Locality-aware parallel block-sparse matrix-matrix multiplication using the Chunks and Tasks programming model

We present a method for parallel block-sparse matrix-matrix multiplication on distributed memory clusters. By using a quadtree matrix representation, data locality is exploited without prior information about the matrix sparsity pattern. A distributed quadtree matrix representation is straightforward to implement due to our recent development of the Chunks and Tasks programming model [Parallel Comput. 40, 328 (2014)]. The quadtree representation combined with the Chunks and Tasks model leads to favorable weak and strong scaling of the communication cost with the number of processes, as shown both theoretically and in numerical experiments. Matrices are represented by sparse quadtrees of chunk objects. The leaves in the hierarchy are block-sparse submatrices. Sparsity is dynamically detected by the matrix library and may occur at any level in the hierarchy and/or within the submatrix leaves. In case graphics processing units (GPUs) are available, both CPUs and GPUs are used for leaf-level multiplication work, thus making use of the full computing capacity of each node. The performance is evaluated for matrices with different sparsity structures, including examples from electronic structure calculations. Compared to methods that do not exploit data locality, our locality-aware approach reduces communication significantly, achieving essentially constant communication per node in weak scaling tests.Comment: 35 pages, 14 figure

Constellation Queries over Big Data

A geometrical pattern is a set of points with all pairwise distances (or, more generally, relative distances) specified. Finding matches to such patterns has applications to spatial data in seismic, astronomical, and transportation contexts. For example, a particularly interesting geometric pattern in astronomy is the Einstein cross, which is an astronomical phenomenon in which a single quasar is observed as four distinct sky objects (due to gravitational lensing) when captured by earth telescopes. Finding such crosses, as well as other geometric patterns, is a challenging problem as the potential number of sets of elements that compose shapes is exponentially large in the size of the dataset and the pattern. In this paper, we denote geometric patterns as constellation queries and propose algorithms to find them in large data applications. Our methods combine quadtrees, matrix multiplication, and unindexed join processing to discover sets of points that match a geometric pattern within some additive factor on the pairwise distances. Our distributed experiments show that the choice of composition algorithm (matrix multiplication or nested loops) depends on the freedom introduced in the query geometry through the distance additive factor. Three clearly identified blocks of threshold values guide the choice of the best composition algorithm. Finally, solving the problem for relative distances requires a novel continuous-to-discrete transformation. To the best of our knowledge this paper is the first to investigate constellation queries at scale

Towards Building Deep Networks with Bayesian Factor Graphs

We propose a Multi-Layer Network based on the Bayesian framework of the Factor Graphs in Reduced Normal Form (FGrn) applied to a two-dimensional lattice. The Latent Variable Model (LVM) is the basic building block of a quadtree hierarchy built on top of a bottom layer of random variables that represent pixels of an image, a feature map, or more generally a collection of spatially distributed discrete variables. The multi-layer architecture implements a hierarchical data representation that, via belief propagation, can be used for learning and inference. Typical uses are pattern completion, correction and classification. The FGrn paradigm provides great flexibility and modularity and appears as a promising candidate for building deep networks: the system can be easily extended by introducing new and different (in cardinality and in type) variables. Prior knowledge, or supervised information, can be introduced at different scales. The FGrn paradigm provides a handy way for building all kinds of architectures by interconnecting only three types of units: Single Input Single Output (SISO) blocks, Sources and Replicators. The network is designed like a circuit diagram and the belief messages flow bidirectionally in the whole system. The learning algorithms operate only locally within each block. The framework is demonstrated in this paper in a three-layer structure applied to images extracted from a standard data set.Comment: Submitted for journal publicatio

A quadtree-polygon-based scaled boundary finite element method for image-based mesoscale fracture modelling in concrete

A quadtree-polygon scaled boundary finite element-based approach for image-based modelling of concrete fracture at the mesoscale is developed. Digital images representing the two-phase mesostructure of concrete, which comprises of coarse aggregates and mortar are either generated using a take-and-place algorithm with a user-defined aggregate volume ratio or obtained from X-ray computed tomography as an input. The digital images are automatically discretised for analysis by applying a balanced quadtree decomposition in combination with a smoothing operation. The scaled boundary finite element method is applied to model the constituents in the concrete mesostructure. A quadtree formulation within the framework of the scaled boundary finite element method is advantageous in that the displacement compatibility between the cells are automatically preserved even in the presence of hanging nodes. Moreover, the geometric flexibility of the scaled boundary finite element method facilitates the use of arbitrary sided polygons, allowing better representation of the aggregate boundaries. The computational burden is significantly reduced as there are only finite number of cell types in a balanced quadtree mesh. The cells in the mesh are connected to each other using cohesive interface elements with appropriate softening laws to model the fracture of the mesostructure. Parametric studies are carried out on concrete specimens subjected to uniaxial tension to investigate the effects of various parameters e.g. aggregate size distribution, porosity and aggregate volume ratio on the fracture of concrete at the meso-scale. Mesoscale fracture of concrete specimens obtained from X-ray computed tomography scans are carried out to demonstrate its feasibility

Sparse component separation for accurate CMB map estimation

The Cosmological Microwave Background (CMB) is of premier importance for the cosmologists to study the birth of our universe. Unfortunately, most CMB experiments such as COBE, WMAP or Planck do not provide a direct measure of the cosmological signal; CMB is mixed up with galactic foregrounds and point sources. For the sake of scientific exploitation, measuring the CMB requires extracting several different astrophysical components (CMB, Sunyaev-Zel'dovich clusters, galactic dust) form multi-wavelength observations. Mathematically speaking, the problem of disentangling the CMB map from the galactic foregrounds amounts to a component or source separation problem. In the field of CMB studies, a very large range of source separation methods have been applied which all differ from each other in the way they model the data and the criteria they rely on to separate components. Two main difficulties are i) the instrument's beam varies across frequencies and ii) the emission laws of most astrophysical components vary across pixels. This paper aims at introducing a very accurate modeling of CMB data, based on sparsity, accounting for beams variability across frequencies as well as spatial variations of the components' spectral characteristics. Based on this new sparse modeling of the data, a sparsity-based component separation method coined Local-Generalized Morphological Component Analysis (L-GMCA) is described. Extensive numerical experiments have been carried out with simulated Planck data. These experiments show the high efficiency of the proposed component separation methods to estimate a clean CMB map with a very low foreground contamination, which makes L-GMCA of prime interest for CMB studies.Comment: submitted to A&