In the heart of Europe…

The mountain at the Buda side as captured from the Pest side

In the heart of Europe and more specifically in Budapest, the capital of Hungary, I will spend my summer. The city is split in two parts by the Danube River, the Buda and the Pest. The Pest side, where both the NIIFI and we reside in, is urbanised with many shops, large malls and a vivid night life, while the Buda side is more residential with many trees and also hosting the famous Buda castle. The two sides are connected by numerous bridges, which are beautifully lighted in the night creating a wonderful majestic atmosphere.

The supercomputers hosted in the basement of NIIFI at Budapest, Hungary

During the first day at NIIFI, we met our mentors and they showed us the infrastructure that was hosted in their facilities. In general, the first week was introductory, teaching us how to use the supercomputers and how to visualize molecules, which will be the final outcome of our project here (Visualization and Performance Analysis of PRACE Material Science Community Codes: Quantum Espresso and Siesta). The initial objective was to familiarize with the visualization tools and for this reason we employed molecules uploaded on the internet by other scientists for our first visualization attempts. As an example, below you can see an image of a protein, which is the result of my first visualization effort. Later, we will learn how to extract molecule structures using the Quantum Espresso and the Siesta programs. Finally, we will work on improving the rendering techniques for better visualization of the structures that were created in the previous phase of this SoHPC program. Stay tuned…

Visualization with VMD (structure obtained from: Rossi, P. et al. Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome. Nucl. Acids Res. 41, 2756-2768 (2013).)