1. ANTON D.E Shaw Research

2. Force Fields: Typical Energy Functions
Bond stretches
Angle bending
Torsional rotation
Improper torsion (sp2)
Electrostatic interaction
Lennard-Jones interaction

3. MD Simulator Requirements
Parallelization
(getting an idea of the level of computation needed)
For every time step, every atom must communicate within its cutt-off radius with every other atom.
A lot of inter-processor communication that can be scaled well is needed.

4. Why Specialized Hardware?
1) Need a huge number of arithmetic processing elements
2) A lot of inter-processor communication that can be scaled well is needed.
3) Memory is not an issue
With 25,000 atoms (64bytes each) total=1.6MB over 512 nodes =3.2KB/node which is < most L1
Memory
Communication
Computation
Needs

5. Anton System-Level Organization
Multiple segments (probably 8 in first machine)
512 nodes (each consists of one ASIC plus DRAM) per segment
Organized in an 8 x 8 x 8 toroidal mesh
Each ASIC equivalent performance to roughly 500 general purpose microprocessors
ASIC power similar to a single microprocessor

6. Anton
33M gate ASIC
Two computational subsystems connected by communication ring
Hardware datapaths compute over 25 billion interactions/s
Full machine has 512 ASICs in a 3D torus
13 embedded processors

7. Example: Particle Interaction Pipeline (one of 32)

8. Where We Use Flexible Hardware
Use programmable hardware where:
Algorithm less regular
Smaller % of total computation
E.g., local interactions (fewer of them)
More likely to change
Examples:
Bonded interactions
Bond length constraints
Experimentation with
New, short-range force field terms
Alternative integration techniques

9. Overview of the Flexible Subsystem
GC = Geometry Core (each a VLIW processor)

10. Anton in Action

11. Simulation Evaluations
500X NAMD X Desmond X Blue Matter

12. GPU+FPGA ??? FFT and LJ 6*GDDR5 LVDS LVDS FPGA GPU
HIGH SPEED SERIAL I/O
UP TO 2 Tbit/S
16*PCIe