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Advanced research computing on the Great Lakes cluster
January 30, 2020 @ 1:00 pm - 4:00 pm
Venue: Modern Languages Building (MLB), Room 2001A
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 High Performance Computing Consultant in the Research Computing Services group of LSA TS 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
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 Flux user login, you don’t need to do anything. Otherwise, go to the Flux user login application page at: https://arc-ts.umich.edu/fluxform/ .
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 do not need to bring your own laptop to class. The classroom contains Windows or Mac computers, which require your uniqname and UMICH (AKA Level 1) password to login, and that have all necessary software pre-loaded.
If you want to use a laptop for the course, you are welcome to do so: please see our web page on Preparing your laptop to use Flux. However, if there are problems connecting your laptop, you will be asked to switch to the provided computer for the class. We cannot stop to debug connection issues with personal or departmental laptops during the class.
