How to use RSPH cluster

Prerequisite

If you want to access the culster from outside the Emory (e.g. using Emory wifi), you need to connect to Emory VPN first.

A useful toolkit COMBO

• Windows User:
  1. Windows PowerShell
  2. WinSCP
• Mac user:
  1. terminal
  2. a. Cyberduck or FileZilla
     b. Remote mounting using sshfs (details of this method can be found below.)

Login to the cluster

This is where we interact with cluster, e.g. installing packages, submitting jobs, etc.

How:
Open terminal (or PowerShell) on your computer, and then login using ssh with command:

ssh netid@clogin01.sph.emory.edu

Note: NetID is your official network ID that is used to access all resources throughout Emory.

Details about mounting remote directory to local computer:
After following the steps, you don’t need to use any SFTP client to move your file back and forth.
There is one caveat: beware of deleting files in the mounted folder if you only have one copy here.

1. Install sshfs and macFUSE.
   Note: If you encountered any issues in installing these for M1 chip, please see this page.

2. Create a local directory (destination on your own computer).

   mkdir /Users/yutong/local_HPC_folder
   

3. Mount cluster directory to your local directory. Here is an example of mount remote folder /home/yjin85 to local folder /Users/yutong/yjin85/:

   sshfs yjin85@clogin01.sph.emory.edu:/home/yjin85 /Users/yutong/yjin85/ -o auto_cache -o follow_symlinks
   

4. If you mount with error in step 3 and want to re-mount, you should unmount first with the following:

   sudo umount /Users/yutong/yjin85/ 
   

Additional Resources

1. Some useful tips provided by the RSPH IT:
   • The HPC Getting Started Guide.
   • website for BIOS at RSPH: HPC Documentation.
2. SLURM quick start.
3. Dr. Wu’s post and Dr. Yang’s post.