The Cooperative Computing Lab
2009 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 grants NSF-CCF-0621434 and NSF-CNS-0643229.

Before You Arrive

Keep in email contact Prof. Thain (dthain@nd.edu) and with Dian Wordinger (Dian.Wordinger.3@nd.edu), our secretary who will keep track of all your paperwork and other necessary items. Note that Prof. Thain will be out of town May 19-24, so direct any last-minute questions to Dian.

Dian will help you to complete the three following distinct items:

Apply to the summer session.

Enroll in the REU course for the summer session.

Complete paperwork for employment.

Do not apply for housing, we will do so for you. Here are the costs for housing and meal options.

Make sure that you collect and bring your employment verification documents to Notre Dame, otherwise you will have a hard time getting paid.

When You Arrive

You may arrive on campus anytime between Sunday, May 24th and Tuesday, May 26th. However, note that many campus offices (including food service) will be closed on Sunday and Monday, due to the holiday.

Here is a Campus Map and driving directions.

Check into your dorm and move in. Women will be in Badin Hall and men in Sorin 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 26th at 1PM in 382 Fitzpatrick Hall. There will be an 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. Due to the short session, there are no vacation days. If you are sick, please contact Prof Thain (dthain@nd.edu / 631-6845) in the morning. Full or partial days not worked will be unpaid.

You will be assigned a desk, computer, and laptop 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. The biocompute group meets weekly at 10AM in the CSE conference room. The BXGrid group meets weekly at 1PM in the CSE conference room. Everyone is expected to show a few slides and explain what they learned or accomplished in the last week. (Use your laptop and PowerPoint.)

To help you gain some background in our research area, I will assign one research paper for you to read each week. We will meet a once week at 11AM on Mondays in my office, 382 Fitzpatrick to discuss the paper in detail. You should be prepared to explain the algorithms or system described in the paper, and have a list of questions for us to discuss.

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 26th 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, Chirp, and Parrot.

Condor - (http://condor.cse.nd.edu) 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.

Parrot and Chirp - (http://www.cse.nd.edu/~ccl) Download, build, and install the CCTools package on your workstation. Use Parrot to access our distributed storage pool. Run your own Chirp server, and learn how to manipulate the access controls. Try to discover and use as many options and features as you can find.

Wednesday, May 27th we will have two "all-hands" meetings for the biocompute and bxgrid projects, so that you can gain a high level understanding of the research project, as well as meet some of our "customers". All students should attend both meetings in the CSE conference room:

10-12 Biocompute Group Meeting

11:45-12:15 - Lunch

12-2 BXGrid Group meeting

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.

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, July 31st.

The final activity for the summer will be a lunch and closing ceremony on Friday, July 31st. You may check out of your dormitory and depart that afternoon, or on the following day.

The Cooperative Computing Lab2009 Summer Undergraduate Research Instructions