Logging on to pupil system: Difference between revisions

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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.
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.  
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.


<HR>
<HR>


<H2>Details</H2>
<H2>Details</H2>
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<p>To be able to perform the exercises and project you will need an account to log in to the cloud computers. Open the
<p>To be able to perform the exercises and project you will need an account to log in to the cloud computers. Open the
[https://docs.google.com/spreadsheets/d/1wdx1LjRXNiMDmUCy7GfYD5j-iDEX1q0UFSTEwxm-egA/edit?usp=sharinggoogle doc], find the student id and determine which server you need to use. This will be your server that you must use for the rest of the course.</p>
[https://docs.google.com/spreadsheets/d/1wdx1LjRXNiMDmUCy7GfYD5j-iDEX1q0UFSTEwxm-egA/edit?usp=sharing 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.</p>


<H4>User ID/username</H4>
<H4>User ID/username</H4>


Your cloud <b>username</b> or '''user ID''' is one entered in the '''username''' column (ex: s123456).
Your cloud <b>username</b> or '''user ID''' is the one entered in the '''username''' column (ex: s123456).


<H4>Server (host)/CPU/RAM</H4>
<H4>Server (host)/CPU/RAM</H4>
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{| class="wikitable"
{| class="wikitable"
| '''Server'''
| '''Server''' | '''Full host name''' | '''CPUs''' | '''RAM'''
| '''Full host name'''  
| '''CPUs'''  
| '''RAM'''
|-
|-
| pupil1
| pupil1 | pupil1.healthtech.dtu.dk | 40 | 252G
| pupil1.healthtech.dtu.dk
| 40
| 252G
|-
|-
| pupil2
| pupil2 | pupil2.healthtech.dtu.dk | 24 | 110G
| pupil2.healthtech.dtu.dk
| 24
| 110G
|-
|-
| pupil3
| pupil3 | pupil3.healthtech.dtu.dk | 24 | 94G
| pupil3.healthtech.dtu.dk
| 24
| 94G
|-
|-
| pupil4
| pupil4 | pupil4.healthtech.dtu.dk | 48 | 126G
| pupil4.healthtech.dtu.dk
| 48
| 126G
|-
|-
| pupil5
| pupil5 | pupil5.healthtech.dtu.dk | 48 | 126G
| pupil5.healthtech.dtu.dk
| 48
| 126G
|}
|}


<H4>Password</H4>


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


<H4>Password</H4>
<H4>2 factor authentication</H4>
 
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.
 
<HR>
 
<H3>Connection testing and first-time login tips</H3>
 
• 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:
<pre>
whoami
uname -a
pwd
</pre>
 
• 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: <code>ssh -v USER@HOST</code>
 
<HR>
 
<H3>Disk space and resource usage</H3>
 
• Disk space is limited. Do not download large datasets unless instructed. 
• Check your disk usage with:
<pre>
df -h
du -sh .
</pre>


The password is the '''same''' as the DTU one. <b> Remember: If you lose your DTU password we can not help you! Check with DTU.</b>
• Delete intermediate files when no longer needed.
• Be considerate: running large jobs on the wrong server affects your classmates.
<H4>2 factor authentication</H4>


You will be prompted for a 2-factor authentication code, using the same system as for logging in to your DTU mail. Look at your phone.
<HR>
<!--
This should be set up already - according to DTU IT (AIT). If you continue to fail at logging in, it might not be set up for you on Azure.<br>
To do the setup yourself, go to: [https://account.activedirectory.windowsazure.com/proofup.aspx?proofup=1 https://account.activedirectory.windowsazure.com/proofup.aspx?proofup=1]. Use your DTU username/password to enroll.
-->


<H3>Windows computer</H3>
<H3>Windows computer</H3>
Line 76: Line 87:
<H4>Terminal</H4>
<H4>Terminal</H4>


You have 3 choices here:
You have 3 choices:
# MobaXterm. Described [https://teaching.healthtech.dtu.dk/22113/index.php/Course_preparation#MobaXterm.2C_not_really_recommended here]. Install MobaXterm. Download [https://mobaxterm.mobatek.net/download.html here]<br>Once installed you must create an '''ssh session''' in Mobaxterm and log on to your cloud server (Look at the Google docs depending on user ID and use the IP above). Easy choice if you do not plan for more programming in the future.
 
