Introduction Research Results Future Work HPC Research Group Jiří Filipovič et al. Institute of Computer Science Masaryk University 15. září 2023 Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group Introduction Research Results Future Work E ur Group Main topics: ► generic technologies in HPC ► scientific computing Important synergy ► scientific programs use generic technologies ► generic technologies are inspired and tested on scientific software Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group Introduction Research Results Future Work generic tecnnoiogies All about software adaptability ► software efficiency depends on HW and input ► autotuning CUDA/OpenCL kernels, by Kernel Tuning Toolkit ► autotuning FFT settings by cuFFTAdvisor ► autotuning graphic pipelines by Umpalumpa Typical output ► computer science papers ► software Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group Standardization ► how to test and compare autotuning searchers/frameworks (collaboration with NTNU, eScience Centre)? ► unified specification for tunable code (collaboration with multiple institutions) ► autotuning benchmark (collaboration with NTNU, eScience Centre) ► mainly Filip's work, now abandoned Umpalumpa ► specification of pipeline (what to do with data) decoupled with details, such as distribution on heterogeneous node and autotuning ► data-centric architecture, describe physical and logical properties of data ► in principle allows autotuning on level of the pipeline ► David's PhD Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group Introduction Research Results Future Work ecent wor Tuning space analysis ► how to be sure we have defined a good tuning space? ► detect opportunity for adding faster configurations ► detect always-poor configurations ► collaboration with UAB Tuning budget estimation ► autotuning optimizes the runtime... and requires runtime ► how to decide how much resources invest into autotuning? ► Jaro's PhD Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group Introduction Research Results Future Work DCientmc compuimg Holistic approach ► change mathematics/introduce approximative solution: CaverDock, 4D-GRAPHS ► parallelize/optimize the code: CaverDock, Xmipp ► introduce GPU acceleration: Xmipp, some small projects Typical output ► non-computer science papers (e.g., structural biology), some computer science papers ► software Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group Introduction Research Results Future Work ecent wor CaverDock 2.0 ► utilizing RRT algorithm as an alternative for the original CD algorithm ► allowing the receptor to change conformance ► Petra's PhD Xmipp ► GPU acceleration of continuous heterogeneity ► improving accelerated FlexAlign ► David's PhD, multiple bachelor's and master's thesis Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group Journal papers ► O. Vävra et al. pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support. Bioinformatics. (IF 6.9, Ql) ► D. Streläk et al. Umpalumpa: a framework for efficient execution of complex image processing workloads on heterogeneous nodes. Computing. (IF 3.2, Q2) ► F. Petrovic, J. Filipovic. Kernel Tuning Toolkit. SoftwareX. (IF 3.4, Q2) ► D. Herreros et al. ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis. Journal of Molecular Biology. (IF 5.6, Ql). ► D. Herreros et al. Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials. Nature Communications. (IF 16.6, Dl) Conferences/workshops ► J. O. T0rring et al. Towards a Benchmarking Suite for Kernel Tuners. IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group Introduction Research Results Future Work Ql Q2 Q3 confs/books sum 2017 0 0 0 1 1 2018 0 0 0 1 1 2019 2 2 0 1 5 2020 2 0 2 0 4 2021 3 1 2 1 7 2022 0 1 0 2 3 2023 3 2 0 1 6 Tabulka: Papers of our group where Fila is an co-author. Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group Introduction Research Results Future Work utotuning Searching and analysis of tuning spaces ► analysis of performance counters allows to understand limitations of tuning space ► potential for visual tool ("tuning space profiler") ► further development of profile-based searcher Dynamic autotuning ► new playground: spMV (CUSP) ► practical implementation of tuning budget planing Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group Introduction Research Results Future Work MM! DCientmc L-omputing CaverDock ► we are finishing the version 2.0 ► unclear what to do next Xmipp ► we expect to continue Other projects ► rather limited by our capacity Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group igger ric Introduction Research Results Future Work What goes well ► quite good publication record ► strenghten international collaboration Challenges ► projects ► people Jiří Filipovič et al.Institute of Computer Science Masaryk University HPC Research Group