Based on a parallel scalable library for Coulomb interactions in particle systems, a comparison between the fast multipole method (FMM), multigrid-based methods, fast Fourier transform (FFT)-based methods, and a Maxwell solver is provided for the case of three-dimensional periodic boundary conditions. These methods are directly compared with respect to complexity, scalability, performance, and accuracy. To ensure comparable conditions for all methods and to cover typical applications, we tested all methods on the same set of computers using identical benchmark systems. Our findings suggest that, depending on system size and desired accuracy, the FMM- and FFT-based methods are most efficient in performance and stability.

Abstract-High-performance computing (HPC) is recognized as one of the pillars for further advance of science, industry, medicine, and education. Current HPC systems are being developed to overcome emerging challenges in order to reach Exascale level of performance, which is expected by the year 2020. The much larger embedded and mobile market allows for rapid development of IP blocks, and provides more flexibility in designing an application-specific SoC, un turn giving possibility in balancing performance, energy-efficiency and cost. In the Mont-Blanc project, we advocate for HPC systems be built from such commodity IP blocks, currently used in embedded and mobile SoCs.As a first demonstrator of such approach, we present the MontBlanc prototype; the first HPC system built with commodity SoCs, memories, and NICs from the embedded and mobile domain, and offthe-shelf HPC networking, storage, cooling and integration solutions. We present the system's architecture, and evaluation including both performance and energy efficiency. Further, we compare the system's abilities against a production level supercomputer. At the end, we discuss parallel scalability, and estimate the maximum scalability point of this approach across a set of applications.

Many scientific and medical researchers are working towards the creation of a virtual human—a personalized digital copy of an individual—that will assist in a patient’s diagnosis, treatment and recovery. The complex nature of living systems means that the development of this remains a major challenge. We describe progress in enabling the HemeLB lattice Boltzmann code to simulate 3D macroscopic blood flow on a full human scale. Significant developments in memory management and load balancing allow near linear scaling performance of the code on hundreds of thousands of computer cores. Integral to the construction of a virtual human, we also outline the implementation of a self-coupling strategy for HemeLB. This allows simultaneous simulation of arterial and venous vascular trees based on human-specific geometries.

Abstract:We investigate the conformational properties of polymers in ionic microgels in the presence of salt ions by molecular dynamics simulations and analytical theory. A microgel particle consists of coarse-grained linear polymers, which are tetra-functionally crosslinked. Counterions and salt ions are taken into account explicitly, and charge-charge interactions are described by the Coulomb potential. By varying the charge interaction strength and salt concentration, we characterize the swelling of the polyelectrolytes and the charge distribution. In particular, we determine the amount of trapped mobile charges inside the microgel and the Debye screening length. Moreover, we analyze the polymer extension theoretically in terms of the tension blob model taking into account counterions and salt ions implicitly by the Debye-Hückel model. Our studies reveal a strong dependence of the amount of ions absorbed in the interior of the microgel on the electrostatic interaction strength, which is related to the degree of the gel swelling. This implies a dependence of the inverse Debye screening length κ on the ion concentration; we find a power-law increase of κ with the Coulomb interaction strength with the exponent 3/5 for a salt-free microgel and an exponent 1/2 for moderate salt concentrations. Additionally, the radial dependence of polymer conformations and ion distributions is addressed.

We analyzed hydrodynamic fluctuations in nematic liquid crystals simulated by Multi-particle Collision Dynamics. Velocity effects on orientation were incorporated by allowing mesoscopic velocity gradients to exert torques on nematic particles. Backflow was included through an explicit application of angular momentum conservation during the collision events. We measured the spectra of hydrodynamic fluctuations and compared them with those derived from a linearized hydrodynamic scheme. Numerical results were found to reproduce the expected coupling between hydrodynamic modes, thus showing that the implementation simulates proper nematodynamic effects at the mesoscopic level.