Message-Passing Multi-Cell Molecular Dynamics on the Connection Machine 5

We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5) and demonstrate that meso-scale molecular dynamics with more than $10^8$ particles is now possible on massively parallel MIMD computers. Typical runs show single particle update-times of $0.15 \mu s$ in 2 dimensions (2D) and approximately $1 \mu s$ in 3 dimensions (3D) on a 1024 node CM-5 without vector units, corresponding to more than 1.8 GFlops overall performance. We also present a scaling equation which agrees well with actually observed timings.Comment: 17 pages, Uuencoded compressed PostScript fil

A wrapper generation tool for the creation of scriptable scientific applications

Journal ArticleIn recent years, there has been considerable interest in the use of scripting languages as a mechanism for controlling and developing scientific software. Scripting languages allow scientific applications to be encapsulated in an interpreted environment similar to that found in commercial scientific packages such as MATLAB, Mathematica, and IDL. This improves the usability of scientific software by providing a powerful meachanism for specifyling and controlling cimplex problems as well as giving users an interactive and exploratory problem solving environment. Scripting languages also provide a framework for building and integrating software components that allows tools be used in a more efficient manner. This streamlines the problem solving process and enable scientists to be more productive

SWIG users manual (version 1.1)

technical reportSWIG is a tool for solving problems. More specifically, SWIG is a simple tool for building interactive C, C++, or Objective-C programs with common scripting languages such as Tel, Perl, and Python. Of course, more importantly, SWIG is a tool for making C programming more enjoyable and promoting laziness (an essential feature). SWIG is not part of an overgrown software engineering project, an attempt to build some sort of monolithic programming environment, or an attempt to force everyone to rewrite all of their code (ie. code reuse). In fact, none of these things have ever been a priority. SWIG was originally developed in the Theoretical Physics Division at Los Alamos National Laboratory for building interfaces to large materials science research simulations being run on the Connection Machine 5 supercomputer

Training Big Random Forests with Little Resources

Without access to large compute clusters, building random forests on large datasets is still a challenging problem. This is, in particular, the case if fully-grown trees are desired. We propose a simple yet effective framework that allows to efficiently construct ensembles of huge trees for hundreds of millions or even billions of training instances using a cheap desktop computer with commodity hardware. The basic idea is to consider a multi-level construction scheme, which builds top trees for small random subsets of the available data and which subsequently distributes all training instances to the top trees' leaves for further processing. While being conceptually simple, the overall efficiency crucially depends on the particular implementation of the different phases. The practical merits of our approach are demonstrated using dense datasets with hundreds of millions of training instances.Comment: 9 pages, 9 Figure

The primary visual system of adult lizards demonstrates that neurogenesis is not obligatorily linked to central nerve regeneration but may be a prerequisite for the restoration of maps in the brain

AbstractFollowing optic nerve crush in the adult lizard Ctenophorus ornatus, most retinal ganglion cells regrow their axons into visual brain centres: however, the regenerated projections lack retinotopic order and the animals are blind via the experimental eye. Here we have used 3H-thymidine autoradiography to demonstrate that cell division is no longer taking place in the retina of normal adult lizards. We conclude that the optic nerve can regenerate in lizard even though cells are no longer being added to the retina, However, continued retinal neurogenesis may be linked to the ability to restore topographic maps

User interfaces for computational science: a domain specific language for OOMMF embedded in Python

Computer simulations are used widely across the engineering and science disciplines, including in the research and development of magnetic devices using computational micromagnetics. In this work, we identify and review different approaches to configuring simulation runs: (i) the re-compilation of source code, (ii) the use of configuration files, (iii) the graphical user interface, and (iv) embedding the simulation specification in an existing programming language to express the computational problem. We identify the advantages and disadvantages of different approaches and discuss their implications on effectiveness and reproducibility of computational studies and results. Following on from this, we design and describe a domain specific language for micromagnetics that is embedded in the Python language, and allows users to define the micromagnetic simulations they want to carry out in a flexible way. We have implemented this micromagnetic simulation description language together with a computational backend that executes the simulation task using the Object Oriented MicroMagnetic Framework (OOMMF). We illustrate the use of this Python interface for OOMMF by solving the micromagnetic standard problem 4. All the code is publicly available and is open source

Pathways to care in at-risk mental states: a systematic review

Aim: Pathways to care are well studied in the First Episode Psychosis field, but less attention has been given to At‐Risk Mental States or prodromal psychosis. This is important because accessing appropriate help at the earliest opportunity is likely to improve outcomes, particularly for those who make transition to psychosis. The present systematic review aimed to synthesize the available literature on pathways to care in ARMS or prodromal psychosis, and investigate the barriers and facilitators to receiving care for ARMS. Methods: The CINAHL Complete, EMBASE, Medline Complete, PsycINFO and PubMED databases were searched. Studies were included if they were published in English between 1985 and 2019, where reported data came exclusively from an At‐Risk Mental State population, and the study described or related to pathways to care. Results: Ten studies met the inclusion criteria, of which 8 were quantitative. Screening tools and pathways to care instruments varied. Mental health professionals, and general practitioners played a key role in help seeking. Family involvement was also found to be an important factor. Conclusions: Pathways to care research in At‐Risk Mental States are more scarce than in the field of First Episode Psychosis. More research is warranted, especially concerning the role of patient‐level characteristics on pathways to care. A validated measure of pathways to care may also be of benefit

Management of the Industry/Research Organisation Interface

The purpose of a consultancy undertaken to assess management processes in research projects to improve communication between research organisations and the mining industry through the development of an improved mode of operation and customer interface is discussed. The consultancy was conducted using the Nadler and Tushman Congruency Model of Organisational Behaviour to asses components of a project\u27s inputs, transformation process and outputs for their degree of congruence or \u27fit\u27. As an example the University of Queensland (UQ) managed ACARP Project \u27Maximising Coal Production in the Presence of Hydrogen Sulphide (H₂S) Seam Gas\u27 was used for illustration. An action research process was used to collect data on the project organisation and history, observations made of group project meetings and interviews undertaken with project staff and representatives of the mining industry and the UQ. The findings highlighted major differences in culture between the university and industry, inadequate planning and strategy development, ineffective intergroup communication, high and conflicting demands on time, and in some cases a poor fit between individuals and tasks. Recommendations proposed to address these issues are presented as two groups, those applicable to the current H₂S Project and those for future similar research projects. They involve improved strategies for intergroup and interpersonal communication, role clarification, project administration and organisational learning and assessment. The proposed interventions are relatively simple, easily implemented and inexpensive. They have the potential to improve the fit between the components of the organisation as well as between the organisation and its environment, enhance efficiency and effectiveness and improve the relationship between the university and industry to ensure future collaborative research projects and access to external funding