Linux and MobaXterm for bachelor students

Linux and MobaXterm for bachelor students

This page is the first stop if you have only ever used Windows. By the end you will be able to install MobaXterm, type basic Linux commands on your own computer, and open a remote session on the lab cluster, Agustina.

You do not need to memorize the commands. Type them once, read what comes back, and keep this page open.

Why the lab uses Linux

The lab computers and Agustina run Linux. Linux is an operating system, like Windows, with a different way of talking to the machine.

Think of the computer as a building. Folders are rooms. Files are the things inside a room. On Windows you walk around by clicking. In Linux you mostly send short text messages. The window where you type those messages is the terminal. The program inside it that reads each line is the shell.

A command is one of those messages. You type it after the prompt (the text that already sits on the line, often ending in $) and press Enter. Do not type the $ itself.

Install MobaXterm

MobaXterm is a free Windows program that gives you a Linux-style terminal and a way to connect to other computers.

1. Open the MobaXterm download page.
2. Choose the Home edition. It is free.
3. Choose the Installer edition, not the portable zip.
4. Run the downloaded installer and accept the default options.
5. Open MobaXterm from the Start menu.

The first screen has a big button that starts a local terminal. “Local” means this terminal is running on your laptop, not on Agustina. Click Start local terminal.

You should see a line that ends with $ and a blinking cursor. That cursor is where your typing goes.

Three parts of the window matter:

• The black (or dark) area is the terminal. You type commands there.
• Session, at the top, is how you phone another computer later.
• The left panel is a file browser. After you connect to Agustina it shows the remote files, and you can drag a file between your laptop and the cluster. You do not need it for the practice below.

Your Windows Desktop is not the first place this terminal opens. MobaXterm keeps its own home folder, often /home/mobaxterm. Stay there while you practice, so you do not change real Windows files.

Your first commands

Type each block one line at a time. Press Enter after each line. Wait until the $ prompt comes back before you type the next command.

pwd

pwd means “print working directory”. A directory is a folder. This command tells you which folder you are standing in. You should see a path such as /home/mobaxterm.

A path is the address of a file or folder. Slashes separate the rooms. /home/mobaxterm means: start at the root of the disk (/), go into home, then into mobaxterm.

ls

ls lists the names in the current folder. An empty answer is fine. It means the folder has nothing to show yet.

mkdir linux-practice
cd linux-practice
pwd

mkdir makes a new folder. cd changes into it (“change directory”). After pwd, the path should end in linux-practice.

Now make a tiny text file. vi is the editor you will use in the terminal. It starts in Normal mode, where the keys are commands, not letters on the page.

vi hello.txt

• Press i to enter Insert mode. The bottom of the window should say -- INSERT --.
• Type one sentence, for example Hello from the terminal.
• Press Esc to go back to Normal mode.
• Type :wq and press Enter. That writes the file and quits.

If you get stuck, press Esc, then type :q! and press Enter. That leaves without saving. The rest of the editor, including vim, is in Vi and Vim Basics.

You are back at the $ prompt. Check that the sentence was saved:

cat hello.txt

cat prints a whole file. You should see the sentence you typed.

cp hello.txt hello-copy.txt
mv hello-copy.txt renamed.txt
ls

cp copies a file. mv moves or renames a file. ls should now show hello.txt and renamed.txt.

Delete only the copy you just made:

rm renamed.txt
ls

renamed.txt is gone. hello.txt should still be there. Do not run rm on a name you did not create yourself.

Step back out of the practice folder. Two dots means “the folder above this one”:

cd ..
pwd

You should be back in the folder you started from, and linux-practice is still there for next time.

Three keys that save time

• Tab finishes a name. Type cd linux-prac and press Tab. The shell should complete linux-practice. If nothing happens, the name matches more than one file, or the spelling is off.
• Up arrow brings back the previous command. Press Enter to run it again.
• Ctrl+C cancels the line you are typing, or stops a command that is still running. Use this when you are stuck. It does not turn the computer off.

Paths, in one picture

Try this:

cd ~
pwd
ls -a

cd ~ jumps home from anywhere. ls -a lists hidden names too. A hidden name starts with a dot. You will probably see .bashrc.

.bashrc is a settings file the shell reads each time it starts. Later guides ask you to add lines to it. Do not edit it today. Seeing the name is enough.

Windows files, if you need them, live under a path like /drives/c/Users/YourName/Desktop. You can cd there. For this practice, stay in the MobaXterm home.

Phone another computer with SSH

SSH is a phone call to another computer. You type commands in the same kind of window, but they run on the far machine. The far machine for this lab is Agustina, a shared supercomputer. A shared front door called the bridge sits in front of it.

You need the username and password the lab gave you. If you do not have them yet, stop after the local practice and ask.

1. In MobaXterm, click Session, then SSH.
2. In Remote host, type bridge.bifi.unizar.es.
3. Tick Specify username and type your username.
4. Click OK.
5. If it asks whether you trust the host, type yes and press Enter. This happens the first time only.
6. Type your password and press Enter.

The prompt should change. You are on the bridge, not on your laptop. MobaXterm remembers this session in the left sidebar, so next time you double-click it instead of filling the form again.

From the bridge, call Agustina:

ssh username@agustina.bifi.unizar.es

Replace username with your real username. Type your password again when asked.

Check where you landed:

pwd
ls

pwd should show a path under /home/ with your username. ls shows your files on the cluster, which may be empty.

The left panel should now list those remote files. Dragging a file between that panel and your computer is the easy way to move one file. You do not need another program for that.

Leave the same way you would hang up a phone. exit drops one connection:

exit

The first exit leaves Agustina and returns you to the bridge. A second exit leaves the bridge and returns you to the local terminal.

There is a shorter version of this double call. You do not need it today. The Using Agustina page asks you to save these two nicknames, called aliases, inside .bashrc on your own computer:

alias tob='ssh -X username@bridge.bifi.unizar.es'
alias toa='ssh -J username@bridge.bifi.unizar.es username@agustina.bifi.unizar.es'

After that, toa opens Agustina in one step. Replace username before you paste them. That page also explains the cluster itself: storage, conda, and job scripts. This page stops at the door.

If the session waits a long time and then fails, you are probably off the network the cluster expects. Try again from the university network, then ask in the lab. Do not keep guessing passwords.

What to read next

Stay in this order. Each page assumes you can already do what the previous one taught.

1. Linux Sysadmin Basics repeats these commands and adds .bashrc, PATH, and small scripts.
2. Using Agustina is the cluster: the tob and toa aliases, conda, and how to submit a job.
3. Git tips can be done in this same MobaXterm local terminal.
4. Vi and Vim Basics is the rest of the editor you just used: moving around, changing text, and comparing files.
5. Coding tips points at the Software Carpentry Unix shell lessons, which are the right next practice once this page feels easy.
6. Local Conda and VS Code Setup is for Python on your laptop, after the terminal feels ordinary.

If a command prints an error, copy the error, say which page you were on, and ask. That is faster than trying random flags.