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Connecting to HPC 4 Research

HPC 4 Research is only available via the Charité, MDC, and BIH internal networks. VPN access requires additional measures which are described in Connecting from External Networks.

There are two primary methods for interacting with BIH HPC:

  1. Through the “Ondemand” web portal.
  2. Via SSH and Slurm.

This part of the documentation only described direct console access via SSH. For information regarding the web portal, please read OnDemand Portal. In case you're not familiar with SSH, you should probably start via the web portal or (if you are determined to learn) read through our SSH basics page.

In brief

Follow these steps to connect to BIH HPC via the command line:

  1. Register an account via your PI. 📝
  2. Generate a SSH key pair 🔑 in Linux or Windows
  3. Submit your public key ⬆ to Charite or to MDC.
  4. Connect to one of the two login nodes.

    # Charite Users
    $ ssh
    $ ssh
    # MDC Users
    $ ssh
    $ ssh


    There are two login nodes, hpc-login-1 and hpc-login-2. There are two for redundancy reasons. Please do not perform big file transfers or an sshfs mount via the login nodes. For this purpose, we have hpc-transfer-1 and hpc-transfer-2.

    Please also read Advanced SSH for more custom scenarios how to connect to BIH HPC. If you are using a Windows PC to access BIH HPC, please read Connecting via SSH on Windows

  5. Allocate resources on a computation node using Slurm. Do not compute on the login node!

    # Start interactive shell on computation node
    $ srun --pty bash -i
  6. Bonus: Configure your SSH client 🔧 on Linux and Mac or Windows.

  7. Bonus: Connect from external networks 🛸.


  • Web Access:
  • SSH-Based Access:

    # Interactive login (choose one)
    srun --pty bash -i
    # File Transfer (choose one)
    sftp local/file
    sftp local/file
    # Interactive login into the transfer nodes (choose one)

What is my username?

Your username for accessing the cluster are composed of your username at your primary organization (Charité/MDC) and a suffix:

  • Charite user: <Charite username>_c -> doej_c
  • MDC user: <MDC username>_m -> jdoe_m

How can I connect from the outside?

Please read Connecting from External Networks

I have problems connecting

Please read Debugging Connection Problems