Construction and diagonalization of the Hamiltonian matrix is the rate-limiting step in most low-energy electron -- molecule collision calculations. Tennyson (J Phys B, 29 (1996) 1817) implemented a novel algorithm for Hamiltonian construction which took advantage of the structure of the wavefunction in such calculations. This algorithm is re-engineered to make use of modern computer architectures and the use of appropriate diagonalizers is considered. Test calculations demonstrate that significant speed-ups can be gained using multiple CPUs. This opens the way to calculations which consider higher collision energies, larger molecules and / or more target states. The methodology, which is implemented as part of the UK molecular R-matrix codes (UKRMol and UKRMol+) can also be used for studies of bound molecular Rydberg states, photoionisation and positron-molecule collisions.
A hybrid scheme that utilizes MPI for distributed memory parallelism and OpenMP for shared memory parallelism is presented. The work is motivated by the desire to achieve exceptionally high Reynolds numbers in pseudospectral computations of fluid turbulence on emerging petascale, high core-count, massively parallel processing systems. The hybrid implementation derives from and augments a well-tested scalable MPI-parallelized pseudospectral code. The hybrid paradigm leads to a new picture for the domain decomposition of the pseudospectral grids, which is helpful in understanding, among other th…
Level set method has been used to capture interface motion. Narrow band algorithm is applied to localize the solving of level-set PDE on global domain to a tube around interface. Due to the unknown evolving interface, narrow band algorithm brings load balance problem for parallelizing computing. This work presents a tool for evenly distributing work loads on CPUs. On the other hand, numerically solving level-set PDE only needs simple operations but on large grid points. This work also presents a GPU acceleration for solving level-set PDE using finite difference method.
QuOp_MPI is a Python package designed for parallel simulation of quantum variational algorithms. It presents an object-orientated approach to quantum variational algorithm design and utilises MPI-parallelised sparse-matrix exponentiation, the fast Fourier transform and parallel gradient evaluation to achieve the highly efficient simulation of the fundamental unitary dynamics on massively parallel systems. In this article, we introduce QuOp_MPI and explore its application to the simulation of quantum algorithms designed to solve combinatorial optimisation algorithms including the Quantum Approx…
The use of Euler-Lagrange methods on unstructured grids extends their application area to more versatile setups. However, the lack of a regular topology limits the scalability of distributed parallel methods, especially for routines that perform a physical search in space. One of the most prominent slowdowns is the search for halo elements in physical space for the purpose of runtime communication avoidance. In this work, we present a new communication-free halo element search algorithm utilizing the MPI-3 shared memory model. This novel method eliminates the severe performance bottleneck of m…
In this paper, we present a parallel algorithm for Monte Carlo simulation of the 2D Ising Model to perform efficiently on a cluster computer using MPI. We use C++ programming language to implement the algorithm. In our algorithm, every process creates a sub-lattice and the energy is calculated after each Monte Carlo iteration. Each process communicates with its two neighbor processes during the job and they exchange the boundary spin variables. Finally, the total energy of lattice is calculated by map-reduce method versus the temperature. We use multi-spin coding technique to reduce the interp…
QSW_MPI is a python package developed for time-series simulation of continuous-time quantum stochastic walks. This model allows for the study of Markovian open quantum systems in the Lindblad formalism, including a generalisation of the continuous-time random walk and continuous-time quantum walk. Consisting of a python interface accessing parallelised Fortran libraries utilising sparse data structures, QSW_MPI is scalable to massively parallel computers, which makes possible the simulation of a wide range of walk dynamics on directed and undirected graphs of arbitrary complexity.
