About me

sdr

I work as a Research Scientist at Varian Medical Systems Finland Oy.

Before joining Varian, I conducted research on eigenvalue problem solvers, numerical linear algebra, high performance computing and task-based parallelism at Umeå University, Sweden. I graduated from University of Jyväskylä, Finland. My PhD dissertation focused on GPU computation, fast direct linear system solvers and image denoising.

Curriculum vitae (CV): 1. June, 2021

Emails: mirko.myllykoski (a) google dot com

Other: ORCID [0000-0002-3689-0899], Umeå university, LinkedIn, ResearchGate, Google Scholar, Github, ArXiv, jyx repository, DiVA repository.

Software

StarNEig library

StarNEig library aims to provide a full suite of task-based algorithms for solving nonsymmetric dense standard and generalized eigenvalue problems. The library is built on top of the StarPU runtime system and targets both shared memory and distributed memory machines. Some components of the library support GPUs.

The library is open source and published under the BSD 3-Clause licence. The library and the accompanying documentation are available at https://nlafet.github.io/StarNEig.

Teaching and training

  • Training courses (HPC2N/PRACE):
    • Introduction to GPU programming: When and how to use GPU-acceleration?, 1 day, fall 2019 (hpc2n, git repository)
    • Introduction to HPC2N, 1 day, co-organizer, biannual since spring 2020 (hpc2n)
    • Also involved (helper/mentor): Scientific computing in R (hpc2n), Using R in an HPC environment (hpc2n), AI For Science Bootcamp – NVIDIA/ENCCS (ENCCS)
  • University courses (University of Jyväskylä):
    • Multicore Programming (TIEA342)
      • organizer,spring/summer 2016, in Finnish (TIM)
      • co-organizer,spring 2011, in Finnish
    • Numerical Methods (TIEA381), assistant, 2013, in Finnish

Publications

In press and submitted

Peer-reviewed publications

  • Mirko Myllykoski, Carl Christian Kjelgaard Mikkelsen: Task-based, GPU-accelerated and Robust Library for Solving Dense Nonsymmetric Eigenvalue Problems, Concurrency and Computation: Practice and Experience, 33 (11), 2021 (online since 2020; e5915), doi: 10.1002/cpe.5915 (postprint, DiVA, arXiv:2002.05024, source code)
  • Mirko Myllykoski, Carl Christian Kjelgaard Mikkelsen: Introduction to StarNEig — A Task-based Library for Solving Nonsymmetric Eigenvalue Problems, In Parallel Processing and Applied Mathematics, 13th International Conference, PPAM 2019, Bialystok, Poland, September 8–11, 2019, Revised Selected Papers, Part I, Lecture Notes in Computer Science, Vol. 12043, Wyrzykowski R., Deelman E., Dongarra J., Karczewski K. (eds), Springer International Publishing, pp. 70-81, 2020, doi: 10.1007/978-3-030-43229-4_7 (postprint, DiVA, arXiv:1905.04975, source code)
  • Carl Christian Kjelgaard Mikkelsen, Mirko Myllykoski: Parallel Robust Computation of Generalized Eigenvectors of Matrix Pencils, In Parallel Processing and Applied Mathematics, 13th International Conference, PPAM 2019, Bialystok, Poland, September 8–11, 2019, Revised Selected Papers, Part I, Lecture Notes in Computer Science, Vol. 12043, Wyrzykowski R., Deelman E., Dongarra J., Karczewski K. (eds), Springer International Publishing, pp. 58-69, 2020, doi: 10.1007/978-3-030-43229-4_6 (postprint, DiVA, arXiv:2003.04776, source code)
  • Mirko Myllykoski: A Task-Based Algorithm for Reordering the Eigenvalues of a Matrix in Real Schur Form, In Parallel Processing and Applied Mathematics, 12th International Conference, PPAM 2017, Lublin, Poland, September 10-13, 2017, Revised Selected Papers, Part I, Lecture Notes in Computer Science, Vol. 10777, Wyrzykowski R., Dongarra J., Deelman E., Karczewski K. (eds), Springer International Publishing, pp. 207-216, 2018, doi: 10.1007/978-3-319-78024-5_19 (postprint, DiVA, source code)
  • Mirko Myllykoski, Tuomo Rossi, Jari Toivanen: On solving separable block tridiagonal linear systems using a GPU implementation of radix-4 PSCR, Journal of Parallel and Distributed Computing, 115, pp. 56-66, 2018, doi: 10.1016/j.jpdc.2018.01.004 (postprint, jyx, DiVA, source code)
  • Mirko Myllykoski, Roland Glowinski, Tommi Kärkkäinen, Tuomo Rossi: A GPU-Accelerated Augmented Lagrangian Based L¹-mean Curvature Image Denoising Algorithm Implementation, In WSCG 2015 : 23rd International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision’2015 : Full Papers Proceedings, Gavrilova M., Skala V. (eds.), Union Agency, pp. 119-128, ISBN 978-80-86943-65-7, 2015 (link, full paper, jyx, source code)
  • Mirko Myllykoski, Roland Glowinski, Tommi Kärkkäinen, Tuomo Rossi: A New Augmented Lagrangian Approach for L¹-mean Curvature Image Denoising, SIAM Journal on Imaging Sciences, 8 (1), pp. 95-125, 2015, doi: 10.1137/140962164 (full paper, jyx, source code)
  • Mirko Myllykoski, Tuomo Rossi: A parallel radix-4 block cyclic reduction algorithm, Numerical Linear Algebra with Applications, 21 (4), pp. 540-556, 2014, doi: 10.1002/nla.1909 (postprint, jyx)
  • Mirko Myllykoski, Tuomo Rossi, Jari Toivanen: Fast Poisson Solvers for Graphics Processing Units, In Applied Parallel and Scientific Computing, 11th International Conference, PARA 2012, Helsinki, Finland, Lecture Notes in Computer Science, Vol. 7782, Manninen P., Öster P. (eds), Springer Berlin Heidelberg: Berlin, Germany, pp. 265-279, 2013, doi: 10.1007/978-3-642-36803-5_19 (postprint, jyx, source code)

