A quick start for external users to connect to the BioHPC server

For more detailed information, see this page: https://biohpc.cornell.edu/lab/doc/BioHPCLabexternal.pdf

1. Prerequisite: Set up 2-factor authentication with BioHPC

BioHPC requires two-factor authentication (2FA) for logins outside the Cornell network; both to login machines and the BioHPC webpage (as well as some enhanced security compute machines). The 2FA protocol is different from what is used by other Cornell services. Rather than a push notification, you will need to supply a time-based one-time password (TOTP) as well as your BioHPC username/password. The TOTP is provided by an app installed on your smartphone and linked to your BioHPC account (the app can also be installed on laptops/desktops/browsers if you prefer). To enroll in two-factor authentication, and for more details, visit http://biohpc.cornell.edu/lab/2fa_setup.aspx. This only needs to be done once, though you can re-visit this site to link additional devices to your BioHPC account. When connecting to BioHPC login machines or the BioHPC webpage, you will be prompted for a TOTP after providing your BioHPC password, but this is only required once per week per IP address. There are a few applications that do not support 2FA – such as when using ‘QuickConnect’ in FileZilla. In this case, we recommend first logging into the BioHPC website (https://biohpc.cornell.edu/login_bio.aspx). You will supply your 2-factor code there, and then will be able to use other apps without needing a TOTP from that IP address for the next week.

2. Connect to the server

2.1 Set up a tunnel to bypass Cornell network firewall

• Open Terminal (Mac) or Command Prompt (Win).

• Run this command to setup a tunnel to cbsuxxxxxxx port 22.

  ssh -N -L 22:cbsuxxxxxxx:22 YOUR_BIOHPC_ID@cbsulogin.biohpc.cornell.edu
  

  1. Replace "cbsuxxxxxxx" in the command with the server you want to connect to. Replace "YOUR_BIOHPC_ID" with your BioHPC use name.

  2. When prompted for password, enter your BioHPC password. When typing the password, you would not see anything on the screen, just finish the typing and then press "Enter".

  3. Keep this terminal window open, and move on to the next step 2.2.

2.2 To connect to the computing server cbsuxxxxxxx, open another Terminal (Mac) or Command Prompt (Win), and connect to localhost (localhost port 22 is now tunneled into the Cornell Linux server cbsuxxxxxxx.biohpc.cornell.edu port 22).

xxxxxxxxxx
ssh xxxxx@localhost

2.3 To upload/download files.

Open Filezilla, enter following information and press "Quickconnect":

​x
Host: localhost

Username and password: BioHPC user name and password

Port: 22

Once connected, the left panel is your laptop, the right panel is the remote server. To upload/download files or directories, just drag the files/directories between the two panels.

2.4 To Connect to the Rstudio server running on cbsuxxxxxxx server

2.4.1 Set up another tunnel for Rstudio server, which runs on port 8016 of cbsuxxxxxxx

xxxxxxxxxx
ssh -N -L 8016:cbsuxxxxxxx:8016 xxxxx@cbsulogin.biohpc.cornell.edu

2.4.2 Open a web browser, connect to http://localhost:8016