Getting and Using Interactive Sessions

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This pathway is a step-by-step introduction to interactive sessions in the Rhino/Gizmo compute environment.

Pre-requisites

  • Basic Unix/Linux commands cd, ls, and pwd
  • Connection to Campus Network (VPN or on-campus)
  • A terminal emulator ( Terminal on Mac, Putty, or WSL on Windows)

  • Node An individual server in a collection of networked servers that make up a computing cluster.

  • Shell A command line user interface for Unix-like operating systems.

  • Prompt A “prompt” indicates that the terminal session is ready for input. Prompts typically have a structure indicating the username and host, followed by a blinking square. AKA “command prompt”.

  • Session A temporary and interactive information interchange between two or more communicating devices, or between a computer and user.

  • Slurm A type of workload manager used at the Fred Hutch’s gizmo computing cluster.

  • HutchNet ID A user ID specific to the Fred Hutch.

  • rhino The login node (actually several nodes) of the Fred Hutch high performance computing cluster.

  • gizmo The name of the Fred Hutch high performance computing cluster’s computing nodes.

Steps

Get a Hutchnet ID

In order to use Fred Hutch batch computing resources you must have valid Fred Hutch credentials. Sepcicially a HutchNet ID.

This HutchNet ID needs to be associated with a PI account in order to submit jobs.

Connect to the Campus Network

Batch computing resources require that your local computer be connected to the campus network. This authentication process happens differently when you’re on vs off campus.

When on campus

When off campus

Start a Terminal

A terminal provides a text-based interface to computers (the “command line”).

Apple OSX has a built in terminal application. It can be found in Applications->Utilities->Terminal. Other options are available that are more full featured such as iterm2, which is one free option (please consider donating!)

Windows has a few different terminals built in, but many of these are unsuitable for accessing Linux systems. Two easy options are the Microsoft Terminal app (available in the App Store) and PuTTY.

Shell Connection to the ‘rhino’ Login Nodes

Once you have a connection to the Hutch network and a suitable terminal, the next step is to connect to the login nodes known as rhino.

This will present you with a command prompt on one of the rhino nodes- from here you can run commands, view data, and start cluster jobs.

Home Directory

The “home” directory on Linux is used for storing user-specific data and is the directory you will begin in when you login to rhino.

If you get an error like Home directory not found when you log in, please email SciComp to get that set up.

The common storage options are available in the rhino-gizmo compute environment. These paths are available in the same location on each of these hosts.

You’ll be started (by default) with a bash shell and most of the common GNU/Linux utilities

Where to go Next

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