Server Guide#

As a user of MBO servers, you will be given a login to MBO servers, which will give you access to the servers.

Connecting with RDP#

MBO processing servers are accessible via Microsoft Remote Desktop Protocol (RDP).

There are a few common applications, depending on your operating system:

via Windows App#

You will need the following information to access the servers:

  • Server IP address

  • Username

  • Password

../_images/rdp_base.png

To add an MBO User Account:

  • Add (+) -> PC

  • Enter IP address (XXX.XX.X.XX) in PC name

  • Enter Username in User account

  • Enter Password in Password

  • Choose an optional display name

../_images/rdp_certif.png

Accept the certificate notification popup to continue connecting to your MBO server.#

You should now be able to connect to the MBO servers!

Logging out#

Warning

If you don’t properly sign-out, you will use more login-sessions than you are afforded and your account will need to be logged out forcefully.

To sign out, Windows Menu -> Username -> Sign Out

Filesystem#

Each server has an ID that prepends the computer name.

Each directory for this system will have this ID prepended to the directory name.

Warning

Both workstation and compute file-systems are NOT backed up.

Users should have their own copies of all data on MBO servers.

The D: drive is read-only and contains:

  • D:/ID_SOFT/repos : Data processing software

  • D:/ID_SOFT/apps : Applications

  • D:/ID_DATA/username : Raw data that users will frequenly access will be saved here.

The E: drive is the user sandbox, with a directory E:/ID_USER_DATA/username for each user.

This is where your intermediate results should go.

Internet Access

Users are strongly discouraged to browse the internet on the compute server, browsing should be done on your local machine only. A browser is available for Jupyter notebooks, but internet access is discouraged.

Software#

Python#

Each user has access to uv and miniforge3 for managing python installations and environments.

USER@SERVER MINGW64 ~/repos
$ which uv
/c/Users/USER/.local/bin/uv

USER@SERVER MINGW64 ~/repos
$ which conda
/c/Users/USER/miniforge3/Scripts/conda

There are important differences to consider depending on whether you use uv or conda to manage environments.

See the mbo guide on virtual environments to learn more.

Warning

For conda, DO NOT install any software in the base environment as that will cause conflicts between all installed environments and require a reinstallation of miniforge3.

The recommended method for interacting with conda is the miniforge_prompt (other terminals will work but consistent behavior is not guaranteed).

UV should be accessible from any terminal you choose.

Other Software#

  • MATLAB

  • Fiji / ImageJ

  • Visual Studio Code

  • git bash

  • wezterm

Contact a server administrator to inquire about adding additional software. Please do not install software without consulting an MBO admin.

Connecting to Network Servers#

Computers on the Rockefeller network (with network discoverability turned on) can be accessed via SMB as \\server-name or \\ip-address.

../_images/rdp_access_other_server.png

You will be prompted for username/password credentials the first time you connect.

SSH Connections#

TLDR

Generate a new ssh key:

ssh-keygen -t ed25519 -C "your_email@example.com"

Send the .pub output to an MBO administrator.

ssh is a communication protocol that will allow you to access MBO servers from the command line.

To establish a connection, the computer you are connecting from (the ‘client’) must have a private ssh key.

This guide provides an example of generating this key to authenticate github.com, but the process is the same.

This process will generate 2 files:

Private key

  • ed25519

  • Never share this

  • Stored in your .ssh/ folder

Public key

  • ed25519.pub

  • This is what you send to MBO

  • Can be safely shared

Depending on the algorithm you choose, the filename may be different.
What matters is that the .pub file (e.g. ed25519.pub) is installed on the MBO servers.

Talk to an MBO admin to add your ssh-key to the server.

Guidelines#

  • Store raw and processed data in your allocated user space ID_USER_DATA.

  • Delete unused data when no longer needed to conserve shared storage.

  • Do not browse the internet on the MBO servers.

  • Do not install software on your own. Consult with the MBO admins with a request.

  • Log out from Windows after each session.