Do you have tens to hundreds of TBs of data that you want to process
in a uniform and reproducible manner
with software that can be uniformly distributed
and actively collaborate, share your results with, colleagues without having to transfer the data or reinstall the software?
The objective of the workshop is to provide hands-on experience on the upcoming elastic high throughput Spider platform with features designed to cater to such needs. If you are also curious in integrating additional functionalities such as software containers or Jupyter Notebooks in your workflows, access to external storage systems or would like to have your own cluster specifically tailored to your project needs, join us in Utrecht on August 28!
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.
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.
Running data analysis and using collaboration features
16:15
Additional features on the platform and conclusion
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.
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.
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
(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.
