Accelerating AIREBO: Navigating the Journey from Legacy to High-Performance Code

Despite initiatives to improve the quality of scientific software, there still is a large presence of legacy code. The focus of such code is usually on domain-science features, rather than maintainability or highest performance. Additionally, architecture specific optimizations often result in less maintainable code. In this article, we focus on the AIREBO potential from LAMMPS, which exhibits large and complex computational kernels, hindering any systematic optimization. We suggest an approach based on complexity-reducing refactoring and hardware abstraction and present the journey from the C++ port of a previous Fortran code to performance-portable, KNC-hybrid, vectorized, scalable, and optimized code supporting full and reduced precision. The journey includes extensive testing that fixed bugs in the original code. Large-scale, full-precision runs sustain speedups of more than 4× (KNL) and 3× (Skylake). © 2019 Wiley Periodicals, Inc.     

Horizontal vectorization of electron repulsion integrals

We present an efficient implementation of the Obara–Saika algorithm for the computation of electron repulsion integrals that utilizes vector intrinsics to calculate several primitive integrals concurrently in a SIMD vector. Initial benchmarks display a 2–4 times speedup with AVX instructions over comparable scalar code, depending on the basis set. Speedup over scalar code is found to be sensitive to the level of contraction of the basis set, and is best for quartets when l_D = 0 or , which makes such a vectorization scheme particularly suitable for density fitting. The basic Obara–Saika algorithm, how it is vectorized, and the performance bottlenecks are analyzed and discussed. © 2016 Wiley Periodicals, Inc.     

工程图的快速半自动矢量化和点阵拾取算法

针对当前对工程图尤其是图纸质量较差的旧图纸的全自动矢量化还没有完全成熟可靠的算法，提出了一种新颖快速的半自动矢量化方法，即通过少量的人机交互，在点阵上进行跟踪，得到工程图纸上的矢量，同时也可将矢量所对应的光栅提取出来．既可对工程图纸进行矢量化，又可对其进行智能编辑．算法的特点是快速，准确，并具有良好的鲁棒性，对较差的蓝图也能取得理想的结果     

基于回溯的二级圆弧拟合算法

本文根据用最小二乘法拟合二次曲线的原理，在分析了一些其它文献中算法的基础上，提出了一种以圆弧或圆拟合平面曲线的改进的二级曲线拟合算法。     

光绘制版技术研究

分析了ＳＰＴ图像文件格式和ＰＣＢ图形文件格式。并应用图像矢量化技术完成了ＳＰＴ文件到ＰＣＢ文件的格式转换。从而达到了用低挡的矢量式光绘仪输出各种图文进行制版的目的。     

区域边界无缝矢量化方法

提出一种通过比较连接边坐标方位角大小实现边界无缝矢量化的方法,并给出具体算法及演示实验.该算法克服以往矢量化中边界线不闭合或存在双边界线等问题,矢量化结果可直接用于GIS的空间分析,不需要额外进行人工合缝或边界闭合等操作.利用该算法可大幅降低人工劳动的强度.     

基于混凝土裂纹数字图像的有限元网格生成

通过结合数字图像处理技术、边界矢量化技术与有限元网格自动生成技术,提出了基于数字图像的混凝土构件裂纹有限元分析方法。本文以混凝土裂纹为研究对象,先采用Canny算子提取裂纹边缘,对中断的边缘和伪边缘利用顺序边缘连接算法进行连接和剔除;然后,通过矢量化技术将裂纹边界拟合成小线段;最后在矢量化边界的基础上,利用自动生成技术生成裂纹结构的有限元网格,实现对裂纹区域受力情况的分析。实验结果表明:本文提出的方法可实现混凝土结构裂纹的图像监测与力学分析的一体化,能够大幅提高现役结构的评估速度和效率。     

Vectorized search for single clusters

Breadth-first search for a single cluster on a regular lattice is shown to be vectorizable. It is applied to construct clusters in the single-cluster variant of the Swendsen-Wang algorithm. On a Cray-YMP, total CPU time has been reduced by factors of 3.5–7 in large-scale applications. A multiple-cluster version is also described.     

Implementation and performance of the time integration of a 3D numerical transport model

The total solution of a three-dimensional model for computing the transport of salinity, pollutants, suspended material (such as sediment or mud), etc. in shallow seas involves many aspects, each of which has to be treated in an optimal way in order to cope with the tremendous computational task involved. In this paper we focus on one of these aspects, i.e. on the time integration, and discuss two numerical solution methods. The emphasis in this paper is on the performance of the methods when implemented on a vector/parallel, shared memory computer such as a Cray-type machine. The first method is an explicit time integrator and can straightforwardly be vectorized and parallelized. Although a stabilizing technique has been applied to this method, it still suffers from a severe time step restriction. The second method is partly implicit, resulting in much beter stability characteristics; however, as a consequence of the implicitness, it requires in each step the solution of a large number of tridiagonal systems. When implemented in a standard way, the recursive nature would prevent vectorization, resulting in a very long solution time. Following a suggestion of Golub and Van Loan, this part of the algorithm has been tuned for use on the Cray C98/4256. On the basis of a large-scale test problem, performance results will be presented for various implementations.     

使用图形矢量化软件实现气候曲线向数据的转化

不同区域的气候对比是全球变化研究的重要内容和手段.气候对比通常表现为气候曲线的对比.对文献中的气候曲线进行扫描并加以数字化(矢量化)处理得到屏幕坐标序列,由屏幕坐标和实际坐标的比例系数计算文献中的气候曲线拐点的实际坐标值,最终可使用这些数值再造所需的高质量的气候曲线图形.本文探讨了地理信息系统的辅助软件之一R2V的气候曲线数字化流程.