Getting started on the high-throughput data processing platform

Aug 28, 2019

13:00 - 17:00 pm

Instructors: Maithili Kalamkar Stam (SURFsara), Natalie Danezi (SURFsara)

Helpers: Mateusz Kuzak (DTL)


General Information

Vastly increasing data volumes and data complexity imply that researchers require novel solutions to large scale cluster computing. This workshop aims to provide an introduction and hands-on experience with our new solution to this problem: “a new and versatile platform for high-throughput data processing”. The objective of the workshop is to distinguish the different functionalities of the platform, to provide information on applying for access, and to give participants hands-on experience with basic job processing, software distribution and portability, using internal and external storage systems, and how to collaborate on data analysis within a project. Participants will acquire first hand experience with the flexibility, interactivity and interoperability offered by the platform.

Who: Anyone who wants to start processing large data volumes (tens to hundreds of terabytes or even more)

Where: SURF Utrecht. Kantoren Hoog Overborch (Hoog Catharijne), Moreelsepark 48, 3511 EP Utrecht. Room 3.5. Get directions with OpenStreetMap or Google Maps.

When: Aug 28, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). Basic knowledge of UNIX commandline, bash scripting and cluster computing is expected.

Contact: Please email mateusz.kuzak@dtls.nl , carlos.teijeiro@surfsara.nl or maithili.kalamkar-stam@surfsara.nl for more information.

Schedule

13:00 Introduction to the high throughput platform
13:30 Login to the platform (ssh key troubleshooting)
14:00 Demo of data manager and software manager role
15:00 Coffee
15:15 Submitting jobs and using collaboration features
16:15 More demos of additional features and Wrap up
17:00 END

Sponsors

This workshop is sponsored and supported by ELIXIR-EXCELERATE. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.

EXCELERATE

Setup

You will be granted access to the SURFsara computing facilities during this workshop. In order to participate, you will need access to the software described below on your laptop.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. Select “Use the nano editor by default” and click on “Next”.
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Select "Use Windows' default console window" and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are BBEdit or Sublime Text.

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.