Design and Analysis of a Task-based Parallelization over a Runtime System of an Explicit Finite-Volume CFD Code with Adaptive Time Stepping

FLUSEPA (Registered trademark in France No. 134009261) is an advanced simulation tool which performs a large panel of aerodynamic studies. It is the unstructured finite-volume solver developed by Airbus Safran Launchers company to calculate compressible, multidimensional, unsteady, viscous and reactive flows around bodies in relative motion. The time integration in FLUSEPA is done using an explicit temporal adaptive method. The current production version of the code is based on MPI and OpenMP. This implementation leads to important synchronizations that must be reduced. To tackle this problem, we present the study of a task-based parallelization of the aerodynamic solver of FLUSEPA using the runtime system StarPU and combining up to three levels of parallelism. We validate our solution by the simulation (using a finite-volume mesh with 80 million cells) of a take-off blast wave propagation for Ariane 5 launcher.Comment: Accepted manuscript of a paper in Journal of Computational Scienc

The Steam Factory

IMPACT. 1: Collaboration: The STEAM Factory provides a space where researchers from all disciplines can broaden their perspectives, share resources, spark creative research ideas and form collaborations across areas of common interest. -- 2. Dissemination: The STEAM Factory helps to bridge the gap between Ohio State and the Columbus community through research dissemination and outreach that is accessible, approachable and combines formal and informal learning.OSU PARTNERS: College of Arts and Sciences; College of Food, Agricultural, and Environmental Sciences; Office of Research; Office of Outreach and Engagement; College of Engineering; University Libraries; College of MedicineCOMMUNITY PARTNERS: 400 West Rich; Jami Goldstein, Greater Columbus Arts Council; Loose Films; Alex Bandar, Columbus Idea Foundry; Jim Sweeney, Franklinton Develpment Association Tom Murnane, ARC Business Advisors; Jenny Pope, Franklin Park Conservatory; David Spurlock, Hilton Columbus DowntownPRIMARY CONTACT: Roman Holowinski, Charlene Brenner ([email protected])Founded by a collection of young and energetic Ohio State faculty, postdocs and staff, the STEAM Factory is a diverse and inclusive grass-roots network in the Ohio State community that facilitates creative and interdisciplinary collaboration, innovation and dissemination

Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors.

Genome-wide association studies have identified over 70 single-nucleotide polymorphisms (SNPs) associated with breast cancer. A subset of these SNPs are associated with quantitative expression of nearby genes, but the functional effects of the majority remain unknown. We hypothesized that some risk SNPs may regulate alternative splicing. Using RNA-sequencing data from breast tumors and germline genotypes from The Cancer Genome Atlas, we tested the association between each risk SNP genotype and exon-, exon-exon junction- or transcript-specific expression of nearby genes. Six SNPs were associated with differential transcript expression of seven nearby genes at FDR < 0.05 (BABAM1, DCLRE1B/PHTF1, PEX14, RAD51L1, SRGAP2D and STXBP4). We next developed a Bayesian approach to evaluate, for each SNP, the overlap between the signal of association with breast cancer and the signal of association with alternative splicing. At one locus (SRGAP2D), this method eliminated the possibility that the breast cancer risk and the alternate splicing event were due to the same causal SNP. Lastly, at two loci, we identified the likely causal SNP for the alternative splicing event, and at one, functionally validated the effect of that SNP on alternative splicing using a minigene reporter assay. Our results suggest that the regulation of differential transcript isoform expression is the functional mechanism of some breast cancer risk SNPs and that we can use these associations to identify causal SNPs, target genes and the specific transcripts that may mediate breast cancer risk

MPMD parallelization of an aerodynamic code with bodies in relative motion

International audienceFLUSEPA is an advanced simulation tool which performs a large panel of aerodynamic studies. It is the unstructured finite-volume solver developed by Airbus Defence & Space company to calculate compressible, multidimensional, unsteady, viscous and reactive flows around bodies in relative motion. The numerical strategy in FLUSEPA is designed for highly compressible flows and keeps its accuracy in non-Cartesian grids. According the desired accuracy, a second-order accurate shock-capturing scheme is generally used for RANS and URANS simulations and a fourth order accurate vortex-centered scheme is used for hybrid RANS/LES simulations. The meshing strategy is based on multi-overlapping grid intersection which is conservative and allows to quickly and properly mesh 3D complex geometries. It can be seen as a CHIMERA strategy without interpolation. Each body is meshed independently and immersed in background grids.MPMD parallelisation of this code is presented

