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Advanced research computing on the Great Lakes Cluster
September 30, 2020 @ 1:00 pm - 4:00 pm
Venue: Your Desktop
OVERVIEW
This workshop will cover some more advanced topics in computing on the U-M Great Lakes Cluster. Topics to be covered include a review of common parallel programming models and basic use of Great Lakes; dependent and array scheduling; workflow scripting using bash; high-throughput computing using launcher; parallel processing in one or more of Python, R, and MATLAB; and profiling of parallel code using Allinea Performance Reports and Allinea MAP.
PRE-REQUISITES
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.
INSTRUCTORS
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
MATERIALS
- Lecture Notes
- Great Lakes Slurm HPC cluster
- Great Lakes User Guide
- Two-page Cheat Sheet
- MPI Profiling with Allinea MAP
COURSE PREPARATION
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.
USER LOGIN
If you already have a Great Lakes user login, you don’t need to do anything. Otherwise, go to the Great Lakes user login application page at: http://arc-ts.umich.edu/login-request/ .
Please note that obtaining a user account requires human processing, so be sure to do this at least two business days before class begins.
SLURM ACCOUNT
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 AUTHENTICATION
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.
LAPTOP PREPARATION
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 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. This document describes how to download and use this software, except please note you will be connecting to greatlakes.arc-ts.umich.edu 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 1.2 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.Please note this session will be recorded.