ASC Workshop Catalogue Brochure CSIRO ASC Version 1.0 August 2, 2013

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1 INFORMATION MANAGEMENT AND TECHNOLOGY ASC Workshop Catalogue Brochure CSIRO ASC Version 1.0 August 2, 2013 Commercial In Confidence

2 CSIRO Advanced Scientific Computing GPO Box 1289, Melbourne, Victoria 3001, Australia Telephone : Fax : Copyright and disclaimer 2013, CSIRO CSIRO To the extent permitted by law, all rights are reserved and no part of this publication covered by copyright may be reproduced or copied in any form or by any means except with the written permission of CSIRO. Important disclaimer CSIRO advises that the information contained in this publication comprises general statements based on scientific research. The reader is advised and needs to be aware that such information may be incomplete or unable to be used in any specific situation. No reliance or actions must therefore be made on that information without seeking prior expert professional, scientific and technical advice. To the extent permitted by law, CSIRO (including its employees and consultants) excludes all liability to any person for any consequences, including but not limited to all losses, damages, costs, expenses and any other compensation, arising directly or indirectly from using this publication (in part or in whole) and any information or material contained in it.

3 CONTENTS 1 ASC Workshops 2 2 Introductory Courses Audience Introduction to CSIRO s Advanced Scientific Computing Facilities Intermediate and Language Specific Courses Audience High Performance Computing in C/C++ & Fortran High Performance Computing in Python High Performance Computing in R Accelerator Programming with OpenACC Advanced Courses Audience Advanced Topics in Program Optimisation and Parallelisation Heterogeneous Programming with CUDA & OpenCL i

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5 ASC Workshop Catalogue Brochure, Release 1.0 This document lists the HPC training courses provided by IM&T s Advanced Scientific Computing group. CONTENTS 1

6 CHAPTER ONE ASC WORKSHOPS Do you want your scientific computing to run hundreds of times faster? Do you have a shelf full of external hard drives to manage your data and no tools for management or protection of your data? Are you interested in parallel programming but don t know where to start? If you answered yes, then one of our free workshops is for you. At eresearch Accelerated Computing Workshops you will meet members of IM&T s Advanced Scientific Computing team, learn about the CSIRO high performance scientific computing services on offer, and how to take advantage of vast compute resources and virtually unlimited storage. ASC s multi-day hands-on workshops cover a number of topics in High Performance Computing (HPC) including: CSIRO s high performance computing capabilities Data management Profiling and optimising your applications Parallel programming theory and tools Code debugging Accelerator theory and programming We also provide programming language specific coverage of these HPC topics in: C/C++ & Fortran R statistical package Python CUDA OpenCL OpenACC For further information see the ASC workshop website. 2

7 CHAPTER TWO INTRODUCTORY COURSES 2.1 Audience These workshops provide fairly low-level, tutorial style, exposure to topics of HPC, computational science, and the use of ASC systems. They are targeted at researchers and others who may need to: 1. Run scientific or numerical software in a HPC environment 2. Manage data on HPC systems 3. Develop or modify scripts to launch jobs in a batch system These workshops are not intended as a high level overview of high performance or scientific computing for managers, decision makers, or others with such interests, nor are they intended to be a conference style workshop consisting of science project presentations. If you are interested in HPC workshops and conferences you should consider the CSIRO CSS/eResearch annual conference and the eresearch Australasia conference. 2.2 Introduction to CSIRO s Advanced Scientific Computing Facilities Skills Acquired Basic understanding of modern Supercomputers Logging into remote Linux systems using commandline and VNC desktops Running jobs through Supercomputer batch systems Basic data management and software access on CSIRO Supercomputers Running simple parallel workflows using a batch system Course Content What is a Supercomputer Introduction to IM&T Advanced Scientific Computing The HPC Environment 3

8 ASC Workshop Catalogue Brochure, Release 1.0 Accessing Linux systems using Secure Shell (ssh/putty) Accessing Linux systems using Virtual Network Computing (VNC) The batch system Running jobs through the Portable Batch System (PBS) Data management Accessing software and tools Compiling & debugging programs Simple parallel batch execution and parametric sweeps Other ASC services 2.2. Introduction to CSIRO s Advanced Scientific Computing Facilities 4

