VSC School Seminar: Vienna Protein Simulator – a case study for scientific code optimization

    Authors:

    Francesca Nerattini1, Luca Tubiana1, Ivan Coluzza2 and Christoph Dellago1

    1 Computational Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
    2 CIC biomaGUNE, Paseo Miramon 182, 20014 San Sebastian, Spain

    Abstract:

    The “Vienna Protein Simulator” (ViPS) VSC School Project is aimed at the realization of a Monte Carlo based simulation package for protein folding and protein design. Protein folding consists in the prediction of the folded protein structure from the amino acid sequence, while for the design one needs to find a sequence which will fold into a given target structure. The configurational and sequence space that needs to be explored for such processes is extremely vast and sampling it with atomistic models is not currently feasible. ViPS tackles these problems through the use of three complementary strategies: a coarse-grained protein model, the caterpillar [1], reduces the dimension of the configurational space; an advanced and scalable Monte Carlo scheme, the Virtual Move Parallel Tempering (VMPT) [2] enhances sampling; large-scale parallelization takes advantage of modern cluster architectures. These characteristics make ViPS an ideal code to be run on high-performance, highly parallelized clusters such as VSC. While code optimization if of capital importance, a code like ViPS must also remain easy to extend by other research groups. We thus focused not only on implementing more efficient numerical algorithms, but also on building a modular framework to extend the physical observables measured by ViPS. Here we present the work stream used: from the profiling tools to identify bottlenecks, optimisation of serial operations, loop vectorization, all the way to the insertion of a new Monte Carlo move to improve the sampling of the conformational space of a polymer. We also showcase possible applications of the package, that is now able to handle single protein folding, protein design and protein-protein interactions, producing free energy profiles onto many different order parameters.

    This talk is based on work supported by the VSC Research Center funded by the Austrian Federal Ministry of Education, Science and Research (BMBWF) and reports about the VSC School Project "Development of a protein design and protein folding package for HPC: The Vienna Protein Simulator".

    [1]   Coluzza, I., PloS one 6.7 (2011).
    [2]   Coluzza, I., and Frenkel, D., Chem.Phys.Chem. 6, 1779 (2005).

    Speaker:

    Francesca Nerattini
    Computational Physics, University of Vienna

    Language:

    English

    Date, Time, and Location:

    12.03.2018, 15:00 - 18:00, FH Hörsaal 2 (TU Wien, Wiedner Hauptstraße 8-10, 2nd floor, yellow area)

    Registration:

    If you would like to join us for this event, please email to: vsc-seminar@list.tuwien.ac.at
    (so we will know how many persons will come)

    Slides:

    The course material will be available for registered attendees only.

     

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