Abstract
We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bonded force calculations and run at 0.8 GHz. Additionally, it has 65 Tensilica Xtensa LX cores with single-precision floating-point units that are used for other calculations and run at 0.6 GHz. At peak performance levels, each SoC can evaluate 51.2 G interactions per second. It also has 1.8 MB of embedded shared memory banks and six network units with a peak bandwidth of 7.2 GB s−1 for the three-dimensional torus network. The system consists of 512 (8×8×8) SoCs in total, which are mounted on 64 node modules with eight SoCs. The optical transmitters/receivers are used for internode communication. The expected maximum power consumption is 50 kW. While MDGRAPE-4 software has still been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE-4 system will enable long-time molecular dynamics simulations of small systems. It is also useful for multiscale molecular simulations where the particle simulation parts often become bottlenecks.
Highlights
The development of the GRAvity PipE (GRAPE) systems started with accelerators for astrophysical N-body simulations, and they have been extended for molecular dynamics (MD) simulations such as MDGRAPE [16]
We report on the architecture of the fourth-generation special-purpose computer for MD simulations, MDGRAPE4
The MDGRAPE-4 takes a similar approach and uses a system on chip (SoC) to integrate the functions of a host and an accelerator into a single chip
Summary
Recent advances in structural biology have revealed the structural basis of biological molecules and have enabled various computational analyses on them Among these methods, molecular dynamics (MD) simulation is one of the most important methods for studying the thermodynamic and dynamic properties of molecules, because they are flexible, complex and fluctuating [1]. A typical system size for protein simulations is approximately 105 atoms, which requires a computational cost of approximately 5 G operations per timestep This means that the elapsed time to perform a single simulation step is only 5 μs when using a machine with sustained PFLOPS-level performance. The MDGRAPE-4 takes a similar approach and uses a SoC to integrate the functions of a host and an accelerator into a single chip.
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