Mobaxterm Configuration

Mobaxterm is a Windows application that provides an ssh client, scp client and X11 server all in one program.  It is a very convenient tool for accessing the JHPCE cluster and utilizing the many features of the cluster.  There is some configuration that needs to be done though in order to effectively use Mobaxterm in the JHPCE environment.  This FAQ will take you through the steps needed to configure Mobaxterm.  Before your proceed you should have your Google Authenticator app available.

– The first thing you will need to do is download the MobaXterm program from their web site

– Be sure to use the “Installer Edition” instead of the “Portable Edition”


– Once the program has been downloaded, install it as you would any other Windows program.

– Once the program is installed, start the MobaXterm program.  You should see a screen like this:


– From this screen, click on the “Sessions” icon mobxterm-sessions-icon in the upper left corner.

– On the “Session settings” screen, click on “SSH”


– Enter “” as the “Remote host”.  Click on the “Specify username” checkbox, and enter your JHPCE username in the next field.  Then click the “OK” button.

– When you click OK, you will initiate an SSH session to the JHPCE cluster.  You will be prompted for your Google Authenticator “Verification Code”, and then your password.

– Once you enter your password correctly, you will see a number of boxes pop up (usually 3) prompting for another Verification Code.  Click “Cancel on these boxes.  You will then be prompted to save your password.  In the lower left, check the box that says “Do not ask this again” and then click “No”.  (We will get rid of these annoying boxes in a couple of steps).


– At this point you should be logged into the JHPCE cluster and sitting at a shell prompt.


To make logging in more streamlined and avoid the pop-up windows when you login, you can create an SSH key pair in MobaXterm.  To create the key pair:

– First bring up a second local Mobaxterm session by clicking on the “+” tab that is to the right of your JHPCE session tab.

– In this local session, type “ssh-keygen -t rsa”.  You will be prompted for a passphrase.  For security reasons, we recommend that you use a passphrase to protect your key.  Going forward, when you start Mobaxterm, you will only be prompted for your passphrase, and not for your JHPCE password and Google Authenticator PIN.  The output from “ssh-keygen” should look something like:


-This will generate a public key and private key on you local system.  We will need to copy the public key to the JHPCE cluster.  Change Directory into the the .ssh directory in your local session (typically /home/mobaxterm/.ssh), and cat the file “”


– Copy the contents of this output with your mouse.  NOTE: to do Copy/Paste in MobaXterm, you should not use <CTRL>-C and <CTRL>-V.  Instead, select the text you want to copy, then use the right mouse button to bring up the context menu, and select  Copy or select Paste when you are pasting.

– Next go back to the tab where you JHPCE ssh session is running.  From your home directory, cd into the .ssh directory.  In this directory, you should see a file called “authorized_keys”.  Edit this file with your text editor of choice (nano, vi, emacs):


– Paste in the public key that you copied from your local session.  Depending on your editor, the new key may only show up on one long line, or it may wrap to multiple lines.  Save the “authorized_keys” file when you are done.


– Now, in the MobaXerm application, on the left pane, you should see a list of “Saved sessions”, including a session for the “jhpce01” login node.  Right-Click on the “jhpce01” session, and select “Edit Session”.  This will open a window that looks like:


– Select the “Use private key” checkbox.
– The field next to the checkbox should populate with the path to your local private key.  If it does not, then click the blue icon on the right side of the field, and navigate to the location of your “id_rsa”.


– Click OK to save your changes.
– Now, in the left pane of Saved Sessions, you should be able to double click on the “jhpce01” session, and a new tab should open up, and log you into the JHPCE cluster without having to enter a password or Google Authenticator PIN.
– Once you have verified that you can login, exit out of all of your SSH sessions, and close the MobaXterm app.  Reopen the MobaXterm application, double click on the “jhpce01” session.  As before, a new tab should open up, and log you into the JHPCE cluster without having to enter a password or Google Authenticator PIN.