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Logging in to SCINet

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All users should have received their login credentials in an email. If you have not, please email the Virtual Research Support Core at scinet_vrsc@USDA.GOV.

Note that home directories on Atlas are not created right away, so it is recommended to wait a day after receiving email with the credentials before logging to Atlas cluster.

LincPass Users Please contact your IT Specialist if you need help with installing Step on your USDA controlled machine.

If you are encountering errors after completing the below steps, see SmallStepCLI Install Troubleshooting for LincPass Users

Creating a Config File

It is recommended to create a config file on your computer. You may do so using Notepad. The file you create must be titled “config” with no extension for this method to work properly (i.e. “config” not “config.txt”). This will send a “keepalive” signal every 20 seconds and keep retrying for up to 30 failures. Note: Do not copy the code into the terminal itself, it must be in a separate file.

Create a ~/.ssh/config file replacing USER.NAME with your actual username, all in lowercase. The path to the .ssh file is as follows: C>Users>(Your Account)>.ssh

Note: If you are using a Mac, the .ssh file may be hidden to you. To reveal the hidden files, you will press and hold CMD+SHIFT+. (Period Key) when choosing a location to save your file. The .ssh file will now be visible for you to save the config file.

Host ceres-login
TCPKeepAlive yes
ServerAliveInterval 20
ServerAliveCountMax 30

Host atlas-login
TCPKeepAlive yes
ServerAliveInterval 20
ServerAliveCountMax 30

ForwardAgent yes

If you don’t want to use the config file method above, add the following title to the ssh command replacing USER.NAME with your actual username, all in lowercase.

ssh -o TCPKeepAlive=yes -o ServerAliveInterval=20 -o ServerAliveCountMax=30


ssh -o TCPKeepAlive=yes -o ServerAliveInterval=20 -o ServerAliveCountMax=30

Step-Based Access Via SSH - Small Step Installation Instructions

Please Note: If you previously manually created a ssh host key, you may need to delete it as the hosts will now have a new signed key. Delete your .ssh/known_hosts file OR run: ssh-keygen -R This process will remain the same for all GUI services.

Installation Instructions:

  • OpenSSH needs to be installed. This is standard on recent Windows 10 and 11, MacOS, and Linux installs. However your local admin may have removed it or restricted access to it. Check by running “ssh” in a PowerShell or terminal window. You should get Usage instrctions.
  • ssh-agent needs to to running as a system service. If it is not running SmallStep will NOT work. You must assure it is running before proceeding
    • For Linux and MacOS this is probably already running so this step can be skipped.
    • For Windows this has to be enabled by an administator, it is not on by default even if openssh is installed. To enable it an administor must:
      • Make sure you’re running as an Administrator.

        Get-Service ssh-agent | Set-Service -StartupType Automatic
      • Start the service

        Start-Service ssh-agent
      • This should return a status of Running

        Get-Service ssh-agent

Step needs to be installed on your machine.

  • If you are on a USDA controlled Windows laptop or workstation, you can install SmallStepsCLI directly from the Software Center.
  • After installing, you may need to restart your terminal for step to be in your path.
  • If you do need to perform the installation yourself, see:
    • For windows we recommend the winget installer, we’ve had the best lusk with that. Again, please be aware that you will only be able to complete the installation yourself if you have admin rights (i.e. you will have admin rights on your home machine rather than an USDA controlled machine.)
    • For MacOS the instrcutions are more straightforward and can be done by the user without admin access. Please be aware that Homebrew will need to be installed first. There is a link to install this at the link above.
    • Linux will require root/sudo if you want to use the system packager rpm,deb,pacman. But can be done in userspace it you just download the binary directly.

After Step Installation:

  • Open a Terminal, CMD shell, or PowerShell window and run the following:

    step ca bootstrap --ca-url --fingerprint adb703fd18f176937743b20228d52af7a705d63a0471cd67428660be5fd006bf 
    step ssh config --set Provisioner=keycloak --set
    • Be sure to change “” to your own SCINet username
    • If the step config command fails, ssh-agent probably isnt running. See instructions above.

These commands will do the following:

  • Gets the initial cert from the certificate authority.
  • Sets up your ssh profile to simplify future logins

These commands only need to be done once. The second command updates your .ssh/config file. If you already have a complicated structure in there you may wish to review it. The changes are fine for most, but particularly if you already have ceres entries in yours there could be conflicts.

SSH Access After Step Installtion:

  • Each morning on your first attempt to ssh to Ceres with ssh or Atlas with ssh, (changing to your own SCINet username), you will see the following screen:

screenshot of Login Screen with Legacy Selection

  • Your default web browser should open automatically to the SCINet authentication page. Choose “ or USDA LincPass” as your sign-in option.
  • From there, if you havea LincPass, you will authenticate as usual with eAuth. If you are using, please follow the steps outlined below

  • Go back to your shell and you should see “CA:” followed by your regular login.

screenshot of Login Screen with Legacy Selection

After these steps, command line ssh works normally. The only different is that it will not prompt you for a password for the day (16 hours). Note: With the below examples, you will swap for your own SCINet username.

scp file1 file2 

Access Using Linux and LincPass

Ensure that you have the following prior to continuing:

  • Your card reader must work with your distro
  • Your Lincpass must be detected by your distro
  • The root certs installed properly for your distro which can be found here
  • The Intermediates as well can be found here

To test that everything is functioning properly, you must log into something that requires eAuth, such as your USDA Office 365 account.

Once you have successfully authenticated using eAuth, you will need to install Step following the instructions here

  • A current version can be found here

You will then configure Step according to our instructions above.

Finally, you will test eAuth access to SCINet using ssh, making sure to change “” to your own SCINet username.

Notes and Limitations

  • If you use multiple profiles in Chrome, step will open a new window in whichever profile was used last. If you end up in the wrong one just close it, do something in your work profile and rerun the ssh login command.
  • Windows users will find most tools other than the built-in windows ssh command line tools no longer work.
  • Mac and Linux users may have a bit more luck, but anything beyond command line tools probably won’t work anymore.
  • For graphical file transfers globus is still the preferred method and will continue to work.
  • After logging in via OIDC you will not have any automatic Kerberos tickets. You will need to kinit if you need them.

If you have any questions or issues, please contact the VRSC at

Accessing SCINet after Step is Installed

This process will be the same for all GUI based SCINet Services. Please follow the instructions below. If you have further questions or issues, please email

Accessing Using LincPass

If you are a LincPass holder, you will only select the option of “USDA LincPass” when logging into GUI services such as Open OnDemand, Galaxy, and the SCINet Forum.

After selcting this, you will be automatically directed to login using your usual eAuth based login.

Accessing Using

  • When logging into a GUI based system, you will be presented with the following image
    • You will select “ or USDA LincPass”

  • If prompted, you will then select “Customer”

  • Then, you will select “”

  • This will redirect you to for you to sign in. If you already have an existing account, there is no need for you to create a new one. You can simply sign in with your existing information.
    • However, if you need to create an account, you will toggle from “Sign In” to “Create an account.”

  • Once you fill out the required information, you will be sent an email to confirm your account. Confirming your email will redirect you back to for you to set up a password and second authentication method.

  • More information on account set up can be found here

  • Once you have completed the account setup, you will need to select “Continue without linking to an existing eAuth account” to move forward.

  • Once you have successfully authenticated with, you should see a similar image to the successful logins for LincPass/Yubikey:

If you need assistance with this login process, please email your questions to