Bura HPC

Using supercomputing resources at University of Rijeka for academic and industrial goals

Vedran Miletić, Faculty of Informatics and Digital Technologies, University of Rijeka

FIDIT

• founded in 2008. as Dept. of Inf. at UniRi, became Faculty of Informatics and Digital Technologies in 2022.
• research (computer vision, pattern recognition, natural language processing, machine translation, e-learning, digital transformation, supercomputing) and teaching

• Image source: Wikimedia Commons File:FIDIT-logo.svg

GASERI

• Group for Applications and Services on Exascale Research Infrastructure
• focus: optimization of computational biochemistry applications for running on modern exascale supercomputers
• vision: high performance algorithms readily available for academic and industrial use in state-of-the-art open-source software

Details about Bura HPC

• hosted at and maintained by Center for Advanced Computing and Modelling at University of Rijeka
• Top 500 in November 2015 ranked it in 441th place
• computing resources
• cooling system and efficiency, data center
• software
• access
• tutorials

Accessing Bura HPC

bura.uniri.hr

Slurm workload manager

• quick start user guide
• sinfo
• squeue
• scontrol
• srun
• sbatch
• scancel

GROMACS molecular dynamics simulation software

• popular open-source molecular dynamics simulation software focused on supercomputer usage
• examples: freezing of ice, bacterial cytoplasm
• paralelization techniques

Input files for GROMACS

• we'll be using a free GROMACS benchmark set prepared by Cartsen Kutzner
  • credit: Theoretical and Computational Biophysics Research Group of Helmut Grubmüller, Max Planck Institute for Multidisciplinary Sciences
  • we'll use wget or curl to download them to Bura

Further reading

• projects
• publications

Author: Vedran Miletić