Related papers: A hybrid algorithm for parallel molecular dynamics…
The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…
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…
B-spline based orbital representations are widely used in Quantum Monte Carlo (QMC) simulations of solids, historically taking as much as 50% of the total run time. Random accesses to a large four-dimensional array make it challenging to…
We study the opportunities for parallelism for the simulation of surface reactions. We introduce the concept of a partition and we give new simulation methods based on Cellular Automaton using partitions. We elaborate on the advantages and…
The approximate minimum degree algorithm is widely used before numerical factorization to reduce fill-in for sparse matrices. While considerable attention has been given to the numerical factorization process, less focus has been placed on…
This paper studies parallelization schemes for stochastic Vector Quantization algorithms in order to obtain time speed-ups using distributed resources. We show that the most intuitive parallelization scheme does not lead to better…
Comprehensive simulations of the entire biochemistry of cells have great potential to help physicians treat disease and help engineers design biological machines. But such simulations must model networks of millions of molecular species and…
Sample-based quantum diagonalization (SQD) is an algorithm for hybrid quantum-classical molecular simulation that has been of broad interest for application with noisy intermediate scale quantum (NISQ) devices. However, SQD does not always…
Atomistic simulation drives scientific advances in modern material science and accounts for a significant proportion of wall time on High Performance Computing facilities. It is important that algorithms are efficient and implementations…
We present an algorithm for cluster dynamics to efficiently simulate large systems on MIMD parallel computers with large numbers of processors. The method divides physical space into rectangular cells which are assigned to processors and…
Parallel algorithms for ab initio calculations of vibrations modes of solids are presented and implemented under PVM. Load balancing and communication problems are dealt with in order to increase parallelism efficiency. For accurate time…
Practical applicability of quantum optimisation on near term devices is constrained by limited qubit counts and hardware noise, which restricts the scalability of quantum optimisation algorithms for combinatorial problems. The simulation of…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Among the many possible approaches for the parallelization of self-organizing networks, and in particular of growing self-organizing networks, perhaps the most common one is producing an optimized, parallel implementation of the standard…
The study of controlled hybrid systems requires practical tools for approximation and comparison of system behaviors. Existing approaches to these problems impose undue restrictions on the system's continuous and discrete dynamics.…
In this paper, we present a new multibody physics simulation framework that utilizes the subsystem-based structure and the Alternating Direction Method of Multiplier (ADMM). The major challenge in simulating complex high degree of freedom…
Recent advances in computing architectures and networking are bringing parallel computing systems to the masses so increasing the number of potential users of these kinds of systems. In particular, two important technological evolutions are…
Interest in parallel architectures applied to real time selections is growing in High Energy Physics (HEP) experiments. In this paper we describe performance measurements of Graphic Processing Units (GPUs) and Intel Many Integrated Core…
Agent-based modeling (ABM) is a bottom-up modeling approach, where each entity of the system being modeled is uniquely represented as an independent decision-making agent. Large scale emergent behavior in ABMs is population sensitive. As…
In this paper, we propose an efficient parallelization strategy for boundary element method (BEM) solvers that perform the electromagnetic analysis of structures with lossy conductors. The proposed solver is accelerated with the adaptive…