HeTM: Transactional Memory for Heterogeneous Systems

Modern heterogeneous computing architectures, which couple multi-core CPUs with discrete many-core GPUs (or other specialized hardware accelerators), enable unprecedented peak performance and energy efficiency levels. Unfortunately, though, developing applications that can take full advantage of the potential of heterogeneous systems is a notoriously hard task. This work takes a step towards reducing the complexity of programming heterogeneous systems by introducing the abstraction of Heterogeneous Transactional Memory (HeTM). HeTM provides programmers with the illusion of a single memory region, shared among the CPUs and the (discrete) GPU(s) of a heterogeneous system, with support for atomic transactions. Besides introducing the abstract semantics and programming model of HeTM, we present the design and evaluation of a concrete implementation of the proposed abstraction, which we named Speculative HeTM (SHeTM). SHeTM makes use of a novel design that leverages on speculative techniques and aims at hiding the inherently large communication latency between CPUs and discrete GPUs and at minimizing inter-device synchronization overhead. SHeTM is based on a modular and extensible design that allows for easily integrating alternative TM implementations on the CPU's and GPU's sides, which allows the flexibility to adopt, on either side, the TM implementation (e.g., in hardware or software) that best fits the applications' workload and the architectural characteristics of the processing unit. We demonstrate the efficiency of the SHeTM via an extensive quantitative study based both on synthetic benchmarks and on a porting of a popular object caching system.Comment: The current work was accepted in the 28th International Conference on Parallel Architectures and Compilation Techniques (PACT'19

BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images

In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM (BioEM) formalism. By ranking structural models using posterior probabilities calculated for individual images, BioEM in principle addresses the challenge of working with highly dynamic or heterogeneous systems not easily handled in traditional EM reconstruction. However, the calculation of these posteriors for large numbers of particles and models is computationally demanding. Here we present highly parallelized, GPU-accelerated computer software that performs this task efficiently. Our flexible formulation employs CUDA, OpenMP, and MPI parallelization combined with both CPU and GPU computing. The resulting BioEM software scales nearly ideally both on pure CPU and on CPU+GPU architectures, thus enabling Bayesian analysis of tens of thousands of images in a reasonable time. The general mathematical framework and robust algorithms are not limited to cryo-electron microscopy but can be generalized for electron tomography and other imaging experiments

GNA: new framework for statistical data analysis

We report on the status of GNA --- a new framework for fitting large-scale physical models. GNA utilizes the data flow concept within which a model is represented by a directed acyclic graph. Each node is an operation on an array (matrix multiplication, derivative or cross section calculation, etc). The framework enables the user to create flexible and efficient large-scale lazily evaluated models, handle large numbers of parameters, propagate parameters' uncertainties while taking into account possible correlations between them, fit models, and perform statistical analysis. The main goal of the paper is to give an overview of the main concepts and methods as well as reasons behind their design. Detailed technical information is to be published in further works.Comment: 9 pages, 3 figures, CHEP 2018, submitted to EPJ Web of Conference

Scalable Rejection Sampling for Bayesian Hierarchical Models

Bayesian hierarchical modeling is a popular approach to capturing unobserved heterogeneity across individual units. However, standard estimation methods such as Markov chain Monte Carlo (MCMC) can be impracticable for modeling outcomes from a large number of units. We develop a new method to sample from posterior distributions of Bayesian models, without using MCMC. Samples are independent, so they can be collected in parallel, and we do not need to be concerned with issues like chain convergence and autocorrelation. The algorithm is scalable under the weak assumption that individual units are conditionally independent, making it applicable for large datasets. It can also be used to compute marginal likelihoods

Exploring Task Mappings on Heterogeneous MPSoCs using a Bias-Elitist Genetic Algorithm

Exploration of task mappings plays a crucial role in achieving high performance in heterogeneous multi-processor system-on-chip (MPSoC) platforms. The problem of optimally mapping a set of tasks onto a set of given heterogeneous processors for maximal throughput has been known, in general, to be NP-complete. The problem is further exacerbated when multiple applications (i.e., bigger task sets) and the communication between tasks are also considered. Previous research has shown that Genetic Algorithms (GA) typically are a good choice to solve this problem when the solution space is relatively small. However, when the size of the problem space increases, classic genetic algorithms still suffer from the problem of long evolution times. To address this problem, this paper proposes a novel bias-elitist genetic algorithm that is guided by domain-specific heuristics to speed up the evolution process. Experimental results reveal that our proposed algorithm is able to handle large scale task mapping problems and produces high-quality mapping solutions in only a short time period.Comment: 9 pages, 11 figures, uses algorithm2e.st