Introduction to Linux in HPC/Shell scripting

HPC.NRW
Other HPC Courses
1.	Gprof Tutorial
2.	OpenMP in Small Bites
Introduction to Linux in HPC
1.	Background and History
2.	The Command Line
3.	Directory structure
4.	Files
5.	Text display and search
6.	Users and permissions
7.	Processes
8.	The vim text editor
9.	Shell scripting
10.	Environment variables
11.	System configuration
12.	SSH Connections
13.	SSH: Graphics and File Transfer
14.	Various tips

Video

( Slides as pdf)

Quiz

Which bash command below assigns "value" to variable var?

	var="value"
	var = "value"
	var=="value"

Exercises in Terminal

1. a. Write a script that
   b. Prints an environment variable
   c. Saves the output of the date command to a variable
   d. Sleeps briefly
   e. Prints the new and old date and time

Answer:

     One possible way to write the script is

      #!/bin/bash

      echo "I am $USER, my home directory is $HOME"

      olddate=$(date)
      sleep 10s
      echo "old date: ${olddate}"
      echo "new date: $(date)"

     Explanation:
        #!/bin/bash: the shebang line for bash script
        echo "I am $USER, my home directory is $HOME": the variables $USER and $HOME are your username and home directory, respectively. This line prints a sentence embedded with your username and home directory.
        olddate=$(date) assigns the output of the date command to the variable olddate as a string.
        sleep 10s puts the terminal into idle for 10 seconds.
        echo "old date: ${olddate}" prints the previously saved date in the olddate variable. The form of ${olddate} is for using (or referencing) this variable.
        echo "new date: $(date)" prints the current date, in which the output of the command date will take the place of $(date).

2. Find a way to execute a script without setting execute permissions.

Answer: bash script.sh Explanation: bash will be used as an interpreter to execute script.sh and the commands contained in script.sh will be executed sequentially.

3. Find out how to do other programming things in bash (e.g. functions, classes). How convenient do they look?

Answer:

    To define a function hello in bash, which prints a message "hello, world" on the terminal. bash script.sh 

       function hello {
           echo "hello, world"
       }

    To use this function in bash (after defining it):

       hello

4. Look at different ways you can define if conditions.

Answer:

     Both single square brackets [] and double square brackets [[]] can be used to define if conditions. But the effects are different. For example, we define a variable str by using a string with spaces:

        str="a  b"

     The if condition with double square brackets works fine.

       if [[ $str = "a  b" ]]; then
          echo "it works"
       fi

     However, the if condition with single square brackets will emit a syntax error.

       if [ $str = "a  b" ]; then
          echo "it works"
       fi

     To have the correct syntax for if condition with single square brackets, the variable str must be double quoted inside the if condition.

       if [ "$str" = "a  b" ]; then
          echo "it works"
       fi

5. Find out what different types of quotes (single ' vs. double ") do?

Answer:

     single quote ' gives literal string, the variable will not be interpreted, e.g.

       var=abc
       echo '$var'

     This script prints the literal string $var (instead of its value abc) to terminal.
     double quote " allows the variable to be interpreted, e.g.

       var=abc
       echo "$var"

     This script prints the value of var, which is abc (instead of the literal string $var) to terminal. 

6. create an shell variable MYIDENTITY and export it as below: 
   $ export MYIDENTITY=whoami
   How will you list the shell variable MYIDENTITY?
   Execute the shell variable MYIDENTITY, what is the output? 

Answer:

     you can list the variable by using the echo command as follows

        $ echo $MYIDENTITY
        whoami

     The arguments passed to echo are printed to the standard output.

        $ $MYIDENTITY     
        username

     The shell variable upon execution runs the command whoami, which is assigned to it. whoami command prints the user name of the effective user ID

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