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Maciej Cytowski, PhD

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Publications, whitepapers & documentation:

  • "Offloading over Fabric for the Timothy application: Running agent-based parallel tissue modeling framework on a heterogeneous system with Intel Xeon and Xeon Phi Processors.",Piotr Uminski, Maciej Cytowski, Zuznna Szymanska, Krzysztof Raszkowski and Grzegorz Andrejczuk, IXPUG Spring Conference 2017 [website]
  • "Enabling large scale modelling of personalised stem cells therapy through High Performance Computing", J.Jurek, D.Bakalarz, M.Cytowski, Supercomputing Frontiers 2017 Conference [website]
  • "Computational modelling of cancer growth and invasion: Modelling at multiple scales and multiscale modelling", Szymanska, Z., Cytowski, M., Mitchell, E., Macnamara, C.K., Chaplain, M.A.J., Bull. Math. Biol., accepted
  • "Implementation of an Agent-Based Parallel Tissue Modelling Framework for the Intel MIC Architecture", Maciej Cytowski, Zuzanna Szymanska, Piotr Uminski, Grzegorz Andrejczuk, Krzysztof Raszkowski, Scientific Programming, 2017, Article ID 8721612, 11 pages, doi:10.1155/2017/8721612
  • "The Copernicus Complexio: a high-resolution view of the small-scale Universe", Wojciech A Hellwing, Carlos S Frenk, Marius Cautun, Sownak Bose, John Helly, Adrian Jenkins, Till Sawala, Maciej Cytowski, Monthly Notices of the Royal Astronomical Society, 2016/4/21, Vol. 457/4, pp.2492-3509 [pdf]
  • "Enabling Large Scale Individual-Based Modelling through High Performance Computing", M.Cytowski, Z.Szymanska, Conference: Workshop on Multiscale and Hybrid Modelling in Cell and Cell Population Biology, UPMC, Paris, March 16-17, 2015,ITM Web of Conferences 5, 00014 (2015), DOI: 10.1051/itmconf/20150500014 [pdf]
  • "Large Scale Computational Modelling of Cellular Biosystems", M.Cytowski, PhD Thesis [pdf]
  • "Large Scale Parallel Simulations of 3-D Cell Colony Dynamics. II. Coupling with continuous description of cellular environment", M.Cytowski, Z.Szymanska, IEEE Computing in Science and Engineering, vol.PP, no.99, pp.1,1, doi: 10.1109/MCSE.2015.66 [preprint]
  • "SOMPARlib: Simple OpenMP Adaptive Runtime Library", M.Cytowski, The Journal of Supercomputing, Springer, submitted
  • "Best Practice Guide - IBM Power 775", M.Cytowski, PRACE Best Practice Guide available on-line at www.prace-ri.eu [pdf]
  • "Best Practice Guide - IBM Blue Gene/Q", P.Wautelet, M.Boiarciuc, J.-M.Dupays, S.Giuliani, M.Guarrasi, G.Muscianisi, M.Cytowski, PRACE Best Practice Guide available on-line at www.prace-ri.eu [pdf]
  • "Large Scale Parallel Simulations of 3-D Cell Colony Dynamics", M.Cytowski, Z.Szymanska, IEEE Computing in Science and Engineering, vol.16, no.5, pp.86,95, Sept.-Oct. 2014, doi: 10.1109/MCSE.2014.2 [pdf]
  • "A 2-D Large-scale Individual-based model of solid tumour growth", M.Cytowski, Z.Szymanska, B.Borucki, GAKUTO International Series, Mathematical Sciences and Applications, Vol.36(2013), pp.43-56
  • "Scalability Analysis and OpenMP Hybridization of a Code for Direct Numerical Simulation of a Real Wing", M.Cytowski, M.Bernardini, PRACE Whitepaper available on-line at www.prace-ri.eu [pdf]
  • "Towards Autotuning of OpenMP Applications on Multicore Architectures", J.Katarzynski, M.Cytowski, arXiv:1401.4063 [cs.DC] [link]
