Related papers: Performance metrics in a hybrid MPI-OpenMP based m…
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…
Particle collisions are the primary mechanism of inter-particle momentum and energy exchange for dense particle-laden flow. Accurate approximation of this collision operator in four-way coupled Euler-Lagrange approaches remains challenging…
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…
Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available…
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…
Matrix Distributed Processing (MDP) is a C++ library for fast development of efficient parallel algorithms. It constitues the core of FermiQCD. MDP enables programmers to focus on algorithms, while parallelization is dealt with…
The integration of quantum chemical methods with high-performance computing is indispensable for handling large systems with modest accuracy or even small systems but with high accuracy. Continuing with the unified implementation of…
With the ever-increasing computing power of supercomputers and the growing scale of scientific applications, the efficiency of MPI collective communications turns out to be a critical bottleneck in large-scale distributed and parallel…
MPI derived datatypes are an abstraction that simplifies handling of non-contiguous data in MPI applications. These datatypes are recursively constructed at runtime from primitive Named Types defined in the MPI standard. More recently, the…
Matrix-accelerated stencil computation is a hot research topic, yet its application to three-dimensional (3D) high-order stencils and HPC remains underexplored. With the emergence of matrix units on multicore CPUs, we analyze matrix-based…
Matrix-matrix multiplication is a basic operation in linear algebra and an essential building block for a wide range of algorithms in various scientific fields. Theory and implementation for the dense, square matrix case are well-developed.…
Cooperative Distributed Model Predictive Control (DiMPC) architecture employs local MPC controllers to control different subsystems, exchanging information with each other through an iterative procedure to enhance overall control…
w-Projection is a wide-field imaging technique that is widely used in radio synthesis arrays. Processing the wide-field big data generated by the future Square Kilometre Array (SKA) will require significant updates to current methods to…
Machine learned interatomic potentials, particularly equivariant message-passing (MP) models, have demonstrated high fidelity in representing first-principles data, revolutionizing computational studies in materials science, biophysics, and…
We present a new approach for the two-temperature molecular dynamics (MD) model for coupled simulations of electronic and phonon heat conduction in nanoscale systems. The proposed method uses a master equation to perform heat conduction of…
Exactly solving multi-objective integer programming (MOIP) problems is often a very time consuming process, especially for large and complex problems. Parallel computing has the potential to significantly reduce the time taken to solve such…
Asynchronous programming models (APM) are gaining more and more traction, allowing applications to expose the available concurrency to a runtime system tasked with coordinating the execution. While MPI has long provided support for…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
Computationally-intensive loops are the primary source of parallelism in scientific applications. Such loops are often irregular and a balanced execution of their loop iterations is critical for achieving high performance. However, several…
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…