Accelerating molecular dynamics simulations on playstation 3 platform using virtual-grape programming model

Tetsu Narumi, Shun Kameoka, Makoto Taiji, Kenji Yasuoka

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Molecular dynamics (MD) simulation requires huge computational power because each atom interacts with another by long-range forces, such as Coulomb and van der Waals forces. Therefore, parallel computers or special accelerators, such as MDGRAPE-3, are required for accelerating MD simulations. A video game processor in a Sony PlayStation 3 or NVIDIA's graphic accelerator card is also a candidate hardware for accelerating MD simulations, because the peak performance of the latest video game processors exceeds that of a current PC's CPU, and they are also very cost-effective. However, the software development for these processors requires much more time compared to CPUs of PCs because the hardware has a lot of parallel processing. We propose the virtual-GRAPE programming model to utilize the hardware resource of video game processors with minimum time for software development. GRAPE is a special-purpose computer used to accelerate particle-based simulations: astrophysical or MD simulations. Under the Virtual-GRAPE model, the subroutine whose calculation speed is accelerated by the special hardware, GRAPE, is replaced with a specially tuned subroutine to be used without the accelerator. We implemented this model in a PlayStation 3 to accelerate the "sander" MD module in the AMBER software package. We were able to achieve an acceleration of 20 times, compared to a serial job using an Intel Xeon 5160 processor. Its performance cost is far superior to that of a PC or an MDGRAPE-3. To obtain the highest performance from the subroutine, most of the arithmetic operations in the tuned routine were performed with single precision accuracy, which is sufficient for MD simulations.

Original languageEnglish
Pages (from-to)3108-3125
Number of pages18
JournalSIAM Journal on Scientific Computing
Volume30
Issue number6
DOIs
Publication statusPublished - 2008

Fingerprint

Computer programming
Molecular Dynamics Simulation
Programming Model
Molecular dynamics
Video Games
Accelerator
Program processors
Hardware
Subroutines
Computer simulation
Particle accelerators
Software Development
Accelerate
Computer hardware
Software engineering
Van Der Waals Force
Sanders
Costs
Parallel Computers
Van der Waals forces

Keywords

  • Cell broadband engine
  • GRAPE
  • Molecular dynamics simulation
  • PlayStation 3
  • Special-purpose computer

ASJC Scopus subject areas

  • Applied Mathematics
  • Computational Mathematics

Cite this

Accelerating molecular dynamics simulations on playstation 3 platform using virtual-grape programming model. / Narumi, Tetsu; Kameoka, Shun; Taiji, Makoto; Yasuoka, Kenji.

In: SIAM Journal on Scientific Computing, Vol. 30, No. 6, 2008, p. 3108-3125.

Research output: Contribution to journalArticle

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