Many studies point to the difficulty of scaling existing computer architectures to meet the needs of an exascale system (i.e., capable of executing 10 18 floating-point operations per second), consuming no more than 20 MW in power, by around the year 2020. This paper outlines a new architecture, the Active Memory Cube, which reduces the energy of computation significantly by performing computation in the memory module, rather than moving data through large memory hierarchies to the processor core. The architecture leverages a commercially demonstrated 3D memory stack called the Hybrid Memory Cube, placing sophisticated computational elements on the logic layer below its stack of dynamic random-access memory (DRAM) dies. The paper also describes an Active Memory Cube tuned to the requirements of a scientific exascale system. The computational elements have a vector architecture and are capable of performing a comprehensive set of floating-point and integer instructions, predicated operations, and gather-scatter accesses across memory in the Cube. The paper outlines the software infrastructure used to develop applications and to evaluate the architecture, and describes results of experiments on application kernels, along with performance and power projections.

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Mansonella ozzardi and Mansonella perstans infections both cause mansonellosis but are usually treated differently. Using a real-time polymerase chain reaction assay and deep sequencing, we reveal the presence of mansonellosis coinfections that were undetectable by standard diagnostic methods. Our results confirm mansonellosis coinfections and have important implications for the disease’s treatment and diagnosis.

Abstract-Big data analytics is an indispensable tool in transforming science, engineering, medicine, health-care, finance and ultimately business itself. With the explosion of data sizes and need for shorter time-to-solution, in-memory platforms such as Apache Spark gain increasing popularity. In this context, data shuffling, a particularly difficult transformation pattern, introduces important challenges. Specifically, data shuffling is a key component of complex computations that has a major impact on the overall performance and scalability. Thus, speeding up data shuffling is a critical goal. To this end, state-of-the-art solutions often rely on overlapping the data transfers with the shuffling phase. However, they employ simple mechanisms to decide how much data and where to fetch it from, which leads to sub-optimal performance and excessive auxiliary memory utilization for the purpose of prefetching. The latter aspect is a growing concern, given evidence that memory per computation unit is continuously decreasing while interconnect bandwidth is increasing. This paper contributes a novel shuffle data transfer strategy that addresses the two aforementioned dimensions by dynamically adapting the prefetching to the computation. We implemented this novel strategy in Spark, a popular in-memory data analytics framework. To demonstrate the benefits of our proposal, we run extensive experiments on an HPC cluster with large core count per node. Compared with the default Spark shuffle strategy, our proposal shows: up to 40% better performance with 50% less memory utilization for buffering and excellent weak scalability.

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Tuning configurations of Spark jobs is not a trivial task. State-of-the-art auto-tuning systems are based on iteratively running workloads with different configurations. During the optimization process, the relevant features are explored to find good solutions. Many optimizers enhance the time-to-solution using black-box optimization algorithms that do not take into account any information from the Spark workloads. In this paper, we present a new method for tuning configurations that uses information from one run of a Spark workload. To achieve good performance, we mine the SparkEventLog that is generated by the Spark engine. This log file contains a large amount of information from the executed application. We use this information to enhance a performance model with low-level features from the workload to be optimized. These features include Spark Actions, Transformations, and Task metrics. This process allows us to obtain application-specific workload information. With this information our system can predict sensible Spark configurations for unseen jobs, given that it has been trained with reasonable coverage of Spark applications. Experiments show that the presented system correctly produces good configurations, while achieving up to 80% speedup with respect to the default Spark configuration, and up to 12x speedup of the time-to-solution with respect to a standard Bayesian Optimization procedure.