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Profiles

Research Interests

  • Hardware acceleration
  • Parallel programming

Short CV

  • Since 2015

    DAAD Research Scholar at the “Embedded Systems and Applications” (ESA) group

  • 2010-2013

    M.Sc. Electronic Engineering, Politecnico di Torino (Italy)

  • 2004-2009

    B.Sc. Electronic Engineering, Universidad Nacional de Ingenieria (Peru)

Publications

  1. Santos-Martins, D., Solis-Vasquez, L., Tillack, A. F., Sanner, M. F., Koch, A., and Forli, S. (2021). Accelerating AutoDock4 with GPUs and Gradient-Based Local Search. Journal of Chemical Theory and Computation (JCTC). doi: 10.1021/acs.jctc.0c01006
    Preprint
    Bibtex 
    @article{solis2020jctc,
  title = {Accelerating AutoDock4 with GPUs and Gradient-Based Local Search},
  author = {Santos-Martins, Diogo and Solis-Vasquez, Leonardo and Tillack, Andreas F and Sanner, Michel F and Koch, Andreas and Forli, Stefano},
  journal = {Journal of Chemical Theory and Computation (JCTC)},
  year = {2021},
  doi = {10.1021/acs.jctc.0c01006},
  preprint = {https://pubs.acs.org/doi/10.1021/acs.jctc.0c01006}
}
  2. Solis-Vasquez, L., Santos-Martins, D., Tillack, A. F., Koch, A., Eberhardt, J., and Forli, S. (2020). Parallelizing Irregular Computations for Molecular Docking. In 10th Workshop on Irregular Applications: Architectures and Algorithms (IA3). doi: 10.1109/IA351965.2020.00008
    Preprint Slides
    Bibtex 
    @inproceedings{solis2020ia3,
  author = {Solis-Vasquez, Leonardo and Santos-Martins, Diogo and Tillack, Andreas F. and Koch, Andreas and Eberhardt, J\'{e}r\^{o}me and Forli, Stefano},
  title = {Parallelizing Irregular Computations for Molecular Docking},
  booktitle = {10th Workshop on Irregular Applications: Architectures and Algorithms (IA3)},
  year = {2020},
  doi = {10.1109/IA351965.2020.00008}
}
  3. LeGrand, S., Scheinberg, A., Tillack, A. F., Thavappiragasam, M., Vermaas, J. V., Agarwal, R., Larkin, J., et al. (2020). GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research. In Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB). doi: 10.1145/3388440.3412472
    Preprint
    Bibtex 
    @inproceedings{legrand2020bcb,
  author = {LeGrand, Scott and Scheinberg, Aaron and Tillack, Andreas F. and Thavappiragasam, Mathialakan and Vermaas, Josh V. and Agarwal, Rupesh and Larkin, Jeff and Poole, Duncan and Santos-Martins, Diogo and Solis-Vasquez, Leonardo and Koch, Andreas and Forli, Stefano and Hernandez, Oscar and Smith, Jeremy C. and Sedova, Ada},
  title = {GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research},
  booktitle = {Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB)},
  year = {2020},
  preprint = {https://arxiv.org/abs/2007.03678},
  doi = {10.1145/3388440.3412472}
}
  4. Vinçon, T., Weber, L., Bernhardt, A., Riegger, C., Hardock, S., Knoedler, C., Stock, F., et al. (2020). nKV in Action: Accelerating KV-Stores on Native Computation Storage with Near-Data Processing. In Proceedings of the VLDB Endowment, Volume 13.
    Preprint Slides Video
    Bibtex 
    @inproceedings{weber2020vldb,
  author = {Vin\c{c}on, Tobias and Weber, Lukas and Bernhardt, Arthur and Riegger, Christian and Hardock, Sergey and Knoedler, Christian and Stock, Florian and Solis-Vasquez, Leonardo and Tamimi, Sajjad and Koch, Andreas},
  title = {nKV in Action: Accelerating KV-Stores on Native Computation Storage with Near-Data Processing},
  booktitle = {Proceedings of the VLDB Endowment, Volume 13},
  year = {2020},
  video = {https://www.youtube.com/watch?v=iiGh6Pj_A9k}
}
