From Physics Model to Results: An Optimizing Framework for Cross-Architecture Code Generation

Starting from a high-level problem description in terms of partial differential equations using abstract tensor notation, the Chemora framework discretizes, optimizes, and generates complete high performance codes for a wide range of compute architectures. Chemora extends the capabilities of Cactus, facilitating the usage of large-scale CPU/GPU systems in an efficient manner for complex applications, without low-level code tuning. Chemora achieves parallelism through MPI and multi-threading, combining OpenMP and CUDA. Optimizations include high-level code transformations, efficient loop traversal strategies, dynamically selected data and instruction cache usage strategies, and JIT compilation of GPU code tailored to the problem characteristics. The discretization is based on higher-order finite differences on multi-block domains. Chemora's capabilities are demonstrated by simulations of black hole collisions. This problem provides an acid test of the framework, as the Einstein equations contain hundreds of variables and thousands of terms.Comment: 18 pages, 4 figures, accepted for publication in Scientific Programmin

Geometry-Oblivious FMM for Compressing Dense SPD Matrices

We present GOFMM (geometry-oblivious FMM), a novel method that creates a hierarchical low-rank approximation, "compression," of an arbitrary dense symmetric positive definite (SPD) matrix. For many applications, GOFMM enables an approximate matrix-vector multiplication in $N \log N$ or even $N$ time, where $N$ is the matrix size. Compression requires $N \log N$ storage and work. In general, our scheme belongs to the family of hierarchical matrix approximation methods. In particular, it generalizes the fast multipole method (FMM) to a purely algebraic setting by only requiring the ability to sample matrix entries. Neither geometric information (i.e., point coordinates) nor knowledge of how the matrix entries have been generated is required, thus the term "geometry-oblivious." Also, we introduce a shared-memory parallel scheme for hierarchical matrix computations that reduces synchronization barriers. We present results on the Intel Knights Landing and Haswell architectures, and on the NVIDIA Pascal architecture for a variety of matrices.Comment: 13 pages, accepted by SC'1

Polyhedral+Dataflow Graphs

This research presents an intermediate compiler representation that is designed for optimization, and emphasizes the temporary storage requirements and execution schedule of a given computation to guide optimization decisions. The representation is expressed as a dataflow graph that describes computational statements and data mappings within the polyhedral compilation model. The targeted applications include both the regular and irregular scientific domains. The intermediate representation can be integrated into existing compiler infrastructures. A specification language implemented as a domain specific language in C++ describes the graph components and the transformations that can be applied. The visual representation allows users to reason about optimizations. Graph variants can be translated into source code or other representation. The language, intermediate representation, and associated transformations have been applied to improve the performance of differential equation solvers, or sparse matrix operations, tensor decomposition, and structured multigrid methods

An ontology enhanced parallel SVM for scalable spam filter training

This is the post-print version of the final paper published in Neurocomputing. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2013 Elsevier B.V.Spam, under a variety of shapes and forms, continues to inflict increased damage. Varying approaches including Support Vector Machine (SVM) techniques have been proposed for spam filter training and classification. However, SVM training is a computationally intensive process. This paper presents a MapReduce based parallel SVM algorithm for scalable spam filter training. By distributing, processing and optimizing the subsets of the training data across multiple participating computer nodes, the parallel SVM reduces the training time significantly. Ontology semantics are employed to minimize the impact of accuracy degradation when distributing the training data among a number of SVM classifiers. Experimental results show that ontology based augmentation improves the accuracy level of the parallel SVM beyond the original sequential counterpart