1. Support for Adaptive Computations Applied to Simulation of Fluids in Biological Systems
Immersed Boundary Method Simulation in Titanium
Objectives
Immersed Boundary Method
Titanium
High performance Java dialect
Explicitly parallel SPMD model
Bulk synchronous style
Global address space
Language level enhancements to support parallelism and performance
Immutable “value” classes
Multi-dimensional arrays
Region-based memory management
Compiled into C with light weight message passing
Developed by Peskin and McQueen
Models elastic fibers in an incompressible fluid.
Used for heart, blood clotting, embryos, ciliated cells, and more.
The heart model used to design artificial heart valves.
NYU software runs on vector and shared memory machines
4 phase algorithm:
Provide easy-to-use, high performance tool for simulation of fluid flow in biological systems.
Two specific goals:
Scalable, parallel version of heart simulation to run on machines like Blue Horizon.
Toolkit for general Immersed Boundary Method Simulation.
Fiber activation &
force calculation
Interpolate
Velocity
Spread
Force
Navier Stokes
Solver
Titanium Implementation Status
Immersed Boundary Software in Titanium
Compiler and runtime systems for:
Uniprocessors
SMPs running POSIX threads
Clusters with:
Shared memory -- SGI Origin (ANL), Tera MTA (SDSC)
Global Address space – T3E (NERSC)
Active Messages -- NOW & Millennium (UCB)
LAPI -- IBM SP2, 3 (SDSC)
Immersed Boundary Method Software package written in Titanium
Based on “Generic” software from NYU
Sufficient for the heart model
Functionally complete as of 10/2000
A contractile torus simulation run on the Berkeley NOW and ANL Origin.
Challenges to Parallelization
Scalability of the current algorithm:
Irregular fiber points interact with regular fluid lattice
Elliptic solver is communication-intensive
Scalability of future algorithm:
Add adaptivity to fluid solver for accuracy
Further complicates communication
Conclusions
Performance tuning started
Uniprocessor performance:
Compiler enhancements underway
Data collected with C code for 2 kernels
Communication:
Alternate data layouts
Extension for irregular communication
Titanium support aided development
~7 months to develop running version
Indication for small language extensions
Future plans:
Add Adaptivity in Fluid Solver
Performance tuning, especially for the IBM SP
Add IB functionality for other biological systems (bending angles, anchorage points, source & sink)