Support for Adaptive Computations Applied to Simulation of Fluids in Biological Systems Immersed Boundary Method Simulation in Titanium Siu Man Yau, Katherine Yelick and the Titanium group

Objectives Provide easy-to-use, high-performance tool for simulation of fluid flow in biological systems. Demonstrate Titanium Allow heart simulation on large-scale parallel machines like Millennium. –Used for artificial valves.

Immersed Boundary Method Developed at NYU –models biological systems with elastic fibers in an incompressible fluid –heart, platelets, embryos Fibers (e.g., heart muscles) modeled by list of fiber points Fluid space modeled by a regular lattice

Challenges to Parallelization Irregular fiber list interacts with fluid grid –Trade-off between load balancing of fibers and minimizing communication Need a scalable elliptic solver –Plan to use multigrid & Adaptive Mesh Refinement Fiber activation & force calculation Interpolate Velocity Navier-Stokes Solver Spread Force

Titanium Motivation Applications are increasingly complex –Want classes, overloading, linked data structures –C++ is hard to read, modify and tune Machines are increasingly complex –Want compiler help for optimizations –Want clear performance model and programmer control Java is a better C++ +Safe: strongly typed, garbage collected –Performance is poor due to

Titanium for Scientific Computing Java dialect for high performance Added constructs for performance & expressiveness –Immutable, value classes –SPMD parallelism with a global address space –Multidimensional arrays –Templates –Region-based memory management Compiled to C (no JVM) with lightweight messaging (Active Messages, LAPI, shmem)

Titanium Implementation Run time system and compiler for: –Uniprocessors and SMPs with POSIX threads –Clusters with: Shared memory - SGI Origin cluster (ANL), Tera MTA Global Address Space - T3E (NERSC) Active Messages - NOW & Millennium (UCB) LAPI - IBM SP2, SP3 (SDSC) Millennium port: –Runs on AM on VIA Anxiously awaiting Myrinet 2000 –Many executions models in a single language 1 thread per node, 1 per processor, k per node, 1 node…

Immersed Boundary in Titanium IB rewritten in Titanium. Running since October Contractile torus –Has been run on Berkeley NOW and SGI Origin –Performance tuning needed to run full heart model

Future work Improve performance –Especially on SMP clusters like Millennium Add functionality –Bending angles, anchorage points, source & sinks) to the software package. Add adaptability to NS solver (AMR) –Needed for scaling and more accurate modeling of fluid features in heart