Job Scheduling with Slurm

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  • Instructor:  Oliver Stueker
  • Level: Beginner
  • Duration: 1.5 hours
  • Helpers: Ross Dickson
  • Date:  September 27, 2024 | 10:00 - 11:30 am (Atlantic)
  • Prerequisite: Intro to Shell Scripting or similar experience
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COURSE DESCRIPTION

The national systems use a job scheduler called “Slurm”. In this session you will learn how Slurm works and how it allocates jobs, helping you to: minimize wait time by framing reasonable requests; ask for only the resources you need, to improve efficiency; increase throughput; run more jobs simultaneously; and troubleshoot and address crashes.

This workshop is designed for either new HPC users familiar with Linux and Shell Scripting, but who have not had experience with using Slurm, or, for experienced users transitioning to Slurm or seeking to improve efficiency with the scheduler.

This session will be delivered online.

To get the most from ACENET basics, please register for a Digital Research Alliance of Canada (the Alliance) account. To register contact your supervising professor, ask for their CCRI, then visit https://ccdb.alliancecan.ca/account_application. If your professor is not registered with the Alliance, please have them register, then follow up with you. In addition to an Alliance account, you will want a computer with Windows, MacOS X, or a Unix-based operating system (not a ChromeBook), and a stable internet connection. A registered account is not mandatory, just recommended to get the most out of our lessons. You can attend the first session to see how ACENET can assist in accelerating your computational research before you decide to obtain an account, if you wish.

SETUP REQUIREMENTS
  • You will want a computer with Windows, MacOS X, or a Unix-based operating system (not a ChromeBook), and a stable internet connection. A registered alliance account is not mandatory, just recommended to get the most out of our lessons. You can attend the first session to see how ACENET can assist in accelerating your computational research before you decide to obtain an account.
  • For windows users, download MobaXterm.

Meet your teaching team

Oliver Stueker

Instructor

Research Consultant

Dr. rer. nat. Computational Chemistry, University of Paderborn, Germany

Oliver is based at Memorial University and has been with ACENET since 2015. He has over 15 years of computational research experience in the fields of molecular modelling, chemistry, and bioinformatics. He has held post-doctoral positions at the Donnelly Centre for Cellular & Biomolecular Research at the University of Toronto, doing computational network biology working on active cell maps, and at the NRC’s National Institute for Nanotechnology in Edmonton, where he performed molecular dynamics studies on the interactions between proteins and functionalized Gold nano-particles. Most recently, Oliver has been working with Dr. Ray Poirier at Memorial University, and Dr. Jason Pearson at the University of Prince Edward Island on ‘Retrievium’, a repository for quantum-mechanical information.

Tannia Chevez

Host

Digital Training Specialist
BSc Computational Chemistry, Memorial University

Tannia joined ACENET in 2023 and is based in St. John’s. She has held positions as a research assistant in various departments, with responsibilities ranging from developing algorithms for an online animal sound repository, to crafting chemical composite films. Proficient in Python, Java, and JavaScript, she has focused on spectral data analysis, SEM image-based nanoparticle detection, and software development for data analysis. Tannia contributed significantly to the publication of a research paper by analyzing potential environmental toxicants, generating millions of chemical structure IDs, and conducting data extraction and analysis using Python, R, and JavaScript, as well as enhancing algorithms for simulating potential environmental toxicants’ behavior in water, soil, and air environments. Tannia’s teaching experience includes a Leader Instructor at Brilliant Labs where she taught a range of digital topics, and a Digital Literacy Instructor for the Association for New Canadians.

Ross Dickson

Helper

Lead Research Consultant

Ph.D. Computational Chemistry, Queen’s University

ITIL Foundation Certificate

Based at Dalhousie University, Ross joined ACENET in 2007 as a Research Consultant. His responsibilities span education, documentation, and client support, and he manages job scheduling policies on ACENET’s high-performance computing clusters. He has worked with users across many disciplines including chemistry, physics, biology, oceanography, neuroscience, several engineering disciplines, philosophy, and management studies. Following his doctoral and postdoctoral studies in computational chemistry, Ross worked in software development for Hypercube Inc., makers of HyperChem for Windows, and for Molecular Mining Corporation where he helped specify some of the earliest software for analyzing high-throughput gene expression data.