Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters

The classical method of determining the atomic structure of complex molecules by analyzing diffraction patterns is currently undergoing drastic developments. Modern techniques for producing extremely bright and coherent X-ray lasers allow a beam of streaming particles to be intercepted and hit by an ultrashort high energy X-ray beam. Through machine learning methods the data thus collected can be transformed into a three-dimensional volumetric intensity map of the particle itself. The computational complexity associated with this problem is very high such that clusters of data parallel accelerators are required. We have implemented a distributed and highly efficient algorithm for inversion of large collections of diffraction patterns targeting clusters of hundreds of GPUs. With the expected enormous amount of diffraction data to be produced in the foreseeable future, this is the required scale to approach real time processing of data at the beam site. Using both real and synthetic data we look at the scaling properties of the application and discuss the overall computational viability of this exciting and novel imaging technique

BrainFrame: A node-level heterogeneous accelerator platform for neuron simulations

Objective: The advent of High-Performance Computing (HPC) in recent years has led to its increasing use in brain study through computational models. The scale and complexity of such models are constantly increasing, leading to challenging computational requirements. Even though modern HPC platforms can often deal with such challenges, the vast diversity of the modeling field does not permit for a single acceleration (or homogeneous) platform to effectively address the complete array of modeling requirements. Approach: In this paper we propose and build BrainFrame, a heterogeneous acceleration platform, incorporating three distinct acceleration technologies, a Dataflow Engine, a Xeon Phi and a GP-GPU. The PyNN framework is also integrated into the platform. As a challenging proof of concept, we analyze the performance of BrainFrame on different instances of a state-of-the-art neuron model, modeling the Inferior- Olivary Nucleus using a biophysically-meaningful, extended Hodgkin-Huxley representation. The model instances take into account not only the neuronal- network dimensions but also different network-connectivity circumstances that can drastically change application workload characteristics. Main results: The synthetic approach of three HPC technologies demonstrated that BrainFrame is better able to cope with the modeling diversity encountered. Our performance analysis shows clearly that the model directly affect performance and all three technologies are required to cope with all the model use cases.Comment: 16 pages, 18 figures, 5 table

About multi-resolution techniques for large eddy simulation of reactive multi-phase flows

A numerical technique for mesh refinement in the HeaRT (Heat Release and Transfer) numerical code is presented. In the CFD framework, Large Eddy Simulation (LES) approach is gaining in importance as a tool for simulating turbulent combustion pro- cesses, also if this approach has an high computational cost due to the complexity of the turbulent modeling and the high number of grid points necessary to obtain a good numerical solution. In particular, when a numerical simulation of a big domain is performed with a structured grid, the number of grid points can increase so much that the simulation becomes impossible: this problem can be overcomed with a mesh refinement technique. Mesh refinement technique developed for HeaRT numerical code (a staggered finite difference code) is based on an high order reconstruction of the variables at the grid interfaces by means of a least square quasi-eno interpolation: numerical code is written in modern Fortran (2003 standard of newer) and is parallelized using domain decomposition and message passing interface (MPI) standard