Models in the Cloud: Exploring Next Generation Environmental Software Systems

There is growing interest in the application of the latest trends in computing and data science methods to improve environmental science. However we found the penetration of best practice from computing domains such as software engineering and cloud computing into supporting every day environmental science to be poor. We take from this work a real need to re-evaluate the complexity of software tools and bring these to the right level of abstraction for environmental scientists to be able to leverage the latest developments in computing. In the Models in the Cloud project, we look at the role of model driven engineering, software frameworks and cloud computing in achieving this abstraction. As a case study we deployed a complex weather model to the cloud and developed a collaborative notebook interface for orchestrating the deployment and analysis of results. We navigate relatively poor support for complex high performance computing in the cloud to develop abstractions from complexity in cloud deployment and model configuration. We found great potential in cloud computing to transform science by enabling models to leverage elastic, flexible computing infrastructure and support new ways to deliver collaborative and open science

The Astrophysical Multipurpose Software Environment

We present the open source Astrophysical Multi-purpose Software Environment (AMUSE, www.amusecode.org), a component library for performing astrophysical simulations involving different physical domains and scales. It couples existing codes within a Python framework based on a communication layer using MPI. The interfaces are standardized for each domain and their implementation based on MPI guarantees that the whole framework is well-suited for distributed computation. It includes facilities for unit handling and data storage. Currently it includes codes for gravitational dynamics, stellar evolution, hydrodynamics and radiative transfer. Within each domain the interfaces to the codes are as similar as possible. We describe the design and implementation of AMUSE, as well as the main components and community codes currently supported and we discuss the code interactions facilitated by the framework. Additionally, we demonstrate how AMUSE can be used to resolve complex astrophysical problems by presenting example applications.Comment: 23 pages, 25 figures, accepted for A&

The GeoClaw software for depth-averaged flows with adaptive refinement

Many geophysical flow or wave propagation problems can be modeled with two-dimensional depth-averaged equations, of which the shallow water equations are the simplest example. We describe the GeoClaw software that has been designed to solve problems of this nature, consisting of open source Fortran programs together with Python tools for the user interface and flow visualization. This software uses high-resolution shock-capturing finite volume methods on logically rectangular grids, including latitude--longitude grids on the sphere. Dry states are handled automatically to model inundation. The code incorporates adaptive mesh refinement to allow the efficient solution of large-scale geophysical problems. Examples are given illustrating its use for modeling tsunamis, dam break problems, and storm surge. Documentation and download information is available at www.clawpack.org/geoclawComment: 18 pages, 11 figures, Animations and source code for some examples at http://www.clawpack.org/links/awr10 Significantly modified from original posting to incorporate suggestions of referee

Sussing merger trees: a proposed merger tree data format

We propose a common terminology for use in describing both temporal merger trees and spatial structure trees for dark-matter halos. We specify a unified data format in HDF5 and provide example I/O routines in C, FORTRAN and PYTHON

Towards quantum-chemical method development for arbitrary basis functions

We present the design of a flexible quantum-chemical method development framework, which supports employing any type of basis function. This design has been implemented in the light-weight program package molsturm, yielding a basis-function-independent self-consistent field scheme. Versatile interfaces, making use of open standards like python, mediate the integration of molsturm with existing third-party packages. In this way both rapid extension of the present set of methods for electronic structure calculations as well as adding new basis function types can be readily achieved. This makes molsturm well-suitable for testing novel approaches for discretising the electronic wave function and allows comparing them to existing methods using the same software stack. This is illustrated by two examples, an implementation of coupled-cluster doubles as well as a gradient-free geometry optimisation, where in both cases, an arbitrary basis functions could be used. molsturm is open-source and can be obtained from https://molsturm.org.Comment: 15 pages and 7 figure