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Molecular dynamics accelerating method based on CUP (Central Processing Unit) and GPU (Graphics Processing Unit) cooperation

A molecular dynamics and molecular technology, applied in the field of molecular dynamics acceleration based on CPU and GPU collaboration, can solve problems such as low efficiency

Inactive Publication Date: 2013-05-15
NAT UNIV OF DEFENSE TECH
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Problems solved by technology

[0007] The technical problem to be solved by the present invention is: aiming at the low efficiency of the current GPU-based molecular dynamics acceleration method, a method for accelerating the use of CPU and GPU in coordination is proposed, so that both CPU and GPU in the system can perform efficient calculations, thereby Accelerating molecular dynamics while keeping costs low

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  • Molecular dynamics accelerating method based on CUP (Central Processing Unit) and GPU (Graphics Processing Unit) cooperation
  • Molecular dynamics accelerating method based on CUP (Central Processing Unit) and GPU (Graphics Processing Unit) cooperation

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Embodiment Construction

[0043] specific implementation plan

[0044] figure 1 Is the general flowchart of the present invention.

[0045] Step 1), building a computer system configured with Q core CPU and GPU;

[0046] Step 2), read in the molecular system parameters from the hard disk including the truncation radius R c and molecular data volume;

[0047] Step 3), setting the simulation parameters including the target grid weight TW, the target simulation step number T and the actual simulation step number t, and initializing the actual simulation step number t as 0.

[0048] Step 4), establish a "grid-unit" structure for the target molecular system, including the structure array SCell and the linked list SPatch;

[0049] Step 5), start No. 0 thread and No. 1 thread control GPU and CPU to calculate, will N 0 Point to SPatch, put N 1 Point to SPatch→Next, set N 0 → R is True, set N 1 → R is True, thread No. 0 goes to step 6), thread No. 1 goes to step 9);

[0050] Step 6), No. 0 thread contr...

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Abstract

The invention discloses a molecular dynamics accelerating method based on CUP (Central Processing Unit) and GPU (Graphics Processing Unit) cooperation, which aims to provide a molecular dynamics accelerating method based on CUP and GPU cooperation at a lower cost. The technical scheme is executed by the following steps that: a ''grid-unit'' structure for storing molecular information is built on a to-be-simulated molecular system by a computer configured with a CPU and a GPU; the grids are dynamically applied and processed by the CPU and GPU; when the grids are processed, the CPU processes the grids by regarding cells as the unit; and the whole grid is processed by the GPU for simulating the molecular dynamics by efficient cooperation of CPU and GPU. The molecular dynamics accelerating method disclosed by the invention can balance loads among the CPU cores and avoid the phenomenon that the CPU and GPU are in idle and waiting state in statically distributing the calculating tasks. Therefore, the CPU and GPU can both fully develop the calculating properties. The use ratio of the whole computer system is improved and acceleration of molecular dynamics at lower cost is realized.

Description

technical field [0001] The invention relates to a molecular dynamics acceleration method, in particular to a molecular dynamics acceleration method based on cooperation between a CPU and a GPU. Background technique [0002] The molecular dynamics method is a method that relies on Newton's laws of mechanics to simulate the motion of molecular systems, thereby calculating the macroscopic properties of molecular systems. It is an important means of studying nanoscale physical phenomena and is widely used in the fields of materials science, biophysics and drug design. With the improvement of simulation accuracy and the increase of simulation scale, the simulation time of molecular dynamics also increases, which has a great impact on its practical application. The current common practices are as follows: [0003] 1. Simulate in parallel by setting up a cluster system. However, this method has high hardware costs and requires developers to continuously improve parallel algorith...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F17/50
Inventor 廖湘科杨灿群吴强陈娟李春江杜云飞彭林左克石志才
Owner NAT UNIV OF DEFENSE TECH
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