善用高效能計算，不僅可以解決大型科學或工程問題，也能開發重要的產業應用軟體。在這個兩星期的密集課程裡，我們將簡介 (A) 手把手數學軟體工具應用，(B) CUDA GPU 程式設計，(C) CPU/GPU 的 OpenMP/OpenACC 程式設計。這個短期課程提供一個非常難得的機會，利用東京大學的超級電腦 Reedbush，學習最先進的高效能計算軟體語言與開發環境。歡迎教師、碩博士生、大學部同學報名參加，建議具備 C 程式語言基本能力。

• 6/26 ( Day 1 ) : https://github.com/wlab-pro/scsc17summer0/releases
• 6/28 ( Day 3 ) : https://github.com/wlab-pro/scsc17summer/releases

https://drive.google.com/open?id=0B6vku8qPKNhdeFlYRVFoR3dDRlE

In order to make full use of modern supercomputer systems with multicore/manycore architectures, hybrid parallel programming with message-passing and multithreading is essential. While MPI is widely used for message-passing, OpenMP for CPU and OpenACC for GPU are the most popular ways for multithreading on multicore/manycore clusters. In this 4-day course, we focus on optimization of single node performance using OpenMP and OpenACC for CPU and GPU. We “parallelize” a finite-volume method (FVM) code with Krylov iterative solvers for Poisson’s equation on Reedbush supercomputer at the University of Tokyo with 1.93 PF peak performance (http://www.cc.u-tokyo.ac.jp/system/reedbush/index-e.html), which consists of the most recent CPU’s (Intel Xeon E5-2695 v4 (Broadwell-EP)) and GPU’s (NDIVIA Tesla P100 (Pascal)).

It is assumed that all the participants have already finished “邁向 Petascale 高速計算 (February 2016)” or “國家理論中心數學組「高效能計算 」短期課程 (February 2017)”, or they have equivalent knowledge and experiences in numerical analysis and parallel programming by MPI and OpenMP.

In the winter schools in February 2016 and February 2017, the target application was a 3D FVM code for Poisson’s equation by Conjugate Gradient (CG) iterative method with very simple Point Jacobi preconditioner. This time our target is same FVM code, but linear equations are solved by ICCG (CG iterative method with Incomplete Cholesky preconditioning), which is more complicated, powerful and widely used in practical applications. Because ICCG includes “data dependency”, where writing/reading data to/from memory could occur simultaneously, parallelization using OpenMP/OpenACC is not straight forward. We need certain kind of reordering in order to extract parallelism. In this 4-day course, lectures and exercise on the following issues will be provided:

• Overview of Finite-Volume Method (FVM)
• Krylov Iterative Method, Preconditioning
• Implementation of the Program
• Introduction to OpenMP/OpenACC
• Reordering/Coloring Method
• Parallel FVM by OpenMP/OpenACC

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)

• July 4, 2017 (T)
  • Introduction
  • Finite-Volume Method (FVM)
  • Login to Reedbush System
  • OpenMP
  • Reordering (1/2)
• July 5, 2017 (W)
  • Reordering (2/2)
  • Parallel FVM by OpenMP
• July 6, 2017 (Th)
  • Introduction to GPU Programming
  • OpenACC (1/2)
• July 7, 2017 (F)
  • OpenACC (2/2)
  • Parallel FVM by OpenACC
  • Exercises

• Completion of one of the following two short courses:
  • 邁向 Petascale 高速計算 (February 2016) https://sites.google.com/site/school4scicomp/previous/2016-a-winter
  • 國家理論中心數學組「高效能計算 」短期課程 (February 2017) https://sites.google.com/site/school4scicomp/previous/2017-b-spring (or equivalent knowledge and experiences in numerical analysis (FVM, preconditioned iterative solvers) and parallel programming using OpenMP and MPI )
  • 6月28日課程將會幫同學複習這部分的內容
• Experiences in Unix/Linux (vi or emacs)
• Fundamental numerical algorithms (Gaussian Elimination, LU Factorization, Jacobi/Gauss-Seidel/SOR Iterative Solvers, Conjugate Gradient Method (CG))
• Experiences in SSH Public Key Authentication Method

• Windows
  • Cygwin with gcc/gfortran and OpenSSH
    • Please make sure to install gcc (C) or gfortran (Fortran) in “Devel”, and OpenSSH in “Net”
    • ParaView
• MacOS, UNIX/Linux
  • ParaView
• Cygwin: https://www.cygwin.com/
• ParaView: http://www.paraview.org/

• http://nkl.cc.u-tokyo.ac.jp/NTU2017S/
• http://nkl.cc.u-tokyo.ac.jp/17s/ (Lectures at the University of Tokyo (OpenMP only))
• http://nkl.cc.u-tokyo.ac.jp/NTU2015/
• http://nkl.cc.u-tokyo.ac.jp/files/multicore-c.tar
• http://nkl.cc.u-tokyo.ac.jp/files/multicore-f.tar

• Putty 產生金鑰投影片