C2110 UNIX and programming Lesson 1 / Module 1 -1C2110
UNIX and programming
Petr Kulhánek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science
Masaryk University, Kamenice 5, CZ-62500 Brno
Lesson 1 / Module 1
PS/2020 Distance form of teaching: Rev2
C2110 UNIX and programming Lesson 1 / Module 1 -2Teaching
Organization
➢ Schedule
➢ Form of teaching
➢ Knowledge assessment
C2110 UNIX and programming Lesson 1 / Module 1 -3-
Schedule
Teaching: October 5, 2020 – January 15, 2021
Examination period: January 18, 2021 - February 26, 2021
Total number of lectured hours: 13 x 2 hours = 26 hours
Final exam: colloquium (2 + 1 credits)
Total hourly load of the subject:
1 ECTS credit -> 26 hours of study load
3 credits -> 3x 26 hours = 78 hours of study load
Self-study, homework,
preparation for the exam:
52 hours
Full-time form of teaching Distance form of teaching
Full-time teaching:
26 hours
All in one ☺
78 hours of study load
C2110 UNIX and programming Lesson 1 / Module 1 -4Form
of teaching
Full-time form of teaching
▪ Course in form of a seminar, attendance is
compulsory
▪ Two absences excused in advance allowed
▪ Teaching takes place in the computer room
1.18 /C04/UKB on computers with Ubuntu
OS
▪ Lectures with exercises solved during the
lesson with the possibility of consultation
▪ Two continuous tests (part of the lesson)
▪ Unscored algorithms
▪ Exam (full-time, in classroom 1.18 / C04 /
UKB)
Distance form of teaching
▪ Teaching takes place remotely with the
possibility of online consultation at the
time for which the lessons are planned in
the schedule
▪ Absences are only excused for in term tests
for serious health reasons
▪ Teaching takes place on personal
computers of students with MS Windows
10, MS Windows <10*, OS Linux*, macOS*
▪ The lessons are divided into modules
ending with exercises
▪ The modules are accommodated by a prerecorded
verbal commentary with practical
examples.
▪ Three continuous tests (online)
▪ Scored algorithm of your choice
▪ Exam (full-time form, in classroom
1.18/C04/UKB)
* Must be reported to the teacher
C2110 UNIX and programming Lesson 1 / Module 1 -5Form
of Teaching
Self-study, homework, preparation for the exam
Full-time teaching / On-line teaching
Self-study of extra knowledge that will not be required to pass the
exam
C2110 UNIX and programming Lesson 1 / Module 1 -6Submitting
Assignments
Teamwork is essential. It allows you to
blame someone else.
L.M.E.T
lesson number
exercise number
task number
Task numbering:
module number
For some tasks, I recommend noting the answers for yourself by writing either into a
notebook, printed presentations, or in an electronic document. Each task is uniquely
numbered in the following format:
Complete tasks independently, you can consult the problems and work in teams in case of
ambiguity. I strongly discourage teamwork in a style where one solves the tasks, and the
others only follow.
C2110 UNIX and programming Lesson 1 / Module 1 -7Online
Consultation
Self-study
on-line
consultations
Lesson 1 Lesson 13
Test I Test II Test III
on-line consultations:
• MS Teams * (functional microphone and desktop sharing, camera not required)
• Dates (without registration for seminar groups):
• Monday 12:00-13:50
• Tuesday 16:00-17:50
• Tuesday 18:00-19:50
* Available under MS Windows, Linux, macOS
Assigned Algorithm
C2110 UNIX and programming Lesson 1 / Module 1 -8Knowledge
Assessment
Three tests: (20 minutes) 3x 20 points
Algorithm according to the assignment: 10 points
Final assessment:
- final test (1 hour) 50 points
- assigned script (1 hour) 30 points
=======================================================
Total: 150 points
Passed: >= 110 points
Distance form of teaching
The course is DEMANDING (do not underestimate its easy start)
Course success > 90%
Follow-Up Course C2115 Practical Introduction to Supercomputing
• block teaching January / February 2021
• possibility of enrollment during the semester
• I grant exception to the students who have C2110 registered
at the same time
C2110 UNIX and programming Lesson 1 / Module 1 -9Knowledge
Assessment
Tests:
• 20 questions, 20 minutes
• It will be possible to take the test online anytime within two days (Monday,
Tuesday) from any computer
• one try (one possibility of composition)
• we expect you to take the test by yourself
Algorithm:
• algorithm of the given problem (flow chart)
• submitted in pdf format to the Homework Vaults in IS: "Algorithm"
Exam:
• final test (50 questions, 60 minutes)
• solving one of the three assigned tasks (60 minutes, writing a script)
Tests:
• multiple-choices (none to all answers may be correct)
• the answers are evaluated
• correctly chosen answer +1 point
• incorrectly chosen answer -0.25 points
C2110 UNIX and programming Lesson 1 / Module 1 -10Knowledge
Assessment
During the tests and solving the final task:
You can use all the study materials, any books and the Internet. When writing a test and
creating a script, you can use a computer (even your own), you can use scripts from
exercises or homeworks.
However, you must not collaborate with other people (Facebook, mobile, etc.).
Example of the final task (script):
• the student solves one task, which he chooses from the three available assignments
Assignment A: The file prod006.out contains the result of a molecular dynamics simulation in an explicit solvent at a
temperature of 300 K and a pressure of 100 kPa. Extract the current temperature (TEMP (K)) versus time (TIME (PS))
from the file and display it as a graph (5 points). Calculate the average value of temperature <T> and its fluctuation sN
from the data given in the file prod006.out (10 points). Display the average value and temperature fluctuation
together with the time course of the temperature (5 points) in one graph. The name of the analyzed file is presented
as the first argument of the script, which performs the analysis and displays the graph (5 points). Treatment of the
wrong input (5 points): the specified file must exist.
𝑇 = ෍
𝑖=1
𝑁
𝑇𝑖
𝑠 𝑁 =
1
𝑁
෍
𝑖=1
𝑁
𝑇𝑖 − 𝑇 2
where N is the number of analyzed values ​​of temperatures Ti.
C2110 UNIX and programming Lesson 1 / Module 1 -11Lecture
Overview
1. Getting started, remote access (ssh, putty)
2. Remote access (scp, VNC), Linux as a desktop system
3. File system
4. Processes
5. Programs vs scripts, algorithms, bash
6. Bash scripting
7. bash - control structures (conditions, cycles)
8. bash - completion (almost)
9. gnuplot, bash
10. awk
11. Practice: bash + gnuplot + awk
12. awk - continued
13. Compilation of programs from source code
Test I
Test II
Test III
Algorithm
according to
assignment
assignment
submission