Foundations of Theoretical and Computational Science School

26 Jan 2019, 09:00 → 6 Feb 2019, 18:00 Africa/Johannesburg

Premier Resort Sani Pass, Drakensberg

The 9th CHPC Introductory   Programming School

                                  And

The 30th Chris Engelbrecht (NITheP) Theoretical Physics Summer School

                            26 January- 06 February 2019

                                   Premier Resort Sani Pass, Drakensberg

The Summer School is jointly organised by the Centre for High Performance Computing (CHPC) of the Council of Scientific and Industrial Research and the National Institute for Theoretical Physics (NITheP). This specific Summer School is motivated by a concept paper of the South African Department of Science and Technology (DST) that explores the possibility to broaden the scope of NITheP into a national institute/centre for theoretical and computational science.

Aim of the School

The School is aimed at postgraduate students in the fields of physics, chemistry, mathematics, applied mathematics, biology, bioinformatics, computer science, engineering with an interest in both theoretical and computational science. In particular the School aims at bridging the gap between theoretical studies and high performance computing.

The School will start with a Basic Scientific Programming Course to introduce students to Linux (Ubuntu) Command line and bash scripting and the Python programming Language. This will be followed by introductions to topics as

• Foundations of Theoretical and Computational Physics,
• Foundations of Theoretical and Computational Biology,
• Foundations of Theoretical and Computational Chemistry,
• Foundations of Quantum Information Processing and Computation,
• Machine Learning as a Tool for Theoretical and Computational Science,

and advanced tutorials and workshops to put the theoretical material into practice. The School is structured in such a way to encourage students to actively solve challenging problems that the lectures will pose. Students will learn by doing!

School Syllabus

The School syllabus will cover:

Introduction to Linux. It will cover basic introduction to Linux command line, bash scripting and Introduction to PBS Pro and job submission at CHPC (Dr Krishna Govender, Centre for High Performance Computing, CSIR).

Introduction to Python Programming: It will cover basic of python and syntax, advanced function and using matplotlib with python and the use of advanced mathematical packages such as numpy and scipy (Dr Andrew Gill, Centre for High Performance Computing, CSIR).

Foundations of Theoretical Physics [Title to be confirmed] (Prof Neil Turok, Perimeter Institute)

The Square Kilometer Array and Its Science: Indirect imaging in the SKA era; Real time classification at SKA-scale for time domain astrophysics; Data-centric machine learning for SKA post-processing (Prof Anna Scaife, University of Manchester)

Foundations of Quantum Technology [Title to be confirmed] (Prof Artur Ekert, National University of Singapore and University of Oxford)

Foundations of Quantum Biology and Chemistry [Title to be confirmed] (Prof Birgitta Whaley, University of California, Berkeley)

Computational Biology (Prof Johann Rohwer)

Application and Registration

The CHPC and NITheP call for all talented students to submit their applications. As public funded institutions, the CHPC and NITheP support the transformation of South Africa and thus the School organizers highly encourage students from previously disadvantaged backgrounds to submit their applications. Applicants that require a sponsorship must be registered for postgraduate (MSc and PhD) degrees in Science and Engineering with South African Universities. A background of scientific programming skills and basic Linux will be an advantage. It is a requirements that ALL SUCCESSFUL APPLICANTS MUST BRING THEIR OWN LAPTOPS.

The CHPC and NIThep will cover cost for travel and accommodation of students selected to attend the school. We would like to encourage Institutions and supervisors to financially support their students (e.g. travel cost). Due to budgetary reasons, only a limited number of scholarships is available for suitably qualified students. Should you wish to attend the School, kindly complete the application form and register online before the closing date.

Important dates

Arrival at Venue: 25 January 2018

School start: 26 January 2018

Closing date for scholarship applications: 18h00 Sunday 04 November 2018

Notification of Successful Candidates: will be notified by 30 November 2018

Closing dates for registration (not sponsored applicants): 25 November 2018

School end: 6 February 2018

Departure day: 7 February 2018

School Organizing Committee

Prof Francesco Petruccione (UKZN & NITheP)

Dr Maria Schuld (UKZN & NITheP)

Prof Amanda Weltman (UCT)

Dr. Daniel Moeketsi (CHPC, CSIR))

Dr Krishna Govender (CHPC, CSIR)

General Inquiries

For general inquiries please contact: Dr. Daniel Moeketsi at dmoeketsi@csir.co.za and Prof. Francesco Petruccione at petruccione@ukzn.ac.za

2018-10-05 Draft Programme.pdf

Saturday, 26 January

09:00 → 09:30 Welcome and Introduction: Dr. Daniel Moeketsi (CHPC), Prof Francesco Petruccione (UKZN, NITheP)

09:30 → 10:30 Introdution to Shell: Dr Krishna Govender (CHPC)

10:30 → 11:00 Tea Break

11:00 → 12:30 Running commands and getting help

12:30 → 14:00 Lunch Break

14:00 → 15:30 Standard I/O Pipes and Filters; Loops and Scripts

15:30 → 16:00 Tea Break

16:00 → 17:30 Linux Text Editors; Manual Pages

Sunday, 27 January

09:00 → 10:30 Linux file system in depth; Regular expressions: sed, grep and find

Linux file system in depth;
Regular expressions: sed, grep and find

10:30 → 11:00 Tea Break

11:00 → 12:30 Introduction to bash scripting

12:30 → 14:00 Lunch Break

14:00 → 15:30 Advanced bash scripting and exercises

15:30 → 16:00 Tea Break

16:00 → 17:30 Advanced bash scripting and exercises and Data Visualization using GNU Plot

