Supercomputing Technologies Research Group SC@FIT

Hardware topics

• Architecture of parallel systems
• Performance and scaling models of parallel systems
• HPC systems based on GPUs and other accelerators
• Low power systems, power-performance optimization

Software topics

• Domain decomposition for spectral methods
• Automatic load balancing on heterogeneous systems
• Multi-scale and multi-physics model coupling
• Asynchronous input/output in HPC applications
• System for managing and monitoring supercomputers
• Modern programming languages in HPC (Python, OpenACC, Thrust)

Applications

• Simulation of ultrasound propagation in human body
• Acceleration of photoacoustic imaging
• Design of ultrasound sensors
• High performance scientific applications

The research group currently works on the PAMMOTH project on the photoacoustic breast screening. The group is involved in the data collection, on-the fly data quality assessment, and the offline processing on the supercomputer. The image reconstruction is done using our massively parallel implementation of the k-Wave toolbox based on the local decomposition of spectral methods. The full processing automation and monitoring is ensured by the in-house tool k-Dispatch

The group also participates in the project focusing on neurostimulation and neurosurgery. Here, we have been developing the elastic wave simulator accounting for both compression, and shear waves and a novel numeric method for solving problems with jump discontinuities. 

• Prof Hlavička Award for the best presentation at PhD conference  PAD 2019 - Filip Vaverka
• Excellent Poster Presentation Award - Signal Frequency Content and Appearance of Tumors in Photoacoustic Breast Tomography: A Simulation by Maura Dantuma, Felix Lucka, Bradley Treeby, Jiri Jaros, Ben Cox, and Srirang Manohar -  Ultrasonics 2018, Caparica, Portugal.
• Research Poster Award - GPU-accelerated Simulation of Elastic Wave Propagation by  Kristian Kadlubiak, Jiří Jaroš, and Bradley Treeby - HPC applications, ISC 2018, Frankfurt, Germany.
• PRACE HPC Ambassador Award, Marta Čudová, Summer Of HPC, 2016.
• Best paper award, BREITENBACHER Dominik, HOMOLIAK Ivan, JAROŠ Jiří and HANÁČEK Petr. Impact of Optimization and Parallelism on Factorization Speed of SIQS. In: Proceedings of The 20th World Multi-Conference on Systemics, Cybernetics and Informatics. Orlando: The International Institute of Informatics and Systemics, 2016, pp. 55-62. ISBN 978-1-941763-41-4.

Software

• k-Wave toolbox - 20,000+ registered users

Publications

• Modeling nonlinear ultrasound propagation in heterogeneous media with power law absorption using a k-space pseudospectral method - Journal paper, JASA (110 citations)
• Parallel Genetic Algorithm on the CUDA Architecture - Conference paper, EvoStar (50 citations)
• Parallel Genetic Algorithm Solving 0/1 Knapsack Problem Running on the GPU - Conference paper, Mendel (15 citations)

Conferences

• Supercomputing - every year attendance at the best conference in the field, poster 2017, poster 2018
• ISC HPC - every year attendance at the best European conference in the field, poster 2018

PRACE Summer of HPC

• Martin Stodůlka, ULux-University of Luxembourg, Lux, 2021
• Filip Kukliš, SURFsara, Amsterdam, NL, 2018
• Petr Stehlík , CINECA, Bologna, It, 2017
• Marta Čudová , EPCC, Edinburgh, UK, 2016
• Ondřej Vysocký , EPCC, Edinburgh, UK, 2015
• Vojtech Nikl, CINECA, Bologna, It, 2014

Computing resources

• IT4Innovation, CZ, 17 milion core hours
• National Computing Infrastructure, AU, 1 million core hours
• PRACE, EU, 1 million core hours
• Swiss National Supercomputing Centre, CH, 24 thousand core hours

Collaboration offer

The SC@FIT research group offers collaboration in the design and development of applications demanding high compute power, large operational memory and big data. We have deep experience in the R&D of scientific codes for shared memory systems (high-end servers), distributed systems (clusters) and hybrid systems with processors and graphics processing units.

The group also offers the application of the k-Wave toolbox for the nonlinear simulation of ultrasound wave propagation in medical and industrial problems.

Current Collaboration

• Biomedical Ultrasound Group, University College London, UK - development of the simulation toolbox k-Wave for modelling ultrasound propagation in human body
• Institute of Biomedical Engineering, Ludwig Cancer Research, University of Oxford, UK - Kidney cancer treatment planning
• Turku High-Intensity Focused Ultrasound (HIFU) Research Centre, Turku, Finland - Ultrasound Prostate cancer treatment
• IT4Innovations národní superpočítačové centrum, VŠB - Technical University Ostrava, CZ - Research and development on the Anselm and Salomon supercomputer, collaboration in the READEX project
• The University of Twente, Twente, NL - acceleration of the photoacoustic imaging of breast (PAMMTOH project)
• University of Bern, Bern, CH - acceleration of the photoacoustic imaging of breast (PAMMTOH project)
• Medisch Spectrum Twente, Twente, NL - acceleration of the photoacoustic imaging of breast (PAMMTOH project)
• Imasonic SAS, Voray sur l'Ognon, FR -acceleration of the photoacoustic imaging of breast (PAMMTOH project)
• EKSPLA, Vilnius, Lt - acceleration of the photoacoustic imaging of breast (PAMMTOH project)
• Continental, Ostrava - Research and development of  ultrasound sensors
• Faculty of Civil Engineering, Brno University of Technology, CZ - Simulation of fraction tests in quasi-brittle materials

• k-Wave toolbox
• PAMMOTH

Brno University of Technology
Faculty of Information Technology
Department of Computer Systems
Bozetechova 2, Room L334
612 66 Brno, Czech Republic

Phone: +420 54114-1207
E-mail: jarosjir@fit.vutbr.cz

see web pages of the group http://speech.fit.vutbr.cz/

Brno University of Technology
Faculty of Information Technology
Department of Computer Systems
Bozetechova 2 612 66 Brno, Czech Republic

Phone: +420 54114-1207
E-mail: jarosjir@fit.vutbr.cz