ASTRONOMY

Keen to maximize tightening IT budgets, dozens of academic and scientific institutions across Asia are choosing to build Intel®-based HPC clusters or servers, to take advantage of leading price-performance levels. Fifteen recent deployments include University of Melbourne, Queensland Parallel Supercomputer Foundation (Australia) HK Baptist University, HK University (Hong Kong) Institute of Bioinformatics and Applied Biotechnology, Indian Institute of Science’s Supercomputing Education Research Center, Indian Institute of Technology and Center for Scientific and Industrial Research (India) Tsinghua University (People’s Republic of China) Bioinformatics Institute, Genome Institute of Singapore, Nanyang Polytechnic, School of BioInformatics, National University of Singapore Supercomputing and Visualisation Unit, and Singapore MIT Alliance (Singapore) and Kaohsiung City Government’s Bio-Informatics Grid (Taiwan). IDC estimates that around US$50 billion will be injected into the region’s Life Sciences markets from both public and private sources, and expects bio-IT revenue to reach US$2.6 billion in Asia/Pacific* by 2006, at a compound annual growth rate of 46%. “We are seeing two significant trends in Asia today. First, Life Sciences organizations are spending up to 50% of capital expenditure on the required ‘technology stack’ to support their programs, as they constantly demand more computing power to accelerate their discoveries. Second, we are seeing growing interest in cost-effective, industry-standard HPC platforms, as the fledgling industry attempts to maximize the return on their ‘capex’ investments,” commented IDC’s director of life sciences for the Asia Pacific region. “The increasing demand for HPC power in the Life Sciences industry will be a major driver of computing innovation throughout the next decade. We expect Intel-based clusters and grids, using open standard building-blocks based on Intel® Itanium® 2, Intel® Xeon™ and Intel® Pentium® 4 processors, to deliver the performance and affordability required by the industry,” said Jason Fedder, regional director of Intel Asia-Pacific’s solutions group, keynoting at today’s BioITWorld Hong Kong 2003 conference. In November 2002 Intel announced it was increasing its focus on Life Sciences and Mr Fedder described how Intel delivers an integrated HPC solution, including platform architectures, interconnect and networking building-blocks, software tools and libraries and services. Intel-based Platforms Powering Asian Life Sciences Programs At least fifteen leading Asian organizations have recently selected Intel-based HPC clusters or servers, and are using them, or are planning to use them, to help power Life Sciences programs. These organizations are involved in a variety of initiatives, ranging from gene sequencing, protein folding and functional genomics, to Chinese medicine projects. “Buying an Intel-based cluster running Linux** gives us more bang for the buck, plus we have access to the plethora of open-source software developed for this environment,” said Professor Fred J Hickernell of the Hong Kong Baptist University Department of Mathematics. The university has a multi-disciplinary research effort in Chinese medicine that involves the identification and classification of Chinese herbs as well as understanding the biochemical mechanism of herbal remedies. This research involves substantial data analysis that will be facilitated by the department’s new Intel® Xeon™ dual processor-based 64-node cluster from Dell** Computer. An Asian Bio-IT Ecosystem Emerging The projects are typically headed by world-class academic teams, often with connections to overseas institutions, and supported by an emerging breed of specialist Asian HPC solution-providers. These include the Singapore Computer Systems’ Linux Competency Centre and India’s CDC Linux, which specializes in building HPC solutions for Life Sciences, Computational Fluid Dynamics (CFD) and other applications. Growing Popularity of Clusters Clusters are part of a worldwide trend, which has seen a dramatic increase in the number of Intel-based systems being used for HPC deployments. A cluster is a collection of connected, independent computers that work in unison to solve a problem. The latest worldwide TOP500 Supercomputers List***, previously made up almost exclusively of proprietary, RISC-based supercomputers, now includes 56 Intel-based systems, versus just two systems only three years ago. The University of Hong Kong’s Gideon 300 Cluster is currently ranked 175 on the world’s Top500 Supercomputer