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All simulation approaches eventually face limits in computational scalability when applied to large spatiotemporal domains. This challenge becomes especially apparent in molecular-level particle simulations, where high spatial and temporal…
Development of models and dedicated numerical methods for dynamics in fractured rocks is an active research field, with research moving towards increasingly advanced process couplings and complex fracture networks. The inclusion of coupled…
Future experiments in high-energy physics will pose stringent requirements to computing, in particular to real-time data processing. As an example, the CBM experiment at FAIR Germany intends to perform online data selection exclusively in…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
OpenCL is a standard for parallel programming of heterogeneous systems. The benefits of a common programming standard are clear; multiple vendors can provide support for application descriptions written according to the standard, thus…
Harnessing modern parallel computing resources to achieve complex multi-physics simulations is a daunting task. The Multiphysics Object Oriented Simulation Environment (MOOSE) aims to enable such development by providing simplified…
We describe a methodology for designing efficient parallel and distributed scientific software. This methodology utilizes sequences of mechanizable algebra--based optimizing transformations. In this study, we apply our methodology to the…
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),…
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…
Simflowny is an open platform which automatically generates efficient parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support simultaneously a quite…
Particle-in-Cell (PIC) Monte Carlo (MC) simulations are central to plasma physics but face increasing challenges on heterogeneous HPC systems due to excessive data movement, synchronization overheads, and inefficient utilization of multiple…
The numerical simulation of the diffusion MRI signal arising from complex tissue micro-structures is helpful for understanding and interpreting imaging data as well as for designing and optimizing MRI sequences. The discretization of the…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
In the era of data-driven science, conducting computational experiments that involve analysing large datasets using heterogeneous computational clusters, is part of the everyday routine for many scientists. Moreover, to ensure the…
MiMiC is a flexible and efficient framework for multiscale simulations in which different subsystems are treated by individual client programs. In this work, we present a new interface with OpenMM to be used as an MM client program and we…
Task based parallel programming has shown competitive outcomes in many aspects of parallel programming such as efficiency, performance, productivity and scalability. Different approaches are used by different software development frameworks…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
Numerical investigation of compressible flows faces two main challenges. In order to accurately describe the flow characteristics, high-resolution nonlinear numerical schemes are needed to capture discontinuities and resolve wide…
As quantum computers continue to improve and support larger, more complex computations, smart control hardware and compilers are needed to efficiently leverage the capabilities of these systems. This paper introduces a novel approach to…
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…