CMPUT 497: Cluster Challenge and Computational Science

Paul Lu
Department of Computing Science
January 2009

Assignment 1: Setting up SGE using Virtual Machines

Report Due Date: Thursday, March 12, 2009, in class.
Demonstrations to be scheduled for March 13 and 16.

Description:

This assignment is to be done individually and is worth 12.5% of your mark in the course.

The purpose of the assignment is for you to learn more about setting up the SGE batch scheduler, especially in a virtual machine (VM) environment. In contrast, the next assignment will be about parallel programming and benchmarking.

There are 3 main components to the assignment:

  1. Set Up Your Virtual Machines: Follow the instructions in the document about SGE and VMs (Feb. 27/09 updated to point to Version 3) (March 4/09 Erkan's slides are now available too) created by Erkan Unal. The goal (see the Demonstration component below) is to be able to demonstrate that you have created a cluster of virtual machines that run the SGE batch scheduler. Note that Erkan has previously (in class) demonstrated the final product/result.

    Although great care has been taken in preparing this document, mistakes and omissions are possible. Please immediately ask your questions by email to both Erkan (unal@cs.ualberta.ca) and myself.

  2. Install an Application (of the Student's Choice): Choose any application that you wish. For example, some of you have experience with applications such as RAxML, GROMACS, etc. Install this application inside your VMs such that you can run batch-scheduled jobs that use this chosen application.

    The application does not have to be from computational science; in the worst case, you can always use an application such as gnuplot. The point of this part of the assignment is to install an application that was not previously installed in the VM, and to demonstrate that you can run that application using the SGE batch scheduler.

  3. Demonstration and Report: On either March 13 or 16 (other dates are possible), we will set up a 1-on-1 meeting (of about 15 minutes) for you to demonstrate that your SGE/VM setup works with the application that you have chosen. There is no set format for this demonstration. You should design a series of steps to convince me that SGE is working and show me that your chosen application produces the right output.

    The choice of actual input data and parameters for running your application are entirely up to you.

    Write a 1-page report (1 inch margins, at least 12 point font, single-spaced) answering the following questions:

    1. What was the most challenging aspect of installing SGE under the VMs? (This is mostly feedback to Erkan and myself.)
    2. Why did you select your chosen application?
    3. Was it difficult to get the application to work under SGE? Why or why not?

      For example, in terms of the current working directory (and paths required by the application), in terms of getting the right input files to the application, and in terms of copying the output files to a given location, what were the issues that you had to solve?

    Obviously, given the 1-page limit, I am not expecting a long discussions. Be precise and concise in answering the above questions.

    Be aware of the Code of Student Behaviour and it how applies to referencing source material, if applicable.

What to hand in:

On the due date, hand in via paper copy and email of your electronic files, your report. We will try to set up meeting times for the demonstration during class.

Marking:

The assignment is worth 12.5% of your final mark in the course. This is an individual assignment. Do not work in groups. You may discuss the assignment with other students, but the report and the setup of SGE and the application must be your individual work.

70% of the marks will be for the demonstration. 30% of the marks will be for the report.

General comments on assignments:

  1. In formal writing, such as this assignment or a report to your boss, be careful to not use contractions (e.g., that's, can't, doesn't) and do not use overly colloquial words or phrases (e.g., huge chunk, deal breaker, new kid on the block).
  2. Be careful of making statements that you cannot support with evidence. Your statement might be right. The instructor might have even said it in class. But, unless you can make the argument with the support of facts, or cite a paper or the lecture notes, then it is risky to make such statements.
  3. Be sure to answer all the required questions in your report.