list, which makes it the 4th most powerful Intel®-based supercomputer in Asia-Pacific. The Gideon cluster is used by the University’s Department of Computer Science and Information Systems (CSIS) to power various research programs, including Life Sciences projects involving molecular dynamic, N-body simulations. According to Dr. Francis Lau, Head of the CSIS, “In less than a decade, computer clusters have come to prominence as the most convenient and cost-effective tool for solving complex computational problems. Being able to bring together enough computing cycles together in a pool is one thing, to be able to use these cycles efficiently so that the aggregate power of a cluster can be fully harnessed is another. Research and development effort must continue to explore better strategies to make clusters an even greater tool when facing up to the grandest challenges of this age.” Intel Itanium Processor Family & Grid Computing: the Next HPC Wave Amongst the fifteen Asian organizations, at least five of them have chosen systems based on the new Itanium architecture. The 64-bit Itanium processor family addresses the requirements of scientific researchers, including superior floating-point performance, memory performance, and support for large data sets. Several leading global research institutions have begun to deploy Itanium-based systems, including The National Center for Supercomputing Applications (NCSA), the Cornell Theory Center and the European Organization for Nuclear Research (CERN). The NCSA deploys a large-scale computational center powered by Itanium 2-based systems, and soon expects to complete deployment of 10 teraflops (a trillion calculations per second) of clusters. Grid computing takes the HPC philosophy and extends it by linking desktops, clusters and large symmetric multiprocessing (SMP) systems across multiple geographic locations – creating a single, virtual computing resource. Intel is already participating in new grid deployments in Asia-Pacific, including the Singapore BioMedical Grid and the Kaohsiung City Government’s Bio-Informatics Grid. * International Data Corporation (IDC), Nov. 2002. ** Other names and brands may be claimed as the property of others. *** TOP500 Supercomputers List, http://www.top500.org. These organizations are running or planning to run a variety of initiatives, ranging from gene sequencing, protein folding and functional genomics, to Chinese medicine projects seeking to classify Chinese herbs and understand the biochemical mechanism of herbal remedies. Australia – University of Melbourne The University of Melbourne, as part of its Research Infrastructure, has established the Melbourne Advanced Research Computing Centre (MARCCentre) to provide advanced computing and visualization facilities for research workers within the University and in partnership with VPAC, the Victorian Partnership for Advanced Computing. BioIT initiatives under research include protein folding, and Biological sequence analysis. The recent investment in an Intel Architecture system was driven by a "building blocks" design to enable easy expansion to meet future upgrade and changing usage requirements. The investment consists of 96 Intel® Xeon™ 2.4 GHz processors configured in a supercomputing Linux cluster running a combination of Gaussian98 and user written codes. Australia - Queensland Parallel Supercomputer Foundation In January 2003, the Queensland Parallel Supercomputer Foundation (QPSF), a technology consortium of six universities in Australia's Queensland State, announced it would shortly take delivery of two SGI® AltixTM 3000 supercomputing systems, powered by Intel® Itanium® 2 processors and based on the Linux® operating system. Scientists at the six Queensland universities will access the SGI Altix clusters, both of which are powered by Intel Itanium 2 processors, across the state's high-bandwidth research network, which will soon be upgraded to 2.5Gb under the national Grangenet initiative. QPSF members will use a 64-processor server primarily for batch processing and a 16-processor system for open-source applications development. Among the research groups expressing strong interest in the new SGI® platform are teams in bioinformatics, systems modeling, computational physics, computational chemistry and engineering. Hong Kong – HK Baptist University Hong Kong Baptist University has a multi-disciplinary research effort in Chinese medicine that involves the identification and classification of Chinese herbs as well as understanding the biochemical mechanism of herbal remedies. This