We introduce Lemon, an MPI parallel I/O library that is intended to allow for efficient parallel I/O of both binary and metadata on massively parallel architectures. Motivated by the demands of the Lattice Quantum Chromodynamics community, the data is stored in the SciDAC Lattice QCD Interchange Message Encapsulation format. This format allows for storing large blocks of binary data and corresponding metadata in the same file. Even if designed for LQCD needs, this format might be useful for any application with this type of data profile. The design, implementation and application of Lemon are …
A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are computed with the pseudospectral method. The code is pa…
To leverage the last two decades' transition in High-Performance Computing (HPC) towards clusters of compute nodes bound together with fast interconnects, a modern scalable CFD code must be able to efficiently distribute work amongst several nodes using the Message Passing Interface (MPI). MPI can enable very large simulations running on very large clusters, but it is necessary that the bulk of the CFD code be written with MPI in mind, an obstacle to parallelizing an existing serial code. In this work we present the results of extending an existing two-phase 3D Navier-Stokes solver, which was …
In this paper, we propose an efficient and accurate message-passing interface (MPI)-based parallel simulator for streamer discharges in three dimensions using the fluid model. First, we propose a new second-order semi-implicit scheme for the temporal discretization of the model that relaxes the dielectric relaxation time restriction. Moreover, it requires solving the Poisson-type equation only once at each time step, while the classical second-order explicit scheme typically needs to do twice. Second, we introduce a geometric multigrid preconditioned FGMRES solver that dramatically improves th…
A parallelized quantum dynamics package using the Smolyak algorithm for general molecular simulation is introduced in this work. The program has no limitation of the Hamiltonian form and provides high flexibility on the simulation setup to adapt to different problems. Taking advantage of the Smolyak sparse grids formula, the simulation could be performed with high accuracy, and in the meantime, impressive parallel efficiency. The capability of the simulation could be up to tens of degrees of freedom. The implementation of the algorithm and the package usage are introduced, followed by typical …
We report on the latest additions to our open-source, block-grid adaptive framework MPI-AMRVAC, which is a general toolkit for especially hyperbolic/parabolic partial differential equations (PDEs). Applications traditionally focused on shock-dominated, magnetized plasma dynamics described by either Newtonian or special relativistic (magneto)hydrodynamics, but its versatile design easily extends to different PDE systems. Here, we demonstrate applications covering any-dimensional scalar to system PDEs, with e.g. Korteweg-de Vries solutions generalizing early findings on soliton behaviour, shallo…
We present an efficient MPI-parallel geometric multigrid library for quadtree (2D) or octree (3D) grids with adaptive refinement. Cartesian 2D/3D and cylindrical 2D geometries are supported, with second-order discretizations for the elliptic operators. Periodic, Dirichlet, and Neumann boundary conditions can be handled, as well as free-space boundary conditions for 3D Poisson problems, for which we use an FFT-based solver on the coarse grid. Scaling results up to 1792 cores are presented. The library can be used to extend adaptive mesh refinement frameworks with an elliptic solver, which we de…
We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nanoindentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr Cr interaction and the Morse potential for Cr C interactions. We study the performance of our algorithm for …
A parallel code has been written in FORTRAN90, C, and MPI for the analysis of biological simulation data. Using a master/slave algorithm, the software operates on AMBER generated trajectory data using either UNIX or MPI file IO, and it supports up to 15 simultaneous function calls. This software has been performance tested on the Ranger Supercomputer on trajectory data of an aqueous bacterial reaction center micelle. Although the parallel reading is poor, the analysis algorithm itself shows embarrassingly parallel speedup up to 1024 compute nodes. At this CPU count the overall scaling of the s…
Traditional solution approaches for problems in quantum mechanics scale as $\mathcal O(M^3)$, where $M$ is the number of electrons. Various methods have been proposed to address this issue and obtain linear scaling $\mathcal O(M)$. One promising formulation is the direct minimization of energy. Such methods take advantage of physical localization of the solution, namely that the solution can be sought in terms of non-orthogonal orbitals with local support. In this work a numerically efficient implementation of sparse parallel vectors within the open-source finite element library deal.II is pro…
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also explained. A simple spatial-decomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processo…
We develop a "semi-parallel" simulation technique suggested by Pretorius and Lehner, in which the simulation spacetime volume is divided into a large number of small 4-volumes which have only initial and final surfaces. Thus there is no two-way communication between processors, and the 4-volumes can be simulated independently without the use of MPI. This technique allows us to simulate much larger volumes than we otherwise could, because we are not limited by total memory size. No processor time is lost waiting for other processors. We compare a cosmic string simulation we developed using the …
acousticHelmholtzFoam: an MPI-parallel unstructured finite-volume solver for frequency-domain acoustics in heterogeneous two-phase media with perfectly matched layers
