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Day 1: UNIX and CSC

Connecting to Puhti

Windows users

  • Launch PuTTY
  • In “Host Name (or IP address)”, type puhti.csc.fi and click “Open”
  • In the following dialogue window, choose “Yes”
  • Type your CSC username and hit "Enter"
  • Type your password and hit "Enter"
  • To logout just type exit and hit "Enter"

MacOS users

  • Launch Terminal (e.g. open the Launchpad and type terminal)
  • Type ssh user@puhti.csc.fi and hit "Enter" (change "user" for your own CSC username)
  • In the following dialogue, type yes and hit "Enter"
  • Type your password and hit "Enter"
  • To logout first type exit, hit "Enter", and close the Terminal window

Playing around with basic UNIX commands

Important notes

Things inside a box like this...

mkdir MMB114
cd MMB114

...represent commands you need to type in the shell. Each line is a command. Commands have to be typed in a single line, one at a time. After each command, hit “Enter” to execute it.

Things starting with a pound sign (or hashtag)...

# This is a comment and is ignored by the shell

...represent comments embedded in the code to give instructions to the user. Anything in a line starting with a "#" is ignored by the shell. You can type it if you want, but nothing will happen (provided you start with a "#").

We will be using different commands with different syntaxes. Different commands expect different types of arguments. Some times the order matters, some times it doesn't. If you are unsure, the best way to check how to run a command is by taking a look at its manual with the command man. For example, if you want to look at the manual for the command mkdir you can do:

man mkdir

# You can scroll down by hitting the space bar
# To quit, hit "q"

Creating and navigating directories

First let's see where we are:

pwd

Are there any files here? Let's list the contents of the folder:

ls

Let's now create a new folder called "MMB114". In addition to the command (mkdir), we are now passing a term (also known as an argument) which, in this case, is the name of the folder we want to create:

mkdir MMB114

Has anything changed? How to list the contents of the folder again?

HINT (CLICK TO EXPAND)

ls

And now let's enter the "MMB114" folder:

cd MMB114

Did it work? Where are we now?

HINT

pwd

Creating a new file

Let's create a new file called "myfile.txt" by launching the text editor nano:

nano myfile.txt

Now inside the nano screen:

  1. Write some text

  2. Exit with ctrl+x

  3. To save the file, type y and hit "Enter"

  4. Confirm the name of the file and hit "Enter"

List the contents of the folder. Can you see the file we have just created?

Copying, renaming, moving and deleting files

First let's create a new folder called "myfolder". Do you remember how to do this?

HINT

mkdir myfolder

And now let's make a copy of "myfile.txt". Here, the command cp expects two arguments, and the order of these arguments matter. The first is the name of the file we want to copy, and the second is the name of the new file:

cp myfile.txt newfile.txt

List the contents of the folder. Do you see the new file there?

Now let's say we want to copy a file and put it inside a folder. In this case, we give the name of the folder as the second argument to cp:

cp myfile.txt myfolder

List the contents of "myfolder". Is "myfile.txt" there?

ls myfolder

We can also copy the file to another folder and give it a different name, like this:

cp myfile.txt myfolder/copy_of_myfile.txt

List the contents of "myfolder" again. Do you see two files there?

Instead of copying, we can move files around with the command mv:

mv newfile.txt myfolder

Let's list the contents of the folders. Where did "newfile.txt" go?

We can also use the command mv to rename files:

mv myfile.txt myfile_renamed.txt

List the contents of the folder again. What happened to "myfile.txt"?

Now, let's say we want to move things from inside "myfolder" to the current directory. Can you see what the dot (.) is doing in the command below? Let's try:

mv myfolder/newfile.txt .

Let's list the contents of the folders. The file "newfile.txt" was inside "myfolder" before, where is it now?

The same operation can be done in a different fashion. In the commands below, can you see what the two dots (..) are doing? Let's try:

# First we go inside the folder
cd myfolder

# Then we move the file one level up
mv myfile.txt ..

# And then we go back one level
cd ..

Let's list the contents of the folders. The file "myfile.txt" was inside "myfolder" before, where is it now?

We have so many identical files in our folders. Let's clean things up and delete some files :

rm newfile.txt

Let's list the contents of the folder. What happened to "newfile.txt"?

When deleting files, pay attention in what you are doing: if you accidently remove the wrong file, it is gone forever!

And now let's delete "myfolder":

rm myfolder

It didn't work did it? An error message came up, what does it mean?

rm: cannot remove ‘myfolder’: Is a directory

To delete a folder we have to modify the command further by adding the recursive flag (-r). Flags are used to pass additional options to the commands:

rm -r myfolder

PS: the following command also works, but only if the folder is empty:

rmdir myfolder

Let's list the contents of the folder. What happened to "myfolder"?

Finished and want to learn more?

Try taking some online tutorials, e.g.: