A5028832623- Parallel Computing and Optimization Techniques
- Distributed and Parallel Computing Systems
- Advanced Data Storage Technologies
- Matrix Theory and Algorithms
- Protein Structure and Dynamics
- Mass Spectrometry Techniques and Applications
- Cloud Computing and Resource Management
- Fluid Dynamics and Heat Transfer
- Computational Fluid Dynamics and Aerodynamics
- Advanced Numerical Methods in Computational Mathematics
- Scientific Computing and Data Management
- Spectroscopy and Quantum Chemical Studies
- Lattice Boltzmann Simulation Studies
- Advanced Optimization Algorithms Research
- Advanced Chemical Physics Studies
- Fluid Dynamics and Thin Films
- Algorithms and Data Compression
- Numerical Methods and Algorithms
- Polynomial and algebraic computation
- Molecular Junctions and Nanostructures
- Thermal Regulation in Medicine
- Computability, Logic, AI Algorithms
- Respiratory Support and Mechanisms
- Service-Oriented Architecture and Web Services
- Analytic Number Theory Research
Science and Technology Facilities Council
2020
Sci-Tech Daresbury
2018-2020
University of Edinburgh
2011-2019
Daresbury Laboratory
2018
El Paso Community College
2013-2015
University of Belgrade
2014
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, biological systems. It especially aimed at massively parallel linear-scaling methods state-of-the-art ab initio simulations. Excellent performance for calculations achieved using novel algorithms implemented modern high-performance computing This review revisits the main capabilities efficient accurate The emphasis put on density functional...
The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse process, reasonable timescales, the large generated amounts molecular data. In light this, we have developed present here pyPcazip: a suite for compression analysis dynamics (MD) compatible with trajectory file formats by most contemporary MD engines such as AMBER, CHARMM, GROMACS NAMD, MPI parallelised to permit efficient processing very datasets. pyPcazip Unix based open-source...
Abstract We consider the linear and nonlinear stability of two-phase density-matched but viscosity-contrasted fluids subject to laminar Poiseuille flow in a channel, paying particular attention formation three-dimensional waves. A combination Orr–Sommerfeld–Squire analysis (both modal non-modal) with direct numerical simulation Navier–Stokes equations is used. For parameter regimes under consideration, theory, most unstable waves are two-dimensional. Nevertheless, we demonstrate several...
Ever-increasing core counts create the need to develop parallel algorithms that avoid closely coupled execution across all cores. We present performance analysis of several asynchronous implementations Jacobi’s method for solving systems linear equations, using MPI, SHMEM and OpenMP. In particular we have solved over 4 billion unknowns up 32,768 processes on a Cray XE6 supercomputer. show precise implementation details can strongly affect resulting convergence behaviour our solvers in...
CoCo ("complementary coordinates") is a method for ensemble enrichment based on principal component analysis (PCA) that was developed originally the investigation of NMR data. Here we investigate potential method, in combination with molecular dynamics simulations (CoCo-MD), to be used more generally enhanced sampling conformational space. Using alanine penta-peptide as model system, find an iterative workflow, interleaving short multiple-walker MD long-range jumps through space informed by...
Macro-modeling of cerebral blood flow can help determine the impact thermal intervention during instances head trauma to mitigate tissue damage. This work presents a bioheat model using 3D fluid-porous domain coupled with intersecting 1D arterial and venous vessel trees. combined vascular porous (VaPor) resolves both energy equations, including heat generated by metabolism, vasculature extracted from MRI data is extended tree generation algorithm. Counter-current flows are expected increase...
For many macromolecular systems the accurate sampling of relevant regions on potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient sampling. We present design and implementation Extensible Toolkit for Advanced Sampling analYsis (Ex-TASY) building executing advanced workflows HPC systems. ExTASY provides Python based "templated scripts" that interface an interoperable high-performance pilot-based...
Multiplication of two sparse matrices is a key operation in the simulation electronic structure systems containing thousands atoms and electrons. The highly optimized linear algebra library DBCSR (Distributed Block Compressed Sparse Row) has been specifically designed to efficiently perform such matrix-matrix multiplications. This basic building block for scaling theory low correlated methods CP2K. It parallelized using MPI OpenMP, can exploit GPU accelerators by means CUDA. We describe...
We introduce a modified and simplified version of the pre-existing fully parallelized three-dimensional Navier–Stokes flow solver known as TPLS. demonstrate how can be used pedagogical tool for study computational fluid dynamics (CFDs) parallel computing. TPLS is at its heart two-phase solver, uses calls to range external libraries accelerate performance. However, in present context we narrow focus basic hydrodynamics computing techniques, code therefore simulate pressure-driven single-phase...
CP2K is a widely used application for atomistic simulation that can execute on range of architectures. Consisting more than one million lines Fortran 95 code, the tested correctness with set about 2,500 inputs using dedicated regression testing environment. be built many compilers and executed different serial parallel platforms, thus making comprehensive even challenging. This paper presents an effort to improve existing process in order better support its continuing development....