GNA: new framework for statistical data analysis

We report on the status of GNA --- a new framework for fitting large-scale physical models. GNA utilizes the data flow concept within which a model is represented by a directed acyclic graph. Each node is an operation on an array (matrix multiplication, derivative or cross section calculation, etc). The framework enables the user to create flexible and efficient large-scale lazily evaluated models, handle large numbers of parameters, propagate parameters' uncertainties while taking into account possible correlations between them, fit models, and perform statistical analysis. The main goal of the paper is to give an overview of the main concepts and methods as well as reasons behind their design. Detailed technical information is to be published in further works.Comment: 9 pages, 3 figures, CHEP 2018, submitted to EPJ Web of Conference

Obvious: a meta-toolkit to encapsulate information visualization toolkits. One toolkit to bind them all

This article describes “Obvious”: a meta-toolkit that abstracts and encapsulates information visualization toolkits implemented in the Java language. It intends to unify their use and postpone the choice of which concrete toolkit(s) to use later-on in the development of visual analytics applications. We also report on the lessons we have learned when wrapping popular toolkits with Obvious, namely Prefuse, the InfoVis Toolkit, partly Improvise, JUNG and other data management libraries. We show several examples on the uses of Obvious, how the different toolkits can be combined, for instance sharing their data models. We also show how Weka and RapidMiner, two popular machine-learning toolkits, have been wrapped with Obvious and can be used directly with all the other wrapped toolkits. We expect Obvious to start a co-evolution process: Obvious is meant to evolve when more components of Information Visualization systems will become consensual. It is also designed to help information visualization systems adhere to the best practices to provide a higher level of interoperability and leverage the domain of visual analytics

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

The ALPS project: open source software for strongly correlated systems

We present the ALPS (Algorithms and Libraries for Physics Simulations) project, an international open source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models such as quantum magnets, lattice bosons, and strongly correlated fermion systems. Development is centered on common XML and binary data formats, on libraries to simplify and speed up code development, and on full-featured simulation programs. The programs enable non-experts to start carrying out numerical simulations by providing basic implementations of the important algorithms for quantum lattice models: classical and quantum Monte Carlo (QMC) using non-local updates, extended ensemble simulations, exact and full diagonalization (ED), as well as the density matrix renormalization group (DMRG). The software is available from our web server at http://alps.comp-phys.org.Comment: For full software and introductory turorials see http://alps.comp-phys.or

Gunrock: A High-Performance Graph Processing Library on the GPU

For large-scale graph analytics on the GPU, the irregularity of data access and control flow, and the complexity of programming GPUs have been two significant challenges for developing a programmable high-performance graph library. "Gunrock", our graph-processing system designed specifically for the GPU, uses a high-level, bulk-synchronous, data-centric abstraction focused on operations on a vertex or edge frontier. Gunrock achieves a balance between performance and expressiveness by coupling high performance GPU computing primitives and optimization strategies with a high-level programming model that allows programmers to quickly develop new graph primitives with small code size and minimal GPU programming knowledge. We evaluate Gunrock on five key graph primitives and show that Gunrock has on average at least an order of magnitude speedup over Boost and PowerGraph, comparable performance to the fastest GPU hardwired primitives, and better performance than any other GPU high-level graph library.Comment: 14 pages, accepted by PPoPP'16 (removed the text repetition in the previous version v5