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HPC news


Biophysicist targets protein with supercomputer

Chenglong Li, an assistant professor of medicinal chemistry and pharmacognosy at The Ohio State University (OSU), USA, is using a cluster at the Ohio Supercomputer Center (OSC) to develop a drug that will block the small protein molecule Interleukin-6 (IL-6). The body normally produces this immune- response messenger to combat infections, burns, traumatic injuries, etc. Scientists have found, however, that in people who have cancer, the body fails to turn off the response and overproduces IL-6. Last year, Li partnered with an organic chemist and a cancer biologist at OSU’s James Cancer

Hospital to investigate this further, using an OSC supercomputer to construct malleable, three- dimensional colour simulations of the protein complex. Li accessed 64 nodes of OSC’s Glenn IBM 1350 Opteron cluster to simulate IL-6 and the two additional helper proteins needed to convey the signal: the receptor IL-6R and the common signal-transducing receptor GP130. Two full sets of the three proteins combine to form a six-sided molecular machine, or ‘hexamer’, that transmits the signals that will, in time, cause cellular infl ammation and, potentially, cancer.

New supercomputing institute established

Cray and Sandia National Laboratories have formed the Supercomputing Institute for Learning and Knowledge Systems (SILKS) – a Cooperative Research and Development Agreement (CRADA) focused on knowledge discovery, data management and

informatics computing. Located at Sandia National Laboratories in Albuquerque, USA, SILKS will bring together hardware resources, software assets and researchers that are profi cient in knowledge discovery, data management and informatics computing at large scale.


Japan’s Semiconductor Energy Laboratory (SEL) has purchased a high-performance computing solution consisting of an SGI Altix ICE 8400 to accelerate the research and development of semiconductor technology. The system will have 3,840 processor cores built with Intel Xeon processor 5600 series, along with up to 15TB of memory, and

is projected to achieve up to a 10-fold increase in application performance over the previous solution. It will be used for research and development work on thin fi lm integrated circuits, liquid crystal and electroluminescent displays, semiconductor thin-fi lm transistors, solar cells, and batteries. The system is expected to be in place and operational in July 2011.

Supercomputer to be deployed at the University of Stuttgart energy laboratory

At the University of Stuttgart in Germany, the High Performance Computing Centre Stuttgart (HLRS) will install the fi rst stage of a system called Hermit, a one-Pfl op Cray system, in the autumn of 2011. This initial step is to be followed by a four-to fi ve-Pfl op second step in 2013. The contract with Cray includes the delivery of a Cray XE6 supercomputer and the future delivery of the company’s next-generation supercomputer code-named ‘Cascade’. The XE6 combines Cray’s current Gemini system interconnect with AMD Opteron processors and is designed to deliver production petascale computing. Fully

upgradeable from the XT5 and XT6 line of supercomputers, the XE6 system offers improved interconnect performance and features additional enhancements such as improved network resiliency, a mature and scalable software environment and the ability to run a broad array of ISV applications with the latest version of the Cray Linux Environment. The next-generation Cascade supercomputer will feature a continuing evolution of the Cray Linux Environment, Cray’s HPC-optimised programming environment, a next-generation interconnect chipset follow-on to Gemini, and support for future Intel Xeon processors.

TERI institute acquires supercomputer

The Energy and Resources Institute (TERI) has acquired a supercomputer from IT services company Wipro, to develop a better understanding of climate variability and change at different spatial and temporal scales. Headquartered in Delhi, India, and with locations worldwide, TERI has been improving its computing capabilities in order to better predict climate change at both a global and regional

scale. Impacts of climate change in India are unique due to the diversity of ecosystems and topography. Some of the key collaborations on climate research include those with Bjerknes Center for Climate Research, Norway; the United Kingdom Meteorological Offi ce, UK; and Asian Disaster Preparedness Center, Thailand. TERI is also contributing to the state action plans on climate change in a number of states in India.


now online Performance optimisation speeds plant genetic studies

Future challenges within HPC Supercomputing transforms study of evolutionary relationships JUNE/JULY 2011 17

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