Registering for and logging in to HPC - EpiModel/EpiModeling GitHub Wiki

Initial Access Requests

To get access to the Emory HPC, you need to follow these steps:

  1. Email PI Sam ([email protected]) to request access to the HPC. Include your NETID in your request email. Sam will then send an request email to RSPH IT help ([email protected]) to request access to the cluster, with specific assignment to the epimodel group there. This might take a day or two for IT to respond.

  2. Once IT has granted access, you will receive a welcome email with initial instructions. It will include a link to IT's HPC guide. Feel free to read that, although it may be outdated and include information not immediately relevant to our EpiModel workflows.

  3. Connection to the HPC is through the Emory VPN. As noted in the welcome email, you should visit the Emory VPN site to download a VPN client for your system. For Macs this is the Big-IP Edge Client. Once you log in to the VPN, follow the instructions in the HPC welcome email: "Once you have successfully connected to the VPN, send an email a reply confirming your VPN account is working. At that point, a necessary privilege escalation will be requested on your behalf which will allow your connection to reach the HPC Cluster." Once you get a response confirming that, you should be ready to go!

Logging in to the HPC

Start your VPN session (the VPN must be running to access to the HPC). In Rstudio (or your other favorite terminal program like iTerm2 for Mac or PowerShell for Windows), start a new terminal window (Tools -> Terminal -> New Terminal Window). We recommend that you have two terminal windows running in parallel, one on your local computer, and then another to connect to the HPC. In Rstudio, you can open multiple terminals, then toggle back and forth with them with the arrow keys just to the left of the Terminal drop-down menu.

Windows Note

To use the ssh command in Rstudio's terminal window, you must type this every time you open a terminal window:

set DISPLAY=

Initial ssh login

When ready, type the following in one of the open terminal windows:

ssh [email protected]

replacing netid with your specific NETID. Note: your NETID is case sensitive, all lowercase; it must be typed as such. Type in the password provided to you by RSPH IT; you will likely be prompted to change your password.

If successful, you should see something like this:

Welcome to the

██████╗ ███████╗██████╗ ██╗  ██╗
██╔══██╗██╔════╝██╔══██╗██║  ██║
██████╔╝███████╗██████╔╝███████║
██╔══██╗╚════██║██╔═══╝ ██╔══██║
██║  ██║███████║██║     ██║  ██║
╚═╝  ╚═╝╚══════╝╚═╝     ╚═╝  ╚═╝

High Performance Computing (HPC) Cluster

***  AUTHORIZED USE ONLY ***


-->>>  DO NOT RUN APPLICATIONS ON THE LOGIN NODE <<<---
       Please submit ALL computations, including small
       interactive ones, to compute nodes.


Last login: Wed Jan 26 11:58:41 2022 from 10.110.83.203
[sjennes@clogin01 ~]$

This is your home directory. Only you have access here, but space is limited. So don't use this for storing EpiModel simulations. Instead change directory with cd to our group folder here:

cd /projects/epimodel/

Finally, make your own subdirectory with your NETID like this:

mkdir netid

Change into that directory with cd netid and back out to the group directory with cd ... You can also return to your home directory with cd with no arguments after.