Calculation of capillary jet

The Arbitrary Lagrangian Eulerian (ALE) framework coupled with some boundary tracking techniques is proven to be an effective method for simulation of free‐surface flows. In this paper, a special ALE framework is derived with clarification of three velocities, the notion of mesh‐frozen and field‐frozen, and the notion of tentatively inertial coordinates. A weighted integral ALE governing equations are formulated on generic coordinates and discretized with a finite element method and linear implicit time scheme. The system is solved with a discrete operator splitting technique and superposition‐based logistic parallelization. The formulation and implementation are verified through several fixed‐geometry problems and a reasonably good parallel performance is observed. Capillary jet flow is the main problem of the paper and the numerical techniques for boundary tracking are elaborated, which include an indirect boundary tracking of flux method and an iterative direct boundary tracking method. Also, a high‐order compact scheme for dynamic boundary condition and a squeeze technique for kinematic boundary condition are adopted. The axisymmetric jet breakup is studied in detail and numerical results match with the published data very well. Numerical accuracy and sensitivity are studied, including effects of element type, time scheme, compact scheme, and boundary tracking techniques. Copyright © 2010 John Wiley & Sons, Ltd.     

RedMD—Reduced molecular dynamics package

We developed a software package (RedMD) to perform molecular dynamics simulations and normal mode analysis of reduced models of proteins, nucleic acids, and their complexes. With RedMD one can perform molecular dynamics simulations in a microcanonical ensemble, with Berendsen and Langevin thermostats, and with Brownian dynamics. We provide force field and topology generators which are based on the one‐bead per residue/nucleotide elastic network model and its extensions. The user can change the force field parameters with the command line options that are passed to generators. Also, the generators can be modified, for example, to add new potential energy functions. Normal mode analysis tool is available for elastic or anisotropic network models. The program is written in C and C++ languages and the structure/topology of a molecule is based on an XML format. OpenMP technology for shared‐memory architectures was used for code parallelization. The code is distributed under GNU public licence and available at http://bionano.icm.edu.pl/software/ . © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

密度矩阵重正化群的异构并行优化

密度矩阵重正化群方法（DMRG）在求解一维强关联格点模型的基态时可以获得较高的精度，在应用于二维或准二维问题时，要达到类似的精度通常需要较大的计算量与存储空间.本文提出一种新的DMRG异构并行策略，可以同时发挥计算机中央处理器（CPU）和图形处理器（GPU）的计算性能.针对最耗时的哈密顿量对角化部分，实现了数据的分布式存储，并且给出了CPU和GPU之间的负载平衡策略.以费米Hubbard模型为例，测试了异构并行程序在不同DMRG保留状态数下的运行表现，并给出了相应的性能基准.应用于4腿梯子时，观测到了高温超导中常见的电荷密度条纹，此时保留状态数达到10⁴，使用的GPU显存小于12 GB.     

Parallelization alternatives and their performance for the convex hull problem

High performance machines have become available nowadays to an increasing number of researchers. Most of us might have both an access to a supercomputing center and an algorithm that could benefit from these high performance machines. The aim of the present work is to revisit all existing parallelization alternatives, including emerging technologies like software-only speculative parallelization, to solve on different architectures the same representative problem: The computation of the convex hull of a point set.     

密度矩阵重正化群的异构并行优化

密度矩阵重正化群方法（DMRG）在求解一维强关联格点模型的基态时可以获得较高的精度，在应用于二维或准二维问题时，要达到类似的精度通常需要较大的计算量与存储空间.本文提出一种新的DMRG异构并行策略，可以同时发挥计算机中央处理器（CPU）和图形处理器（GPU）的计算性能.针对最耗时的哈密顿量对角化部分，实现了数据的分布式存储，并且给出了CPU和GPU之间的负载平衡策略.以费米Hubbard模型为例，测试了异构并行程序在不同DMRG保留状态数下的运行表现，并给出了相应的性能基准.应用于4腿梯子时，观测到了高温超导中常见的电荷密度条纹，此时保留状态数达到10⁴，使用的GPU显存小于12 GB.     

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used.     

Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers

A message passing interface (MPI)-based implementation (Autodock4.lga.MPI) of the grid-based docking program Autodock4 has been developed to allow simultaneous and independent docking of multiple compounds on up to thousands of central processing units (CPUs) using the Lamarkian genetic algorithm. The MPI version reads a single binary file containing precalculated grids that represent the protein-ligand interactions, i.e., van der Waals, electrostatic, and desolvation potentials, and needs only two input parameter files for the entire docking run. In comparison, the serial version of Autodock4 reads ASCII grid files and requires one parameter file per compound. The modifications performed result in significantly reduced input/output activity compared with the serial version. Autodock4.lga.MPI scales up to 8192 CPUs with a maximal overhead of 16.3%, of which two thirds is due to input/output operations and one third originates from MPI operations. The optimal docking strategy, which minimizes docking CPU time without lowering the quality of the database enrichments, comprises the docking of ligands preordered from the most to the least flexible and the assignment of the number of energy evaluations as a function of the number of rotatable bounds. In 24 h, on 8192 high-performance computing CPUs, the present MPI version would allow docking to a rigid protein of about 300K small flexible compounds or 11 million rigid compounds.     

基于点球弹簧修匀法的混合网格变形并行算法

针对二维/三维混合网格,提出基于点球弹簧修匀法的并行网格变形算法。按特定模板将混合网格中的非三角形/四面体单元分解成三角形/四面体单元。针对每个内部节点及其相邻节点建立相应的子弹簧系统,并通过增加Ball-Vertex弹簧避免弹簧系统的塌陷问题。由于点球弹簧法在计算中逐点对网格内部节点进行计算,在计算过程中具有良好的弱耦合性质,因此有利于算法并行化。在并行化时仅需对网格进行虚拟分区操作,不必进行复杂的几何分区操作,同时避免了混合网格不同单元之间的兼容性问题。该方法适用于具有复杂外形的大规模混合网格的变形问题,能够显著提高网格变形的效率,同时具有良好的适应性。     

密度矩阵重正化群的异构并行优化

密度矩阵重正化群方法(DMRG)在求解一维强关联格点模型的基态时可以获得较高的精度,在应用于二维或准二维问题时,要达到类似的精度通常需要较大的计算量与存储空间.本文提出一种新的DMRG异构并行策略,可以同时发挥计算机中央处理器(CPU)和图形处理器(GPU)的计算性能.针对最耗时的哈密顿量对角化部分,实现了数据的分布式存储,并且给出了CPU和GPU之间的负载平衡策略.以费米Hubbard模型为例,测试了异构并行程序在不同DMRG保留状态数下的运行表现,并给出了相应的性能基准.应用于4腿梯子时,观测到了高温超导中常见的电荷密度条纹,此时保留状态数达到104,使用的GPU显存小于12 GB.     

密度矩阵重正化群的异构并行优化

密度矩阵重正化群方法（DMRG）在求解一维强关联格点模型的基态时可以获得较高的精度，在应用于二维或准二维问题时，要达到类似的精度通常需要较大的计算量与存储空间.本文提出一种新的DMRG异构并行策略，可以同时发挥计算机中央处理器（CPU）和图形处理器（GPU）的计算性能.针对最耗时的哈密顿量对角化部分，实现了数据的分布式存储，并且给出了CPU和GPU之间的负载平衡策略.以费米Hubbard模型为例，测试了异构并行程序在不同DMRG保留状态数下的运行表现，并给出了相应的性能基准.应用于4腿梯子时，观测到了高温超导中常见的电荷密度条纹，此时保留状态数达到10⁴，使用的GPU显存小于12 GB.