research involves substantial data analysis that will be facilitated by the new Intel® Xeon™ DP-based, 64-node cluster from Dell Computer. “We have seen the computational power of the desktop PC grow much faster than that of traditional workstations. Moreover, there has been an explosion in the support for inexpensive clusters that allow multiple CPUs to attack computational problems. Buying an Intel-based cluster running Linux gives us more bang for the buck, plus we have access to the plethora of open-source software developed for this environment,” said Professor Fred J Hickernell of the Hong Kong Baptist University Department of Mathematics. Hong Kong - HK University The University of Hong Kong’s Gideon 300 Cluster is currently ranked 175 on the world’s Top500 Supercomputer list, which makes it the 4th most powerful Intel®-based supercomputer in Asia-Pacific. The cluster consists of 300 Intel® Pentium® 4-based Legend PCs, interconnected by a single, high-port density Fast Ethernet switch, delivering a peak floating point performance of 1.2 Teraflops (trillion floating point operations per second). The Gideon cluster is used by the University’s Department of Computer Science and Information Systems (CSIS) to power various research programs, including Life Sciences projects involving molecular dynamic, N-body simulations. In the words of Dr. Francis Lau, Head of CSIS, “In less than a decade, the "lowly" computer clusters have come to prominence as the most convenient and cost-effective tool for solving complex computational problems. Being able to bring together enough computing cycles together in a pool is one thing, to be able to use these cycles efficiently so that the aggregate power of a cluster can be fully harnessed is another. Research and development effort must continue to explore better strategies to make clusters an even greater tool when facing up to the grandest challenges of this age.” India - Institute of Bioinformatics and Applied Biotechnology (IBAB) Intel® Xeon™-based cluster running Bioinformatics applications India - Indian Institute of Science’s Supercomputing Education Research Center (IISc SERC) A 32-way Intel® Itanium® 2-based system. "Intel® Itanium® 2 processors offer the scalability, performance and reliability that HPC users need to solve the large, complex problems of both science and industry,” said Dr. S.M Rao, Chairman of the Supercomputing Education Research Center at IISc, Bangalore. “At SERC, we have always believed in having the best computing platforms for our scientific research needs. Our recent decision to extend this to the next-generation Intel Itanium 2- based systems, powered by the forthcoming Itanium processor code-named ‘Madison’, is keeping in tune with this belief.” India - Indian Institute of Technology (IIT) Cluster running Bioinformatics applications India - Center for Scientific and Industrial Research (CSIR) Intel® Pentium® III-based cluster for Bioinformatics People’s Republic of China – Tsinghua University Tsinghua University, the leading research university in PRC, has under the School of Information Science & Technology established the Institute of Bioinformatics which is a cross-disciplinary research institute combining the faculties and researchers from the Departments of Biology, Computing Science and Automation. The Institute of Bioinformatics seeks to conduct leading edge bioinformatics research and explore breakthroughs in gene sequencing/expression to functional genomics using the latest Intel Xeon processor based cluster systems. According to Prof. Weimin Zheng, Director of the High Performance Computing Center which is a part of the bioinformatics research effort, “Tsinghua University’s 144 Intel Xeon processor based cluster system provides us with a high performance and cost effective solution to meet the high computing requirements of bioinformatics research. The Intel software tools and compiler also give us the ability to maximize the performance of our gene sequencing algorithms on the Intel Architecture based cluster systems.” Singapore – Singapore Computer Systems’ Linux Competency Centre The SCS Linux Competency Centre (SCS-LCC) has deployed several Linux HPC clusters based on Intel’s processors. The team has worked closely with Singapore's foremost teaching and research institutions that include the Genome Institute of Singapore, National University of Singapore (NUS) Supercomputing and Visualisation Unit, the NUS School of Computing and the Singapore MIT Alliance, "SCS Linux Competency Centre closely collaborates with the San