C2115 Practical Introduction to Supercomputing

Faculty of Science
Spring 2025
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: k (colloquium).
Taught in person.
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (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
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
there are 27 fields of study the course is directly associated with, display
Language of instruction
Czech
Further Comments
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 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2024
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: k (colloquium).
Taught in person.
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (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
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
there are 27 fields of study the course is directly associated with, display
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
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 2021, Autumn 2022, Autumn 2023, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2023
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: k (colloquium).
Taught in person.
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (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 (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: 6/42, only registered: 1/42, only registered with preference (fields directly associated with the programme): 0/42
fields of study / plans the course is directly associated with
there are 27 fields of study the course is directly associated with, display
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
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 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2022
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: k (colloquium).
Taught in person.
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (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
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: 6/42, 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
there are 27 fields of study the course is directly associated with, display
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 2021, Autumn 2023, Autumn 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
autumn 2021
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: k (colloquium).
Taught in person.
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
there are 27 fields of study the course is directly associated with, display
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.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2020
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: k (colloquium).
Taught in person.
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
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
Timetable of Seminar Groups
C2115/CZ: No timetable has been entered into IS. T. Bouchal, I. Durník, P. Kulhánek
C2115/EN: No timetable has been entered into IS. T. Bouchal, I. Durník, P. Kulhánek
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: 3/42, 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
there are 27 fields of study the course is directly associated with, display
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 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 2021, Autumn 2022, Autumn 2023, Autumn 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2019
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Ivo Durník, Ph.D. (seminar tutor)
Petra Ludvová Hašková, DiS. (assistant)
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
there are 27 fields of study the course is directly associated with, display
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 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2018
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
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
there are 27 fields of study the course is directly associated with, display
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.
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 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
autumn 2017
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, 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: 1/42, 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
there are 27 fields of study the course is directly associated with, display
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.
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 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2016
Extent and Intensity
0/2. 2 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Jakub Štěpán, 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
there are 27 fields of study the course is directly associated with, display
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.
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 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2015
Extent and Intensity
0/2. 2 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Jakub Štěpán, 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
there are 27 fields of study the course is directly associated with, display
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.
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 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2014
Extent and Intensity
0/2. 2 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Jakub Štěpán, 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
there are 27 fields of study the course is directly associated with, display
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.
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 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2013
Extent and Intensity
0/2. 2 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Jakub Štěpán, 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
there are 27 fields of study the course is directly associated with, display
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.
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 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2012
Extent and Intensity
0/2. 2 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Jakub Štěpán, 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
there are 27 fields of study the course is directly associated with, display
Course objectives
The course is mainly intend for the student working on projects in computational chemistry, biochemistry and biophysics. Students will practically train the usage of supercomputing center environment and the main impact will be given to the effective job management.
Syllabus
  • Introduction of UNIX. Cluster WOLF / hardware, software, environment. MetaCentrum registration

  • MetaCentrum environment. Job management:(torque, Pbspro) – Infinity.

  • software benchmark, practical application - students projects

  • Frequently asked questions

Literature
  • Dokumentace MetaCentra, software Infinity
Teaching methods
the courses in computer room
Assessment methods
final test
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 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2011
Extent and Intensity
0/2. 2 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Zora Střelcová, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
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
there are 30 fields of study the course is directly associated with, display
Course objectives
The course is mainly intend for the student working on projects in computational chemistry, biochemistry and biophysics. Students will practically train the usage of supercomputing center environment and the main impact will be given to the effective job management.
Syllabus
  • Introduction of UNIX. Cluster WOLF / hardware, software, environment. MetaCentrum registration

  • MetaCentrum environment. Job management:(torque, Pbspro) – Infinity.

  • software benchmark, practical application - students projects

  • Frequently asked questions

Literature
  • Dokumentace MetaCentra, software Infinity
Teaching methods
the courses in computer room
Assessment methods
final test
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 - 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, Autumn 2024, Spring 2025.

C2115 Practical Introduction to Supercomputing

Faculty of Science
Autumn 2011 - acreditation

The information about the term Autumn 2011 - acreditation is not made public

Extent and Intensity
0/2. 2 credit(s). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Zora Střelcová, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
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
there are 29 fields of study the course is directly associated with, display
Course objectives (in Czech)
Předmět je primárně určen pro studenty věnující se výpočtům v oblasti biochemie, chemie i biofyziky (mateřský obor Chemoinformatika a bioinformatika). Cílem předmětu je zvýšení schopnosti studentů efektivně využívat dostupných výpočetních zdrojů a má za úkol rozvíjet základní znalosti ze skriptování ve smyslu analýzy získaných dat. Zároveň je ve výuce kladen důraz na praktickou aplikaci dostupného software, ať již komerčního, nebo vyvíjeného na Národním centru pro výzkum biomolekul.
Syllabus (in Czech)
  • Stručný úvod do UNIXu. Seznámení se s prostředím výpočetního clusteru (struktura, stavba, software) – cluster WOLF, registrace uživatelů do MetaCentra

  • Seznámení s prostředím MetaCentra, systém modulů, úvod do rozhraní na správu výpočetních úloh (torque, Pbspro) – Infinity.

  • Metodika testování použitelnosti software pro paralelní spouštění, efektivní správa výpočetních úloh; procvičování praktických úkolů v rozhraní Infinity na specifických výpočtech studentů

  • Analýza získaných dat, využití znalostí ze skriptování pro zjednodušení správy výpočetních úloh a násobné spouštění výpočtů

  • Diskuse praktických problémů

Teaching methods (in Czech)
bloková výuka v počítačové učebně
Assessment methods (in Czech)
závěrečný test
Language of instruction
Czech
Follow-Up Courses
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught: in blocks.
The course is also listed under the following terms Autumn 2011, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024, Spring 2025.