  5. Sommer, L., Stock, F., Solis-Vasquez, L., and Koch, A. (2020). DAPHNE - An Automotive Benchmark Suite for Parallel Programming Models on Embedded Heterogeneous Platforms. In D. Ziegenbein, S. Saidi, X. S. Hu, and S. Steinhorst (Eds.), Future Automotive HW/SW Platform Design (Dagstuhl Seminar 19502), Dagstuhl Reports (Vol. 9, pp. 28–66). Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik. doi: 10.4230/DagRep.9.12.28
    Preprint
    Bibtex 
    @inproceedings{sommer2020dagstuhl,
  author = {Sommer, Lukas and Stock, Florian and Solis-Vasquez, Leonardo and Koch, Andreas},
  title = {DAPHNE - An Automotive Benchmark Suite for Parallel Programming Models on Embedded Heterogeneous Platforms},
  booktitle = {{{Future Automotive HW/SW Platform Design (Dagstuhl Seminar 19502)}}},
  year = {2020},
  editor = {Ziegenbein, Dirk and Saidi, Selma and Hu, Xiaobo Sharon and Steinhorst, Sebastian},
  volume = {9},
  series = {Dagstuhl Reports},
  pages = {28--66},
  publisher = {{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik}},
  address = {Dagstuhl, Germany},
  url = {https://drops.dagstuhl.de/opus/volltexte/2020/12010},
  urn = {urn:nbn:de:0030-drops-120101},
  doi = {10.4230/DagRep.9.12.28},
  annote = {Keywords: automotive, hw/sw platforms, real-time systems, systems design automation},
  preprint = {http://dx.doi.org/10.4230/DagRep.9.12.28}
}
  6. Solis-Vasquez, L., Santos-Martins, D., Koch, A., and Forli, S. (2020). Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking. In 28th EUROMICRO International Conference on Parallel, Distributed and Network-Based Processing (PDP’20).
    Preprint Slides
    Bibtex 
    @inproceedings{solis2020pdp,
  author = {Solis-Vasquez, Leonardo and Santos-Martins, Diogo and Koch, Andreas and Forli, Stefano},
  booktitle = {28th EUROMICRO International Conference on Parallel, Distributed and Network-Based Processing (PDP'20)},
  title = {Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking},
  year = {2020}
}
  7. Sommer, L., Stock, F., Solis-Vasquez, L., and Koch, A. (2020). Using Parallel Programming Models for Automotive Workloads on Heterogeneous Systems - a Case Study. In 28th EUROMICRO International Conference on Parallel, Distributed and Network-Based Processing (PDP’20).
    Preprint
    Bibtex 
    @inproceedings{sommer2020pdp,
  author = {Sommer, Lukas and Stock, Florian and Solis-Vasquez, Leonardo and Koch, Andreas},
  booktitle = {28th EUROMICRO International Conference on Parallel, Distributed and Network-Based Processing (PDP'20)},
  title = {Using Parallel Programming Models for Automotive Workloads on Heterogeneous Systems - a Case Study},
  year = {2020},
  keywords = {embedded, automotive, parallel programming, heterogeneous, OpenMP, OpenCL, CUDA}
}
  8. Solis-Vasquez, L. (2019). Accelerating Molecular Docking by Parallelized Heterogeneous Computing - A Case Study of Performance, Quality of Results, and Energy-Efficiency using CPUs, GPUs, and FPGAs (PhD thesis). Technische Universität Darmstadt, Germany.
    Preprint
    Bibtex 
    @phdthesis{solis2019diss,
  author = {Solis-Vasquez, Leonardo},
  title = {Accelerating Molecular Docking by Parallelized Heterogeneous Computing - 
                 A Case Study of Performance, Quality of Results, and Energy-Efficiency 
                 using CPUs, GPUs, and FPGAs},
  school = {Technische Universität Darmstadt, Germany},
  year = {2019},
  preprint = {https://tuprints.ulb.tu-darmstadt.de/9288/}
}
  9. Santos-Martins, D., Eberhardt, J., Bianco, G., Solis-Vasquez, L., Ambrosio, F. A., Koch, A., and Forli, S. (2019). D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU. Journal of Computer-Aided Molecular Design.
    Preprint
    Bibtex 
    @article{santosmartins2019posepred,
  title = {D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU},