Reports and deliverables

  • João Bispo et al.: Best Practice Guide: Modern Accelerators, PRACE Best Practice Guide, 2021 (download, link)
  • Mirko Myllykoski, Carl Christian Kjelgaard Mikkelsen, Angelika Schwarz, Bo Kågström: D2.7 Eigenvalue solvers for nonsymmetric problems, public NLAFET deliverable, 2019 (download, link, DiVA)
  • Lars Karlsson, Mahmoud Eljammaly, Mirko Myllykoski: D6.5 Evaluation of auto-tuning techniques, public NLAFET deliverable, 2019 (download, link, DiVA)
  • Bo Kågström et al.: D7.8 Release of the NLAFET library, public NLAFET deliverable, 2019 (download, link, DiVA)
  • Mirko Myllykoski, Lars Karlsson, Bo Kågström, Mahmoud Eljammaly, Srikara Pranesh, Mawussi Zounon: D2.6 Prototype Software for Eigenvalue Problem Solvers, public NLAFET deliverable, 2018 (download, link, DiVA)
  • Mirko Myllykoski, Carl Christian Kjelgaard Mikkelsen, Lars Karlsson, Bo Kågström: Task-Based Parallel Algorithms for Reordering of Matrices in Real Schur Forms, NLAFET Working Note WN-11, 2017. Also as Report UMINF 17.11, Department of Computing Science, Umeå University, SE-901 87 Umeå, Sweden (download, UMINF, DiVA)
  • Carl Christian Kjelgaard Mikkelsen, Mirko Myllykoski, Björn Adlerborn, Lars Karlsson, Bo Kågström: D2.5 Eigenvalue Problem Solvers, public NLAFET deliverable, 2017 (download, link, DiVA)

