AMRA: An Adaptive Mesh Refinement Hydrodynamic Code for Astrophysics

Implementation details and test cases of a newly developed hydrodynamic code, AMRA, are presented. The numerical scheme exploits the adaptive mesh refinement technique coupled to modern high-resolution schemes which are suitable for relativistic and non-relativistic flows. Various physical processes are incorporated using the operator splitting approach, and include self-gravity, nuclear burning, physical viscosity, implicit and explicit schemes for conductive transport, simplified photoionization, and radiative losses from an optically thin plasma. Several aspects related to the accuracy and stability of the scheme are discussed in the context of hydrodynamic and astrophysical flows.Comment: 41 pages, 21 figures (9 low-resolution), LaTeX, requires elsart.cls, submitted to Comp. Phys. Comm.; additional documentation and high-resolution figures available from http://www.camk.edu.pl/~tomek/AMRA/index.htm

Extensions of the siesta dft code for simulation of molecules

We describe extensions to the siesta density functional theory (dft) code [30], for the simulation of isolated molecules and their absorption spectra. The extensions allow for: - Use of a multi-grid solver for the Poisson equation on a finite dft mesh. Non-periodic, Dirichlet boundary conditions are computed by expansion of the electric multipoles over spherical harmonics. - Truncation of a molecular system by the method of design atom pseudo- potentials of Xiao and Zhang[32]. - Electrostatic potential fitting to determine effective atomic charges. - Derivation of electronic absorption transition energies and oscillator stren- gths from the raw spectra produced by a recently described, order O(N3), time-dependent dft code[21]. The code is furthermore integrated within siesta as a post-processing option

RIACS

Topics considered include: high-performance computing; cognitive and perceptual prostheses (computational aids designed to leverage human abilities); autonomous systems. Also included: development of a 3D unstructured grid code based on a finite volume formulation and applied to the Navier-stokes equations; Cartesian grid methods for complex geometry; multigrid methods for solving elliptic problems on unstructured grids; algebraic non-overlapping domain decomposition methods for compressible fluid flow problems on unstructured meshes; numerical methods for the compressible navier-stokes equations with application to aerodynamic flows; research in aerodynamic shape optimization; S-HARP: a parallel dynamic spectral partitioner; numerical schemes for the Hamilton-Jacobi and level set equations on triangulated domains; application of high-order shock capturing schemes to direct simulation of turbulence; multicast technology; network testbeds; supercomputer consolidation project

Invasive Computing in HPC with X10

High performance computing with thousands of cores relies on distributed memory due to memory consistency reasons. The resource management on such systems usually relies on static assignment of resources at the start of each application. Such a static scheduling is incapable of starting applications with required resources being used by others since a reduction of resources assigned to applications without stopping them is not possible. This lack of dynamic adaptive scheduling leads to idling resources until the remaining amount of requested resources gets available. Additionally, applications with changing resource requirements lead to idling or less efficiently used resources. The invasive computing paradigm suggests dynamic resource scheduling and applications able to dynamically adapt to changing resource requirements. As a case study, we developed an invasive resource manager as well as a multigrid with dynamically changing resource demands. Such a multigrid has changing scalability behavior during its execution and requires data migration upon reallocation due to distributed memory systems. To counteract the additional complexity introduced by the additional interfaces, e. g. for data migration, we use the X10 programming language for improved programmability. Our results show improved application throughput and the dynamic adaptivity. In addition, we show our extension for the distributed arrays of X10 to support data migrationThis work was supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Centre “Invasive Computing” (SFB/TR 89)