The Kernel Polynomial Method (KPM) is one of the fast diagonalization methods used for simulations of quantum systems in research fields of condensed matter physics and chemistry. The algorithm has a difficulty to be parallelized on a cluster computer or a supercomputer due to the fine-gain recursive calculations. This paper proposes an implementation of the KPM on the recent graphics processing units (GPU) where the recursive calculations are able to be parallelized in the massively parallel environment. This paper also illustrates performance evaluations regarding the cases when the actual simulation parameters are applied, the one for increased intensive calculations and the one for increased amount of memory usage. Finally, it concludes that the performance on GPU promises very high performance compared to the one on CPU and reduces the overall simulation time.
In this paper, the OpenACC heterogeneous parallel programming model is successfully applied to modification and acceleration of the three-dimensional Tokamak magnetohydrodynamical code (CLTx). Through combination of OpenACC and MPI technologies, CLTx is further parallelized by using multiple-GPUs. Significant speedup ratios are achieved on NVIDIA TITAN Xp and TITAN V GPUs, respectively, with very few modifications of CLTx. Furthermore, the validity of the double precision calculations on the above-mentioned two graphics cards has also been strictly verified with m/n=2/1 resistive tearing mode …
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes. Though great efforts have been put into developing efficient PBE numerical models, challenges still remain due to the high dimensionality of typical biomolecular systems. In this study, we implemented and analyzed commonly used linear PBE solvers for the ever-improving graphics processing units (GPU) for biomolecular simulations, including both standard and preco…
We present an efficient open-source implementation of the multiparticle collision dynamics (MPCD) algorithm that scales to run on hundreds of graphics processing units (GPUs). We especially focus on optimizations for modern GPU architectures and communication patterns between multiple GPUs. We show that a mixed-precision computing model can improve performance compared to a fully double-precision model while still providing good numerical accuracy. We report weak and strong scaling benchmarks of a reference MPCD solvent and a benchmark of a polymer solution with research-relevant interactions …
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these benefits, it has been necessary to reformulate some of the most fundamental algorithms, including the Verlet list, pair searching and cut-offs. Here, we present the heterogeneous parallelization and acceleration design of molecular dynamics implemented in the GROMACS codebase over the last decade. The setup involves a general cluster-based approach to pair …
We demonstrate the first implementation of recently-developed fast explicit kinetic integration algorithms on modern graphics processing unit (GPU) accelerators. Taking as a generic test case a Type Ia supernova explosion with an extremely stiff thermonuclear network having 150 isotopic species and 1604 reactions coupled to hydrodynamics using operator splitting, we demonstrate the capability to solve of order 100 realistic kinetic networks in parallel in the same time that standard implicit methods can solve a single such network on a CPU. This orders-of-magnitude decrease in compute time for…
Time dependent density matrix renormalization group (TD-DMRG) has become one of the cutting edge methods of quantum dynamics for complex systems. In this paper, we comparatively study the accuracy of three time evolution schemes in TD-DMRG, the global propagation and compression method with Runge-Kutta algorithm (P&C-RK), the time dependent variational principle based methods with matrix unfolding algorithm (TDVPMU) and with projector-splitting algorithm (TDVP-PS), by performing benchmarks on the exciton dynamics of Fenna-Matthews-Olson (FMO) complex. We show that TDVP-MU and TDVP-PS yield the…
Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force exp…
This paper presents a Graphics Processing Units (GPUs) acceleration method of an iterative scheme for gas-kinetic model equations. Unlike the previous GPU parallelization of explicit kinetic schemes, this work features a fast converging iterative scheme. The memory reduction techniques in this method enable full three-dimensional (3D) solution of kinetic model equations in contemporary GPUs usually with a limited memory capacity that otherwise would need terabytes of memory. The GPU algorithm is validated against the DSMC simulation of the 3D lid-driven cavity flow and the supersonic rarefied …
Empirical potential structure refinement (EPSR) is a neutron scattering data analysis algorithm and a software package. It was developed by the British spallation neutron source (ISIS) Disordered Materials Group in 1980s, and aims to construct the most-probable atomic structures of disordered liquids. It has been extensively used during the past decades, and has generated reliable results. However, it is programmed in Fortran and implements a shared-memory architecture with OpenMP. With the extensive construction of supercomputer clusters and the widespread use of graphics processing unit (GPU…
Elegant is an accelerator physics and particle-beam dynamics code widely used for modeling and design of a variety of high-energy particle accelerators and accelerator-based systems. In this paper we discuss a recently developed version of the code that can take advantage of CUDA-enabled graphics processing units (GPUs) to achieve significantly improved performance for a large class of simulations that are important in practice. The GPU version is largely defined by a framework that simplifies implementations of the fundamental kernel types that are used by Elegant: particle operations, reduct…
The Monte Carlo method is a powerful technique for computing thermodynamic magnetic states of otherwise unsolvable spin Hamiltonians, but the method becomes computationally prohibitive with increasing number of spins and the simulation of real materials and nanostructures is cumbersome. This paper presents the acceleration of Monte Carlo simulations of the three-dimensional anisotropic Heisenberg model on Graphics-Processing Units (GPU). The GPU implementation of the method presented here provides an acceleration of two orders of magnitude over conventional implementations and enables the simu…
