Related papers: Langevin dynamics simulations of biomolecules on g…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Utilizing GPUs is critical for high performance on heterogeneous systems. However, leveraging the full potential of GPUs for accelerating legacy CPU applications can be a challenging task for developers. The porting process requires…
Simulations of physical phenomena are essential to the expedient design of precision components in aerospace and other high-tech industries. These phenomena are often described by mathematical models involving partial differential equations…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
Splotch is a rendering algorithm for exploration and visual discovery in particle-based datasets coming from astronomical observations or numerical simulations. The strengths of the approach are production of high quality imagery and…
Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial…
Graphical processing units (GPUs) promise to revolutionize scientific computing in the near future. Already, they allow almost real-time integration of simplified numerical models of cardiac tissue dynamics. However, the integration methods…
The answers to data assimilation questions can be expressed as path integrals over all possible state and parameter histories. We show how these path integrals can be evaluated numerically using a Markov Chain Monte Carlo method designed to…
Last several years, GPUs are used to accelerate computations in many computer science domains. We focused on GPU accelerated Support Vector Machines (SVM) training with non-linear kernel functions. We had searched for all available GPU…
Structural parameters are normally extracted from observed galaxies by fitting analytic light profiles to the observations. Obtaining accurate fits to high-resolution images is a computationally expensive task, requiring many model…
Process mapping asks to assign vertices of a task graph to processing elements of a supercomputer such that the computational workload is balanced while the communication cost is minimized. Motivated by the recent success of GPU-based graph…
Training a Graph Neural Network (GNN) model on large-scale graphs involves a high volume of data communication and computations. While state-of-the-art CPUs and GPUs feature high computing power, the Standard GNN training protocol adopted…
Large-scale molecular dynamics simulations with high accuracy have been increasingly popular for their capability to bridge the gap between atomistic modeling and mesoscale phenomena. Both machine learning potentials and enhanced sampling…
We introduce the Velocity Jumps approach, denoted as JUMP, a new class of Molecular dynamics integrators, replacing the Langevin dynamics by a hybrid model combining a classical Langevin diffusion and a piecewise deterministic Markov…
The recent accelerated growth in the computing power has generated popularization of experimentation with dynamic computer models in various physical and engineering applications. Despite the extensive statistical research in computer…
In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM…
We develop a novel parallel resampling algorithm for fully parallelized particle filters, which is designed with GPUs (graphics processing units) or similar parallel computing devices in mind. With our new algorithm, a full cycle of…
This article presents an optimized algorithm and implementation for calculating resolution-of-the-identity Hartree-Fock (RI-HF) energies and analytic gradients using multiple Graphics Processing Units (GPUs). The algorithm is especially…
This work proposes a novel approach to evaluate and analyze the behavior of multi-population parallel genetic algorithms (PGAs) when running on a cluster of multi-core processors. In particular, we deeply study their numerical and…
We present the results of gravitational direct $N$-body simulations using the commercial graphics processing units (GPU) NVIDIA Quadro FX1400 and GeForce 8800GTX, and compare the results with GRAPE-6Af special purpose hardware. The force…