This pathway will get you to a first non-interactive computing job on the
gizmo computing cluster using the command-line interface at the Fred Hutch.
A desktop computer, access to the internet, a good text editor.
If you are unfamiliar with any of these terms, hover over them to find more information.
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.
Scripts A script is set of commands that are executed by an operating system or application.
Session A temporary and interactive information interchange between two or more communicating devices, or between a computer and user.
Workload manager Software that coordinates job submission to nodes on a cluster.
HutchNet ID A user ID specific to the Fred Hutch.
Workflow manager Software that coordinates the submission of jobs, inputs and outputs of individual jobs in a scientific workflow.
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.
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 authenticaiton process happens differently when you’re on vs off campus.
Start a Terminal
A terminal provides a text-based interface to computers (the “command line”).
Macintosh 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 Connections 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
The “home” directory on Linux is used for storing user-specific data and is the directory you will begin in when you login to
If you get an error like
Home directory not found when you log in, please email
SciComp to get that set up.
Navigating the Compute Environment
The common storage options are available in the
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
Familiarize Yourself with SLURM
SLURM is the workload manager for our
gizmo computing cluster. Review the documentation for basic information about how SLURM works. Once you have logged into the login nodes (
rhino), you will be sending non-interactive instructions to the compute nodes (
gizmo) via these instructions.
Create a Script
For the purpose of this pathway we will use a pre-existing script in this template GitHub repository. Copy this file to a location you can access from
rhino by using:
wget https://github.com/FredHutch/slurm-examples/blob/master/introduction/1-hello-world/01.sh .
Submit the Script
Use the sbatch command to submit the script to
gizmo. Output should appear in the form of a log file in the current driectory with the jobID in the filename.
Where to go from here
This documentation provides more information on managing jobs that are queued and running on the cluster, including steps to take when jobs don’t run.
Writing More Complicated Scripts
This was a simple script - you’ll need more advanced scripts to run workload on the cluster. These resources are great starting points:
- The Linux Documentation Project manual on bash scripting
- The Advanced Guide for bash scripting
Larger Compute Needs
We’ve described a single job - when your work requires many jobs or many steps, more advanced tools are necessary, and you begin to delve into parallel computing. Two commonly used approaches at the Fred Hutch include:
- SLURM job arrays provide an easy mechanism for submitting thousands of homogenous jobs
- Workflow managers are the gold-standard for managing computational workflows, particularly valuable for managing multi-step analyses. Cromwell and Nextflow are the two preferred workflow manager tools at the Hutch.
Updated: September 6, 2022Edit this Page via GitHub Comment by Filing an Issue Have Questions? Ask them here.