C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2024
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: k (colloquium).
In-person direct teaching
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Július Zemaník (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Tue 13:00–14:50 C04/118
Prerequisites
The basics of working with a computer, the basics of working in the Linux operating system, or completion of the C2110 UNIX Operating System and the basics of programming are an advantage.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 42 student(s).
Current registration and enrolment status: enrolled: 11/42, only registered: 0/42, only registered with preference (fields directly associated with the programme): 0/42
fields of study / plans the course is directly associated with
Course objectives
The goal of the course is to introduce students to the key concepts of supercomputing, including supercomputer architectures, parallel computing, and typical problems solved on supercomputers. Students will learn practical skills while working in the MetaCenter supercomputing centre. They will learn basic commands, operating system operation, data storage management, and effective task management in a multi-user environment. Hands-on demonstrations will include simple numerical computations, simulations of molecular systems, quantum-chemical computations, and artificial intelligence applications using large language models (LLM) for data processing.
Learning outcomes
Student will be able to:
- work with CESNET data storages;
- work in the MetaCentrum and IT4I supercomputer centers;
- analyze the demands of scientific and technical applications;
- choose a suitable strategy for launching jobs in supercomputer centers;
- submit computational tasks into the PBS (OpenPBS) and Slurm batch system;
Syllabus
  • The history, use, and future of computing. Examples of real problems solved in the computational chemistry group. Overview of supercomputing centres in the Czech Republic: MetaCentre, CERIT-SC, IT4Innovation. Foreign supercomputing centres.
  • A brief introduction to UNIX. The computational cluster WOLF, structure, architecture, software. User registration into MetaCentre.
  • Computer architecture. Representation of numerical values ​​in digital form. From problem to the result. Error propagation in numerical calculations.
  • Fortran as a major language used in supercomputing. History. Syntax. Compilers. Numerical libraries.
  • Speeding up calculations via parallelization. Types of parallelization. A practical example of using OpenMP and MPI. Effectiveness of parallelization.
  • Batch systems PBS (OpenPBS) and Slurm. Submitting jobs in Gaussian and AMBER into MetaCentre. Infinity as an extension of batch systems.
  • Hardware accelerators. Molecular simulation using GPU accelerators. Using artificial intelligence for data processing.
Literature
  • CHIVERS, Ian and Jane SLEIGHTHOLME. Introduction to Programming with Fortran: With Coverage of Fortran 90, 95, 2003, 2008 and 77. Springer. 2012, 619 pp. ISBN 978-0-85729-232-2. info
  • CLERMAN, Walter. Modern Fortran: style and usage. New York. Cambridge University Press, 2012, 334 pp. ISBN 978-0-521-51453-8. info
  • PACHECO, Peter S. An introduction to parallel programming. Amsterdam; Boston: Morgan Kaufmann, 2011. ISBN 978-0-12-374260-5. info
  • High performance computing: from grids and clouds to exascale. Washington, DC: IOS Press, 2011. Advances in parallel computing, v. 20. ISBN 978-1-60750-802-1. info
Teaching methods
lectures, class discussion, group projects in the computer room
Assessment methods
approved written protocols of students' projects, final test, the test consists of 50 questions, multiple choices, correct answer plus one point, incorrect answer minus quarter point, at least 35 points is needed to pass
Language of instruction
Czech
Follow-Up Courses
Study support
https://is.muni.cz/auth/el/sci/podzim2024/C2115/index-XFhLTD.qwarp
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Spring 2025.
  • Enrolment Statistics (recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2024/C2115