marie quickstart

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The SteenLab server is named marie for Marie Tharp, a pioneering oceanographer who used sounding data collected by others to create the first high-quality bathymetric map of the world’s oceans. In that spirit, we hope that you will use marie to gain a new understanding of how the planet and the microbial world work.

Getting an account

To access marie, you will need the following:

  • A University of Tennessee email account.
  • An account on marie. If you don’t have one already, ask permission from Drew Steen.
  • A virtual private network (VPN) client, such as PulseSecure, connected to University of Tennessee’s VPN.
  • A shell on your computer.
    • If you are using a Mac, it is easiest to use the Bash or zsh shells that come default with OS X. This is what you get when you open the ‘Terminal’ program.
    • If you are using a PC, it is a little more complicated. In newer versions of Windows 10, you can enable a true, Linux-based Bash shell by enabling Windows Subsystem for Linux. If that isn’t possible, the best alternative is probably to use Git Bash. It is also possible to use the Windows-native PowerShell, but this will require you to learn two different shell languages.
  • A very basic understanding of how to use a Linux shell such as Bash, and a basic idea of how to use conda environments.

Getting started

Take the following steps to access marie:

  • Make sure that you are connected to UT’s VPN. If you are using PulseSecure, there will be a little green arrow on the PulseSecure logo when you are connected.
  • Open your shell (Terminal on OS X, Git Bash or similar on Windows).
  • Type ssh <username>@marie.bio.utk.edu, replacing with your username, and enter your password when prompted. You will now be connected to marie, so that any commands you type into your shell are executed on marie.
  • Activate a conda environment. Note to self: I’d like to edit everyone’s .bashrc so that it will automatically start a lab-default conda environment on login.
  • Congratulations! You can now run jobs on marie to your heart’s content.

Rules

  • Taylor Royalty is marie’s system administrator. What he says, goes.

Passwords and security

marie is subject to frequent hacking attempts. We have already had to wipe the system clean once due to a successful takeover by hackers. Thus, please take these rules seriously.

  • When you are given a marie account, your password will be set to a random 8-character string. I urge you to keep your password in a password manager such as LastPass, rather than an unencrypted file such as a Word document or similar.
  • You may change your password, but if you do, change it to another randomly-generated 8-or-more character string, for example one generated by a password manager. Please do not use a password containing real words, birthdays, etc.
  • We will inform you of your password in person or via text message or similar. Please do not write your password in an email.
  • All of this is on the honor system. However, violation of password rules is grounds for having your marie account revoked.

Use of conda environments

  • Use a conda environment for all of your work.
  • If you think you need to install software outside of a conda environment, check with Taylor or Drew first.

Hard drive use

  • Right now, hard drive space is not a problem. In the future we may implement limits on hard drive use.
  • Common data sets, such as the SwissProt database, are stored at TBD. All users may read but not write to that space.
  • Users must keep their own data in their own directory, ~/<username>/. If you download data that you think would be useful to others, please contact Taylor or Drew to put it in the public data directory TBD.
  • marie’s hard drives are under RAID control, which give some resilience to hard drive failure. However, each user is responsible for backing up essential data, code and results.
  • Users are urged to organize their directories logically, with one folder for each project. Within each project directory, data should be kept in the data directory, code in dedicated directories, etc.
  • Users are strongly encouraged to keep their code under git control, so that it is easier to recover from mistakes.