The Cooperative Computing Lab
2012 Summer Undergraduate Research Instructions

Welcome to Notre Dame for the summer! I hope you have a productive and enjoyable summer doing a research project with my group. Your summer salary has been funded by the National Science Foundation under grant NSF-CNS-0643229.

Before You Arrive

  • For any questions or concerns, contact BOTH Prof. Thain ( AND Dian Wordinger (, our administrative assistant who will keep track of all your paperwork and other necessary items. Note that Prof. Thain will be out of the office for part of May, so be sure to mail both of us.
  • Housing: If you want to live on campus, look over the housing rates, decide whether you want single or double, A/C or not, and let us know ASAP what you prefer by email. But, don't apply for housing, we will do that for you.
  • Employment: Fill out the following three documents (DD, W-4, I-9) and bring them with you to Notre Dame. Also bring the necessary documents (driver's license, etc) listed on page 5 of the I-9 form.
  • Registration:
  • Current Notre Dame students should use InsideND and register for course EG48999; CRN 2795.
  • Non-Notre Dame Students: You will need to register for summer course using the Summer Session Website.
    1. Click on "First time user account creation" below Login button
    2. Create a Login ID and PIN (PIN must be six numbers)
    3. Choose "Summer Session Undergraduate" from the Application Type
    4. Choose "Summer Session 2012" for Admission Term
    5. Fill in sections for name, permanent address, present address, personal information, international information, colleges attended, and academic status.
    6. On the "Courses for Academic Credit" section, enter the following information:

      In the first box for course selection enter the following information as a, b, and c: REU; Department of Computer Science and Engineering; Working with Dr. Douglas Thain on distributed scientific computing.

      In the second box for course selection enter the following as a, b, and c: Course: EG 48999; CRN: 2795; Research Experience for Undergraduates

    7. Click on continue then "Application is Complete" (once all appropriate data is entered).
    Once your application is received and verified by the department, you will receive a confirmation email from the Summer Session Office. With the confirmation email, you will receive additional campus information regarding parking passes, student IDs, health services, etc. For questions regarding only the above application process, contact or 574-631-7282.
  • When You Arrive

  • Plan to check into your dorm in the afternoon on Monday, May 28th and then begin work on Tuesday, May 29th.
  • Here is a Campus Map and driving directions.
  • Women will be in Walsh Family Hall, and men in Keough Hall.
  • Obtain an ID card and sign up for a meal plan at the Card Services Office.
  • Here are Places to Eat when you first arrive.
  • The REU program will begin on Tuesday, May 29th at 9AM in 382 Fitzpatrick Hall. There will be a group orientation and some additional paperwork before we get down to work.
  • Over the Summer

  • This summer project has two goals. First, you will participate in the construction and improvement of systems for research in bioinformatics and biometrics, which will play an important role in our ongoing research project. Second, you will gain some experience in doing research, which involves programming, making measurements, presenting results, and understanding other research projects in the field. By the end of the summer, you should have a good understanding of what it means to do research, and (we hope) you will consider that career path.

  • Plan to work 9AM-5PM Monday through Friday for ten weeks. You will be paid biweekly. You will be billed directly for housing, which you should pay using your stipend. If you are sick, please contact Prof Thain ( / 631-6845) in the morning. Full or partial days not worked will be unpaid, excepting the July 4th holiday.

  • You will be assigned a desk and computer in Cushing 222 on which to perform your work. You will be given remote access to other machines and equipment as your project requires. These machines are to be used for research purposes only, and should not be used for personal matters, especially not transferring, sharing, or storing copyrighted media. Notre Dame has a site license for Windows and Office software, these are to be used only on ND owned machines.

  • Research is a collaborative activity. You will be working with other students on a daily basis, and should be talking to each other regularly to identify problems and solutions. We will have group meetings at 1PM on Wednesdays in the CSE conference room to review progress. Everyone is expected to give a short demo and explain what they learned or accomplished in the last week.

  • Don't get stuck on a technical problem! Ask others for advice, get a book from the library, search for help on the web, but don't just spin your wheels. It's perfectly ok for you to come knock on my office and get help several times a day until you work through a problem.

  • There will be a number of social activities in conjunction with the ErWin REU Program. You will also be housed in the same dormitory with other students from around the country. Take the opportunity to make friends and relax in the evenings and weekends.

  • The First Week

  • Tuesday, May 29th we will have an initial meeting to talk about expectations for the summer. You will get settled in your offices, meet everyone, and finish any remaining employment paperwork. Once that is done, your job will be to learn how to use the building blocks of our research tools: Condor, Makeflow, Work Queue
  • Condor - ( Use the Condor software out of AFS. Learn how to explore the pool. Read the "Slides and Tutorial" link to learn about Condor, and submit some sample jobs. Do the "In Class Assignment" on the last slide as a homework problem.
  • Makeflow - ( Read the manual, and try out some simple examples your self. Learn how to run jobs locally, on the Condor pool, and using the Work Queue. Try to do something really complicated running on hundreds of cores.
  • Work Queue - ( Read the manual, download the cctools, and try writing a simple application in C, Perl, or Python. Try running with workers submitted to the Condor pool. Modify the work queue program to do something more complex.
  • Wednesday we will have a group meeting at 1PM, where all of the students will give a short update on their work. You will also have another weekly meeting (time TBA) with our "customers" that will be using your software.
  • Thursday and Friday you will work on a "getting started" project decided on Wednesday. This will be a short task to help you get up to speed with our systems and software, and to get you in the right frame of mind for delivering high quality software for our customers. (Even simple things can be hard when they have to be done perfectly!) Once you have completed the starter project, then we will pick out something larger for the rest of the summer.
  • Other Events

  • June 9th at 9am, plan to attend Peter Bui's PhD defense.
  • June 11th and 12th, plan to attend the CCL Workshop
  • Thursday, June 14th - Cedar Point outing with Erwin group.
  • Thursdays at 11AM - REU Seminar in 356 Fitzpatrick
  • Fridays at Noon - Pizza Social in CSE Conference Room
  • At Summer's End

  • You will make two final reports on your summer work. You will develop a detailed technical poster, which will be presented at the REU symposium on Friday, August 3rd.
  • The final activity for the summer will be a lunch and closing ceremony on Friday, August 3rd. You may check out of your dormitory and depart that afternoon, or by noon on Saturday, August 4th.
  • Other Links of Interest

  • Notre Dame
  • Places to Eat at Notre Dame
  • LaFortune Student Center
  • St. Joseph's Beach on Campus
  • St Patrick's County Park
  • City of South Bend
  • South Bend Public Transportation
  • South Shore Railway