New user orientation

A copy of the slides from the Orientation can be download from:

What to do before the JHPCE Orientation Session

Prior to attending the Orientation Session for the JHPCE (pronounced by its letters J-H-P-C-E) cluster, you may need to install some additional applications on you laptop or smart phone.

If you have never used a Linux or Unix system before, we strongly recommend going through the Unix Command Line tutorial offered at the Digital Ocean site at . The cluster is entirely Linux based, so some exposure to the Linux command line environment is recommended before attending the Orientation Session. The tutorial should only take 30 minutes or so to go through.

In order to access the JHPCE cluster and make use of the applications on the cluster, you may need to install additional software on your smart phone and laptop.   If possible, please install this software prior to attending the JHPCE Cluster Orientation session.

  1. Install the 2 Factor Authentication program.  The JHPCE cluster makes use of “Google Authenticator” to provide enhanced security.  You can choose to either install an app on your smartphone or, if you do not have an Apple or Android based smart phone, you can install an extension to the Google Chrome browser.  Prior to the Orientation Session, you will only need to download the GoogleAuthenticator app on your smart phone, or install the Authy Chrome extension. We will be configuring Google Authenticator during the Orientation Session. Please see for instructions.
  2. Install required client software.  You may need to install a couple of programs on your laptop or desktop in order to access the JHPCE Cluster.  You will need 1) an SSH client for logging in, 2) an SFTP client for transferring files to and from the cluster, and 3) an X11 client for displaying graphics back from the JHPCE cluster.  The SSH client is a requirement – the SFTP and X11 clients are preferable but optional.
    • Microsoft Windows
      We have found that the easiest program to use for accessing the JHPCE cluster is MobaXterm as it combines the functionality of all 3 software packages (SSH, SFTP, and X11) in 1 program.  Prior to the Orientation Session, you should install MobaXterm by following the first few steps of .  Alternatively, if you already use an SSH client, (such as putty or Cygwin) and an SCP client  (such as WinSCP), you can continue using that software.
    • Apple Macintosh
      – There are built in command line tools for ssh and scp that can be run from a Terminal window.  The Terminal program can be found in “Applications -> Utilities”.  From a Terminal window, you would type:
             ssh <username>
      and then login with the login id and the password we provided to you.- In order to run graphical programs on the cluster and have them displayed on your Mac, you will need to install XQuartz from Optionally, you can also install a GUI based SFTP program such as “Filezilla“.  One note about Filezilla – if you download the package from the default link on SourceForge, you may be be blocked by your MalWare/Virus Scanner, or prompted to install Potentially Unwanted Programs (PUPs) during installation.  We recommend you follow the alternative download link here to download a clean copy of the program.

Best practices passwords and authentication

Do not share your password with ANYONE.
Choose a “good” password using special characters and letters and digits.
It would be best if your password was unique and
not the same password you use on other systems.
If you believe your password or your computer have been compromised
please let us know immediately so we can reset your password.
If you store passwords on your computer (not recommended),
please let us know immediately if your computer is lost or stolen.

*** NEW ***

Passwords are no longer sufficiently secure!. Don’t believe us? Read this scary article from wired magazine. We strongly recommend that users either use
key-pair authentication with a passphrase, or  use 2-factor authentication  (or both), to  log into the cluster. You may want to set this up now, because it will become a requirement on the new cluster.

Home directory settings

We have set your home directory quota to 100G. If you need more space for static datasets, please contact us.


Hopkins staff will *NEVER* send you an email message asking for your password or login credentials
*NEVER* give out your password and login ID to anyone in an email message or on a web page.

2013 Slides from Orientation:   SGE_lecture.ppt