Monday, 28 January

09:00 → 09:30 Registration

09:30 → 10:00 Introduction to National Institite of Theoretical Physics: Prof. Francesco Petructionne (UZKN, NITheP)

10:00 → 10:30 Introduction to Centre for High Performance Computing: Dr Werner Janse van Rensburg (CHPC)

10:30 → 11:00 Tea Break

11:00 → 12:30 Prof. Neil Turok: Overview of cosmology and recent progress on quantum mechanical aspects (1)

12:30 → 14:00 Lunch Break

14:00 → 15:30 Basic Python Syntax: Dr Andrew Gill(CHPC)

15:30 → 16:00 Tea Break

16:00 → 18:00 Python Basics and Practical Exercise 1

Tuesday, 29 January

09:00 → 10:30 Prof. Anna Scaife (1) : The Square Kilometre Array and its science

10:30 → 11:00 Tea Break

11:00 → 12:30 Prof. Neil Turok: Overview of cosmology and recent progress on quantum mechanical aspects (2)

12:30 → 14:00 Lunch Break

14:00 → 15:30 Python Basics

15:30 → 16:00 Tea Break

16:00 → 18:00 Python Basics and Practical Exercise 2

Wednesday, 30 January

09:00 → 10:30 Prof. Neil Turok: Overview of cosmology and recent progress on quantum mechanical aspects (3)

10:30 → 11:00 Tea Break

11:00 → 12:30 Prof. Anna Scaife (2): Indirect imaging in the SKA era

12:30 → 14:00 Lunch Break

14:00 → 15:30 Prof. Anna Scaife Tutorial 1

15:30 → 16:00 Tea Break

16:00 → 18:00 Data Processing and Visualization with Python (1)

20:30 → 21:20 Dr Adriana Marais: The Allure of the Unknown

Abstract:

We are living at a unique point in the history of life on Earth. Developments in science and technology are taking place at an unprecedented rate, and the expansion of our society beyond this planet is within reach. Adriana will talk about her research in quantum biology and the origins of life, the technology required to sustain terrestrial life on Mars and the various projects aiming to send crewed missions there. She will describe how the establishment, and potential discovery of evidence of, life on Mars, would be one of the most profound possible contributions of science to humanity.

Thursday, 31 January

09:00 → 10:30 Prof. Anna Scaife (3): Real time classification at SKA-scale for time domain astrophysics

10:30 → 11:00 Tea Break

11:00 → 12:30 Prof. Maria Schuld: Introduction to Machine Learning

12:30 → 14:00 Lunch Break

14:00 → 15:30 Prof. Anna Scaife: Tutorial 2

15:30 → 16:00 Tea Break

16:00 → 18:00 Data Processing and Visualization with Python (2): Exercise 3

Friday, 1 February

09:00 → 10:30 Prof. Anna Scaife (4): Data-centric machine learning for SKA post-processing

10:30 → 11:00 Tea Break

11:00 → 12:30 Prof. Artur Ekert: Quantum Computing (1)

12:30 → 14:00 Lunch Break

14:00 → 15:30 Tutorial ML

15:30 → 16:00 Tea Break

16:00 → 18:00 Advanced Matplotlib (1)

Saturday, 2 February

09:00 → 10:30 Prof. Artur Ekert: Quantum Computing (2)

10:30 → 11:00 Tea Break

11:00 → 12:30 Prof. Francesco Petruccione: Programming Quantum Computers

12:30 → 14:00 Lunch Break

14:00 → 15:30 Prof. Maria Schuld: Tutorial Quantum Computing (1)

15:30 → 16:00 Tea Break

16:00 → 18:00 Advanced Matplotlib (2) Practical Exercise 4

Sunday, 3 February

09:00 → 10:30 Free

10:30 → 11:00 Tea Break

11:00 → 12:30 Free

12:30 → 14:00 Lunch Break

14:00 → 15:30 Free

15:30 → 16:00 Tea Break

16:00 → 18:00 Free

Monday, 4 February

09:00 → 10:30 Prof. Artur Ekert: Quantum Computing (3)

10:30 → 11:00 Tea Break

11:00 → 12:30 Prof. Johann Rohwer: Computational Systems Biology (1) The kinetic model of a system of coupled reactions

12:30 → 14:00 Lunch Break

14:00 → 15:30 Tutorial Quantum Computing (2)

15:30 → 16:00 Tea Break

16:00 → 17:30 Mathematical Operations with numpy and scipy (1)

Tuesday, 5 February

09:00 → 10:30 Prof. Johann Rohwer: Computational Systems Biology (2) Energetics and enzyme kinetics of biological reactions (2)

10:30 → 11:00 Tea Break

11:00 → 12:30 Prof. Johann Rohwer: Tutorial Computational Systems Biology

12:30 → 14:00 Lunch Break

14:00 → 15:30 Mathematical Operations with Numpy and scipy (2)

15:30 → 16:00 Tea Break

16:00 → 18:00 Introduction to CHPC cluster login and job submission

Wednesday, 6 February

09:00 → 10:30 Prof. Johann Rohwer: Computational Systems Biology (3) - Metabolic control analysis and simulation of pathways (3)

10:30 → 11:00 Tea Break

11:00 → 12:30 Closing

12:30 → 14:00 Lunch Break

14:00 → 18:00 Summer School ends: Departure of delegates