C2115 Practical Introduction to Supercomputing

Faculty of Science
autumn 2021
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Ivo Durník, Ph.D. (seminar tutor)
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
Prerequisites (in Czech)
C2110 UNIX and Programming
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: 0/42, 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 course is mainly designed for students dealing with the calculations in the field of biochemistry, chemistry and biophysics. The goal is to increase students' ability to efficiently use the available computational resources and aims to develop basic knowledge of scripting for the purposes of data analysis. At the same time, emphasis is put on the practical usage of available software, whether commercial or developed at the National Center for Biomolecular Research.
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 PBSPro batch system;
Syllabus
  • History, use and future of computing. Examples of real problems solved in computational chemistry group. Overview of supercomputing centers in the Czech Republic: MetaCentre, CERIT-SC, IT4Innovation. Foreign supercomputing centers.
  • 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 PBSPro and Torque. Submitting jobs in Gaussian and AMBER into MetaCentre. Infinity as an extension of batch systems.
  • Hardware accelerators. Molecular simulation using GPU accelerators.
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
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
The course is taught: in blocks.
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 2022, Autumn 2023, Autumn 2024, Spring 2025.
  • Enrolment Statistics (autumn 2021, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2021/C2115