Motivation, Design, and Ubiquity: A Discussion of Research Ethics and Computer Science

Modern society is permeated with computers, and the software that controls them can have latent, long-term, and immediate effects that reach far beyond the actual users of these systems. This places researchers in Computer Science and Software Engineering in a critical position of influence and responsibility, more than any other field because computer systems are vital research tools for other disciplines. This essay presents several key ethical concerns and responsibilities relating to research in computing. The goal is to promote awareness and discussion of ethical issues among computer science researchers. A hypothetical case study is provided, along with questions for reflection and discussion.Comment: Written as central essay for the Computer Science module of the LANGURE model curriculum in Research Ethic

nbodykit: an open-source, massively parallel toolkit for large-scale structure

We present nbodykit, an open-source, massively parallel Python toolkit for analyzing large-scale structure (LSS) data. Using Python bindings of the Message Passing Interface (MPI), we provide parallel implementations of many commonly used algorithms in LSS. nbodykit is both an interactive and scalable piece of scientific software, performing well in a supercomputing environment while still taking advantage of the interactive tools provided by the Python ecosystem. Existing functionality includes estimators of the power spectrum, 2 and 3-point correlation functions, a Friends-of-Friends grouping algorithm, mock catalog creation via the halo occupation distribution technique, and approximate N-body simulations via the FastPM scheme. The package also provides a set of distributed data containers, insulated from the algorithms themselves, that enable nbodykit to provide a unified treatment of both simulation and observational data sets. nbodykit can be easily deployed in a high performance computing environment, overcoming some of the traditional difficulties of using Python on supercomputers. We provide performance benchmarks illustrating the scalability of the software. The modular, component-based approach of nbodykit allows researchers to easily build complex applications using its tools. The package is extensively documented at http://nbodykit.readthedocs.io, which also includes an interactive set of example recipes for new users to explore. As open-source software, we hope nbodykit provides a common framework for the community to use and develop in confronting the analysis challenges of future LSS surveys.Comment: 18 pages, 7 figures. Feedback very welcome. Code available at https://github.com/bccp/nbodykit and for documentation, see http://nbodykit.readthedocs.i

Domain-Specific Acceleration and Auto-Parallelization of Legacy Scientific Code in FORTRAN 77 using Source-to-Source Compilation

Massively parallel accelerators such as GPGPUs, manycores and FPGAs represent a powerful and affordable tool for scientists who look to speed up simulations of complex systems. However, porting code to such devices requires a detailed understanding of heterogeneous programming tools and effective strategies for parallelization. In this paper we present a source to source compilation approach with whole-program analysis to automatically transform single-threaded FORTRAN 77 legacy code into OpenCL-accelerated programs with parallelized kernels. The main contributions of our work are: (1) whole-source refactoring to allow any subroutine in the code to be offloaded to an accelerator. (2) Minimization of the data transfer between the host and the accelerator by eliminating redundant transfers. (3) Pragmatic auto-parallelization of the code to be offloaded to the accelerator by identification of parallelizable maps and reductions. We have validated the code transformation performance of the compiler on the NIST FORTRAN 78 test suite and several real-world codes: the Large Eddy Simulator for Urban Flows, a high-resolution turbulent flow model; the shallow water component of the ocean model Gmodel; the Linear Baroclinic Model, an atmospheric climate model and Flexpart-WRF, a particle dispersion simulator. The automatic parallelization component has been tested on as 2-D Shallow Water model (2DSW) and on the Large Eddy Simulator for Urban Flows (UFLES) and produces a complete OpenCL-enabled code base. The fully OpenCL-accelerated versions of the 2DSW and the UFLES are resp. 9x and 20x faster on GPU than the original code on CPU, in both cases this is the same performance as manually ported code.Comment: 12 pages, 5 figures, submitted to "Computers and Fluids" as full paper from ParCFD conference entr

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3) Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.Comment: 72 page