High-throughput discovery of post-transcriptional cis-regulatory elements

Validation of 8mers found in the main screen. (PDF 280 kb

Efficient Helicopter Aerodynamic and Aeroacoustic Predictions on Parallel Computers

This paper presents parallel implementations of two codes used in a combined CFD/Kirchhoff methodology to predict the aerodynamics and aeroacoustics properties of helicopters. The rotorcraft Navier-Stokes code, TURNS, computes the aerodynamic flowfield near the helicopter blades and the Kirchhoff acoustics code computes the noise in the far field, using the TURNS solution as input. The overall parallel strategy adds MPI message passing calls to the existing serial codes to allow for communication between processors. As a result, the total code modifications required for parallel execution are relatively small. The biggest bottleneck in running the TURNS code in parallel comes from the LU-SGS algorithm that solves the implicit system of equations. We use a new hybrid domain decomposition implementation of LU-SGS to obtain good parallel performance on the SP-2. TURNS demonstrates excellent parallel speedups for quasi-steady and unsteady three-dimensional calculations of a helicopter blade in forward flight. The execution rate attained by the code on 114 processors is six times faster than the same cases run on one processor of the Cray C-90. The parallel Kirchhoff code also shows excellent parallel speedups and fast execution rates. As a performance demonstration, unsteady acoustic pressures are computed at 1886 far-field observer locations for a sample acoustics problem. The calculation requires over two hundred hours of CPU time on one C-90 processor but takes only a few hours on 80 processors of the SP2. The resultant far-field acoustic field is analyzed with state of-the-art audio and video rendering of the propagating acoustic signals

A multi-country test of brief reappraisal interventions on emotions during the COVID-19 pandemic.

The COVID-19 pandemic has increased negative emotions and decreased positive emotions globally. Left unchecked, these emotional changes might have a wide array of adverse impacts. To reduce negative emotions and increase positive emotions, we tested the effectiveness of reappraisal, an emotion-regulation strategy that modifies how one thinks about a situation. Participants from 87 countries and regions (n = 21,644) were randomly assigned to one of two brief reappraisal interventions (reconstrual or repurposing) or one of two control conditions (active or passive). Results revealed that both reappraisal interventions (vesus both control conditions) consistently reduced negative emotions and increased positive emotions across different measures. Reconstrual and repurposing interventions had similar effects. Importantly, planned exploratory analyses indicated that reappraisal interventions did not reduce intentions to practice preventive health behaviours. The findings demonstrate the viability of creating scalable, low-cost interventions for use around the world

On Parallel Implementations of Dynamic Overset Grid Methods

This paper explores the parallel performance of structured overset CFD computations for multicomponent bodies in which there is relative motion between component parts. The two processes that dominate the cost of such problems are the flow solution on each component and the intergrid connectivity solution. A two-part static-dynamic load balancing scheme is proposed in which the static part balances the load for the flow solution and the dynamic part re-balances, if necessary, the load for the connectivity solution. This scheme is coupled with existing parallel implementations of the OVERFLOW flow solver and DCF3D connectivity routine and used for unsteady calculations about aerodynamic bodies on the IBM SP2 and IBM SP multi-processors. This paper also describes the parallel implementation of a new solution-adaption scheme based on structured Cartesian overset grids. 1.0 Introduction Unsteady prediction of viscous flows with relative movement between component parts remains an extremel..

On Strand Grids for Complex Flows

The need for highly automated and computationally efficient tools for high fidelity simulation of complex flow fields is recognized. A discretization paradigm that holds significant advantages relative to these needs is described. Problem domains are categorized into near- and offbody partitions. Strand grid technology is applied to near-body partitions, while block-structured Cartesian AMR (Adaptive Mesh Refinement) is applied to the off-body partition. The computational advantages and degrees of automation derivable from the approach are reviewed. A set of software tools that have been developed for grid generation and flow solution using both strand grid and block-structured Cartesian AMR are presented. Demonstration of strand grid technology is provided via time-dependent flow simulations and comparison with experimental data. The degree to which strand grid technology expands the spectrum of problems that can be considered via high performance computing is also considered. T I

Large scale parallel structured AMR calculations using the SAMRAI framework

This paper discusses the design and performance of the parallel data communication infrastructure in SAMRAI, a software framework for structured adaptive mesh refinement (SAMR) multi-physics applications. We describe requirements of such applications and how SAMRAI abstractions manage complex data communication operations found in them. Parallel performance is characterized for two adaptive problems solving hyperbolic conservation laws on up to 512 processors of the IBM ASCI Blue Pacific system. Results reveal good scaling for numerical and data communication operations but poorer scaling in adaptive meshing and communication schedule construction phases of the calculations. We analyze the costs of these different operations, addressing key concerns for scaling SAMR computations to large numbers of processors, and discuss potential changes to improve our current implementation. 1