Anton (computer)
Encyclopedia
Anton is a massively parallel supercomputer designed and built by D. E. Shaw Research
in New York. It is a special-purpose system for molecular dynamics
(MD) simulations of proteins and other biological macromolecules. An Anton machine consists of a substantial number of application-specific integrated circuits
(ASICs)
interconnected by a specialized high-speed three-dimensional torus network.
Unlike earlier special-purpose systems for MD simulations, such as MDGRAPE-3 developed by RIKEN
in Japan, Anton runs its computations entirely on specialized ASICs, instead of dividing the computation between specialized ASICs and general-purpose host processors.
Each Anton ASIC contains two computational subsystems. Most of the calculation of electrostatic and van der Waals forces
is performed by the high-throughput interaction subsystem (HTIS). This subsystem contains 32 deeply pipelined modules running at 800 MHz arranged much like a systolic array
. The remaining calculations, including the bond forces and the fast Fourier transforms (used for long-range electrostatics), are performed by the flexible subsystem. This subsystem contains four general-purpose Tensilica
cores (each with cache and scratchpad memory) and eight specialized but programmable SIMD
cores called geometry cores. The flexible subsystem runs at 400 MHz.
Anton's network is a 3D torus and thus each chip has 6 inter-node links with a total in+out bandwidth of 607.2 Gbit/s. An inter-node link is composed of two equal one-way links (one traveling in each direction), with each one-way link having 50.6 Gbit/s of bandwidth. Each one-way link is composed of 11 lanes, where a lane is a differential pair of wires signaling at 4.6 Gbit/s. The per-hop latency in Anton's network is 50ns. Each ASIC is also attached to its own DRAM bank, enabling large simulations.
The performance of a 512-node Anton machine is over 17,000 nanoseconds of simulated time per day for a protein-water system consisting of 23,558 atoms. In comparison, MD codes running on general-purpose parallel computers with hundreds or thousands of processor cores achieve simulation rates of up to a few hundred nanoseconds per day on the same chemical system. The first 512-node Anton machine became operational in October 2008.
The 6.4 petaFLOP
distributed-computing Folding@home
project has achieved aggregate ensemble simulation timescales similar to those Anton has, specifically achieving the 1.5 millisecond range in January 2010.
The Anton supercomputer is named after Anton van Leeuwenhoek
, who is often referred to as “the father of microscopy” because he built high-precision optical instruments and used them to visualize a wide variety of organisms and cell types for the first time.
D. E. Shaw Research
D. E. Shaw Research is a computational biochemistry research laboratory based in New York City. Under the scientific direction of David E. Shaw, the group's chief scientist, D. E...
in New York. It is a special-purpose system for molecular dynamics
Molecular dynamics
Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
(MD) simulations of proteins and other biological macromolecules. An Anton machine consists of a substantial number of application-specific integrated circuits
(ASICs)
Application-specific integrated circuit
An application-specific integrated circuit is an integrated circuit customized for a particular use, rather than intended for general-purpose use. For example, a chip designed solely to run a cell phone is an ASIC...
interconnected by a specialized high-speed three-dimensional torus network.
Unlike earlier special-purpose systems for MD simulations, such as MDGRAPE-3 developed by RIKEN
RIKEN
is a large natural sciences research institute in Japan. Founded in 1917, it now has approximately 3000 scientists on seven campuses across Japan, the main one in Wako, just outside Tokyo...
in Japan, Anton runs its computations entirely on specialized ASICs, instead of dividing the computation between specialized ASICs and general-purpose host processors.
Each Anton ASIC contains two computational subsystems. Most of the calculation of electrostatic and van der Waals forces
Van der Waals force
In physical chemistry, the van der Waals force , named after Dutch scientist Johannes Diderik van der Waals, is the sum of the attractive or repulsive forces between molecules other than those due to covalent bonds or to the electrostatic interaction of ions with one another or with neutral...
is performed by the high-throughput interaction subsystem (HTIS). This subsystem contains 32 deeply pipelined modules running at 800 MHz arranged much like a systolic array
Systolic array
In computer architecture, a systolic array is a pipe network arrangement of processing units called cells. It is a specialized form of parallel computing, where cells , compute data and store it independently of each other.thumb|240px...
. The remaining calculations, including the bond forces and the fast Fourier transforms (used for long-range electrostatics), are performed by the flexible subsystem. This subsystem contains four general-purpose Tensilica
Tensilica
Tensilica is an IP core company based in Silicon Valley. Tensilica is best known for its customizable microprocessor cores, the Xtensa configurable processor...
cores (each with cache and scratchpad memory) and eight specialized but programmable SIMD
SIMD
Single instruction, multiple data , is a class of parallel computers in Flynn's taxonomy. It describes computers with multiple processing elements that perform the same operation on multiple data simultaneously...
cores called geometry cores. The flexible subsystem runs at 400 MHz.
Anton's network is a 3D torus and thus each chip has 6 inter-node links with a total in+out bandwidth of 607.2 Gbit/s. An inter-node link is composed of two equal one-way links (one traveling in each direction), with each one-way link having 50.6 Gbit/s of bandwidth. Each one-way link is composed of 11 lanes, where a lane is a differential pair of wires signaling at 4.6 Gbit/s. The per-hop latency in Anton's network is 50ns. Each ASIC is also attached to its own DRAM bank, enabling large simulations.
The performance of a 512-node Anton machine is over 17,000 nanoseconds of simulated time per day for a protein-water system consisting of 23,558 atoms. In comparison, MD codes running on general-purpose parallel computers with hundreds or thousands of processor cores achieve simulation rates of up to a few hundred nanoseconds per day on the same chemical system. The first 512-node Anton machine became operational in October 2008.
The 6.4 petaFLOP
distributed-computing Folding@home
Folding@home
Folding@home is a distributed computing project designed to use spare processing power on personal computers to perform simulations of disease-relevant protein folding and other molecular dynamics, and to improve on the methods of doing so...
project has achieved aggregate ensemble simulation timescales similar to those Anton has, specifically achieving the 1.5 millisecond range in January 2010.
The Anton supercomputer is named after Anton van Leeuwenhoek
Anton van Leeuwenhoek
Antonie Philips van Leeuwenhoek was a Dutch tradesman and scientist from Delft, Netherlands. He is commonly known as "the Father of Microbiology", and considered to be the first microbiologist...
, who is often referred to as “the father of microscopy” because he built high-precision optical instruments and used them to visualize a wide variety of organisms and cell types for the first time.