Gromacs在神威蓝光超级计算机上的部署及应用

Gromacs是一个大型的分子动力学模拟软件。国家超算济南中心拥有两套高性能计算系统,分别为基于Intel CPU构建的高性能计算集群(理论峰值超过100T),以及基于国产SW1600 CPU构建的MPP超级计算系统(理论峰值超过1P)。本文介绍了Gromacs软件包在两个高性能计算平台的移植、部署,并以生物大分子作为实例在两个平台上进行了分子动力学模拟测试。     

SOM算法在申威众核上的实现和优化

自组织神经网络(SOM)是一种被广泛使用的经典机器学习算法,但在处理复杂数据时其执行时间将急剧延长。并行化是解决这个问题的有效途径。基于目前TOP500上排名第一的“神威·太湖之光”超算平台,从模型并行和数据并行的角度出发,设计了SOM在申威众核处理器上的单核组和多核组的并行。一方面,通过程序重构将主要计算步骤转换为矩阵运算并利用高性能扩展数学库实现向量计算的并行化;另一方面,针对超算硬件的特性使用多种优化手段进行进一步的性能优化,使算法的性能得到了极大的提升。实验中,当使用64个核组时,所提算法的总加速比超过10000倍,同时最高可达900多倍的从核加速比也证明了所提算法有效发挥了申威核组中众核的能力。     

申威26010众核处理器上一维FFT实现与优化

根据申威26010众核处理器的特点提出了基于两层分解的一维FFT众核并行算法.该算法基于迭代的Stockham FFT计算框架和Cooley-Tukey FFT算法,将大规模FFT分解成一系列的小规模FFT来计算,并通过设计合理的任务划分方式、寄存器通信、双缓冲以及SIMD向量化等与计算平台相关的优化方法来提高FFT的计算性能.最后对所提出算法的性能进行了测试,相比于单主核上运行的FFTW3.3.4库,获得了平均44.53x的加速比,最高加速比可达56.33x,且其带宽利用率最高可达83.45%.     

基于神威蓝光处理器的向量数学软件包

首先介绍了SIMD扩展技术,并分析了使用SIMD扩展的3种方式,认为通过调用特定目标平台优化的第三方库是应用领域软件开发者快速开发高效并行程序的较好的方式;其次,介绍了国产神威处理器SW-1600平台,并利用SIMD扩展和循环展开等技术开发了SW-VML(SW Vector Math Library),开发过程中提出了访存对界、简化向量条件分支的优化方法,解决了非对界访存、向量与标量数组转换影响性能的问题,并根据SW编译器对OpenMP的支持,开发了多线程OpenMp版;最后,在SW-1600平台上采用不同向量规模对SW-VML进行了测试,测试结果显示,SIMD向量化相对于串行程序加速比为2.08,4线程相对单线程平均加速比为2.26.SW-VML是在国产神威系列处理器上开发高效程序的向量函数软件包,也是在神威蓝光高性能计算平台单计算节点开发高性能程序的基础软件工具包.     

基于申威1600的3级BLAS GEMM函数优化

BLAS是当前科学计算领域重要的底层支持数学库之一,其中的3级BLAS函数应用最为广泛.本文基于国产申威1600平台,提出了一种基础线性代数库BLAS的三级函数通用矩阵乘GEMM的高性能实现方法.在单核上,使用乘加指令、循环展开、软件流水线指令重排、SIMD向量化运算、寄存器分块技术等与平台架构相关的技术手段,实现汇编级手工优化;在多核上,提出了适用于该平台的多线程加速方案.实验结果显示,在单核串行性能测试中,与知名开源数学库GotoBLAS相比,我们实现了平均4.72倍的加速效果;在多核并行扩展测试中,4线程版的性能则平均达到了单线程版性能的3.02倍.     