  • "3D-Hit: fast structural comparison of proteins on multicore architectures", L.Bieniasz-Krzywiec, M.Cytowski, L.Rychlewski, D.Plewczynski, Optimization Letters, Springer Berlin Heidelberg,ISSN 1862-4472, p.1-12, 2013 [link]
  • "FLY on Cray: Porting, Optimization and Performance Analysis of Cosmological Simulation Code FLY on Cray XE6 Architecture", V.Antonuccio-Delogu, U.Becciani, M.Cytowski, J.Hein, J.Hertzer, PRACE Whitepaper available on-line at www.prace-ri.eu [pdf]
  • "Performance Analysis of Parallel Applications on Modern Multithreaded Processor Architectures", M.Cytowski, M.Filocha, J.Katarzynski, M.Szpindler, PRACE Whitepaper available on-line at www.prace-ri.eu [pdf]
  • "Large Scale Simulations of the Non-Thermal Universe", C. Gheller, G. Ferini, M. Cytowski, and F. Vazza, PRACE Whitepaper available on-line at www.prace-ri.eu [pdf]
  • "Increasing efficiency of DaCS programming model for heterogeneous systems", M.Cytowski, M.Niezgodka, Parallel Processing and Applied Mathematics 2011, Lecture Notes in Computer Science, Vol. 7203, pp.710-719 [materials]
  • "Analysis of gravitational wave signals on heterogeneous architecture", M.Cytowski, PARA 2010, Part I, LNCS 7133, pp. 347-357, Springer, Heidelberg (2012)
  • "Nautilus - A Testbed for Green Scientific Computing", B.Borucki, M.Cytowski, M.Remiszewski, ERCIM News 79, October 2009 [pdf]
  • "Astronomical period searching on the Cell Broadband Engine", M.Cytowski, M.Remiszewski, I.Soszyński, Parallel Processing and Applied Mathematics 2009 (book chapter), Lecture Notes in Computer Science, Vol. 6067/2010, pp.507-516
  • "Uniqueness and local existence of solutions to an approximate system of a 1D simplified tumor invasion model", M.Cytowski, A.Ito, M.Niezgódka, Banach Center Publ. 86 (2009), 45-58 [Materials]
  • "Numerical Weather Forecasting for Poland", M.Cytowski, M.Szpindler, ERCIM News 74, July 2008 [pdf]
  • "Parallel Position-Specific Iterated Smith-Waterman Algorithm Implementation", W.Rudnicki, R.Maszkowski, L.Bolikowski, M.Cytowski, M.Dobrzynski, M.Fronczak, Proceedings of Cray User Group Conference 2006, Lugano, Switzerland [pdf]
  • "Implementation of the Vectorized Position-Specific Iterated Smith-Waterman Algorithm with Heuristic Filtering Algorithm on Cray Architecture", W.Rudnicki, R.Maszkowski, L.Bolikowski, M.Cytowski, M.Dobrzynski, M.Fronczak, Proceedings of Cray User Group 2005 Conference, Albuquerque, New Mexico. [pdf]
  • "Tuning Vector and Parallel Performance for Molecular Dynamics Codes on the Cray X1e", K.Wawruch, L.Bolikowski, W.Burakiewicz, M.Cytowski, M.Fronczak, M.Kozakiewicz,M.Lopuszynski, F.Rakowski, J.Slowinska, Proceedings of Cray User Group 2005 Conference, Albuquerque, New Mexico.

Contributions:

  • "Final Benchmark Suite (D6.3.2)", Partnership for Advanced Computing in Europe, 21.12.2009, [pdf]
  • "Report on petascale software libraries and programming models (D6.6)", Partnership for Advanced Computing in Europe, 26.10.2009, [pdf]
  • "Report on Porting and Optimisation of Applications (D6.5)", Partnership for Advanced Computing in Europe, 26.10.2009, [pdf]
  • "Report on available Performance Analysis and Benchmark Tools, Representative Benchmark (D6.3.1)", Partnership for Advanced Computing in Europe, 24.11.2008, [pdf]

Posters:

  • "iCell: Multiscale modelling of breast tumour growth", W.Wronowska, G.Bokota, M.Kadlof, J.Sroka, M.Cytowski, A.Kierzek, D.Plewczyński, 7th International Workshop on Biological Processes and Petri Nets (BioPPN 2016).

Selected Conferences and Workshops: