Search results for "Parallel"
showing 10 items of 667 documents
Accelerating metagenomic read classification on CUDA-enabled GPUs.
2016
Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification; i.e. the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes software tools for fast and accurate metagenomic read classification are urgently needed. We present cuCLARK, a read-level classifier for CUDA-enabled GPUs, based on the fast and accurate classification of metagenomic sequences using reduced k-mers (…
mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework
2017
Molecular docking is an important method in computational drug discovery. In large-scale virtual screening, millions of small drug-like molecules (chemical compounds) are compared against a designated target protein (receptor). Depending on the utilized docking algorithm for screening, this can take several weeks on conventional HPC systems. However, for certain applications including large-scale screening tasks for newly emerging infectious diseases such high runtimes can be highly prohibitive. In this paper, we investigate how the massively parallel neo-heterogeneous architecture of Tianhe-2 Supercomputer consisting of thousands of nodes comprising CPUs and MIC coprocessors that can effic…
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters
2016
Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data par…
SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search
2017
Computer architectures continue to develop rapidly towards massively parallel and heterogeneous systems. Thus, easily extensible yet highly efficient parallelization approaches for a variety of platforms are urgently needed. In this paper, we present SWhybrid, a hybrid computing framework for large-scale biological sequence database search on heterogeneous computing environments with multi-core or many-core processing units (PUs) based on the Smith- Waterman (SW) algorithm. To incorporate a diverse set of PUs such as combinations of CPUs, GPUs and Xeon Phis, we abstract them as SIMD vector execution units with different number of lanes. We propose a machine model, associated with a unified …
Evidence of gene orthology and trans-species polymorphism, but not of parallel evolution, despite high levels of concerted evolution in the major his…
2016
17 pages; International audience; The major histocompatibility complex (MHC) is a cornerstone in the study of adaptive genetic diversity. Intriguingly, highly polymorphic MHC sequences are often not more similar within species than between closely related species. Divergent selection of gene duplicates, balancing selection maintaining trans-species polymorphism (TSP) that predate speciation and parallel evolution of species sharing similar selection pressures can all lead to higher sequence similarity between species. In contrast, high rates of concerted evolution increase sequence similarity of duplicated loci within species. Assessing these evolutionary models remains difficult as related…
Optimizing Query Perturbations to Enhance Shape Retrieval
2020
3D Shape retrieval algorithms use shape descriptors to identify shapes in a database that are the most similar to a given key shape, called the query. Many shape descriptors are known but none is perfect. Therefore, the common approach in building 3D Shape retrieval tools is to combine several descriptors with some fusion rule. This article proposes an orthogonal approach. The query is improved with a Genetic Algorithm. The latter makes evolve a population of perturbed copies of the query, called clones. The best clone is the closest to its closest shapes in the database, for a given shape descriptor. Experimental results show that improving the query also improves the precision and complet…
Provoke or encourage improvements? On semantic prosody in English-to-Polish translation
2021
Originally defined as an aura of meaning associated with words used together in a particular context, semantic prosody is a complex linguistic concept, and there is no agreement among researchers as to its precise definition and level of operationalization (word, phrase, text or discourse). Although there have been some studies on semantic prosody in translation, their findings are rather inconclusive and limited to individual words and phrases. Also, there has been no research on semantic prosody conducted so far in Polish-English translation. Intending to fill in this gap, this paper, grounded in corpus linguistics, showcases the role of semantic prosody in a selected English-to-Polish tr…
Cimo: An efficient 2-phases calculator of multimodal itineraries for real trans-territories based on a dynamic programming
2015
In this work we propose an exact solution for calculating multimodal itinerary. This solution is named Cimo (Calculateur d'Itineraires Multimodaux Ordonnes). Cimo is an exact optimal itineraries' calculator wherein itineraries are sorted, multimodal, and trans-territorial. The solution is based on a dynamic programming algorithm "cut", "price" and "share". This solution is multi-objectives and multi-constraints. Several versions of this algorithm are proposed following a methodological approach that enables evaluation of efficiency and complexity's gain : through theoretical calculus and benchmarks. In the first version of realistic problem, we propose a solution with itineraries calculated…
Extending PluTo for Multiple Devices by Integrating OpenACC
2018
For many years now, processor vendors increased the performance of their devices by adding more cores and wider vectorization units to their CPUs instead of scaling up the processors' clock frequency. Moreover, GPUs became popular for solving problems with even more parallel compute power. To exploit the full potential of modern compute devices, specific codes are necessary which are often coded in a hardware-specific manner. Usually, the codes for CPUs are not usable for GPUs and vice versa. The programming API OpenACC tries to close this gap by enabling one code-base to be suitable and optimized for many devices. Nevertheless, OpenACC is rarely used by `standard programmers' and while dif…
"Table 5" of "Search for heavy charged long-lived particles in the ATLAS detector in 31.6 fb$^{-1}$ of proton-proton collision data at $\sqrt{s} = 13…
2019
Expected signal yield and acceptance x efficiency, estimated background and observed number of events in data for the full range of simulated masses in the full-detector R-hadron search.