# MobaXterm

MobaXterm (opens new window) is an application that simplifies SSH connections to your lab from your local Windows machine.


(1) A Windows operating system on your local computer.

(2) A working connection to your lab over SSH as described in the Configure SSH guide section of the How to connect to your lab guide.

(3) The IP address to your lab. This was included in your SSH configuration file that you got on email during your initial onboarding.

(4) The MobaXterm configuration file that your that you got on email during your initial onboarding.

Missing the files? Worry not. You can order a new SSH configuration file and a new MobaXterm configuration file in our do science service desk.

# 1. How to install


Lab users from NTNU can install MobaXterm using the software center.

1.1. Download the Home edition (installer edition) from mobaxterm.mobatek.net (opens new window).

1.2. Unzip the file and install the software.

# 2. Generating SSH Key

This section generates SSH keys that allow you connect to your lab without typing passwords. Jump to section 2.3 if you know you already have a SSH that you want to use.

# 2.1 Open Local terminal

Clicking on Local terminal button opens MobaXterm command line:

Main View - Local terminal

# 2.2 Generate SSH key in local terminal

When you click "Start local terminal", you should see a window similar to this:

Local terminal

2.2.1 Check if you already have a ssh keys in place by running this command in the local terminal:

cat "${USERPROFILE}/.ssh/id_rsa.pub"


Run the above command as is. Keep ${USERPROFILE} (do -not- write your user name).

If you see random letters, jump to section 2.3

If the above command prints several rows of random letters on the screen, you already have a ssh key that can be used. Great! Jump to section 2.3.

If you see no output or an error message (No such file or directory), continue here:

2.2.2 Assure your .ssh directory exists by running:

mkdir -p "${USERPROFILE}/.ssh"

2.2.3 Create your new SSH key:

ssh-keygen -b 4096 -t rsa -f "${USERPROFILE}/.ssh/id_rsa" -q -N ""

# 2.3 Upload your SSH key

2.3.1 Upload your SSH key to your lab machine.

# -- Principal example
ssh-copy-id -i "${USERPROFILE}/.ssh/id_rsa.pub" <username>@<entry-IP>

Note. You need to add your username and lab IP in the above command.

Replace <username> with your username, and replace <entry-IP> with your lab IP address that was included in your ssh-config.txt file. A (non-working) example of the would be: joedeomuser@

Note. Do -not- save your passphrase.

You will be asked to type in your SSH passphrase that you made during your initial lab onboarding.

If you get asked to save your password, refuse by clicking on No to make sure that MobaXterm will authenticate with your SSH keys instead of your passphrase.

# 3. Connect

3.1. Locate your MobaXterm configuration file on your local computer: <your-username>.mobaxterm.

3.2 Click on the file for MobaXterm to pick up your lab session.


With a little bit of luck, you should now be able to connect directly from your client computer to the home machine in your lab.

# Troubleshooting

# Mktemp error

More information
  • If you are getting this error when trying ssh-copy-id: mktemp-error

  • Run this command with TMPDIR variable:

    # -- Non-working example
    TMPDIR="${USERPROFILE}" ssh-copy-id -i "${USERPROFILE}/.ssh/id_rsa.pub" <username>@<entry-IP>

Note. You need to replace <username> with you username (without the brackets), and <entry-IP> with your entry IP from the SSH config file.

  • If permissions error still appears try this alternative approach
    cat "${USERPROFILE}/.ssh/id_rsa.pub" | ssh <username>@<entry-IP> "cat >> ~/.ssh/authorized_keys"

Note. You need to replace <username> with you username (without the brackets), and <entry-IP> with your entry IP from the SSH config file.

# Check SSH keys in session configuration

More information
  • Right click on the session that you want to edit and choose option Edit session. mobaxterm_edit-session
  • Assure SSH option under the Session settings is selected.
  • In Advanced SSH settings make sure that private key option is checked. Then select the path to SSH key file (id_rsa). Step 1
  • Under Network settings, click on Connect through SSH gateway (jump host). Step 2
  • Check Use SSH key option and select the path to SSH key file (id_rsa). Step 3
  • Confirm session settings by clicking OK.

# Agent refused operation

More information

If you see the error message saying: Agent refused operation you need to install Putty.


Once Putty is installed, make sure that MobaXterm is closed and started Pageant. Pageant is part of Putty installation.


Once Pageant is running, you can start MobaXterm.

# Configure custom SSH config

More information

This part might be needed if you plan to use SSH tunneling to other lab machines. It is not part of the recommended workflow.

To setup ssh config to be used in local terminal of MobaXterm use:

cat <<-EOF > /home/mobaxterm/.ssh/config

<Paste content of your ssh-config.txt here>


# Advanced

# Configure custom session

More information
  • Open MobaXterm
  • Select a new session and click on the SSH image on the Session settings.
  • In Basic SSH settings, add as Remote host and type your username into Specify username field. Under Advanced SSH settings uncheck X11-forwarding if not used. Select ssh (private) key file if you already have one. Step 1
  • Under Network settings, click on Connect through SSH gateway (jump host) Step 2
  • Add your labs IP-address to the Gateway SSH server and your user name to the User field (the 10.42.-address from the ssh-config). Select ssh (private) key file if you already have one. Click OK to confirm SSH jump host. Step 3
  • In Bookmark settings, Name your lab session. Click OK to confirm Session settings. Step 4

# Configure MobaAgent

More information
  1. Start MobaXterm and open Settings:


  1. Choose SSH tab and make sure that option Use internal SSH agent "Mobagent" is checked. Then click OK to save the settings.


  1. If you are asked to confirm restart of MobaXterm click Yes to confirm.


  1. (optional) if you have not setup ssh before, follow section 2 above (generating SSH key)

  2. Add SSH key into Mobagent

Check the list of Mobagent SSH keys and make sure that SSH key (id_rsa file) is included.


If MobaXterm included the new key automatically, you can continue to the next step. If your SSH agents list is empty, click on the plus sign (arrow marked "2.") and add your new id_rsa file (key) to the list. You will find the file on your local computer under this path: C:\Users\<yourlocalusername>\.ssh\id_rsa.

# Configure custom session for On-Demand and BLUE machines

More information
  1. Duplicate your current lab session


  1. Edit duplicated session (feel free to rename it as well)


  1. Set options as described below


  1. Add jump host for home machine.



  1. Save and enjoy !
Last Updated: 6/17/2024