HPC 101: High Performance Computing Workshop

Overview

This course will provide an overview of cluster computing in general and how to use the U-M Flux Cluster in particular. Topics to be covered include cluster computing concepts, common parallel programming models, introduction to the Flux Cluster; creating, submitting, observing, and analyzing cluster jobs; common pitfalls and how to avoid them; and some useful tools. We will issue you a temporary allocation to use for the course, or you can use your existing Flux allocations, if any. Short sample programs will be provided, or come to class with your own.

Prerequisites

HPC 100 or equivalent. This course assumes familiarity with the Linux command line.

Instructor

Dr. Charles Antonelli
Advocacy and Research Support Group
LSA Information Technology

Charles is a High Performance Computing Consultant in the Advocacy and Research Support Group of LSAIT at the University of Michigan, where he is responsible for high performance computing support and education, and is 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.

Materials

Preparation

In order to use the Flux cluster successfully, you must have a Flux user account, a Flux allocation, and an MToken. The user account allows you to log in to the cluster, create, compile, and test applications, and prepare Flux jobs for submission. The allocation allows you to submit those jobs, executing those applications in parallel on the cluster and charging their resource use against the allocation. A token is required to authenticate you to the cluster.

Flux user account

A single Flux user account can be used to prepare and submit jobs using various allocations. If you already already possess a user account, you can use it for this course, and you can skip to “Flux allocation” below. If not, please visit https://www.engin.umich.edu/form/cacaccountapplication/ to obtain one. A user account is free to members of the University community.

On the web form you’ll be asked to fill out, you should enter your own project and software information. If you don’t have this, good defaults include: for “Project(s) for which you will use the CAC computers,” enter “HPC 101″; for “What software will you be using,” enter “gcc, icc, ifort.”

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

Flux allocation

We’ll issue you a temporary allocation so you can run jobs on the cluster during the course. If you already have an existing Flux allocation, you can use that as well, if you like.

MToken

An MToken (or a Software Token) is required to login to the cluster. When logging in, you will need to give both the passcode it displays at time of login as well as your Kerberos password in order to authenticate. If you already possess an MToken, you can ignore the rest of this paragraph. Otherwise, you should do one of the following:

  • Obtain a token by visiting the LSAIT Help Desk in Suite 1112 LSA Building, 500 S State St. The Help Desk will issue you an MToken and instructions for activiating it. Your simplest course of action is to activate your MToken before you leave the Help Desk area. If you cannot do so, please activate your MToken before you come to class.
  • Request a token from the LSAIT Help Desk by sending an email to lsa-csg@umich.edu or by calling 734 936 3279, and we will send you an MToken through the campus mail. Please make your request no later than four business days before class, and please activate your MToken before you come to class.
  • Show up for class at 12:30 PM, and we will issue you an MToken and instructions for activating it. Note you will need to be able to send and receive email at that time to complete the activation process.

Laptop Preparation

You do not need to bring your own laptop to class. The classroom contains Mac OS X computers, which require your uniqname and Kerberos password to login, that have all necessary software pre-loaded.

If you want to use a laptop for the course, you’ll minimize in-class distractions if you prepare your laptop as follows well before class begins:

  • You will need an ssh client to connect to the Flux cluster. Mac OS X and Lnux platforms have this built-in. Here are a couple of choices for Windows platforms:
  • Optionally, you can use an X server on your laptop to open GUI displays from the Flux cluster. Mac OS X and Linux platforms have this built-in. If you have a Windows platform, consider downloading and installing Xming (http://sourceforge.net/projects/xming/). Visit the “Project home” link at this URL for additional documentation.

More help

Please use our class mailing list hpc101course@umich.edu for questions, comments, or to seek further assistance.