September 2009MSc: Induction1 MSc 2009/2010 Overview Dr David Henty MSc Programme Director Email: [email protected])

September 2009 MSc: Induction 1

MSc 2009/2010 Overview

Dr David HentyMSc Programme Director

Email: [email protected])

http://www.epcc.ed.ac.uk/msc

http://www.epcc.ed.ac.uk/


Background

• MSc builds on EPCC’s long training history

– initially funded by 5-year Masters Training Package (MTP) from EPSRC

– EPSRC: Engineering and Physical Sciences Research Council– continued under High-End Computing (HEC) scheme

– began in 2001, this is the ninth year that it has been offered– longer-term support from the School of Physics and

Astronomy, the University’s Collaborative Training Account (CTA) and the Postgraduate Students' Allowances Scheme (PSAS)



Aims

• To teach practical skills– not just theory

• In areas relevant to EPCC’s HPC activities– in academic research– in industry

• This involves a number of areas– parallel programming– software development– new architectures and languages– distributed computing– ...



Hidden Aims

• To get to know potential EPCC employees– you!– currently employ seven of our own MSc students from

past years

• To continue our training activities

• To do accredited teaching at a postgraduate level

• Job satisfaction– we enjoy teaching courses



Structure

Physical Sciences

Computer Science

Theory Simulation PureApplied

MSc in HPC

Computational Science



People

• Programme Director– David Henty, room 2254

• Director of Studies– Judy Hardy, room 3403

• Programme Adminstrator– Crystal Lei, School of Physics and Astronomy Teaching Office,

room 4314• Each course taught by a range of EPCC staff

– with a single course organiser in charge of content and assessment

• External examiner– Dr Tony Arber, Centre for Scientific Computing, University of Warwick

• Chair of Board of Examiners– Prof Graeme Ackland, School of Physics, Edinburgh



Information

• Student handbook is the main source– an evolving document, but please read the printed copy– kept up-to-date on the WWW

• We have WWW pages for internal information– https://www2.epcc.ed.ac.uk/msc/students/



Format of EPCC Courses

• Courses are taught over 11 weeks– courses assessed by coursework will finish lectures around week 5 or 6

• Normally take six courses in each of two semesters– most EPCC courses taught in same half-day slot (morning/afternoon) on

same day each week– courses from other programmes may run on two different days each week

• Almost all courses are dedicated to MSc students– including students from other programmes

– Distributed Computing MSc, Maths Operational Research MSc, Informatics MSc (HPC Specialism), fifth-year Computational Physics MPhys students, ...

• Class numbers are relatively small– training room can accommodate around 26 people

• Please ask questions– take advantage of the relatively small classes



Training Room

• The main training facility for the MSc– 26 Sun Ray terminals with dual-processor Sun server (training.epcc)

• Room is often used outside of MSc courses– check the EPCC room booking system– you can use the public access PCs with UNIX via eXceed– or your own laptop and wireless

• You will each have your own smartcard– allows you to access the Sun Ray terminals– we will have to charge if you lose it!

• Ground rules– always arrive promptly for courses– do NOT use your terminal during lectures for reading email etc– ask questions!



Ness Sun HPC System

• ness is the key HPC resource for the MSc– a significant amount of computing power– a cluster of SunFire x4600 servers

– total of 32 Opteron processing cores (each @2.6 GHz)– soon to include a number of Tesla GPU boards

• A number of other HPC systems are hosted at the

University’s Advanced Computing Facility (ACF)– located just south of Edinburgh



Other ACF Machines: QCDoC

• Quantum ChromoDynamics on a Chip– Performance: 11 TFlops (14,000 special-purpose CPUs)

– Note: uses chips specifically designed by IBM, University of

Edinburgh and Columbia



IBM BlueGene

• Performance:– 5.6 TFlops– 2048 PowerPCs

• Notes:– first BlueGene in Europe– low power requirements and

high density of processors– extreme scaling

– hundreds of thousands of processors



HPCx

• The current National UK Supercomputer– http://www.hpcx.ac.uk/– initial service in December 2002 with 1280 [email protected]– now in its final phase with 2560 CPUs

• A six-year contract for £53 million (€ 74M)– includes hardware and support staff

– roughly eight staff at EPCC– consortium of EPCC, Daresbury Laboratory and IBM

– lead by the University of Edinburgh– machine physically located at Daresbury laboratory



The HPCx Consortium



HPCx



HECToR: Cray XT4



HECToR service

• Operated by EPCC / University of Edinburgh– located at the ACF– owned by EPSRC– www.hector.ac.uk

• The UK flagship national supercomputer service– over 22,000 processing cores!– currently ten times more powerful than HPCx– total cost in excess of £100M over six years

• Running for 2 years now



Real machine



Cray spaghetti



Books

• We have reading lists for each course– including at least one book– copies of all books available for review only from Judy’s office– we do not expect you to buy lots of books– many are available online

– or in the library



Programming

• Knowledge of UNIX is essential– as a user only - University provides basic material

• You will be doing a lot of programming– courses are practical-based

• You must be confident with– the language itself– the tools– organising your programming work

