BIOLOGY
Donostia International Physics Center Adds SGI Technology for Materials Science
Published Research Results, Achieved Using SGI Technology, Aids in the Development and Design of New Tailor-Made Materials: The Donostia International Physics Center (DIPC), an SGI customer since 2001, is a leading organization devoted to the promotion of scientific research in basic and applied physics. The recent purchase of four new SGI Altix 4700 systems and an SGI InfiniteStorage solution — in addition to the SGI Altix 4700 system purchased a little over a year ago — has enabled the center in San Sebastian, Spain, to upgrade its technical computing capability to further optimize research results. DIPC selected the new SGI Altix systems to easily meet the demands of larger data sets requiring very fast interconnect. The new systems have also allowed the institute to greatly expand by attracting many new researchers and professors. 
At the heart of DIPC is the Computational Center, created to meet the needs of resident and visiting researchers. The center provides computational resources dedicated to serial and parallel computing and also hosts equipment for facilitating the DIPC's management. "The Altix systems are used to study the prediction and representation of materials structure, properties, inter-relationships, and the structural, electronic and optical properties of solids, surfaces and low-dimensional systems," said Dr. Txomin Romero Asturiano, Director of the Computational Center at DIPC. "Particular attention is paid to systems of nanometer size. We need lots of processors, big amounts of memory and a very fast connection between processors. SGI's shared memory computing is important for our work in materials science because some of our programs need to share a lot of information between processors. We are very happy with the performance of SGI and even happier with the ease of managing the systems." All the SGI Altix systems at DIPC execute a variety of parallel programs related to Materials Physics, and Polymers and Non-Crystalline Solids. Applications such as Vasp, Espresso, Siesta, Materials Studio and Octopus, where the amount of information shared between processors is very large, are generally used. File sizes range from hundreds of small files of several thousands to input/output files of 5GB. Current activities in polymers and non-crystalline materials are focused on molecular motions and relaxation processes in polymer materials and glass-forming systems. This is mainly an experimental approach that combines different techniques — in particular, neutron scattering, broadband dielectric spectroscopy and NMR. The four new SGI Altix 4700 systems, each with 64 Dual-Core Intel Itanium 2 processors are employed for the same purpose, and housed in a new building where more and more researchers are being added. DIPC also purchased a SGI Altix 450 configured with 16 dual core Montvale processors for the execution of the Materials Studio Software application and an SGI InfiniteStorage 120 system consisting 3.6TB. All six SGI systems were installed in November 2007. "With the other clusters, the maintenance and management is very complicated, because they are a lot of nodes to manage and the probability of breakdown is greater, and the network between nodes and the shared disks became bottlenecks," said Dr. Romero. "With the Altix systems, with 128 CPUs in the same node (and only five Altix 4700 nodes) the probability of a breakdown is much lower." Published Results: New Materials Design
More than twenty papers on materials science have been published in international journals by DIPC researchers where results were obtained primarily or solely using SGI Altix systems. These include articles in prestigious journals as Physical Review Letters, Journal of Chemical Physics, Physical Review E, Europhysics Letters, and Macromolecules. Fernando Alvarez and Arantxa Arbe, Scientific Researchers at the Materials Physics Center (and contributing authors of the published papers), described recent results from simulations on polymer blends carried out on the SGI Altix 4700 system: "The combination of fully atomistic molecular dynamics simulations and quasi-elastic neutron scattering measurements on polymer blends with high dynamic asymmetry has evidenced a novel effect: the dynamic confinement of the fast component by the more rigid surrounding chains," said Alvarez. "Approaching the glass transition of the slow component, the long-range motions of the more mobile polymer are restricted and consequently the segmental dynamics of this fast component shows similarities with the localized processes found in systems under confined geometries. The real space analysis possible by the simulations provides a direct proof of this kind of dynamics." "The complete characterization of this phenomenon can be of utmost interest for the development and design of new tailor-made materials, since the mechanical or dielectric properties of plastics are directly determined by the molecular dynamics in the glassy state," concluded Arbe. "Moreover, polymer blending is a cheap and easy method to obtain new polymeric materials, since it is based on already existing polymers. Therefore, the relevance of these investigations is high not only from a basic point of view, but might also have future technological impact." "In less than 10 years of existence, the Donostia International Physics Center has become a major hub of research, impacting the international physics community with accelerated research performed on SGI systems," said Deepak Thakkar, Ph.D., and Higher Education and Research Solutions Manager, SGI. "Science centers, universities and laboratories around the world studying physics, bioinformatics, earth sciences or the origins of galaxies rely on SGI Altix computation and SGI InfiniteStorage systems to handle their largest, most intense data sets while speeding time to discovery."