Diego Supercomputer Centre on the NPACI ROCKS cluster OS, based on Red Hat Linux, to develop a robust and easy-to-use cluster OS. Using Intel processors, NPACI ROCKS and Myrinet-2000 switching technology, we are able to build for our customers a cost-effective, high-performance platform to meet their computational needs. These include intensive computational fluid dynamic simulation and bioinformatics." - Laurence Liew, Manager, SCS Linux Competency Centre. The SCS Linux Competency Centre (LCC) is Singapore's leading Linux and open source solutions provider with operations in Singapore, Malaysia and Thailand. The LCC is a Red Hat Authorised Training and Certification partner and offers the internationally recognised Red Hat Certified Engineer (RHCE) certification. The LCC is also the leading High Performance Computing Cluster (HPCC) solution provider with established cluster deployments in leading research and educational facilities in the region. Singapore - Bioinformatics Institute (BII) In 2002, Intel signed a Memorandum of Understanding (MOU) with Bioinformatics Institute (BII), an institute funded by Singapore’s Agency for Science, Technology and Research (A*STAR), to become a technology partner for the government’s biomedical sciences initiative. As part of the agreement, Intel will provide BII with a range of services, including early access to certain Intel technologies, advanced training of selected staff from leading research institutes, and porting consultancy to help accelerate Singapore’s multiple biotechnology programs. The BII will evaluate the implementation of the Intel Itanium processor family as one of the potential platforms for the Biomedical Grid in Singapore. The Bioinformatics Institute (BII), an institute funded by A*STAR, has been set up to be the focus of research and teaching in bioinformatics in Singapore. Dr Gunaretnam Rajagopal, formerly the Assistant Director of Research from the Cavendish Laboratory in UK’s Cambridge University, was appointed as the Acting Director of the BII from July 2001. For details on Bioinformatics Institute and the BioMedical Grid, please refer to http://www.bii-sg.org Singapore - Genome Institute of Singapore A 32-way Intel® Xeon™-based cluster with NPACI ROCKS cluster OS. Singapore - Nanyang Polytechnic, School of BioInformatics A 32-way Intel® Xeon™-based cluster, NPACI ROCKS cluster OS, Myrinet-2000 supercomputing switch network. Singapore - National University of Singapore (NUS) Supercomputing and Visualisation Unit A 32-way Intel® Xeon™-based cluster with NPACI ROCKS cluster OS. Singapore - Singapore MIT Alliance A system powered by 60 Intel® Itanium® 2 processors, Myrinet-2000 supercomputing switch fabric. “High performance computing systems are increasingly critical in the development cycle of new products. With clustering and grid computing now becoming a reality, engineers across dozens of industries are able to conduct more powerful real-life simulations and achieve substantial design efficiencies. The Intel® Itanium® 2 processor supports vast amounts of data and users and highly complex calculations, making it an important enabling technology for Singapore’s scientific and industrial researchers. SMA continues to emphasize world-class research, and we expect Itanium® 2-based systems to provide our students with valuable exposure to next-generation technologies.” Prof. Khoo Boo-Cheong, Programme Co-Chair, Singapore-MIT Alliance and Associate Professor, Faculty of Engineering, Department of Mechanical Engineering, National University of Singapore Taiwan – Kaohsiung City Government’s Bio-Informatics Grid In July, 2002 Intel Corporation announced an initiative with the city government that aims to transform Kaohsiung into an “e-City” through next-generation technological deployments. The e-Kaohsiung initiative is a collaboration between Kaohsiung (KHCG), the second-largest city in Taiwan, and Intel to deploy Intel® Architecture-based technologies to help accelerate the city’s economic development through cost-effective, high-performance and open standards-based computing and communications platforms. Under the agreement, Intel will serve as the lead technical provider and consultant for KHCG’s initiative. Intel will help KHCG build a world-class Bio-Informatics Grid powered by servers based on the Intel® Itanium® processor family. KHCG intends to build a Bio-Informatics Grid, a clustered grid of high performance computers, to provide the necessary computing power for the city’s researchers to accelerate progress on various Life Sciences initiatives.