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CCL Handbook

Welcome to Notre Dame and the Cooperative Computing Lab! This handbook is a brief introduction to all of the resources available in the lab as well as policies that everyone must follow.

First Week Checklist

Although you will already have a specific research project to work on, take the time to run down this checklist during your first week, so that you are familiar with all of the resources in the lab. Ask Prof. Thain to do the following:
  • Add you to the ccl:team AFS groups.
  • Give you an account on the various ccl machines.
  • Add you to the Condor rank for ccl machines.
  • Add you to the team members page (send him a nice profile picture.)
  • Subscribe yourself to these mailing lists:
    • cctools: The public CCTools forum
    • ccl-team-list: The CCL team private discussion mailing list.
    • cctools-build-list: The private CCTools (auto-)build mailing list. This list gives mails whenever a commit to CCTools is made.
    You may also want to subscribe to these mailing lists: Get yourself set up to work in AFS:
  • Ask for an account at the Center for Research Computing with Prof. Thain as your sponsor.
  • Read about our storage organization and AFS instructions
  • Create a new workspace for yourself: mkdir /afs/crc.nd.edu/group/ccl/work/$USER
  • Add the appropriate cclimport commands to your startup script, as described in the Software Organization
  • Try each of these ways of getting the software:
  • Check out a copy from github
  • Create an account on github and clone cctools into your own repository there.
  • Download and compile a package from the web.
  • Explore the web infrastructure:
  • Browse the bug tracking system Submit a bug report, add a comment, take ownership, and resolve it. If you see a bug that looks easy to fix, then go ahead and take it.
  • Browse the CCTools API. Write a simple program that submits a batch job, or talks to a Chirp server.
  • Browse the github repository, and see who has checked in code lately.
  • Learn how to use Condor;
  • Check out the Condor overview pages.
  • Follow the ND Condor tutorial.
  • See who is on top of the scoreboard.
  • Research Integrity and Intellectual Property

    We expect that you will uphold the highest standards of integrity in your professional lives. There are many dimensions to integrity, but they mostly boil down to tell the truth and tell the whole truth. We will have many opportunities to discuss aspects of research integrity during your time at Notre Dame. However, there are several starting points that everyone must be aware of.

    You must understand and abide by the following codes of conduct.

  • Notre Dame Honor Code
  • IEEE Code of Ethics
  • ACM Code of Ethics
  • You must take and pass the Engineering Basic Course offered by CITI: (a Notre Dame requirement)
  • www.citiprogram.org
  • All of the code and data that you create as part of your employment at Notre Dame is owned by the University. All such code must be marked as "Copyright (C) XXXX The University of Notre Dame", but may also indicate your authorship. Our NSF funding indicates that our software products will be released as open source, and thus are licensed under the GNU General Public License. This license protects everybody: when you leave the University, both you and the CCL will continue to be free to use and modify what you have created.

    The University does not claim copyright on written materials such as journal papers and book chapters; this remains with the authors. Most conferences and journals require that copyright be signed over to the publisher as a condition of publication. Some (but not all) allow authors to continue to simultaneously distributed published papers via the web. Read before you sign.

    At a practical level, we require that all work done in the CCL be stored in a way that it is safely backed up and accessible to others in the lab on a regular basis. For working code and other items that are not yet published, this simply means that they must be stored in AFS under ~ccl/work/YOURNAME. Once a project has reached a reasonably stable point, it should be checked into an appropriate code repository.

    Published work has a higher threshhold. All papers submitted for publication must be checked into the CCL papers repository. The check-in must include the source and data for all figures and graphs, and where possible, the raw data and reduction scripts. The build procedure for the paper should run the data reduction, construct the graph, and embed it in the paper. Should there be any question about the data or methods presented in the paper, the repository will describe exactly how the results were obtained.

    It is not acceptable to embed a raster image transferred from another program, because this does not capture the actual data and makes it difficult to adjust axes, captions, and so forth.

    General Advice

  • Get Organized. Grad school is a busy mix of classwork, meetings, research, and other tasks. So, set up a Google calendar with all of your activities, and share it with Prof. Thain, and overlay the CCL calendar. Make a to-do list for both the short and long term, and put it in plain view on your desk.

  • Mind Your Requirements. It is your responsibility to make sure that you are meeting all of the requirements for graduate school: courses, credits, defense dates, and so on. Double and triple check with Joyce that you are on track every semester.

  • Be a Good Citizen. Help out your fellow students by debugging problems, attending talks, proofreading papers, and generally taking the time to learn what they are doing. Not only is this good karma for when you need help, but it will help you to understand the broader context of research.

  • Keep the Customers Satisfied. Strive to build systems that are truly useful to someone, whether at Notre Dame or elsewhere. A customer that takes the time to complain about bugs is priceless, because they really care about your tool, and want a working solution. Having a real customer is strong evidence that you have solved the right problem and have solved it correctly. Take the time and effort to develop a working relationship, and it will pay off in spades when the time comes to write about the impact of your work.