Quickstart

This quickstart explains how to login to the server jupiter-imphys.tnw.tudelft.nl, copy a Matlab script file to the server, start Matlab, run the matlab script and copy the result file from the server.

We have two servers jupiter-imphys.tnw.tudelft.nl and saturn-imphys.tnw.tudelft.nl. In the examples these names will be used in full, but in the text the will be referred to by jupiter and saturn.

Login to server

Both servers (jupiter and saturn) can only be accessed via an in-between server called a proxy server or a bastion server. For students this proxy server is student-linux.tudelft.nl, for non-students this proxy server is linux-bastion-ex.tudelft.nl. In the example below we will use linux-bastion-ex.

WindowsmacOS

• start Windows PowerShell to start a local shell

• start Terminal to start a local shell

• type ssh <netid>@linux-bastion-ex.tudelft.nl in the shell and press Enter

  If this is the first time you connect with ssh to the proxy server linux-bastion-ex you will be asked to accept the host-key. Answer yes to accept the key and continue.

  Warning

  You will be asked for your password. Note that you will not see the keystrokes on the screen for privacy and security! If you made a mistake you can type Ctrl+U to empty your input and start over.

  Expected output

  After entering your netid password you will now see something like this:

                  ____  ____  ___
   ___ _ ____   _|___ \|___ \( _ )
  / __| '__\ \ / / __) | __) / _ \
  \__ \ |   \ V / / __/ / __/ (_) |
  |___/_|    \_/ |_____|_____\___/
  
  =====
  This server is not meant for storing large files.
  It's mainly for hopping to another server and storing your ssh keys.
  Your homedirectory is therefore limited in space.
  If you store large files on this server anyway we reserve the right to remove them.
  =====
  Last login: <removed> from <removed>
  [<netid>@srv228 ~]$
  

  Info

  • you are logged in to the proxy server linux-bastion-ex
  • <netid> will show your netid, <removed> is used for privacy
  • this last line [<netid>@srv228 ~]$ ending with the dollar sign and followed by a white square is the prompt of the shell. The white square is the cursor where your keyboard input will be written
  • after the prompt you can enter Linux commands or start a program (like Matlab). More on this later

• on the proxy server type ssh jupiter-imphys.tnw.tudelft.nl in the shell and press Enter

  If this is the first time you connect with ssh to the server jupiter you will be asked to accept the host-key. Answer yes to accept the key and continue.

  Expected output

  After entering your netid password you will now see something like this:

  Welcome to Ubuntu 24.04 LTS (GNU/Linux 6.8.0-31-generic x86_64)
  
  * Documentation:  https://help.ubuntu.com
  * Management:     https://landscape.canonical.com
  * Support:        https://ubuntu.com/pro
  
  System information as of Thu May 30 01:19:30 PM UTC 2024
  
  System load:                  0.0
  Usage of /home:               2.0% of 20.96TB
  Memory usage:                 1%
  Swap usage:                   0%
  Temperature:                  55.0 C
  Processes:                    1817
  Users logged in:              2
  IPv4 address for eno12399np0: 131.180.121.118
  
  * Strictly confined Kubernetes makes edge and IoT secure. Learn how MicroK8s
  just raised the bar for easy, resilient and secure K8s cluster deployment.
  
  https://ubuntu.com/engage/secure-kubernetes-at-the-edge
  
  Expanded Security Maintenance for Applications is not enabled.
  
  0 updates can be applied immediately.
  
  Enable ESM Apps to receive additional future security updates.
  See https://ubuntu.com/esm or run: sudo pro status
  
  
  Last login: <removed> from <removed>
  <netid>@jupiter-imphys:~$
  

  Info

  • you are now logged in to the server jupiter
  • note that there is interesting information on this login screen about the conditions of the server

• leave this shell open for later use

Copy the test.m script to the server

Tip

more information about file transport can be found here

Now you have logged in (maybe for the first time) also your homedirectory has been created on the server. Note that this homedirectory is available on both servers! You can now start copying a file from your computer to the server.

This copy also has to be done using the SSH protocol, similar to using ssh to log in. This time we will combine the log in to proxy server and to the jupiter in one command.

WindowsmacOS

• start Windows PowerShell to start a local shell
• navigate to the directory with your Matlab script, e.g.: cd d:\data\test.m

• start Terminal to start a local shell
• navigate to the directory with your Matlab script, e.g.: cd ~/Developer/test.m

• with test.m in your shell’s current directory type:

  scp -o ProxyJump=<netid>@linux-bastion-ex.tudelft.nl test.m <netid>@jupiter-imphys.tnw.tudelft.nl:.
  

  If this is the first time you connect with scp to the server jupiter you will be asked to accept the host-key. Answer yes to accept the key and continue. NOTE: on some shells you will not see the typed characters on the screen!

  Info

  • you have now copied test.m from your computer to your homedirectory on the server
  • read more information on the command here

• check if the file is copied by entering the shell you’ve opened before and typing ls ~. You will see something like this:

  <netid>@jupiter-imphys:~$ ls ~
  test.m
  <netid>@jupiter-imphys:~$
  

Start Matlab

For some major programs multiple versions are installed. To use the right version use the module system. This system will set the right environment for the version you want to use. We will now use the default version of Matlab (R2021b):

• again enter your shell you’ve opened before and type:

  module load matlab
  

  Info

  • you have now setup your shell for Matlab version R2021b
  • if you do not specify a version after the module name like module load matlab/R2023b the default version will be set. In this case this is R2021b
  • to see which modules are available type module avail
  • you need to do this only once for the shell you’ve started with ssh. If the shell is closed and opened again you will need to load the module again.

• start Matlab with matlab -nodisplay

  Explanation command

  • because the default matlab module has been chosen, this matlab will be found here: /opt/apps/MATLAB/R2021b/bin/matlab
  • the -nodisplay option tells Matlab not to use the graphic system
  Expected output

  You will now see something like this:

  rligteringen@jupiter-imphys:~$ matlab -nodisplay
  
                          < M A T L A B (R) >
              Copyright 1984-2021 The MathWorks, Inc.
          R2021b Update 7 (9.11.0.2358333) 64-bit (glnxa64)
                          August 16, 2023
  
  
  To get started, type doc.
  For product information, visit www.mathworks.com.
  
  >>
  

  Info

  • note the version in the header information
  • the prompt of Matlab is >> followed by the cursor a white square
  • after the prompt you can type Matlab commands

Run the test.m script in Matlab

• at the matlab prompt type:

  run('test.m')
  exit
  

  Info

  • run runs the script given as a parameter, in this case the file test.m
  • exit closes matlab

Copy the file test.mat from the server

This is very similar to copying the files to the server from your computer.

• start a new shell on your computer not on the server
• in this shell go to the directory where you want to store the test.mat from the server

• enter this command:

  scp -o ProxyJump=<netid>@linux-bastion-ex.tudelft.nl <netid>@jupiter-imphys.tnw.tudelft.nl:test.mat . 
  

  Info

  • the file test.mat is now copied from the server to your computer
  • note that the proxy server is used

You can now inspect the results from running your Matlab script on the server with your computer.