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Primeur weekly 2014-10-20

Special

High Performance Computing Centre in Stuttgart to focus on Cloudification ...

Cash flow calculations using Monte Carlo simulations ...

The Cloud

IBM and SAP partner to accelerate enterprise Cloud adoption ...

EuroFlash

European Commission to launch survey on EU-Brazil co-operation in the area of ICT - Work Programme 2016-2017 ...

Big Data Value Association and European Commision sign Big Data Public Private Partnership ...

New forecasting method: Predicting extreme floods in the Andes mountains ...

Symposium on HPC and Data-Intensive Applications in Earth Sciences: Challenges and Opportunities@ICTP ...

Jülich renews co-operation with Oak Ridge National Laboratory ...

Johannes Gutenberg University Mainz joins Germany's Gauss-Allianz as a full member ...

PRACE supports HPC for Health ...

HP and VMware dramatically simplify and accelerate the delivery of software-defined infrastructure services with EVO: RAIL ...

Supermicro highlights VMware EVO: RAIL, FatTwin Virtual SAN Ready nodes and NVIDIA GRID vGPU SuperServer at VMworld Barcelona ...

Calling on universities to submit their HPCAC-ISC 2015 Student Cluster Competition application ...

PRACE SHAPE and NSilico pool HPC knowledge to develop faster sequencing methods ...

A novel platform for future spintronic technologies ...

Future computers could be built from magnetic 'tornadoes' ...

USFlash

New SGI UV for SAP HANA enables real-time business for large enterprises ...

Cray adds new advanced analytics solution to its Big Data product portfolio ...

Australian teams set new records for silicon quantum computing ...

IBM announces first commercial application of IBM Watson in Africa ...

Among DOE supercomputing facilities, NERSC is at the forefront of data management and storage innovations ...

SC14 announces ACM/IEEE-CS George Michael HPC Fellowships ...

Fujitsu partners with Singapore to set up Centre of Excellence for sustainable urbanisation ...

UC Santa Cruz leads $11 million Center for Big Data in Translational Genomics ...

Australian volcanic mystery explained ...

Supermicro enhances VMware EVO: RAIL and Virtual SAN offerings with Nexenta ...

Dispelling a misconception about Mg-ion batteries ...

PRACE SHAPE and NSilico pool HPC knowledge to develop faster sequencing methods


13 Oct 2014 Brussels - Via PRACE SHAPE NSilico teamed up with computational experts from CINES, France and ICHEC, Ireland to address the key problem of rapid alignment of short DNA sequences to reference genomes by deploying the Smith-Waterman algorithm on an emerging many-core technology, the Intel Xeon Phi co-processor.

The project entitled high performance computation for short read alignment investigated high performance computational techniques for the analysis of ribosomal RNA, which is the mechanism that cells use to translate an organism's DNA into protein. Next generation sequencing techniques are enabling the capture of vast amounts of data on the ribosomal RNA characteristics of cells in varying conditions. However reads for such RNA fragments are smaller than those typically encountered in sequencing projects, hence most alignment algorithms are optimised for longer reads.

"The SHAPE project has been a very successful collaboration between NSilico and the PRACE partners involved. NSilico has benefited from domain expertise from PRACE in first identifying a bioinformatics codebase with real potential to be deployed on cutting-edge many-core hardware. It has also since gained invaluable insights into the optimisation and parallelisation work involved in porting the code to the Intel Xeon Phi. Next steps are already being discussed on testing and deployment of the code with the release of the next generation 'Knights Landing' hardware, as well as potential incorporation into NSilico's in-house bioinformatics pipelines", stated Paul Walsh of NSilico.

The project team adopted two approaches to optimise and parallelise the SSW library, first using modern SIMD intrinsics and the second using OpenMP. The OpenMP parallelisation work has led to a code that shows good parallel performance results on standard x86 processors and promising results for Xeon Phi many-core hardware. While the resulting SSW library achieves expectedly limited performance gains on the current generation of the Xeon Phi, it has been re-factored in a way to readily take advantage of the next generation of hardware such as Xeon Phi 'Landing' with upcoming AVX 512 features.

The results of the project were presented during the SHAPE parallel track of PRACEdays14 .
Source: PRACE

Back to Table of contents

Primeur weekly 2014-10-20

Special

High Performance Computing Centre in Stuttgart to focus on Cloudification ...

Cash flow calculations using Monte Carlo simulations ...

The Cloud

IBM and SAP partner to accelerate enterprise Cloud adoption ...

EuroFlash

European Commission to launch survey on EU-Brazil co-operation in the area of ICT - Work Programme 2016-2017 ...

Big Data Value Association and European Commision sign Big Data Public Private Partnership ...

New forecasting method: Predicting extreme floods in the Andes mountains ...

Symposium on HPC and Data-Intensive Applications in Earth Sciences: Challenges and Opportunities@ICTP ...

Jülich renews co-operation with Oak Ridge National Laboratory ...

Johannes Gutenberg University Mainz joins Germany's Gauss-Allianz as a full member ...

PRACE supports HPC for Health ...

HP and VMware dramatically simplify and accelerate the delivery of software-defined infrastructure services with EVO: RAIL ...

Supermicro highlights VMware EVO: RAIL, FatTwin Virtual SAN Ready nodes and NVIDIA GRID vGPU SuperServer at VMworld Barcelona ...

Calling on universities to submit their HPCAC-ISC 2015 Student Cluster Competition application ...

PRACE SHAPE and NSilico pool HPC knowledge to develop faster sequencing methods ...

A novel platform for future spintronic technologies ...

Future computers could be built from magnetic 'tornadoes' ...

USFlash

New SGI UV for SAP HANA enables real-time business for large enterprises ...

Cray adds new advanced analytics solution to its Big Data product portfolio ...

Australian teams set new records for silicon quantum computing ...

IBM announces first commercial application of IBM Watson in Africa ...

Among DOE supercomputing facilities, NERSC is at the forefront of data management and storage innovations ...

SC14 announces ACM/IEEE-CS George Michael HPC Fellowships ...

Fujitsu partners with Singapore to set up Centre of Excellence for sustainable urbanisation ...

UC Santa Cruz leads $11 million Center for Big Data in Translational Genomics ...

Australian volcanic mystery explained ...

Supermicro enhances VMware EVO: RAIL and Virtual SAN offerings with Nexenta ...

Dispelling a misconception about Mg-ion batteries ...