# WSL2 + Ubuntu install. Described [https://teaching.healthtech.dtu.dk/22113/index.php/Course_preparation#WSL.2FWSL2.2C_Windows_Subsystem_for_Linux here]. Best choice if taking a course like 22113 later.
# '''MobaXterm''' (recommended). Gives you both terminal and X-server out of the box.
# PuTTY + Xming. A small terminal can be downloaded [https://www.putty.org/ here] and an X-server to be downloaded [https://sourceforge.net/projects/xming/ here].
Download here: https://mobaxterm.mobatek.net/download.html
The cookie-cutter solution is MobaXterm, which gives you the terminal and X-server functionality right out of the box.
Create an '''ssh session''' and log into your assigned pupil server.
# '''WSL2 + Ubuntu'''. Best choice if you plan more programming or future bioinformatics courses (such as 22113).
# '''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'''.


<HR>
<HR>


<H3>Mac computer</H3>
<H3>Mac computer</H3>
Line 89: Line 103:
<H4>Terminal</H4>
<H4>Terminal</H4>


Open your terminal. It is located in: /Applications/Utilities. Or search for "Terminal"
Open Terminal from /Applications/Utilities or via Spotlight.
 
Depending on your server assignment (see the Google sheet), write:
 
<pre>
ssh -XC [USER_ID]@[FULLHOSTNAME]
</pre>


Depending on the server you will be using (see the google sheet), write:
Example:


ssh -XC [USER_ID]@[FULLHOSTNAME]
<pre>
replace the [USER_ID] with the username you have been assigned to and [ID ADDRESS] is the IP of your server (see above).
ssh -XC s123456@pupil3.healthtech.dtu.dk
</pre>


Enter the password..
Enter your password when prompted.
<p>Open the "XQuartz" and "Terminal" in the "Applications/Utilities" folder. You can close the window that the XQuartz program opens, but leave the program running in the background. If you dont have XQuartz installed you can install
 
it from [https://dl.bintray.com/xquartz/downloads/XQuartz-2.7.11.dmg here].
<H4>X11 support</H4>
In the terminal write the command below and enter your password when asked for it. Depending on what you have installed you may have to install "Developer Tools" from Apple. You can also install the program "iTerm2" which is a very neat terminal.<br>
 
Log on to your cloud server using ssh and your cloud username (studXXX) and password (see above).
• 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).


<HR>
<HR>


<H3>Ubuntu/Linux</H3>
<H3>Ubuntu/Linux</H3>
Line 109: Line 134:
<H4>Terminal</H4>
<H4>Terminal</H4>


Open your terminal and ssh using:
Open your terminal and connect using:
  ssh -XC [USER_ID]@[FULLHOSTNAME]
 
<pre>
ssh -XC [USER_ID]@[FULLHOSTNAME]
</pre>
 
Example:
<pre>
ssh -XC s123456@pupil5.healthtech.dtu.dk
</pre>
 
<HR>
 
<H3>File transfer</H3>
 
<H4>Mac/Linux (scp)</H4>
To copy a file to the server:
<pre>
scp myfile.txt s123456@pupil3.healthtech.dtu.dk:~
</pre>
 
<H4>Windows</H4>
• In MobaXterm, use the built-in SFTP browser on the left side.  
• Drag-and-drop files directly.
 
<HR>
 
<H3>ssh without typing passwords (ssh-copy-id)</H3>
 
If you are tired of typing your password and the 2-factor authentication code, you can copy your ssh key to the server:
 
<pre>
ssh-copy-id [USER_ID]@[FULLHOSTNAME]
</pre>
 
This will look like a normal login and then exit. 
Afterwards, you can log in without entering DTU credentials.
 
<b>Important:</b> This applies only to this server. You are responsible for keeping your computer secure.
 
<HR>
 
<H3>Common mistakes</H3>
 
• 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.
 
<HR>


<H3>What NOT to do</H3>


<H3>ssh without any keys</H3>
• 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).


Are you tired of typing your password and the 2-factor authentication code? If so you can automate the process using this on Ubuntu/Linux/MacOS:
<HR>
ssh-copy-id [USERID]@[FULLHOSTNAME]
It will seem like a normal login, which logs you out again immediately. However, in the future, you do no need to supply DTU credentials.

Revision as of 15:28, 19 November 2025

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.

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:

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

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

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.

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.

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).

Ubuntu/Linux

Terminal

Open your terminal and connect using: 

ssh -XC [USER_ID]@[FULLHOSTNAME]

Example: 

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

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.

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.

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.

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).

Retrieved from "https://teaching.healthtech.dtu.dk/22126/index.php?title=Logging_on_to_pupil_system&oldid=205"