HPC NEWS
GenomeQuest and SGI collaborate to offer whole-genome analysis
GenomeQuest and SGI have collaborated to offer whole- genome analysis (WGA) services for researchers, which the companies claim is the world’s first such service offering. As a result, pharmaceutical companies, core labs, biotechs, government agencies, and clinics now have direct access to whole-genome processing previously found only inside genome centres combined with comprehensive, self-serve analysis.
Virtualisation specialist ScaleMP has revealed that the University of Florida’s (UF) Interdisciplinary Center for Biotechnology Research (ICBR) has deployed the company’s virtual symmetric multiprocessing (vSMP) Foundation product. By implementing the vSMP solution, the ICBR is able to better harness its existing infrastructure, allowing scientists and researchers to submit larger interactive jobs to the vSMP system. Large shared-memory pools and increased application
HPC Products
T-Platforms Group will release a range of high-density computing solutions based on Nvidia Fermi architecture and Tesla 20-series GPUs. The heterogeneous HPC blade solution will feature a high- compute density design, with power- saving schemes for heterogeneous environments in its Clustrx OS, dynamically switching GPGPU-based nodes on and off as needed.
www.t-platforms.ru/en The Khronos Group has released version 4.1 of the OpenGL specification, bringing the very latest graphics functionality to the most advanced and widely adopted cross- platform 2D and 3D graphics API.
www.khronos.org
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X-ISS has released DecisionHPC, a web-based monitoring and analytics software package that helps HPC customers achieve maximum system productivity and goal alignment, while serving as a tool to plan for future computing resource needs accurately. DecisionHPC pricing is as low as $2 per node, monthly, and is an ideal software solution for any HPC organisation where monitoring, tracking and reporting on system analytics is important.
x-iss.com AccelerEyes has released version 1.4 of its Jacket software platform for Matlab, adding support the latest Nvidia GPUs based on the Fermi
SCIENTIFIC COMPUTING WORLD OCTOBER/NOVEMBER 2010
architecture (Tesla 20-series and GeForce GTX 4xx-series).
www.accelereyes.com VSG has released version 8.1 of its Open Inventor 3D graphics tool-kit for the development of industrial-strength applications, offering greater performance, higher quality graphics, more interactivity and more robustness for interactive applications. Open Inventor 8.1 delivers a display rate that is now nearly equivalent to graphics hardware peak performance.
www.vsg3d.com The Portland Group has released PGI Visual Fortran (PVF) for Visual Studio 2010, which integrates high-performance parallel Fortran
compilers and tools with Microsoft Visual Studio to offer a high- productivity development solution to scientists and engineers upgrading to the latest 64-bit multicore platforms running Microsoft Windows.
www.pgroup.com/pvf Tech-X has released version 4.2 of Vorpal, its software framework for electromagnetic and electrostatic simulations composed of particles and fluids for 1D, 2D, and 3D geometries. New capabilities will allow researchers to apply Vorpal in new application areas, enabling more advanced simulations of the physics involved in each application.
www.txcorp.com
www.scientific-computing.com
GenomeQuest and SGI co-developed a software and hardware architecture that is optimised for next generation sequencing and enables whole- genome scale and performance. Based on this architecture, the WGA services are available through the just-upgraded GenomeQuest data centre or deployed directly into a customer data centre, as may be required by larger accounts, core labs, and clinics.
performance speeds are offered in a cost-effective way. ICBR’s IT team supports
research at UF and abroad in various biotechnology fields such as proteomics, genomics, bioinformatics and cellomics. ICBR needed to be able to run legacy software as well as proprietary software packages requiring large shared-memory systems. Because of the high price point of traditional SMP systems, the team tried to find other ways to do these jobs. They
‘Data analysis is recognised as the bottleneck of whole-genome research. Traditionally, researchers receive static reports for their sequence runs which, at today’s volumes, are impossible to analyse and increasingly siloed,’ said Jean- Jacques Codani, GenomeQuest chief scientific officer. ‘From its inception, the GQ Engine has provided researchers with rich, interactive reports and the ability to integrate and re-analyse with other work.’
Biotech centre adopts virtual symmetric multiprocessing
ended up stretching their virtual infrastructure to accommodate these large shared memory workloads, resulting in a loss of virtualisation benefits. ICBR chose ScaleMP’s vSMP Foundation for SMP because it was the only solution that could take commodity hardware and aggregate it into one operating environment with a large amount of shared memory, while also allowing multiple threads in a process to address the entire shared memory pool.
PRACE awards 320 million compute hours to ten European research projects
Ten research projects, five from Germany, two from the UK one each from Italy, the Netherlands and Portugal, have been awarded access to the PRACE infrastructure. In total 321.4 million compute core- hours were granted. Sixty-eight applications requesting a total of 1,870 million compute hours were received in this call, which was the first opportunity for researchers to apply for PRACE resources. The successful research
projects are in the fields of astrophysics, earth sciences, engineering, and plasma and particle physics including collaborators from 31 universities and research institutes in 12 countries. These projects will have access to JUGENE, IBM BlueGene/P, hosted by the Gauss-Centre for Supercomputing member site in Jülich, Germany, which is the first Petascale HPC system available to researchers through PRACE.
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