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Acceleration optimization method and system for parallel PME of molecular dynamics simulation software

A technology of molecular dynamics and simulation software, applied in the field of accelerated optimization of parallel PME, can solve problems such as not being able to reflect the advantages of supercomputing platforms, and achieve the effects of improving overall performance, shortening execution time, and improving computing performance

Pending Publication Date: 2020-07-24
SHANDONG UNIV
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Problems solved by technology

[0005] However, as far as the inventor knows, many supercomputer platforms have no way to directly use the existing GROMACS codes because their own architecture is different from Intel and AMD processors, and cannot reflect the advantages of supercomputing platforms

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  • Acceleration optimization method and system for parallel PME of molecular dynamics simulation software
  • Acceleration optimization method and system for parallel PME of molecular dynamics simulation software
  • Acceleration optimization method and system for parallel PME of molecular dynamics simulation software

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Embodiment Construction

[0031] The present disclosure will be further described below in conjunction with the accompanying drawings and embodiments.

[0032] It should be noted that the following detailed description is exemplary and intended to provide further explanation of the present disclosure. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs.

[0033] It should be noted that the terminology used herein is only for describing specific embodiments, and is not intended to limit the exemplary embodiments according to the present disclosure. As used herein, unless the context clearly dictates otherwise, the singular is intended to include the plural, and it should also be understood that when the terms "comprising" and / or "comprising" are used in this specification, they mean There are features, steps, operations, means, components and / or combinations thereof.

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Abstract

The invention provides an acceleration optimization method and system for parallel PME of molecular dynamics simulation software, and the method comprises the steps: a calculation task is divided intoa plurality of parts, the calculation task is distributed to all slave cores of a super calculation platform, and the calculation is carried out through the slave cores; in the fast Fourier transformin the calculation process, data replication of matrix transposition is completed by utilizing data partitioning and a slave core; and the master core obtains the calculation results of the slave cores in a DMA mode, merges and vectorizes the calculation results, and the master core uses an RDMA technology to replace a traditional MPI technology to obtain data of other master cores. According tothe method, the molecular dynamics simulation software can be smoothly loaded on the super computing platform, and meanwhile, the computing performance can be improved.

Description

technical field [0001] The disclosure belongs to the technical field of accelerated optimization of PME, and relates to a method and system for accelerated optimization of parallel PME of molecular dynamics simulation software. Background technique [0002] The statements in this section merely provide background information related to the present disclosure and do not necessarily constitute prior art. [0003] Molecular dynamics simulation refers to the use of computer technology to simulate the motion state of molecules and atoms in the system, so as to analyze the thermodynamic quantity and other macroscopic properties in the system. Now it is widely used in scientific research work in the fields of biochemistry, physics, materials and so on. [0004] GROMACS is a classic molecular dynamics simulation software. Its initial design purpose is mainly to simulate the movement of particles and the overall information changes of the system in biochemical molecular systems (pro...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F15/173G06F15/80G06F13/28G16C10/00
CPCG06F15/17331G06F15/8007G06F13/28G16C10/00
Inventor 刘卫国邵奇张庭坚
Owner SHANDONG UNIV
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