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Recently, constant-depth quantum circuits are proved more powerful than their classical counterparts at solving certain problems, e.g., the two-dimensional (2D) hidden linear function (HLF) problem regarding a symmetric binary matrix. To…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
Recently, task-based programming models have emerged as a prominent alternative among shared-memory parallel programming paradigms. Inherently asynchronous, these models provide native support for dynamic load balancing and incorporate data…
Modern high performance computing (HPC) systems exhibit a rapid growth in size, both "horizontally" in the number of nodes, as well as "vertically" in the number of cores per node. As such, they offer additional levels of hardware…
We address in this thesis the current need to design new parallel algorithms and tools that ease the development of geodynamic modelling applications that are suited for today's and tomorrow's hardware. We present (1) the MATLAB HPC…
Parallel multiphysics simulations often suffer from load imbalances originating from the applied coupling of algorithms with spatially and temporally varying workloads. It is thus desirable to minimize these imbalances to reduce the time to…
Computational Fluid Dynamics (CFD) simulations are often constrained by the memory-bound nature of sparse matrix-vector operations, which eventually limits performance on modern high-performance computing (HPC) systems. This work introduces…
Fast algorithms for the computation of $N$-body problems can be broadly classified into mesh-based interpolation methods, and hierarchical or multiresolution methods. To this last class belongs the well-known fast multipole method (FMM),…
Modern supercomputers allow the simulation of complex phenomena with increased accuracy. Eventually, this requires finer geometric discretizations with larger numbers of mesh elements. In this context, and extrapolating to the Exascale…
We explored the possible benefits of integrating quantum simulators in a "hybrid" quantum machine learning (QML) workflow that uses both classical and quantum computations in a high-performance computing (HPC) environment. Here, we used two…
Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…
Computational systems and methods are often being used in biological research, including the understanding of cancer and the development of treatments. Simulations of tumor growth and its response to different drugs are of particular…
Computing centres, including those used to process High-Energy Physics data and simulations, are increasingly providing significant fractions of their computing resources through hardware architectures other than x86 CPUs, with GPUs being a…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…
Scientific applications often contain large, computationally-intensive, and irregular parallel loops or tasks that exhibit stochastic characteristics. Applications may suffer from load imbalance during their execution on high-performance…
FleCSPH is a smoothed particle hydrodynamics simulation tool, based on the compile-time configurable framework FleCSI. The asynchronous distributed tree topology combined with a fast multipole method allows FleCSPH to efficiently compute…
Accurate simulations of various physical processes on digital computers requires huge computing performance, therefore accelerating these scientific and engineering applications has a great importance. Density of programmable logic devices…
Molecular dynamics (MD) simulates the time evolution of atomic systems governed by interatomic forces, and the fidelity of these simulations depends critically on the underlying force model. Classical force fields (CFFs) rely on fixed…
An application for high-performance computing (HPC) is shown that is relevant in the field of battery development. Simulations of electrolyte wetting and flow are conducted using pore network models (PNM) and the lattice Boltzmann method…