10/21/2009 1 Protein Explorer: A Petaflops Special- Purpose Computer System for Molecular Dynamics Simulations Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Noriyuki Futatsugi, Atsushi Suenaga, Naoki Takada and Akihiko Konagya High-Performance Biocomputing Research Team, Bioinformatics Group, Genomic Sciences Center, Institute of Physical and Chemical Research (RIKEN) ACM/IEEE SC2003 Conference Presented by Jing Xue For Computer Architecture Reading Group
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10/21/20091 Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations Makoto Taiji, Tetsu Narumi, Yousuke Ohno,
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10/21/2009 1
Protein Explorer: A Petaflops Special-Purpose Computer
High-Performance Biocomputing Research Team, Bioinformatics Group, Genomic Sciences Center, Institute of Physical and
Chemical Research (RIKEN) ACM/IEEE SC2003 Conference
Presented by Jing XueFor Computer Architecture Reading Group
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Protein Explorer (PE) System• What is PE system ?
– special-purpose computer system for molecular dynamics simulations particularly protein simulations– PC cluster equipped with special-purpose engines that calculate non-bonded interactions between atoms
• What is MDGRAPE-3 Chip?– A dedicated LSI performs these force calculations
• Why is specialized?– Most time is spent on the calculation of long-range forces
• Gravitational, Coulomb, and Van der Waals forces– Communication-to-computation ratio is 0.25 Gbytes/sec*Tflops
• What is GRAPE?– GRAPE (GRAvity PipE) is a project to develop high-performance competitive special purpose systems– Classical particles (e.g. gravitational N-body problems, Molecular dynamics (MD) simulations)
• What is pioneered?– Delft Molecular Dynamics Processor (DMDP) and FASTRUN processor
• What is the targets of PE system?– High-precision screening for drug design and large scale simulations– Funded by Protein 3000 project started in 2002
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MDGRAPE-3 System
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What Protein Explorer Calculates
• Two-body forces on i-th particle Fi
Where , .
The vectors ri, rj are the position vectors of the i,j-th particles and is an arbitrary smooth function.
Coulomb forces:
Lennard-Jones potential:
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MDGRAPE-3 chip
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Software Cost and Performance Estimation
1. Call pe_start_calc2. Perform other force calculations3. Call pe_wait_calc (force)4. Add other forces such as bonding force to ‘force’, then calculates orbits of
particles, and increments a time
1. Get command sequence from host memory2. Write positions, charges, and species of j-
particles to the chip3. Broadcast positions of 40 i-particles to all the
chip4. Issue the calculation command5. Do calculation6. Read results out from the chip7. Transfer result to host memory8. Repeat from 3-7 for all i-particles9. Tell the end of the calculation to the host
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Anton, a Special-Purpose Machine for Molecular Dynamics Simulation
David E. Shaw et. al.D. E. Shaw Research
ISCA 2007
Presented by Alok Garg
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Force Calculation
• Mechanics force fields on 200,000 molecules/time step
• Total energy– Bonded (linear time complexity)– Non-bonded - O(n2)
• Non-bonded interactions– Range limited interactions– Long-range interactions
• Expresses as a convolution• Computed by: FFT, multiplication, and
inverse FFT
• 73% computation is range limited interactions
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Range-Limited Pair-wise Interactions
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Parallelization Algorithm
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Computation
e.g.A cubical system of 25,000 atomsAtoms in tower: 220Atoms in plate: 430
Total pairs: 94,60023,000 satisfy the selection rule
Each node must import 550 particles
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Specialized Hardware
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Rest of the Machine
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Major Computational Tasks
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System Architecture
• Features– Multicast support– Compressed transfer of