9 CHAPTER THREE INTERMEDIATE AND LANGUAGE SPECIFIC COURSES 3.1 Audience These workshops provide fairly low-level, tutorial style, exposure to topics of HPC, computational science, parallel programming, and the use of ASC systems. They are targeted at researchers and other individuals who may need to: 1. Develop or modify programs that are computationally or data intensive 2. Use or modify scientific / numerical software written by another party 3. Develop or modify scripts to control workflows on a cluster These workshops are not intended as a high level overview of high performance or scientific computing for managers, decision makers, or others with such interests, nor are they intended to be a conference style workshop consisting of science project presentations. If you are interested in HPC workshops and conferences you should consider the CSIRO CSS/eResearch annual conference and the eresearch Australasia conference. 3.2 High Performance Computing in C/C++ & Fortran Prerequisites Introduction to CSIRO s Advanced Scientific Computing Facilities (co-requisite) This course is most often presented in conjunction with the C/C++ and Fortran course Skills Acquired Basic principals of performance tuning and parallel processing Program Debugging Performance profiling Multi-core parallel programming using OpenMP Multi-node (Supercomputer) parallel programming using MPI 5

10 ASC Workshop Catalogue Brochure, Release 1.0 Launching parallel jobs through Supercomputer batch systems Course Content Entire Introduction to CSIRO s Advanced Scientific Computing Facilities Course Introduction to profiling Parallel programming principals 101 What is parallel/concurrent programming Job parallelism Shared memory parallelism Distributed memory parallelism Problem decomposition Implicit parallelism using third party libraries Explicit parallel programming in C/C++ & Fortran Job parallel programming using the batch system Shared memory parallel programming using OpenMP Distributed memory parallel programming using MPI 3.3 High Performance Computing in Python Prerequisites Introduction to CSIRO s Advanced Scientific Computing Facilities (co-requisite) This course is most often presented in conjunction with the Python course Skills Acquired Basic principals of performance tuning and parallel processing Performance profiling in Python Accessing accelerated support libraries from Python Multi-core parallel programming using Python Multi-node (Supercomputer) parallel programming using Python Launching parallel Python jobs through Supercomputer batch systems Course Content Entire Introduction to CSIRO s Advanced Scientific Computing Facilities Course Introduction to profiling Parallel programming principals 101 What is parallel/concurrent programming 3.3. High Performance Computing in Python 6

11 ASC Workshop Catalogue Brochure, Release 1.0 Job parallelism Shared memory parallelism Distributed memory parallelism Problem decomposition Implicit parallelism using third party libraries Explicit parallel programming in Python Job parallel programming using the batch system Shared memory parallel programming Distributed memory parallel programming 3.4 High Performance Computing in R Prerequisites Introduction to CSIRO s Advanced Scientific Computing Facilities (co-requisite) This course is most often presented in conjunction with the R course Skills Acquired Basic principals of performance tuning and parallel processing Performance profiling in R Accessing accelerated support libraries from R Multi-core parallel programming in R Multi-node (Supercomputer) parallel programming in R R to C++ offloading using Rcpp Launching parallel R jobs through supercomputer batch systems Course Content Entire Introduction to CSIRO s Advanced Scientific Computing Facilities Course Introduction to profiling Parallel programming principals 101 What is parallel/concurrent programming Job parallelism Shared memory parallelism Distributed memory parallelism Problem decomposition Implicit parallelism using third party libraries Explicit parallel programming in R 3.4. High Performance Computing in R 7

12 ASC Workshop Catalogue Brochure, Release 1.0 Job parallel programming using the batch system Shared memory parallel programming Distributed memory parallel programming using Rmpi/SNOW Accelerating R programs using C++ offloading and Rcpp package 3.5 Accelerator Programming with OpenACC Prerequisites High Performance Computing in C/C++ & Fortran (recommended prerequisite) Completion of this course is HIGHLY recommended prior to attending the OpenACC course. It will likely include the follow co-requisite in its content Introduction to CSIRO s Advanced Scientific Computing Facilities (co-requisite) For those that opt not to attend the above prerequisite, this course is recommended. It might be presented in conjunction with the OpenACC course on rare occasions Skills Acquired Basic understanding of accelerator architecture and threading model Understanding of directive based acceleration and parallel programming Writing simple OpenACC code to offloading work to an accelerator Managing data movement and placement to and on accelerators in OpenACC Compiling OpenACC code Understanding of compiler actions and the cause/solution to unexpected behaviour Course Content Introduction to accelerators and massively multi-core architectures Directive based parallel programming OpenACC vs OpenMP Writing OpenACC programs Parallel and Kernel regions Variable and Region control clauses * Shared and non-shared variables * Avoiding race conditions * Efficient data movement in accelerator programming Compiling and running OpenACC code * * * Selection of target architecture Displaying and understanding compiler actions Simple OpenACC timing 3.5. Accelerator Programming with OpenACC 8

