Logging on to pupil system

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Overview

In this exercise, we will prepare our computers to log on to our servers called "pupilX", where X is 1/2/3/4/5. These are small but reliable machines. Please read the instructions carefully.

Please be aware: there is no backup. All of your data will be deleted when the class concludes.

IMPORTANT: Do not store large files unnecessarily, and delete temporary files regularly. Disk space on the pupil servers is limited.

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Details

Student accounts

To be able to perform the exercises and project you will need an account to log in to the cloud computers. Open the google doc, find your student ID and determine which server you need to use. This will be your server for the rest of the course — do not log into any other pupil server as this will disrupt other students' work.

User ID/username

Your cloud username or user ID is the one entered in the username column (ex: s123456).

Server (host)/CPU/RAM

The names/CPU/memory of the hosts:

Server	Full host name	CPUs	RAM
pupil1	pupil1.healthtech.dtu.dk	40	252G
pupil2	pupil2.healthtech.dtu.dk	24	110G
pupil3	pupil3.healthtech.dtu.dk	24	94G
pupil4	pupil4.healthtech.dtu.dk	48	126G
pupil5	pupil5.healthtech.dtu.dk	48	126G

Password

The password is the same as your DTU password. If you lose or forget your DTU password, we cannot assist you — you must contact DTU IT.

2 factor authentication

You will be prompted for a 2-factor authentication code, using the same system as when you log in to your DTU mail. Check your authenticator app or SMS depending on your setup.

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Connection testing and first-time login tips

• When you type your password in the terminal, no characters will appear (not even dots). This is normal.

• After login, you can test your session with:

whoami
uname -a
pwd

• If login fails, check the following:

 - Are you using the correct server (pupil1–5)?  
 - Are you using the correct username?  
 - Are you connected to DTU WiFi or eduroam?  
 - Try verbose mode: ssh -v USER@HOST

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Disk space and resource usage

• Disk space is limited. Do not download large datasets unless instructed.

• Check your disk usage with:

df -h
du -sh .

• Delete intermediate files when no longer needed. • Be considerate: running large jobs on the wrong server affects your classmates.

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Windows computer

Terminal

You have 3 choices:

1. MobaXterm (recommended). Gives you both terminal and X-server out of the box.

Download here: https://mobaxterm.mobatek.net/download.html Create an ssh session and log into your assigned pupil server.

1. WSL2 + Ubuntu. Best choice if you plan more programming or future bioinformatics courses (such as 22113).
2. PuTTY + Xming. Download PuTTY from https://www.putty.org/ and Xming from https://sourceforge.net/projects/xming/

The simplest solution for most students is MobaXterm.

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Mac computer

Terminal

Open Terminal from /Applications/Utilities or via Spotlight.

Depending on your server assignment (see the Google sheet), write:

ssh -XC [USER_ID]@[FULLHOSTNAME]

Example:

ssh -XC s123456@pupil3.healthtech.dtu.dk

Enter your password when prompted.

X11 support

• Install XQuartz if you need graphical programs (IGV, etc.): https://www.xquartz.org/

• Open XQuartz once; you may close the blank window, but leave the application running.

• You may also install iTerm2 as a nicer terminal (optional).

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Ubuntu/Linux

Terminal

Open your terminal and connect using:

ssh -XC [USER_ID]@[FULLHOSTNAME]

Example:

ssh -XC s123456@pupil5.healthtech.dtu.dk

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File transfer

Mac/Linux (scp)

To copy a file to the server:

scp myfile.txt s123456@pupil3.healthtech.dtu.dk:~

Windows

• In MobaXterm, use the built-in SFTP browser on the left side.

• Drag-and-drop files directly.

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ssh without typing passwords (ssh-copy-id)

If you are tired of typing your password and the 2-factor authentication code, you can copy your ssh key to the server:

ssh-copy-id [USER_ID]@[FULLHOSTNAME]

This will look like a normal login and then exit. Afterwards, you can log in without entering DTU credentials.

Important: This applies only to this server. You are responsible for keeping your computer secure.

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Common mistakes

• Logging into the wrong pupil server.

• Using the wrong username.

• Forgetting that passwords do not show characters.

• Running large jobs without checking load.

• Not deleting temporary files.

• Not running XQuartz/Xming when using GUI tools.

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What NOT to do

• Do not install software without asking a TA or the instructor.

• Do not share your account with anyone.

• Do not store personal files.

• Do not run multi-hour jobs on login nodes (always ask before running heavy analyses).

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