The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

Parallel Multi-Hypothesis Algorithm for Criticality Estimation in Traffic and Collision Avoidance

Due to the current developments towards autonomous driving and vehicle active safety, there is an increasing necessity for algorithms that are able to perform complex criticality predictions in real-time. Being able to process multi-object traffic scenarios aids the implementation of a variety of automotive applications such as driver assistance systems for collision prevention and mitigation as well as fall-back systems for autonomous vehicles. We present a fully model-based algorithm with a parallelizable architecture. The proposed algorithm can evaluate the criticality of complex, multi-modal (vehicles and pedestrians) traffic scenarios by simulating millions of trajectory combinations and detecting collisions between objects. The algorithm is able to estimate upcoming criticality at very early stages, demonstrating its potential for vehicle safety-systems and autonomous driving applications. An implementation on an embedded system in a test vehicle proves in a prototypical manner the compatibility of the algorithm with the hardware possibilities of modern cars. For a complex traffic scenario with 11 dynamic objects, more than 86 million pose combinations are evaluated in 21 ms on the GPU of a Drive PX~2

Genetic Programming Approach for Classification Problem using GPU

Genetic programming (GP) is a machine learning technique that is based on the evolution of computer programs using a genetic algorithm. Genetic programming have proven to be a good technique for solving data set classification problems but at high computational cost. The objectives of this research is to accelerate the execution of the classification algorithms by proposing a general model of execution in GPU of the adjustment function of the individuals of the population. The computation times of each of the phases of the evolutionary process and the operation of the model of parallel programming in GPU were studied. Genetic programming is interesting to parallelize from the perspective of evolving a population of individuals in paralle

Genetic Programming Approach for Classification Problem using GPU

Genetic programming (GP) is a machine learning technique that is based on the evolution of computer programs using a genetic algorithm. Genetic programming have proven to be a good technique for solving data set classification problems but at high computational cost. The objectives of this research is to accelerate the execution of the classification algorithms by proposing a general model of execution in GPU of the adjustment function of the individuals of the population. The computation times of each of the phases of the evolutionary process and the operation of the model of parallel programming in GPU were studied. Genetic programming is interesting to parallelize from the perspective of evolving a population of individuals in parallel

Paraiso : An Automated Tuning Framework for Explicit Solvers of Partial Differential Equations

We propose Paraiso, a domain specific language embedded in functional programming language Haskell, for automated tuning of explicit solvers of partial differential equations (PDEs) on GPUs as well as multicore CPUs. In Paraiso, one can describe PDE solving algorithms succinctly using tensor equations notation. Hydrodynamic properties, interpolation methods and other building blocks are described in abstract, modular, re-usable and combinable forms, which lets us generate versatile solvers from little set of Paraiso source codes. We demonstrate Paraiso by implementing a compressive hydrodynamics solver. A single source code less than 500 lines can be used to generate solvers of arbitrary dimensions, for both multicore CPUs and GPUs. We demonstrate both manual annotation based tuning and evolutionary computing based automated tuning of the program.Comment: 52 pages, 14 figures, accepted for publications in Computational Science and Discover