  author = {Santos-Martins, Diogo and Eberhardt, Jerome and Bianco, Giulia and Solis-Vasquez, Leonardo and Ambrosio, Francesca Alessandra and Koch, Andreas and Forli, Stefano},
  journal = {Journal of Computer-Aided Molecular Design},
  year = {2019},
  preprint = {https://doi.org/10.1007/s10822-019-00241-9}
}
  10. El Khoury, L., Santos-Martins, D., Sasmal, S., Eberhardt, J., Bianco, G., Ambrosio, F. A., Solis-Vasquez, L., et al. (2019). Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design.
    Preprint
    Bibtex 
    @article{elkhoury2019affrank,
  title = {Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4},
  author = {El Khoury, L{\'e}a and Santos-Martins, Diogo and Sasmal, Sukanya and Eberhardt, J{\'e}r{\^o}me and Bianco, Giulia and Ambrosio, Francesca Alessandra and Solis-Vasquez, Leonardo and Koch, Andreas and Forli, Stefano and Mobley, David L.},
  journal = {Journal of Computer-Aided Molecular Design},
  year = {2019},
  preprint = {https://doi.org/10.1007/s10822-019-00240-w}
}
  11. Sommer, L., Stock, F., Solis-Vasquez, L., and Koch, A. (2019). Work-in-Progress: DAPHNE - Automotive Benchmark Suite for Parallel Programming Models on Embedded Heterogeneous Platforms. In Proceedings of the International Conference on Embedded Software (accepted for publication 07/2019), EMSOFT ’19. Piscataway, NJ, USA: IEEE Press.
    Preprint
    Bibtex 
    @inproceedings{emsoft2019,
  author = {Sommer, Lukas and Stock, Florian and Solis-Vasquez, Leonardo and Koch, Andreas},
  title = {Work-in-Progress: DAPHNE - Automotive Benchmark Suite for Parallel Programming Models on Embedded Heterogeneous Platforms},
  booktitle = {Proceedings of the International Conference on Embedded Software (accepted for publication 07/2019)},
  series = {EMSOFT '19},
  year = {2019},
  location = {New York, NY, USA},
  publisher = {IEEE Press},
  address = {Piscataway, NJ, USA}
}
  12. Sommer, L., Stock, F., Solis-Vasquez, L., and Koch, A. (2019). EPHoS: Evaluation of Programming - Models for Heterogeneous Systems. FAT-Schriftenreihe 317. Forschungsvereinigung Automobiltechik.
    Preprint
    Bibtex 
    @article{fat317,
  title = {EPHoS: Evaluation of Programming - Models for Heterogeneous Systems},
  author = {Sommer, Lukas and Stock, Florian and Solis-Vasquez, Leonardo and Koch, Andreas},
  booktitle = {FAT-Schriftenreihe 317},
  year = {2019},
  publisher = {Forschungsvereinigung Automobiltechik},
  preprint = {https://www.vda.de/de/services/Publikationen/fat-schriftenreihe-317.html}
}
  13. Solis-Vasquez, L., and Koch, A. (2018). A Case Study in Using OpenCL on FPGAs: Creating an Open-Source Accelerator of the AutoDock Molecular Docking Software . In Fifth International Workshop on FPGAs for Software Programmers (FSP).
    Preprint Slides Material
    Bibtex 
    @inproceedings{solis-vasquez2018acsuoclfpgacosaadmds,
  title = {A Case Study in Using OpenCL on FPGAs: Creating an Open-Source Accelerator of the AutoDock Molecular Docking Software },
  author = {Solis-Vasquez, Leonardo and Koch, Andreas},
  booktitle = {Fifth International Workshop on FPGAs for Software Programmers (FSP)},
  year = {2018},
  material = {https://git.esa.informatik.tu-darmstadt.de/docking/ocladock-fpga}
}
  14. Solis-Vasquez, L., and Koch, A. (2017). A Performance and Energy Evaluation of OpenCL-accelerated Molecular Docking. In Fifth International Workshop on OpenCL (IWOCL).
    Preprint Slides Material
    Bibtex 
    @inproceedings{solis-vasquez2017apeeoclmd,
  title = {A Performance and Energy Evaluation of OpenCL-accelerated Molecular Docking},
  author = {Solis-Vasquez, Leonardo and Koch, Andreas},
  booktitle = {Fifth International Workshop on OpenCL (IWOCL)},
  year = {2017},
  material = {https://git.esa.informatik.tu-darmstadt.de/docking/ocladock}
}