MaMiCo: Software design for parallel molecular-continuum flow simulations
MaMiCo: Software design for parallel molecular-continuum flow simulations
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DOI：
10.1016/j.cpc.2015.10.029
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发表时间：
2016-03
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通讯作者：
Philipp Neumann;H. Flohr;Rahul Arora;P. Jarmatz;Nikola Tchipev;H. Bungartz
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作者：
Philipp Neumann;H. Flohr;Rahul Arora;P. Jarmatz;Nikola Tchipev;H. Bungartz
宏微耦合工具（MaMiCo）的开发是为了简化分子连续模拟的开发和模块化，保持顺序和并行性能。我们展示的功能和性能的MaMiCo耦合的空间自适应格子玻尔兹曼框架waLBerla与四个分子动力学（MD）代码：轻量级的Lennard-Jones为基础的implementationSimpleMD，节点级优化软件ls 1 martyn，和社区代码ESPResSo和LAMMPS。我们详细的接口实现连接每个求解器与MaMiCo。每个waLBerla-MD设置的耦合在三维通道流模拟中进行了验证，该模拟通过基于状态的耦合方法来解决。我们提供了连续和强缩放测量的四个分子连续模拟。MaMiCo的开销被发现在总（MD）运行时间的10%-20%。测量结果进一步表明，混合模拟的可扩展性可在多达500个Intel SandyBridge和1000多个AMD Bulldozer计算内核上实现。程序摘要程序标题：MaMiCo目录标识符：AEYW_v1_0程序摘要URL：http://cpc.cs.qub.ac.uk/summaries/AEYW_v1_0.htmlProgram可从以下网站获得：CPC Program Library，Queen's University，贝尔法斯特，N.爱尔兰许可条款：BSD许可证号分布式程序中的行，包括测试数据等：67905号分布式程序的字节数，包括测试数据等：1757334分发格式：tar. gz编程语言：C，C++II.计算机：标准PC，计算集群.操作系统：Unix/Linux.RAM：测试用例消耗ca. 30-50 MB分类：7.7.外部例程：Scons（http：www.scons.org），ESPResSo，LAMMPS，ls 1 martyn，waLBerla问题性质：多分辨率流体动力学的耦合分子连续模拟：部分区域由分子动力学解决，而大部分区域由CFD求解器（例如格子Boltzmann自动机）覆盖求解方法：我们通过MaMiCo（宏微耦合工具）耦合现有的MD和CFD求解器。在MaMiCo中抽象并集成了数据交换和耦合算法。一旦在MaMiCo中设置了算法，即使使用了其他求解器，也可以使用和扩展该算法（只要实现了相应的接口）。限制：目前仅支持单中心Lennard-Jones系统。运行时间：时间取决于底层的耦合问题，可能从几分钟到几天不等。为所有不同的求解器耦合（包括一个完整的AVG耦合周期。域大小）取CA。10小时在一个普通的桌面上。
The macro–micro-coupling tool (MaMiCo) was developed to ease the development of and modularize molecular-continuum simulations, retaining sequential and parallel performance. We demonstrate the functionality and performance of MaMiCo by coupling the spatially adaptive Lattice Boltzmann framework waLBerla with four molecular dynamics (MD) codes: the light-weight Lennard-Jones-based implementationSimpleMD, the node-level optimized softwarels1 mardyn, and the community codes ESPResSo and LAMMPS. We detail interface implementations to connect each solver with MaMiCo. The coupling for each waLBerla-MD setup is validated in three-dimensional channel flow simulations which are solved by means of a state-based coupling method. We provide sequential and strong scaling measurements for the four molecular-continuum simulations. The overhead of MaMiCo is found to come at 10%–20% of the total (MD) runtime. The measurements further show that scalability of the hybrid simulations is reached on up to 500 Intel SandyBridge, and more than 1000 AMD Bulldozer compute cores.Program summaryProgram title:MaMiCoCatalogue identifier:AEYW_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEYW_v1_0.htmlProgram obtainable from:CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions:BSD LicenseNo. of lines in distributed program, including test data, etc.:67905No. of bytes in distributed program, including test data, etc.:1757334Distribution format:tar.gzProgramming language:C, C++II.Computer:Standard PCs, compute clusters.Operating system:Unix/Linux.RAM:Test cases consume ca. 30–50 MBClassification:7.7.External routines:Scons (http:www.scons.org), ESPResSo, LAMMPS, ls1 mardyn, waLBerlaNature of problem:Coupled molecular-continuum simulation for multi-resolution fluid dynamics: parts of the domain are resolved by molecular dynamics whereas large parts are covered by a CFD solver, e.g. a lattice Boltzmann automatonSolution method:We couple existing MD and CFD solvers via MaMiCo (macro–micro coupling tool). Data exchange and coupling algorithmics are abstracted and incorporated in MaMiCo. Once an algorithm is set up in MaMiCo, it can be used and extended, even if other solvers are used (as soon as the respective interfaces are implemented).Restrictions:Currently, only single-centered Lennard-Jones systems are supported.Running time:Runtime depends on the underlying coupled problem and may range from minutes to days. The provided test cases for all different solver couplings (incl. one complete coupling cycle of avg. domain size) take ca. 10 h on a regular Desktop.