2017-b-Spring

國家理論中心數學組「高效能計算 」短期課程

Introduction to Parallel Programming for Multicore/Manycore Clusters

2017年2月21日星期二至2月24日星期五 (9:00-17:00)

國立臺灣大學 天文數學館 301 室

常用連結

• YouTube 課程錄影
• 作業說明
• Prof. Nakajima 課程檔案下載連結：http://nkl.cc.u-tokyo.ac.jp/NTU2017/
• Prof. Katagiri 課程檔案下載連結：http://www.abc-lib.org/MyHTML/Lectures/NU/class-matrNTU2017.htm

最新訊息

• [2012/02/24] We will have a hands-on session on March 1 from 13:00-15:00 in Room 301. Youtube: https://www.youtube.com/watch?v=yubAhlU8Nnw.
• [2017/02/23] A more detailed homework description is available online.
• [2017/02/22] 請將五個作業 (包含程式、結果、說明/討論。檔名：姓名_HW1.pdf,..., 姓名_HW5.pdf) 和一份效能比較報告 (檔名：姓名_RP1.pdf)，在 2017/3/13/6:00am 前上傳到 google 雲端硬碟「2/21-2/24 Short Course Homework」。
• [2017/02/22] 課程錄影可在 YouTube 觀看
• [2017/02/05] Prof. Nakajima 課程檔案下載連結：http://nkl.cc.u-tokyo.ac.jp/NTU2017/
• [2017/01/21] Prof. Katagiri 課程檔案下載連結：http://www.abc-lib.org/MyHTML/Lectures/NU/class-matrNTU2017.htm
• [2017/01/12] 線上註冊網址：https://goo.gl/forms/Gsi5AXujUZtTZrcf1 (報名截止日期： 2017/01/20。本課程不收費用，但名額有限，獲得錄取學員將另行通知。)
• [2017/01/12] 臺灣大學地圖：PDF 檔，Google 版地圖

課程簡介

快速累積的大量數據，以及高速發展的超級電腦，是當今與未來的重要趨勢。具備高速計算能力，才能解決更大更複雜的問題，也能大幅提升進行尖端研究與開發產業應用的競爭力。在這個四天的密集課程，我們將簡介 MPI 與 OpenMP 的平行計算環境，說明如何在此平行環境求解稠密矩陣的特徵值問題，並將有限體積法以及大型線性系統疊代法平行化，求解三維 Poisson 方程。課程中將使用最先進的超級電腦實機操作。(註：帳號須經申請，並依相關規定審核通過後，方得使用。)

這個短期課程提供一個非常難得的機會，可以接觸到目前全世界最尖端的高速平行計算環境。歡迎教師、碩博士生、大學部同學報名參加。本課程以英語講授，課程內容概要如下：

• Fundamental (2/21 -22):
• First 2 days are focusing on training of fundamental MPI and OpenMP. The basic functions and usage of MPI and OpenMP are explained. Several trainings of parallelization by using sample programs based on fundamental numerical computations, such as matrix-matrix multiplication, are provided.
• Advanced (2/23-24):
• On the 3rd and 4th days, MPI and OpenMP/MPI are applied to 3D Poisson equation solver by finite-volume method (FVM) with preconditioned conjugate gradient iterative method (PCG). Detailed lectures on data structure for parallel FVM are also provided.

Overview

In order to make full use of modern supercomputer systems with multicore/manycore architectures, hybrid parallel programming with message-passing and multithreading is essential. MPI for message-passing and OpenMP for multithreading are the most popular ways for parallel programming on multicore/manycore clusters. This 4-day tutorial provides essential knowledge and experiences for parallel programming using MPI and OpenMP. Hands-on exercise by Fujitsu PRIMEHPC FX10 supercomputer at the University of Tokyo (Oakleaf-FX, http://www.cc.u-tokyo.ac.jp/system/fx10/index-e.html) is also given.

預備知識 (Prerequisites)

• Experiences in Unix/Linux
• Experiences in emacs or vi
• Experiences of programming (Fortran or C/C++)
• Fundamental numerical algorithms (Gaussian Elimination, LU Factorization, Jacobi/Gauss-Seidel/SOR Iterative Solvers)
• Experiences in SSH Public Key Authentication Method

課程講義 (Course Handouts)

• http://nkl.cc.u-tokyo.ac.jp/NTU2017/
• http://www.abc-lib.org/MyHTML/Lectures/NU/class-matrNTU2017.htm

相關軟體 (Software)

• Windows: Cygwin with gcc/gfortran, SSH Client (e.g. PUTTY), ParaView
• MacOS, UNIX/Linux: ParaView
• Cygwin: https://www.cygwin.com/
• PuTTY: http://www.chiark.greenend.org.uk/~sgtatham/putty/
• ParaView: http://www.paraview.org/

授課教授 (Instructors)

• Professor Kengo Nakajima (中島 研吾 教授，東京大學 情報基盤中心 超級計算研究部門)

• Professor Takahiro Katagiri (片桐 孝洋 教授，名古屋大學 情報基盤中心 大規模計算支援環境研究部門)

課程內容 (Schedule and Contents)

February 21, 2017 (Tuesday)

09:10-10:00 Introduction

10:10-11:00 FVM code (1/4)

11:10-12:00 FVM code (2/4)

13:10-14:00 FVM code (3/4)

14:10-15:00 FVM code (4/4) and sparse linear solver

15:10-16:00 Overview of OpenMP

17:10-18:00 Functions of OpenMP

February 22, 2017 (Wednesday)

09:10-10:00 Training of OpenMP

10:10-11:00 Overview of MPI

11:10-12:00 How to use the Oakleaf-FX

13:10-14:00 Trainings of Oakleaf-FX

Homework 1

14:10-15:00 Functions of MPI Non-blocking and Persistent Communication

15:10-16:00 Parallelization of dense Matrix-Vector Multiplications (1/2)

16:10-17:00 Parallelization of dense Matrix-Vector Multiplications (2/2)

Homework 2

February 23, 2017 (Thursday)

09:10-10:00 Parallelization of dense Power Method for eigenvalue problem (1/2)

10:10-11:00 Parallelization of dense Power Method for eigenvalue problem (2/2)

Homework 3

11:10-12:00 Parallelization of Fully Distributed dense Matrix-Matrix Multiplication (1/2)

Homework 4

13:10-14:00 Parallelization of Fully Distributed dense Matrix-Matrix Multiplication (2/2)

Homework 5

14:10-15:00 Parallel Data Structure (1/2)

15:10-16:00 Parallel Data Structure (2/2)

16:10-17:00 Parallel FVM (1/4)

February 24, 2017 (Friday)

09:10-10:00 Parallel FVM (2/4)

10:10-11:00 Parallel FVM (3/4)

11:10-12:00 Parallel FVM (4/4)

13:10-14:00 OpenMP/MPI Hybrid (1/4)

14:10-15:00 OpenMP/MPI Hybrid (2/4)

15:10-16:00 OpenMP/MPI Hybrid (3/4)

16:10-17:00 OpenMP/MPI Hybrid (4/4)

Project Report (topics including strong scaling, weak scaling, preconditioning, performance comparison, etc.)

主辦單位與聯絡人

主辦單位：國家理論中心數學組，臺大數學科學中心

協辦單位：東京大學情報基盤中心，臺灣大學數學系與應用數學科學研究所，台灣工業與應用數學學會 GPU與高效能計算活動學群

主持人：王偉仲 (台灣大學數學系與應用數學科學研究所)

聯絡人：冼汶霖 (02-3366-8814, loreinahsien@ncts.ntu.edu.tw)