Conferences, workshops and meetings

  • Task-Based Algorithms and Software for Solving Dense Nonsymmetric Eigenvalue Problems, SIAM Conference on Computational Science and Engineering (CSE21), Online, March 4, 2021 (abstract, slides)
  • Cancelled: Task-based Algorithms and Software for Solving Dense Nonsymmetric Eigenvalue Problems, Householder Symposium XXI on Numerical Linear Algebra, Selva di Fasano (Br), Italy, June 14-19, 2020 (abstract)
  • How two-sided matrix transformation algorithms can benefit from task parallelism, Nordic Numerical Linear Algebra meeting, Stockholm, Sweden, October 21-22, 2019 (abstract, slides)
  • Task-based, GPU-accelerated and Robust Algorithms for Solving Dense Nonsymmetric Eigenvalue Problems, Swedish eScience Academy, Lund, Sweden, October 15-16, 2019 (poster)
  • Introduction to StarNEig — A Task-based Library for Solving Nonsymmetric Eigenvalue Problems, 13th International Conference on Parallel Processing and Applied Mathematics (PPAM 2019), Bialystok, Poland, September 10, 2019 (slides)
  • Co-authored: Parallel Robust Computation of Generalized Eigenvectors of Matrix Pencils (presented by Carl Christian Kjelgaard Mikkelsen), 13th International Conference on Parallel Processing and Applied Mathematics (PPAM 2019), Bialystok, Poland, September 10, 2019 (slides)
  • Poster: Task-Based Algorithms for Eigenvalue Problems, Swedish eScience Academy, Uppsala, Sweden, October 16-17, 2018 (poster)
  • Poster: A Task-Based Algorithm for Reordering the Eigenvalues of a Matrix in Real Schur Form, Swedish eScience Academy, Umeå, Sweden, October 11-12, 2017 (poster, presentation)
  • A Task-Based Algorithm for Reordering the Eigenvalues of a Matrix in Real Schur Form, 12th International Conference on Parallel Processing and Applied Mathematics (PPAM 2017), Dublin, Poland, September 13, 2017 (slides)
  • Poster: How Fast Direct Solvers Can Benefit from GPU-acceleration, Householder Symposium XX on Numerical Linear Algebra, Blacksburg, Virginia, USA, June 20, 2017 (poster)
  • Co-authored: Extreme-Scale Eigenvalue Reordering in the Real Schur Form (presented by Carl Christian Kjelgaard Mikkelsen), SIAM Conference on Computational Science and Engineering (CSE17), Atlanta, Georgia, USA, February 28, 2017 (slides)
  • A GPU-Accelerated Augmented Lagrangian Based L¹-mean Curvature Image Denoising Algorithm Implementation, 23rd International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision 2015, Plzen, Czech Republic, June 9, 2015 (slides)
  • Poster: A New Augmented Lagrangian Approach for L¹-mean Curvature Image Denoising, RICAM Special Semester on New Trends in Calculus of Variations, Workshop 2: Variational methods in imaging, Linz, Austria, October 27-31, 2014 (poster)
  • Cyclic Reduction Type Poisson and Helmholtz Solvers on a GPU, SIAM Conference on Parallel Processing for Scientific Computing, Portland, Oregon, USA, February 18, 2014 (slides)
  • Block Cyclic Reduction Type Fast Poisson Solvers for GPU, Workshop on the State-of-the-Art in Scientific and Parallel Computing (PARA2012), Helsinki, Finland, June 13, 2012 (slides)

Theses

  • PhD thesis: On GPU-Accelerated Fast Direct Solvers and Their Applications in Image Denoising, Jyväskylä, Finland: University of Jyväskylä. Jyväskylä studies in computing, 218, ISBN 978-951-39-6277-7, ISSN 1456-5390, 2015 (download, jyx, Google Docs)
  • Master’s thesis (Pro gradu, in Finnish): Separoituvien yhtälöryhmien ratkaiseminen ohjelmoitavalla näytönohjaimella (Solving separable linear systems on GPU), 2011 (download, Google Docs)
  • Bachelor’s thesis (Kandidaatintutkielma, in Finnish): Rinnakkaistuvat nopeat Poisson-ratkaisijat (Parallel Fast Poisson Solvers), 2010 (download, Google Docs)

Miscellaneous

  • How eigenproblem solvers can benefit from task parallelism, UMIT talk, November 2019 (slides)
  • Task-Based Algorithms for Solving Non-symmetric Eigenvalue Problems, UMIT talk, March 2019 (slides)
  • A quick introduction to StarPU (Google Slides)
  • Cyclic Reduction Type Poisson and Helmholtz Solvers on a GPU (extended version), Farhat Research Group Seminars, Stanford, California, USA, February 26, 2014 (slides)
  • Alberto Quintero, Alexandra Rohde O’Sullivan Freltoft, Anna Igolkina, Mirko Myllykoski, Nitya Dixit, Fabian Rost (instructor): Morphogenesis and Dynamics of Multi-cellular Systems, ECMI Newsletter 52, 2012 (link)