BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images

In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM (BioEM) formalism. By ranking structural models using posterior probabilities calculated for individual images, BioEM in principle addresses the challenge of working with highly dynamic or heterogeneous systems not easily handled in traditional EM reconstruction. However, the calculation of these posteriors for large numbers of particles and models is computationally demanding. Here we present highly parallelized, GPU-accelerated computer software that performs this task efficiently. Our flexible formulation employs CUDA, OpenMP, and MPI parallelization combined with both CPU and GPU computing. The resulting BioEM software scales nearly ideally both on pure CPU and on CPU+GPU architectures, thus enabling Bayesian analysis of tens of thousands of images in a reasonable time. The general mathematical framework and robust algorithms are not limited to cryo-electron microscopy but can be generalized for electron tomography and other imaging experiments

Using machine learning techniques to evaluate multicore soft error reliability

Virtual platform frameworks have been extended to allow earlier soft error analysis of more realistic multicore systems (i.e., real software stacks, state-of-the-art ISAs). The high observability and simulation performance of underlying frameworks enable to generate and collect more error/failurerelated data, considering complex software stack configurations, in a reasonable time. When dealing with sizeable failure-related data sets obtained from multiple fault campaigns, it is essential to filter out parameters (i.e., features) without a direct relationship with the system soft error analysis. In this regard, this paper proposes the use of supervised and unsupervised machine learning techniques, aiming to eliminate non-relevant information as well as identify the correlation between fault injection results and application and platform characteristics. This novel approach provides engineers with appropriate means that able are able to investigate new and more efficient fault mitigation techniques. The underlying approach is validated with an extensive data set gathered from more than 1.2 million fault injections, comprising several benchmarks, a Linux OS and parallelization libraries (e.g., MPI, OpenMP), as well as through a realistic automotive case study

Dynamic Model Averaging for Practitioners in Economics and Finance: The eDMA Package

Raftery, Karny, and Ettler (2010) introduce an estimation technique, which they refer to as Dynamic Model Averaging (DMA). In their application, DMA is used to predict the output strip thickness for a cold rolling mill, where the output is measured with a time delay. Recently, DMA has also shown to be useful in macroeconomic and financial applications. In this paper, we present the eDMA package for DMA estimation implemented in R. The eDMA package is especially suited for practitioners in economics and finance, where typically a large number of predictors are available. Our implementation is up to 133 times faster then a standard implementation using a single-core CPU. Thus, with the help of this package, practitioners are able to perform DMA on a standard PC without resorting to large clusters, which are not easily available to all researchers. We demonstrate the usefulness of this package through simulation experiments and an empirical application using quarterly U.S. inflation data.Comment: 21 pages, 5 figures, 2 table

Afivo: a framework for quadtree/octree AMR with shared-memory parallelization and geometric multigrid methods

Afivo is a framework for simulations with adaptive mesh refinement (AMR) on quadtree (2D) and octree (3D) grids. The framework comes with a geometric multigrid solver, shared-memory (OpenMP) parallelism and it supports output in Silo and VTK file formats. Afivo can be used to efficiently simulate AMR problems with up to about $10^{8}$ unknowns on desktops, workstations or single compute nodes. For larger problems, existing distributed-memory frameworks are better suited. The framework has no built-in functionality for specific physics applications, so users have to implement their own numerical methods. The included multigrid solver can be used to efficiently solve elliptic partial differential equations such as Poisson's equation. Afivo's design was kept simple, which in combination with the shared-memory parallelism facilitates modification and experimentation with AMR algorithms. The framework was already used to perform 3D simulations of streamer discharges, which required tens of millions of cells

A Functional Safety OpenMP∗ for Critical Real-Time Embedded Systems

OpenMP* has recently gained attention in the embedded domain by virtue of the augmentations implemented in the last specification. Yet, the language has a minimal impact in the embedded real-time domain mostly due to the lack of reliability and resiliency mechanisms. As a result, functional safety properties cannot be guaranteed. This paper analyses in detail the latest specification to determine whether and how the compliant OpenMP implementations can guarantee functional safety. Given the conclusions drawn from the analysis, the paper describes a set of modifications to the specification, and a set of requirements for compiler and runtime systems to qualify for safety critical environments. Through the proposed solution, OpenMP can be used in critical real-time embedded systems without compromising functional safety.This work was funded by the EU project P-SOCRATES (FP7-ICT-2013- 10) and the Spanish Ministry of Science and Innovation under contract TIN2015- 65316-P.Peer ReviewedPostprint (author's final draft