申威架构下的虚拟机访存特征提取方法

虚拟化技术是云服务的重要支柱之一,虚拟化充分扩展了物理资源的灵活性,提升了物理资源的利用率。随着国家信息化水平的发展,云服务器核心技术自主可控、安全高效的要求不断提高。近年来,作为国产服务器的典型代表,申威架构服务器的功能不断完善。提出了申威架构上的虚拟机访存特征提取方法,充分利用了申威架构独特优势,实时测算虚拟机的内存缺失率曲线,并最终计算工作集大小,同时利用热页集机制大幅度减少页面追踪的性能开销。实验结果表明,该方法可以准确计算虚拟机工作集大小,平均误差低于3%,平均性能开销不高于8.3%。本工作为申威虚拟机内存动态分配提供条件,最终目标是提高申威云服务器整体性能和内存利用率。     

LQ1600K打印机接口故障的处理方法

论述了ＬＱ１６００Ｋ打印机联机后，不能正常打印数据的故障处理方法，介绍打印机接口芯片的结构原理以及与外围电路的通信原理，用实例介绍了故障测试技术、排除方法及防范措施。     

WETTABILITY AND SURFACE ENERGETICS OF ROUGH FLUOROPOLYMER SURFACES

Hydrophobic solid surfaces with controlled roughness were prepared by coating glass slides with an amorphous fluoropolymer (Teflon® AF1600, DuPont) containing varying amounts of silica spheres (diameter 48?μm). Quasi-static advancing, θ_A, and receding, θ_R, contact angles were measured with the Wilhelmy technique. The contact angle hysteresis was significant but could be eliminated by subjecting the system to acoustic vibrations. Surface roughness affects all contact angles, but only the vibrated ones, θ_V, agree with the Wenzel equation. The contact angle obtained by averaging the cosines of θ_A and θ_R is a good approximation for θ_V, provided that roughness is not too large or the angles too small. Zisman's approach was employed to obtain the critical surface tension of wetting (CST) of the solid surfaces. The CST increases with roughness in accordance with Wenzel equation. Advancing, receding, and vibrated angles yield different results. The θ_A is known to be characteristic of the main hydrophobic component (the fluoropolymer). The θ_V is a better representation of the average wettability of the surface (including the presence of defects).     

DETERMINATION OF SOLID SURFACE TENSION FROM CONTACT ANGLES: THE ROLE OF SHAPE AND SIZE OF LIQUID MOLECULES

Accurate surface tension of Teflon® AF 1600 was determined using contact angles of liquids with bulky molecules. For one group of liquids, the contact angle data fall quite perfectly on a smooth curve corresponding to γ_sv = 13.61 mJ/m², with a mean deviation of only ±0.24 degrees from this curve. Results suggest that these liquids do not interact with the solid in a specific fashion. However, contact angles of a second group of liquids with fairly bulky molecules containing oxygen atoms, nitrogen atoms, or both deviate somewhat from this curve, up to approximately 3 degrees. Specific interactions between solid and liquid molecules and reorientation of liquid molecules in the close vicinity of the solid surface are the most likely causes of the deviations. It is speculated that such processes induce a change in the solid–liquid interfacial tension, causing the contact angle deviations mentioned above. Criteria are established for determination of accurate solid surface tensions.     

Contact Angles and Coating Film Thickness

The effect of film thickness and surface preparation techniques on contact angles of water, 1-bromonaphtalene, and n-hexadecane on Teflon® AF 1600 polymeric surfaces is studied. It was found that contact angles of water on different thicknesses of spin-coated films ranging from 27?nm to 420?nm are essentially constant. This is due to the homogeneity and smoothness of the coating layers as shown by the scanning force microscopy of the samples. Furthermore, the contact angle measurements with these three liquids on both dip-coated and spin-coated films suggested that the film preparation technique does not affect contact angles dramatically. Interestingly, slightly higher contact angles on dip-coated surfaces were measured. It is also argued that the anomaly of the water contact angle—in the sense that the measured contact angle is much higher than the expected ideal value—is due to specific interactions between water and Teflon®.