1 / 12

ANTON D.E Shaw Research

ANTON D.E Shaw Research. Force Fields: Typical Energy Functions. Bond stretches Angle bending Torsional rotation Improper torsion (sp2) Electrostatic interaction Lennard-Jones interaction. MD Simulator Requirements. Parallelization (getting an idea of the level of computation needed)

upton
Download Presentation

ANTON D.E Shaw Research

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. ANTOND.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. 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 Anton

  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 80-100X Desmond 100X 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

More Related