Getting Started with JHPCE

What is JHPCE?

JHPCE or the Joint High-Performance Computing Exchange is a computation resource available to members at the Johns Hopkins Medicial Institute (JHMI). Several research groups across the School of Public Health and School of Medicine tap into the power of JHPCE to run computationally expensive analyses - our transplant epidemiology group included.

The JHPCE introduction to new users describes some use cases. This blog will be a brief introduction to getting your system ready to log onto the JHPCE cluster to use Stata-MP. This multi-core version of Stata is licensed to our group and can be accessed on JHPCE by stakeholders .

Command Line

JHPCE is a linux-based computing system. In order to interact with JHPCE you’ll need to use Linux command line prompts. Basic commands are covered during new user orientation. There are also plenty of Linux resources available online. I’ll provide some basic commands throughout this post.

Mac/Linux Installation Guide

If you are working on a Mac or Linux machine then you don’t need any prerequisites! This is because Mac and Linux both come with command line tools that are robust and pretty easy to use. For Mac users just open up the “Terminal” app. For Linux users - well you probably already know what to do if you’ve installed Linux on your machine.

You can skip past the next section stil you won’t need to install any additional software.

Windows Installation Guide

If you are working on a Windows machine then you’ll need to download some software to make getting on the cluster painless. While I’m sure you can get PowerShell or the Command Prompt to work for you, installing something like MobaXterm or Cygwin is preferable.


MobaXterm is a user-friendly X11 server, SSH client, and command line application. This makes MobaXterm the recommended tool for most people - in fact the JHPCE admins also recommend it.

Since the JHPCE blog already covers the installation and set-up, I’m not going to do a detailed installation guide. If you have any questions or issues with the installation feel free to reach out.


I personally use Cygwin. Cygwin creates a Linux-like environment on your Windows machine. It’s not as user friendly as my next recommendation, but Cygwin better fits my needs and specific use-case. I use Mac and Windows machines on a daily basis. Being able to sync .bash_rc files and the general structure of commands makes my transitions between machines seemless. If you plan to become a JHPCE cluster power-user, or if you use multiple OSes on a daily basis, then I would recommend downloading Cgywin.

There’s definitely a learning curve to Cygwin and I won’t be covering all the details in this post. To get started, I would recommend downloading CygwinX. CygwinX is a version of Cygwin that also comes with an X Window Server. As I mentioned before, interacting with the JHPCE cluster will primarily be through command line prompts. Not everyone is comfortable with command line, and even if you are there are times where it’s nice to see a window with buttons that you can click. X Window allows you to get that classic Stata window on your machine even though you’re technically running it off the cluster.

Installing CygwinX is the same as installing Cygwin for the most part. First go to the Cygwin downloads page. If you have a modern 64-bit verion of Windows, then install the 64-bit version. After opening up the installer, you will be prompted to choose a download source. Any mirror will suffice. You will also need to choose a default location for Cygwin packages. You can keep this anywhere.

Cygwin, by default, only includes the minimal base packages required to get Cygwin running. I really appreciate this, but it does make the installation process very confusing for someone unfamiliar with working with the command line. You can use the serach function to add some additonal packges. You should at least install xinit so that you can use the X Windows System.

  • Here are some recommended packages
  • nano a text editor
  • vim another text editor
  • zip a ZIP file compression utility
  • git a version control language
  • mintty an emulator to given Cygwin a Terminal-like feel
  • xinit X Window utility
  • R a statistical language
  • xclip a command line clipboard grabber

After you finish the installation, boot up Cygwin and move on to the next section

Getting onto JHPCE

During JHPCE orientation, you’ll be introduced to the JHPCE cluster and set-up 2-factor authentication. While the security benefits of 2-factor authentication are valuable, it is not always the easiest practice to abide by when you log onto the cluster multiple times per day. JHPCE admins allow users that abide by Hopkins IT recommendations (encrypted hard drive and password protected machines) to use SSH to bypass 2-factor authentication.

with SSH your cluster account will recognize the machine you’re logging in from and let you get on with no extra fuss. The JHPCE introductions can be found here.

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