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Research computing on the Great Lakes Cluster

May 28, 2020 @ 10:00 am - 1:00 pm

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This workshop will provide a brief overview of the components of the Great Lakes Cluster. The main body of the workshop will cover the resource manager and scheduler, creating submissions scripts to run jobs and the options available in them, and hands-on experience. By the end of the workshop, every participant should have created a submission script, submitted a job, tracked its progress, and collected its output. Participants will have several working examples from which to build their own submissions scripts in their own home directories.

This course assumes familiarity with the Linux command line as might be got from the CSCAR/ARC-TS workshop Introduction to the Linux Command Line. In particular, participants should understand how files and folders work, be able to create text files using the nano editor, be able to create and remove files and folders, and understand what input and output redirection are and how to use them.

Dr. Charles J Antonelli
Research Computing Services
LSA Technology Services

Charles is a member of the LSA Technology Services Research team at the University of Michigan, where he is responsible for high performance computing support and education, and was an Advocate to the Departments of History and Communications. Prior to this, he built a parallel data ingestion component of a novel earth science data assimilation system, a secure packet vault, and worked on the No. 5 ESS Switch at Bell Labs in the 80s. He has taught courses in operating systems, distributed file systems, C++ programming, security, and database application design.

John Thiels
Research Computing Services
LSA Technology Services

Mark Champe
Research Computing Services
LSA Technology Services

Lecture notes
Great Lakes HPC cluster

In order to participate successfully in the workshop exercises, you must have a user login, a Slurm account, and be enrolled in Duo. The user login allows you to log in to the cluster, create, compile, and test applications, and prepare jobs for submission. The Slurm account allows you to submit those jobs, executing the applications in parallel on the cluster and charging their resource use to the account. Duo is required to help authenticate you to the cluster.

If you don’t already have a Great Lakes user login, please visit the application page.

Please note that obtaining a user account requires human processing, so be sure to do this at least two business days before class begins.

We create a Slurm account for the workshop so you can run jobs on the cluster during the workshop and for one day after for those who would like additional practice. The workshop job account is quite limited and is intended only to run examples to help you cement the details of job submission and management. If you already have an existing Slurm account, you can use that, though if there are any issues with that account, we will ask you to use the workshop account.

Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH (AKA Level 1) password as well as authenticate through Duo in order to access Great Lakes.

If you need to enroll in Duo, follow the instructions at Enroll a Smartphone or Tablet in Duo.

Please enroll in Duo before you come to class.


You will need an ssh client to connect to the Great Lakes cluster. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:

Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer.
Download and install PuTTY directly from the developer.Our Great Lakes User Guide in Section 1.2 describes in more detail how to use PuTTY to connect to Great Lakes.
Please prepare and test your computer’s ability to make remote connections before class; we cannot stop to debug connection issues during the class.

A Zoom link will be provided to the participants the day before the class. Registration is required.


May 28, 2020
10:00 am - 1:00 pm
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Your Desktop




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