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Neighbor particle pair search, molecular dynamics calculation method and many-core processing system

A technology of molecular dynamics and search methods, applied in computing, electrical digital data processing, special data processing applications, etc., can solve the problems of data writing conflicts, low parallel efficiency, etc., and achieve the elimination of writing conflicts, correct force, and expanded search range effect

Active Publication Date: 2015-08-12
JIANGNAN INST OF COMPUTING TECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, when GROMACS is transplanted to many-core processors using the existing technology, there are problems such as low parallel efficiency and data writing conflicts.

Method used

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  • Neighbor particle pair search, molecular dynamics calculation method and many-core processing system
  • Neighbor particle pair search, molecular dynamics calculation method and many-core processing system
  • Neighbor particle pair search, molecular dynamics calculation method and many-core processing system

Examples

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no. 1 example

[0060] refer to image 3 , in order to solve the above-mentioned problem of data writing conflicts between slave cores, an embodiment of the present invention provides a neighbor particle pair search method, which is suitable for many-core processing systems configured to perform molecular dynamics calculations.

[0061] As an embodiment of the present invention, the neighbor particle pair search method includes:

[0062] Each particle is used as the main particle to establish the neighbor particle pair of each particle; wherein, for each main particle, the neighbor particles of the main particle are determined among the remaining particles in the calculation area where it is located;

[0063] Thus, the neighbor particle pair information of all particles in the calculation area is established in each calculation area.

[0064] As an embodiment of the present invention, the establishment of neighbor particle pairs of each particle with each particle as the main particle refers...

no. 2 example

[0083] An embodiment of the present invention further provides a molecular dynamics calculation method using the above neighbor particle pair search method. refer to Figure 6 , Figure 6 It is a schematic flowchart of a molecular dynamics calculation method provided by the second embodiment of the present invention.

[0084] As an embodiment of the present invention, the molecular dynamics calculation method is applicable to many-core processing systems; the method includes:

[0085] Each particle is used as the main particle to establish the neighbor particle pair of each particle; wherein, for each main particle, the neighbor particles of the main particle are determined among the remaining particles in the calculation area where it is located;

[0086] Based on the neighbor particle pair information of all particles in the calculation area established in each calculation area, the force of each main particle is calculated.

[0087] In the molecular dynamics calculation ...

no. 3 example

[0110] An embodiment of the present invention also provides a many-core processing system, which is suitable for performing the neighbor particle pair search method and molecular dynamics calculation described in the above embodiments.

[0111] refer to Figure 9 , Figure 9 It is a schematic block diagram of a many-core processing system provided by an embodiment of the present invention.

[0112] As an embodiment of the present invention, the many-core processing system 10 includes a main processor core (master core) and multiple slave processor cores (slave cores), and the many-core processing system includes a neighbor particle pair search module 101 and a calculation module 104; wherein, the neighbor particle pair search module 101 is adapted to use each particle as a main particle to establish a neighbor particle pair of each particle; wherein, for each main particle, it is determined among the remaining particles in the calculation area where it is located Neighboring...

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Abstract

The invention provides a neighbor particle pair searching method, and a many-core processing system suitable for doing the molecular dynamics calculation. The neighbor particle pair searching method comprises the following steps: taking every particle as the main particle to establish the neighbor particle pair for each particle, wherein the neighbor particle of each main particle is determined in the rest particles within the calculation domain where the main particle is arranged so as to establish the neighbor particle information of all the particles in the calculation domain in all the calculation domains. The invention further provides a molecular dynamics calculation method using the neighbor particle pair searching method, and the many-core processing system of the molecular dynamics calculation method. The neighbor particle searching method makes distinction targeting at different domains where the particles are, so that different calculation methods can be adopted according to the domains where the neighbor particles are arranged. Therefore, the processing capacities of sub-cores of the many-core processing system can be developed fully.

Description

technical field [0001] The invention relates to the field of data processing, in particular to a neighbor particle pair search for many-core processors, a molecular dynamics calculation method and a many-core processing system applying the method. Background technique [0002] In recent years, multi-core design has gradually become a trend of high-performance development and a hot spot of academic research. Multi-core processors can be divided into homogeneous multi-core processors and heterogeneous multi-core processors according to the integration method. [0003] A homogeneous multi-core processor integrates multiple homogeneous processor cores in one chip, and all processor cores run a complete operating system for the same workload. Therefore, the design and implementation of the program based on the homogeneous processor is relatively simple. At present, this type of processor has been fully introduced to the market. [0004] Compared with homogeneous multi-core pro...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F17/50G06F9/50
Inventor 张军刘桂英倪颖杰李祖华马飞李弢
Owner JIANGNAN INST OF COMPUTING TECH
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