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Given the current scientific questions of societal significance, such as those related to climate change, there is an urgent need to equip the scientific community with the means to effectively use high-performance and distributed computing (HPDC), Big Data, and tools necessary for reproducible science. The Polar Computing RCN project (http://polar-computing.org) is a National Science Foundation funded...
In this paper we present D.A.V.I.D.E. (Development for an Added Value Infrastructure Designed in Europe), an innovative and energy efficient High Performance Computing cluster designed by E4 Computer Engineering for PRACE (Partnership for Advanced Computing in Europe). D.A.V.I.D.E. is built using best-in-class components (IBM’s POWER8-NVLink CPUs, NVIDIA TESLA P100 GPUs, Mellanox InfiniBand EDR 100...
Driven by the increasing diversity of current and future HPC hardware and software platforms, the HPC community has seen a dramatic increase in research and development efforts into the composability of discrete software systems. While modularity is often desirable from a software engineering, quality assurance, and maintainability perspective, the barriers between software components often hide optimization...
We introduce Dynamic Dual Fixed Point (DDFX) CORDIC, that relies on run-time alteration of the numerical format of the Dual Fixed Point (DFX) CORDIC hardware. This allows for enhanced dynamic range and accuracy. Fixed Point, Dual Fixed Point, Floating Point, and Dynamic Dual Fixed Point CORDIC units are compared in terms of resources and accuracy. Results show that the hardware/software approach achieves...
When using testbeds in the context of experimental computer science, theability to produce trustworthy and reproducible experiments results dependsgreatly on the trustworthiness of the infrastructure itself. Unfortunately, several factors many issues such as software misconfiguration, hardwareheterogeneity, or service failures, can remain undetected and affect thequality of experimental results. This...
One approach of software automatic tuning is the incremental performance parameter estimation (IPPE) method, which is based on discrete spline function (d-Spline). We have applied IPPE to multidimensional performance parameter estimation. IPPE starts with the minimum number of the sampling points. It adds other sampling points by updating d-Spline at every iteration. For multidimensional performance...
The emergence of next generation DNA sequencers has raised interest in short read de novo assembly of whole genomes. Though numerous frameworks were developed in the field, the presence of errors in reads as well as the increasing size of datasets call for scalable preprocessing methods for noise filtering. In this paper we present a filtering algorithm that targets determination of valid k-mers in...
Independent validation of experimental results in the field of systems research is a challenging task, mainly due to differences in software and hardware in computational environments. Recreating an environment that resembles the original is difficult and time-consuming. In this paper we introduce _Popper_, a convention based on a set of modern open source software (OSS) development principles for...
Task-parallelism has been exposed as an efficient approach for the solution of dense and sparse linear algebra problems. Hierarchical matrices lie in-between the dense and sparse scenarios and, therefore, it is natural to target this niche of problems via a runtime-based solution that has reported successful results in the recent past for related linear algebra problems. Concretely, in this paper...
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