• Writing working programs is NOT enough– you must look at their performance (speed, efficiency ...) as well– this makes HPC research more like an experimental science



Programming Languages for MSc

• Everyone should be confident in either C or Fortran– essential for Message-Passing Programming, Shared

Memory Programming, Parallel Decomposition– useful for Applied Numerical Algorithms – Fortran knowledge required for Parallel Decomposition

– training provided in Tools and Techniques and at start of course

• Need Java for Object Oriented Programming for HPC– check requirements for non-EPCC course options

• We will not be teaching C– Java programmers advised to learn Fortran– Fortran programmers should learn Java– C programmers learn basic Fortran and perhaps Java



Compulsory EPCC Courses

• Semester 1

• FC Fundamental Concepts of HPC

• SMP Shared Memory Programming

• MPP Message Passing Programming

• SD Practical Software Development

• Semester 2

• AT Advanced Topics in HPC and e-Science

• PP HPC Project Preparation



Optional EPCC Courses

• Semester 1

• ANA Applied Numerical Algorithms

• TT Tools and Techniques for HPC Programming

• Semester 2

• PD Parallel Decomposition

• HCPP Hardware, Compilers and Performance Programming

• OOP Object Oriented Programming for HPC

• PSMA Performance Scaling on Modern HPC Architectures

• CSTA Computer Simulation using HPC: Techniques and

Applications



Options from Other Programmes

• Informatics courses

• DAPA Design and Analysis of Parallel Algorithms

• AD Applied Databases

• CN Computer Networking

• BI01 Bioinformatics 1

• BI02 Bioinformatics 2

• Distributed Scientific Computing (DSC) MSc

• WP Web Programming

• CDR Computing with Distributed Resources

• IP Internet Computing



Choices

• This year’s programme offers quite a few choices– both within MSc in HPC and from other programmes

• Normally a maximum of three non-EPCC courses

• Students choices must be confirmed by Director of Studies– check for any clashes or pre-requisite knowledge– detailed programme in the handbook

• Certain themes are outlined in the handbook



Timetable

• Semester 1 before Christmas, Semester 2 after Christmas

• See the handbook for details– exams happen at the end of each semester

• Most EPCC Teaching takes place in half day slots (except Wed PM)– teaching takes place in the EPCC training room, 3305– standard morning slot starts at 09:15 and finishes at 12:45– standard afternoon slot starts at 14:00 and finishes at 17:30– half-hour coffee / tea breaks in middle of each session– an hour lunch break– sessions are a mixture of lectures and tutored practical sessions

• Each course organiser will say if their timetable is different from above– Other programmes will have their own timetables – see their WWW pages



Assessment Mechanisms

• Mixture of coursework, exams and dissertation– EPCC courses are assessed entirely be coursework or entirely by

examination

– Informatics and DSC courses may be assessed using both

• If there is a coursework, teaching makes up first half of the semester– second half left free of lectures to allow time for coursework

– any associated tutorials will take place in the usual weekly slot

• Students passing the taught part then do a dissertation– independent project which takes 16 weeks



Marking Breakdown

• MSc comprises 180 credits– each course is 10 credits– either a piece of coursework or a 2-hour exam

• Normal breakdown– Semester 1 60 credits– Semester 2 60 credits– Dissertation 60 credits

• All taught courses have equal weight

• Progression to MSc dissertation based on performance in taught courses– Diploma based purely on taught part



Deadlines• Coursework submission is 100% online: Course Submission Tool

– www.ph.ed.ac.uk/cst/– this allows us to mark anonymously

• All courseworks will have a deadline– normally 12:00 on a Friday– we will deduct marks for late submission to ensure fairness– you are given lots of time free of teaching to do this work

• Lose 5 marks of per working day– or fraction of a working day– imagine a report is worthy of 55%– if handed in at lunchtime on Tuesday it is 2 working days late– and would be awarded 45% (55 – 2*5 = 55-10)

• Note that 8pm on Friday means 5% reduction– the same as 4pm the following Monday



Plagiarism

• Please read the guidelines– copying other people’s work is not acceptable

• We use plagiarism detection software– for both written reports and for submitted code

• If in doubt then– ask for advice

– make it clear which work is yours

• This is an extremely important issue– we give guidance here and as part of HPC Project Preparation



Social Side

• EPCC is a very social place• We want you to feel welcome

– use the coffee room– come to buns (free cakes!) on Friday to meet people– attend any social events, talks etc that you want to

• The email address [email protected] contains everyone– staff– students– visitors (eg from European programme HPC-Europa)– msc-students@epcc contains HPC students only

• Take a chance to enjoy Edinburgh– many historic sites, galleries, museums, walks, ...– eg many buildings open to the public on Doors Open Day

– 26-27 September 2009



Tonight

• Table at Mamma’s pizza place in town centre: 7.30pm– a selection of starters, and pizzas for main course, for around £8



Tonight

• Table at Mamma’s pizza place in town centre: 7.30pm– a selection of starters, and pizzas for main course, for around £8


Documents

September 2009MSc: Induction1 MSc 2009/2010 Overview Dr David Henty MSc Programme Director Email: [email protected])