13 ASC Workshop Catalogue Brochure, Release 1.0 Reductions 3.5. Accelerator Programming with OpenACC 9

14 CHAPTER FOUR ADVANCED COURSES Advanced courses can be provided on request and if demand is sufficient. Given these courses are delivered less often, we can customise their content to specific needs given sufficient audience size. 4.1 Audience These workshops provide fairly low-level, tutorial style, exposure to topics of HPC, computational science, parallel programming, and the use of ASC systems. They are targeted at researchers and other individuals who may need to: 1. Develop or modify programs that are computationally or data intensive 2. Use or modify scientific / numerical software written by another party 3. Develop or modify scripts to control workflows on a cluster These workshops are not intended as a high level overview of high performance or scientific computing for managers, decision makers, or others with such interests, nor are they intended to be a conference style workshop consisting of science project presentations. If you are interested in HPC workshops and conferences you should consider the CSIRO CSS/eResearch annual conference and the eresearch Australasia conference. 4.2 Advanced Topics in Program Optimisation and Parallelisation Prerequisites High Performance Computing in C/C++ & Fortran (prerequisite) Completion of this course is MANDITORY prior to attending the OpenACC course. It will likely include the follow co-requisite in its content Introduction to CSIRO s Advanced Scientific Computing Facilities (co-requisite) This co-requisite will likely be included in the above prerequisite. Otherwise contact ASC staff. 10

15 ASC Workshop Catalogue Brochure, Release Course Content Content is flexible and customisable. Topics may include: Scheduling principles in parallel programming Advanced functionalities of OpenMP and OpenMPI Performance profiling of single and multi-node parallel programs Profiling of MPI communications Debugging of parallel programs CPU code optimisation Efficient cache and memory access Code/Instruction path optimisations 4.3 Heterogeneous Programming with CUDA & OpenCL Prerequisites High Performance Computing in C/C++ & Fortran (prerequisite) Completion of this course is MANDITORY prior to attending the OpenACC course. It will likely include the follow co-requisite in its content Introduction to CSIRO s Advanced Scientific Computing Facilities (co-requisite) This co-requisite will likely be included in the above prerequisite. Otherwise contact ASC staff Skills Acquired Understanding of GPU achitecture and threading model Programming kernels in CUDA and OpenCL Achieving efficient data movement and placement with GPU devices Compiling CUDA and OpenCL programs Profiling and debugging CUDA and OpenCL programs Writing parallel programs over heterogeneous processor by mixing CPU & GPU parallel programing technologies Course Content Content is flexible and customisable. Topics may include: Introduction to NVIDIA GPU architectures Considerations in SIMD execution models Existing GPU enabled libraries CUDA and OpenCL threading models Appropriate problems and decomposition 4.3. Heterogeneous Programming with CUDA & OpenCL 11

16 ASC Workshop Catalogue Brochure, Release 1.0 Profiling GPU programs Debugging GPU programs Exploiting GPU memory hierarchy Advanced optimisations on NVIDIA GPUs Heterogeneous parallel programs Hybrib MPI+GPU for distributed memory clusters Hybrid OpenMP+GPU for heterogeneous workstations 4.3. Heterogeneous Programming with CUDA & OpenCL 12

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18 CONTACT US t e enquiries@csiro.au w YOUR CSIRO Australia is founding its future on science and innovation. Its national science agency, CSIRO, is a powerhouse of ideas, technologies and skills for building prosperity, growth, health and sustainability. It serves governments, industries, business and communities across the nation. FOR FURTHER INFORMATION CSIRO Information Management and Technology Luke Domanski t e luke.domanski@csiro.au w Advanced Scientific Computing CSIRO Information Management and Technology Sam Moskwa t e sam.moskwa@csiro.au w Advanced Scientific Computing

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