MACHISMO IN THE DOCK – A CRITICAL FEMINIST ANALYSIS OF BRAZILIAN CRIMINAL POLICY CONCERNING THE COMBAT OF VIOLENCE AGAINST WOMEN

O presente artigo tem por objetivo realizar uma análise crítica dos discursos feministas, que levaram recentemente à promulgação das leis brasileiras responsáveis por tornar mais severa a punição da violência contra a mulher, de modo a demonstrar como não conseguem escapar das armadilhas cognitivas estabelecidas pela dominação masculina naturalizada nas sociedades ocidentais e como têm servido ao desenvolvimento de uma biopolítica neoliberal.The aim of this article is to critically analyze the feminist discourse that led to the recent enactment of Brazilian laws that increased the penalties for violence against women, in order to demonstrate that they cannot escape the cognitive traps established by male domination naturalized in Western societies and how they have served the development of neoliberal biopolitics

Task-based parallelization of a CFD code over a Runtime System

International audienceFLUSEPA is an advanced simulation tool which performs a large panel of aerodynamic studies. It is the unstructured nite-volume solver developed by Airbus Defence & Space company to calculate compressible, multidimensional, unsteady, viscous and reactive flows around bodies in relative motion [2](Figure 1). The numerical strategy in FLUSEPA is designed for highly compressible tlows and to remain accurate when using non-Cartesian grids. The meshing strategy is based on multi-overlapping grid intersection which is conservative and allows to quickly mesh 3D complex geometries. The time integration in FLUSEPA is done using an explicit temporal adaptive method [3]. Instead of using a time step imposed by the slowest cell, cells are grouped inside temporal classes according to their maximum allowed time step. This method allows to perform a fewer number of operations at the expense of some complexity. An iteration of the aerodynamic solver is separated into several sub-iterations. Every cell is not integrated during each sub-iteration but cells which share a face with a slower one are interpolated. At the end of the iteration, each cell has reached the same time. Between iterations, temporal classes can evolve.The current version of FLUSEPA is parallelized using a classical MPI-OpenMP approach and domain decomposition: border faces are duplicated and ghost cells are used. However, the way the time is integrated leads to important time wasted in synchronization despite computation-communication overlapping. The time integration implies an order for the cells to be processed depending on their temporal class: neighbor cells must be at the same time during processing. This locality information is partially lost with the current parallelization. In this paper, we present a way to overcome this issue by working on sub-domains inside each process. We capture the dependencies more precisely through the use of a task-based parallel expression with the help of a well suited runtime system

FLUSEPA - a Navier-Stokes Solver for Unsteady Problems with Bodies in Relative Motion : Toward a Task-Based Parallel Version over a Runtime System

International audienceFLUSEPA code is designed to handle unsteady problems with bodies in relative motion (stage separation) and strong shocks. A finite volume formulation is used to solve the RANS equations. Time integration consists on an explicit temporal adaptive solver. We present a task based parallel version of the aerodynamic solver designed from the previous MPI/OpenMP one and using a modern runtime system to schedule the tasks. An Ariane 5 booster separation computation will be presented

Towards an efficient Task-based Parallelization over a Runtime System of an Explicit Finite-Volume CFD Code with Adaptive Time Stepping

International audienceFLUSEPA is an advanced simulation tool which performs a large panel of aerodynamic studies. It is the unstruc-tured finite-volume solver developed by Airbus Defence & Space company to calculate compressible, multidimensional, unsteady, viscous and reactive flows around bodies in relative motion. The time integration in FLUSEPA is done using an explicit temporal adaptive method. The current production version of the code is based on MPI and OpenMP. This implementation leads to important synchronizations that must be reduced. To tackle this problem, we present a first study of a task-based parallelization of the solver part of FLUSEPA using the runtime system StarPU and combining up to three levels of parallelism. We validate our solution on the simulation of a takeoff blast wave propagation for Ariane 5 launcher