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.
Anyone who wants to start processing large data volumes (tens to hundreds of terabytes or even more)
SURF Utrecht. Kantoren Hoog Overborch (Hoog Catharijne), Moreelsepark 48, 3511 EP Utrecht. Room 3.5.
Get directions with
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.
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.
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.
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.
Select “Use the nano editor by default” and click on “Next”.
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.
Click on "Next".
Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
Select "Use Windows' default console window" and click on "Next".
Click on "Install".
Click on "Finish".
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press [Enter])
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press [Enter], you should see SUCCESS: Specified value was saved.
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
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
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.