Back to Table of contents

Primeur weekly 2013-08-19

Special

Is 64-bit arithmetic likely to become essential in future scientific computing? ...

Focus

EGI.eu and the University of Messina provided training on Europe's largest scientific federated Cloud at the Cloud Summerschool Almere ...

The Cloud

On our Way towards a New Utility ...

Distributed data safer than centralized Cloud data ...

South Africa's National Airways Corporation securing 20 terabytes of data in HP Autonomy Cloud ...

GAME wins customer loyalty through a Cloud based, IBM smarter commerce approach ...

IBM awarded 10 year $1 billion Cloud hosting services contract to assist US Department of Interior's move to Cloud computing ...

Desktop Grids

.NET GUI RPC binding available ...

EuroFlash

Keynote speakers announced for Altair's Biennial Technology Conference ...

Using high-performance computing to gain new insights into turbulence ...

PRACE to issue Open Calls for Proposals for Regular Access ...

A significant EU supercomputing resource for simulations of interactions between enteroviruses and gold nanoparticles ...

Deutsches Krebsforschungszentrum installs Convey hybrid-core computers to speed next-generation sequencing ...

Teleported by electronic circuit: ETH-physicists beam information ...

Quantum teleportation: Transfer of flying quantum bits at the touch of a button ...

USFlash

GE and Sandia National Lab discover pathway to quieter, more productive wind turbines ...

Western Australian Government invests $26 million in astronomy and the Square Kilometre Array ...

Researchers at Michigan State University use TACC supercomputers to understand DNA bending and repair mechanisms ...

Themis Systems introduces NVIDIA Kepler-based GPGPU and NVIDIA GRID accelerated RES-NT2 high performance computers ...

HP helps software-defined storage customers maximize server investments with data tiering ...

IBM to acquire Trusteer to help companies combat financial fraud and advanced security threats ...

Oracle introduces the Oracle Virtual Compute Appliance ...

Memory breakthrough could bring faster computing, smaller memory devices and lower power consumption ...

SMART Modular Technologies announces new e.MMC product family ...

Scientists find asymmetry in topological insulators ...

Deutsches Krebsforschungszentrum installs Convey hybrid-core computers to speed next-generation sequencing


15 Aug 2013 Richardson - The German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) in Heidelberg, Germany, has installed two Convey hybrid-core (HC) computers. The Convey HC-2ex platforms are being used to accelerate the centre's next-generation sequencing (NGS) pipeline, saving them time and reducing energy consumption.

DKFZ tested their first Convey hybrid-core computer in the summer of 2012, using the server to accelerate a portion of their next-generation pipeline. Results were extremely positive; one of their initial jobs went from over 18 hours on an 8 core system to a mere 48 minutes on the Convey server.

Based on that success, DKFZ purchased two Convey HC-2ex servers a few months later. These hybrid-core systems were integrated into an existing 1,600 compute core cluster. The Convey systems are now routinely used at DKFZ in the production analysis for all BWA algorithms.

"We are extremely pleased with the Convey systems. Depending on the data, we are typically seeing between 10-20x acceleration, which is substantial", explained Dr. Benedikt Brors, Group Leader Computational Oncology, Division Theoretical Bioinformatics at DKFZ. "And our entire work flow from one end to the other is reduced by a factor of two."

Convey's hybrid-core architecture pairs classic Intel x86 microprocessors with a coprocessor comprised of field-programmable gate arrays (FPGAs). Particular algorithms - BWA-based alignment, for example - are optimized and translated into code that's loadable onto the coprocessor at runtime. The result is order of magnitude performance increases with less power, space and cooling requirements.

The Heidelberg DKFZ facility currently processes 5 terabytes of data per day conducting NGS analysis. Prior to the Convey installation, processing massive amounts of data in a timely fashion was a challenge for DKFZ - both from a resource and time perspective.

One of the most time-consuming steps of analyzing a patient's genome involves using the Burrows-Wheeler Aligner (BWA) - the preferred algorithm for fast, accurate alignment to a reference genome of the short reads typical of high-throughput sequencers (HTS). BWA was taking up to 80% of CPU time in the data centre's pipeline.

"Accelerating this portion of our pipeline allows us to get answers substantially faster", noted Dr. Benedikt Brors. "In addition, saving processing time reduces power consumption and cooling - which is a huge advantage in saving money and a step forward in our commitment to pursue green technologies."

This DKFZ effort is part of the International Cancer Genome Consortium (ICGC) to study tumours from more than fifty types of cancers. Their goal is to develop better ways of diagnosing, treating and preventing many types of cancer. The scientists at DKFZ are currently participating in three different ICGC cancer research projects: paediatric brain tumours, malignant lymphoma, and prostate cancer. Their research focuses on mapping how cancer changes the genomes of cells and causes mutations within normal biological pathways.
Source: Convey Computer

Back to Table of contents

Primeur weekly 2013-08-19

Special

Is 64-bit arithmetic likely to become essential in future scientific computing? ...

Focus

EGI.eu and the University of Messina provided training on Europe's largest scientific federated Cloud at the Cloud Summerschool Almere ...

The Cloud

On our Way towards a New Utility ...

Distributed data safer than centralized Cloud data ...

South Africa's National Airways Corporation securing 20 terabytes of data in HP Autonomy Cloud ...

GAME wins customer loyalty through a Cloud based, IBM smarter commerce approach ...

IBM awarded 10 year $1 billion Cloud hosting services contract to assist US Department of Interior's move to Cloud computing ...

Desktop Grids

.NET GUI RPC binding available ...

EuroFlash

Keynote speakers announced for Altair's Biennial Technology Conference ...

Using high-performance computing to gain new insights into turbulence ...

PRACE to issue Open Calls for Proposals for Regular Access ...

A significant EU supercomputing resource for simulations of interactions between enteroviruses and gold nanoparticles ...

Deutsches Krebsforschungszentrum installs Convey hybrid-core computers to speed next-generation sequencing ...

Teleported by electronic circuit: ETH-physicists beam information ...

Quantum teleportation: Transfer of flying quantum bits at the touch of a button ...

USFlash

GE and Sandia National Lab discover pathway to quieter, more productive wind turbines ...

Western Australian Government invests $26 million in astronomy and the Square Kilometre Array ...

Researchers at Michigan State University use TACC supercomputers to understand DNA bending and repair mechanisms ...

Themis Systems introduces NVIDIA Kepler-based GPGPU and NVIDIA GRID accelerated RES-NT2 high performance computers ...

HP helps software-defined storage customers maximize server investments with data tiering ...

IBM to acquire Trusteer to help companies combat financial fraud and advanced security threats ...

Oracle introduces the Oracle Virtual Compute Appliance ...

Memory breakthrough could bring faster computing, smaller memory devices and lower power consumption ...

SMART Modular Technologies announces new e.MMC product family ...

Scientists find asymmetry in topological insulators ...