Lecture Notes

Lecture	Notes
1: Mon Feb 20	Course Introduction (ppt version) National Computational Infrastructure National Computational Infrastructure National Facility Australia's Academic and Research Network Bunyip
2-3: Wed Feb 22	Computational Science Context (LARGE pptx version) National Computational Science Institute Microsoft Computational Science Laboratory NASA Ames wind tunnels The Earth Simulator Project related links Visual Python Visual Python Demos Real time cloth simulation Advanced character physics Approximate models of the real world Large steps in cloth simulation
4: Mon Feb 27	Performance Measuring and Benchmarking (1up version) The Top500 SPEC Organisation SPEC2006 Articles TPC Benchmark STREAM Benchmark IO Profiling with strace
5-6: Wed Feb 29	We will finish discussion of performance measurement first Project related links Molecular Dynamics: display and potential energy
7: Mon Mar 5	Computing with Real Numbers (1up version) What every ANU Computer Science graduate should know about computer arithmetic! Demo Code IEEE Reference IEEE 754 Floating Point Numbers Disasters caused by arithmetic errors ASCI should use intervals Introduction to Interval Analysis Interval Computations Home Page
8-9: Wed Mar 7	High Performance Microprocessors (1up version) Intel 64 and IA-32 Architectures Optimization Manual Contains large amounts of information on Intel processors from a software optimization perspective. This is quite a detailed tutorial on pipelining. It is directed more towards a course in advanced computer architecture than our course in high performance scientific computing, so I would not expect you to know everything given here. Branch Prediction - taken from reference book "Computer Architecture, A Quantitative Approach" by Hennessy and Patterson. Project related links Molecular Dynamics: force, velocity, and movement Here are some sample outputs to help you verify the correctness of your code.
-: Mon Mar 12	Canberra Day, no lecture
10-11: Wed Mar 14	High Performance Microprocessors (continued - see above) Project related links Here are some useful links to help you understand the Python/C interface: Richard Muller on Python/C Interfacing and his complete course web page. A Python/C API example: Python Code, C code , and Makefile More detailed technical material can be found in the following links: Extending Python with C or C++ Python/C API Reference Manual
12: Mon Mar 19	Memory Systems (1up version) Dowd on cache - taken from reference book "High Performance Computing" by Kevin Dowd and Charles Severance Hennessy on cache - taken from reference book "Computer Architecture, A Quantitative Approach" by Hennessy and Patterson. Components to Memory Latency by John McCalpin
13-14: Wed Mar 21	Complete lectures on memory systems Hardware Performance Counters (1up version) Intel Performance Counter Monitor Performance Analysis and Moinitoring PAPI PCL Project related We did not get to this material in lectures. We will hold under after mid semester break. Towards linear scaling MD (1up version) NAMD Performance
15: Mon Mar 26	Optimizing Compilers (1up version) Compiler Operation and Code Generation, from Ch 5 of Write Great Code Vol 2. An introduction to GCC Intel Compiler Guide Selecting best Sun compiler options Sun Compiler Components (scroll down)
16-17: Wed Mar 28	Loop Optimisation (1up version) Project related Cloth Dynamics: Background and modelling Real time cloth simulation Approximate models of the real world Large steps in cloth simulation
18: Mon Apr 2	Mid-Semester Review Lecture
Wed Apr 4	In Class Mid-Semester Exam
19: Mon Apr 23	Shared Memory Computers (1up version) We will also talk abou the assignment and the mid-semester
-: Wed Apr 25	ANZAC Day, no lecture
20: Mon Apr 30	Shared Memory Programming (1up version)
21-22: Wed May 2	OpenMP (1up version) The OpenMP web site LLNL OpenMP Tutorial Project related Cloth Dynamics: OpenGL Implementation Complete OpenGL Tutorial
23: Mon May 7	Loop vectorization/Streaming SIMD Extensions (1up version) A Guide to Vectorization with Intel C++ Compilers Intel C++ Intrinsics Reference
24-25: Wed May 9	The Intel x86 story (1up version)
26: Mon May 14	We will finish discussion the Intel architecture evolution and OpenMP. If time we will also look at the mid-semester.
27-28: Wed May 16	Complete OpenMP Discussion (We will discuss the OpenMP Flush operation - using lecture notes from Vivek Sarkar) From MD Project Towards linear scaling MD (1up version) NAMD Performance Short course on FMM by Beatson and Greengard (just for interest) HPC Futures
29: Mon May 21	Conclude discussion of linear scaling from previous lecture Discussion around the presentation by Jack Dongarra on future of high performance computing The following relates to programming languages for HPC and are just for interest: Fortran/C/Java Fortran Pioneers (New York Times) Brief History of Fortran Fortran2003 User notes on Fortran programming. History of Fortran and comparison with C. Petition to retire fortran! Java and Numerical Computing Java at Middle Age: Enabling Java for Computational Science Benchmarking Java agains C and Fortran for Scientific Applications Some Future Prospects Unified Parallel C Titanium Co-Array Fortran DARPA High Productivity Computing Systems Initiative lead to three programming languages:     Chapel     Fortress     X10 The X10 Option ANUChem (Work at ANU in collaboration with IBM Research US) Concurrent Programming for Modern Architectures X10 Milestone Review HPC Challenge Submission for X10
Wed May 23	Optional visit to the National Facility of the National Computational Initiative. Please go directly to the foyer of the Leonard Huxley Building and be there by 11.15am. Note that it will take you around 15minutes to walk there from the CSIT building.
30: Mon May 28	Conclude and review
31-32: Wed May 30	Conclude and review
9:15 June 22nd MH_G051: Long and Very Hard Exam!

• Putty (to provide terminal from a Windows PC in the lecture theatre)