step n needed for the update of a single cell
sweep method for unsplit stencils5
Sweep Method for Unsplit Stencils
  • At the end of an update we need new values for the fluid quantities Q at time step n+1
  • The new values for Q will depend on the EMF’s calculated at the cell corners
  • As well as the x and y fluxes at the cell faces
  • The EMF’s themselves also depend on the fluxes at the faces adjacent to each corner.
  • Each calculation extends the stencil until we are left with the range of initial values Q at time step n needed for the update of a single cell
distributed tree
Distributed Tree

Level 0 base grid

Level 0 node

distributed tree1
Distributed Tree

Parent-Child

Level 1 nodes are children of level 0 node

Level 1 grids nested within parent level 0 grid

distributed tree2
Distributed Tree

Neighbor

Neighbor

Conservative methods require synchronization of fluxes between neighboring grids as well as the exchanging of ghost zones

distributed tree3
Distributed Tree

Level 2 nodes are children of level 1 nodes

Level 2 grids nested within parent level 1 grids

distributed tree4
Distributed Tree

Since the mesh is adaptive there are successive generations of grids and nodes

distributed tree5
Distributed Tree

New generations of grids need access to data from the previous generation of grids on the same level that physically overlap

distributed tree6
Distributed Tree

Current generation

distributed tree7
Distributed Tree

Current generation

Previous generation

distributed tree8
Distributed Tree

Current generation

Previous generation

distributed tree9
Distributed Tree

Current generation

Level 1 Overlaps

Previous generation

distributed tree10
Distributed Tree

Current generation

Level 2 Overlaps

Previous generation

distributed tree11
Distributed Tree

Current generation

AMR Tree

Previous generation

While the AMR grids and the associated computations are normally distributed across multiple processors, the tree is often not.

distributed tree12
Distributed Tree

Current generation

Previous generation

Each processor only needs to maintain its local sub-tree with connections to each of its grid’s surrounding nodes (parent, children, overlaps, neighbors)

distributed tree13
Distributed Tree

For example processor 1 only needs to know about the following sub-tree

distributed tree14
Distributed Tree

And the sub-tree for processor 2

distributed tree15
Distributed Tree

And the sub-tree for processor 3

distributed tree16
Distributed Tree
  • While the memory and communication required for each node is small to that required for each grid, the memory required for the entire AMR tree can overwhelm that required for the local grids when the number of processors becomes large.
  • Consider a mesh in which each grid is 8x8x8 where each cell contains 4 fluid variables. Lets also assume that each node requires 7 values describing its physical location and the host processor. The memory requirement for the local grids becomes comparable to the AMR tree when there are 8x8x8x4/7 = 292 processors.
  • Even if each processor prunes its local tree by discarding nodes not connected to its local grids, the communication required to globally share each new generation of nodes will eventually prevent the simulation from scaling.
distributed tree17
Distributed Tree
  • When successive generations of level n nodes are created by their level n-1 parent nodes, each processor must update its local sub-tree with the subset of level n nodes that connect to the nodes associated with its local grids.
  • Instead of globally communicating every new level n node to every other processor, each processor determines which other processors need to know about which new level n nodes.
  • Since children are always nested within parent grids, nodes that neighbor or overlap will have parents that neighbor or overlap respectively. This can be used to localize tree communication as follows.
sub tree construction
Sub-tree construction

Tree starts at a single root node that persists from generation to generation

Processor 2

Processor 3

Processor 1

sub tree construction1
Sub-tree construction

Root node creates next generation of level 1 nodes

Processor 2

Processor 3

Processor 1

sub tree construction2
Sub-tree construction

Root node creates next generation of level 1 nodes

It next identifies overlaps between new and old children

Processor 2

Processor 3

Processor 1

sub tree construction3
Sub-tree construction

Root node creates next generation of level 1 nodes

It next identifies overlaps between new and old children

As well as neighbors among new children

Processor 2

Processor 3

Processor 1

sub tree construction4
Sub-tree construction

New nodes along with their connections are then communicated to the assigned child processor.

Processor 2

Processor 3

Processor 1

sub tree construction5
Sub-tree construction

Processor 2

Processor 3

Processor 1

sub tree construction6
Sub-tree construction

Processor 2

Processor 3

Processor 1

sub tree construction7
Sub-tree construction

Level 1 nodes then locally create new generation of level 2 nodes

Processor 2

Processor 3

Processor 1

sub tree construction8
Sub-tree construction

Level 1 nodes then locally create new generation of level 2 nodes

Processor 2

Processor 3

Processor 1

sub tree construction9
Sub-tree construction

Processor 2

Processor 3

Processor 1

Level 1 grids communicate new children to their overlaps so that new overlap connections on level 2 can be determined

sub tree construction10
Sub-tree construction

Processor 2

Processor 3

Processor 1

Level 1 grids communicate new children to their neighbors so that new neighbor connections on level 2 can be determined

sub tree construction11
Sub-tree construction

Processor 2

Processor 3

Processor 1

Level 1 grids and their local trees are then distributed to child processors.

sub tree construction12
Sub-tree construction

Processor 2

Processor 3

Processor 1

Each processor now has the necessary tree information to update their local grids.

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