Researchers can transfer their computing from Google’s Colab to CSC’s environment using a new application. A similar approach can be adapted if one wants to move from one supercomputing environment to another.
Application Specialist Laxmana Yetukuri at CSC – IT Centre for Science and Specialist Researcher Michael Courtney at Turku Bioscience Centre have customised GPU-empowered notebooks originally developed by the Centre’s team, that can apply deep learning models for biological image data in the CSC supercomputing environment. There is also an open-source toolkit, ImageJ/Fiji, for the deep learning models in microscopy and the usage of the toolkit is under exploration at CSC, the Finnish node of the ELIXIR infrastructure.
Researchers can transfer their computing from Google’s Colab to CSC’s environment using an in-house developed container wrapper. The container wrapper allows researchers to define a standardised environment in which they can run scientific software. The program’s code, along with its libraries and settings, is placed within the container. Once the software and its dependent packages are installed as part of the wrapper tool, other users can start using the application without any pre-installations. A similar approach can be adapted if one wants to move from one supercomputing environment to another.
“We make the work of researchers easier by providing easy-to-follow instructions for the installation of user’s custom notebooks. Once a project member installs an application in their project area, other researchers don’t need to install any software to use custom notebooks – they can start working immediately. Accessing CSC’s notebooks in supercomputing environment requires just a few clicks on the web interface (www.puhti.csc.fi),” says Yetukuri.
“Biological image analysis typically needs larger disk space for storing image data. CSC object storage ALLAS provides a good storage environment. The computing environment can be accessed only with a user account obtained from CSC,” Yetukuri says.
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ELIXIR is partly funded by the European Commission