Related papers: Molecular dynamics simulations with many-body pote…
Many-Fermion Dynamics-nuclear, or MFDn, is a configuration interaction (CI) code for nuclear structure calculations. It is a platform-independent Fortran 90 code using a hybrid MPI+X programming model. For CPU platforms the application has…
With the increasing usage of Machine Learning (ML) in High energy physics (HEP), there is a variety of new analyses with a large spread in compute resource requirements, especially when it comes to GPU resources. For institutes, like the…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…
We created an efficient algorithm suitable for graphics processing units (GPUs) to perform Monte Carlo simulations of a subset of reaction-diffusion models. The algorithm uses techniques that are specific to GPU programming, and combines…
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…
Solvent-mediated hydrodynamic interactions between colloidal particles can significantly alter their dynamics. We discuss the implementation of Stokesian dynamics in leading approximation for streaming processors as provided by the compute…
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,…
We describe the use of Graphics Processing Units (GPUs) for speeding up the code NBODY6 which is widely used for direct $N$-body simulations. Over the years, the $N^2$ nature of the direct force calculation has proved a barrier for…
Scalable nonvolatile memory DIMMs will finally be commercially available with the release of the Intel Optane DC Persistent Memory Module (or just "Optane DC PMM"). This new nonvolatile DIMM supports byte-granularity accesses with access…
Modern Machine Learning (ML) training on large-scale datasets is a very time-consuming workload. It relies on the optimization algorithm Stochastic Gradient Descent (SGD) due to its effectiveness, simplicity, and generalization performance.…
GPU-based HPC clusters are attracting more scientific application developers due to their extensive parallelism and energy efficiency. In order to achieve portability among a variety of multi/many core architectures, a popular choice for an…
Hydrodynamics calculations have been successfully used in studies of the bulk properties of the Quark-Gluon Plasma, particularly of elliptic flow and shear viscosity. However, there are areas (for instance event-by-event simulations for…
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…
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…
The continued growth of the computational capability of throughput processors has made throughput processors the platform of choice for a wide variety of high performance computing applications. Graphics Processing Units (GPUs) are a prime…
Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of…
Parallel algorithms on CPU and GPU are implemented for the Unified Gas-Kinetic Scheme and their performances are investigated and compared by a two dimensional channel flow case. The parallel CPU algorithm has a one dimensional block…
Molecular Dynamics (MD) simulations play a central role in physics-driven drug discovery. MD applications often use the Particle Mesh Ewald (PME) algorithm to accelerate electrostatic force computations, but efficient parallelization has…
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…
We develop a neuroevolution-potential (NEP) framework for generating neural network based machine-learning potentials. They are trained using an evolutionary strategy for performing large-scale molecular dynamics (MD) simulations. A…