At the heart of DIPC is the Computational Center, created to meet the needs of resident and visiting researchers. The center provides computational resources dedicated to serial and parallel computing and also hosts equipment for facilitating the DIPC's management. "The Altix systems are used to study the prediction and representation of materials structure, properties, inter-relationships, and the structural, electronic and optical properties of solids, surfaces and low-dimensional systems," said Dr. Txomin Romero Asturiano, Director of the Computational Center at DIPC. "Particular attention is paid to systems of nanometer size. We need lots of processors, big amounts of memory and a very fast connection between processors. SGI's shared memory computing is important for our work in materials science because some of our programs need to share a lot of information between processors. We are very happy with the performance of SGI and even happier with the ease of managing the systems." All the SGI Altix systems at DIPC execute a variety of parallel programs related to Materials Physics, and Polymers and Non-Crystalline Solids. Applications such as Vasp, Espresso, Siesta, Materials Studio and Octopus, where the amount of information shared between processors is very large, are generally used. File sizes range from hundreds of small files of several thousands to input/output files of 5GB. Current activities in polymers and non-crystalline materials are focused on molecular motions and relaxation processes in polymer materials and glass-forming systems. This is mainly an experimental approach that combines different techniques — in particular, neutron scattering, broadband dielectric spectroscopy and NMR. The four new SGI Altix 4700 systems, each with 64 Dual-Core Intel Itanium 2 processors are employed for the same purpose, and housed in a new building where more and more researchers are being added. DIPC also purchased a SGI Altix 450 configured with 16 dual core Montvale processors for the execution of the Materials Studio Software application and an SGI InfiniteStorage 120 system consisting 3.6TB. All six SGI systems were installed in November 2007. "With the other clusters, the maintenance and management is very complicated, because they are a lot of nodes to manage and the probability of breakdown is greater, and the network between nodes and the shared disks became bottlenecks," said Dr. Romero. "With the Altix systems, with 128 CPUs in the same node (and only five Altix 4700 nodes) the probability of a breakdown is much lower." Published Results: New Materials Design
More than twenty papers on materials science have been published in international journals by DIPC researchers where results were obtained primarily or solely using SGI Altix systems. These include articles in prestigious journals as Physical Review Letters, Journal of Chemical Physics, Physical Review E, Europhysics Letters, and Macromolecules. Fernando Alvarez and Arantxa Arbe, Scientific Researchers at the Materials Physics Center (and contributing authors of the published papers), described recent results from simulations on polymer blends carried out on the SGI Altix 4700 system: "The combination of fully atomistic molecular dynamics simulations and quasi-elastic neutron scattering measurements on polymer blends with high dynamic asymmetry has evidenced a novel effect: the dynamic confinement of the fast component by the more rigid surrounding chains," said Alvarez. "Approaching the glass transition of the slow component, the long-range motions of the more mobile polymer are restricted and consequently the segmental dynamics of this fast component shows similarities with the localized processes found in systems under confined geometries. The real space analysis possible by the simulations provides a direct proof of this kind of dynamics." "The complete characterization of this phenomenon can be of utmost interest for the development and design of new tailor-made materials, since the mechanical or dielectric properties of plastics are directly determined by the molecular dynamics in the glassy state," concluded Arbe. "Moreover, polymer blending is a cheap and easy method to obtain new polymeric materials, since it is based on already existing polymers. Therefore, the relevance of these investigations is high not only from a basic point of view, but might also have future technological impact." "In less than 10 years of existence, the Donostia International Physics Center has become a major hub of research, impacting the international physics community with accelerated research performed on SGI systems," said Deepak Thakkar, Ph.D., and Higher Education and Research Solutions Manager, SGI. "Science centers, universities and laboratories around the world studying physics, bioinformatics, earth sciences or the origins of galaxies rely on SGI Altix computation and SGI InfiniteStorage systems to handle their largest, most intense data sets while speeding time to discovery."