Advanced Research Computing on the Great Lakes Cluster

Wednesday, 5/22, 10:00 am-1:00 pm


Advanced Research Computing on the Great Lakes Cluster

This course is remotely over Zoom.  A Zoom link will be provided to all registrants for those who choose to attend remotely.

This workshop will cover some more advanced topics in computing on the U-M Great Lakes Cluster.  Topics to be covered include a brief review of common parallel programming models and basic use of Great Lakes; dependent and array scheduling; workflow scripting; high-throughput computing using launcher; parallel processing in one or more of Python, R, and MATLAB; and profiling of parallel code.


This course assumes familiarity with the Linux command line as might be got from the 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 Antonelli
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
LSA Technology Services



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 already have a Great Lakes user login, you don’t need to do anything.  Otherwise, go to the application page at the ARC log-in request to request a Great Lakes user login.

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 VPN software to access the U-M network.  If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions.  You will need VPN to be able to use the ssh client to connect to Great Lakes. Please use the ‘Campus All traffic’ profile in the Cisco client.

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

  • Download and install U-M PuTTY using these instructions from ITS. Please note you will be connecting to instead of the cited host.  You must have administrative authority over your computer to install this software.
  • Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application.  You do not need administrative authority over your computer to use this software.

Our Great Lakes User Guide in Section 1.3 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 all registrants. Registration is required. Please note this session will be recorded.

If you have questions about this workshop, please send an email to the instructor at

Session Details

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Session level: Advanced
Sponsor(s): Advanced Research Computing
Presenter(s): Charles Antonelli, John Thiels

This session is currently Past.

Registration is currently closed.