Related papers: Tackling Exascale Software Challenges in Molecular…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
Static resource allocations in high-performance computing (HPC) lead to inefficiencies for time-varying workloads, causing idle resources, queue delays, and higher node-hour costs. The Dynamic Management of Resources (DMR) middleware…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
Due to decelerating gains in single-core CPU performance, computationally expensive simulations are increasingly executed on highly parallel hardware platforms. Agent-based simulations, where simulated entities act with a certain degree of…
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes.…
A challenging and fundamental research problem is the better understanding and control of the turbulent transport of heat in present-day tokamak fusion experiments. Recent developments in numerical methods along with enormous gains in…
Local search is a successful approach for solving combinatorial optimization and constraint satisfaction problems. With the progressing move toward multi and many-core systems, GPUs and the quest for Exascale systems, parallelism has become…
The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
Path integral Monte Carlo (PIMC) and path integral molecular dynamics (PIMD) provide the golden standard for the ab initio simulations of identical particles. In this work, we achieved significant GPU acceleration based on PIMD, which is…
Due to its flexible architecture, FPGAs support unique, deep hardware pipeline implementations for accelerating HPC applications. However, these devices are quite new in the HPC space, and thus, have been scarcely explored outside some…
Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to…
We consider the problem of estimating the error when solving a system of differential algebraic equations. Richardson extrapolation is a classical technique that can be used to judge when computational errors are irrelevant and estimate the…
Scientific computing in the exascale era demands increased computational power to solve complex problems across various domains. With the rise of heterogeneous computing architectures the need for vendor-agnostic, performance portability…
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
The accurate description of large molecular systems in complex environments remains an ongoing challenge for the field of computational chemistry. This problem is even more pronounced for photo-induced processes, as multiple excited…
Developing an efficient code for large, multiscale astrophysical simulations is crucial in preparing the upcoming era of exascale computing. RAMSES is an astrophysical simulation code that employs parallel processing based on the Message…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Particle accelerators are invaluable tools for research in the basic and applied sciences, in fields such as materials science, chemistry, the biosciences, particle physics, nuclear physics and medicine. The design, commissioning, and…
Future computing systems, from handhelds to supercomputers, will undoubtedly be more parallel and heterogeneous than todays systems to provide more performance and energy efficiency. Thus, GPUs are increasingly being used to accelerate…