C2110 UNIX and programming

Faculty of Science
Autumn 2019
Extent and Intensity
0/2/0. 2 credit(s) (plus extra credits for completion). 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
Timetable of Seminar Groups
C2110/1: Mon 12:00–13:50 C04/118, T. Bouchal, I. Durník, P. Kulhánek
C2110/2: Tue 16:00–17:50 C04/118, T. Bouchal, I. Durník, P. Kulhánek
C2110/3: Tue 18:00–19:50 C04/118, T. Bouchal, I. Durník, P. Kulhánek
Prerequisites
Basic work with PC (for example MS Windows XX, Word, Excel)
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 63 student(s).
Current registration and enrolment status: enrolled: 0/63, only registered: 0/63, only registered with preference (fields directly associated with the programme): 0/63
fields of study / plans the course is directly associated with
Course objectives
At the end of the course, students should be able to use basic commands of Unix and Linux operating systems, combine them into more complex structures using scripting, create scripts in the AWK and gnuplot programming languages. Students should be able to combine their scripting knowledge to analyze outputs of basic scientific and technical calculations. Acquired skills are a prerequisite for computational chemistry and molecular modeling, and for a follow-up study of compiled programming languages ​​(C/C ++).
Learning outcomes
Student will be able to: - know the basic commands of Unix and Linux;
- combine these commands into more complicated constructions using scripting;
- create scripts in programming languages AWK and gnuplot;
- perform an automated analysis of the results of scientific and technical calculations;
Syllabus
  • 1. Cluster WOLF (structure, usage rules, administrators)
  • 2. Login (local and remote login, display export, password change)
  • 3. Program equipment (system applications, scientific applications)
  • 4. Text editors (vi, graphical text editors)
  • 5. Command line (terminals, structure, history and automatic completition)
  • 6. File system (structure, absolute and relative paths, permissions, special files, disk volumes)
  • 7. Commands (manual pages, overview of commands)
  • 8. Processes (processes, standard input and output, redirections, pipes)
  • 9. Introduction into scripting (what is scripting, advantages and disadvantages, script execution)
  • 10. Scripting in Bash (variables, basic controlling constructions)
  • 11. Scripting in gnuplot (2D and 3D graph drawing, interactive versus non-interactive mode)
  • 12. Scripting in AWK (basic construction, simple text file processing)
  • 13. Application of scripting (analysis of free energy calculations, students projects)
Literature
  • HAHN, Harley and Peter NORTON. Průvodce UNIXEM od Petera Nortona : Jak komunikovat s UNIXEM, jak UNIX ukládá a zobrazuje informace, používání unixového systému souborů, práce s editorem vi : Peter Norton's Guide to UNIX (Orig.). 1.vyd. Brno: UNIS, 1993, XXIV, 562. info
  • BRANDEJS, Michal. UNIX - Linux : praktický průvodce. 1. vyd. Praha: Grada, 1996, 340 s. ISBN 8071691704. info
  • PETRLÍK, Lukáš. Jemný úvod do systému UNIX. 1. vyd. České Budějovice: Kopp, 1995, 189 s. ISBN 80-85828-28-6. info
Teaching methods
lectures, exercising practical examples, class discussion
Assessment methods
Participation in seminars is required (two excused absences are allowed). Two tests (2 x 10 points) will take place during the semestr. The final test (50 points) will take place in the examination period. It will be followed by a task to write a script (30 points) according to written instructions. At least 80 points are required to pass the course.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Spring 2000, Autumn 2010 - only for the accreditation, Spring 2001, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, 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.
  • Enrolment Statistics (Autumn 2019, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2019/C2110