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Bernaschi M.,CNR Institute of Neuroscience | Bisson M.,CNR Institute of Neuroscience | Salvadore F.,CINECA
Computer Physics Communications | Year: 2014

We present and compare the performances of two many-core architectures: the Nvidia Kepler and the Intel MIC both in a single system and in cluster configuration for the simulation of spin systems. As a benchmark we consider the time required to update a single spin of the 3D Heisenberg spin glass model by using the Over-relaxation algorithm. We present data also for a traditional high-end multi-core architecture: the Intel Sandy Bridge. The results show that although on the two Intel architectures it is possible to use basically the same code, the performances of a Intel MIC change dramatically depending on (apparently) minor details. Another issue is that to obtain a reasonable scalability with the Intel Phi coprocessor (Phi is the coprocessor that implements the MIC architecture) in a cluster configuration it is necessary to use the so-called offload mode which reduces the performances of the single system. As to the GPU, the Kepler architecture offers a clear advantage with respect to the previous Fermi architecture maintaining exactly the same source code. Scalability of the multi-GPU implementation remains very good by using the CPU as a communication co-processor of the GPU. All source codes are provided for inspection and for double-checking the results. © 2014 Elsevier B.V. All rights reserved. Source

Beccari A.R.,Dompe S.p.A | Beccari A.R.,University of Parma | Cavazzoni C.,CINECA | Beato C.,University of Parma | Costantino G.,University of Parma
Journal of Chemical Information and Modeling | Year: 2013

Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows. Specific features of LiGen are the use of a pharmacophore-based docking procedure which allows flexible docking without conformer enumeration and accurate and flexible reactant mapping coupled with reactant tagging through substructure searching. The full description of LiGen functionalities is presented. © 2013 American Chemical Society. Source

News Article
Site: http://www.scientificcomputing.com/rss-feeds/all/rss.xml/all

Graduate students and postdoctoral scholars from institutions in Canada, Europe, Japan and the United States are invited to apply for the seventh International Summer School on HPC Challenges in Computational Sciences, to be held June 26 to July 1, 2016, in Ljubljana, Slovenia. Applications are due February 15, 2016. The summer school is sponsored by the Extreme Science and Engineering Discovery Environment (XSEDE) with funds from the U.S. National Science Foundation, Compute/Calcul Canada, the Partnership for Advanced Computing in Europe (PRACE) and the RIKEN Advanced Insti­tute for Computational Science (RIKEN AICS). Leading American, European and Japanese computational scientists and HPC technologists will offer instruction on a variety of topics, including: The expense-paid program will benefit advanced scholars from Canadian, European, Japanese and U.S. institutions who use HPC to conduct research. Interested students should apply by February 15, 2016. Meals and housing will be covered for the selected participants, also travel from outside Europe. Applications from graduate students and postdocs in all science and engineering fields are welcome. Preference will be given to applicants with parallel programming experience, and a research plan that will benefit from the utilization of high performance computing systems. Compute Canada, in partnership with regional organizations ACENET, Calcul Québec, Compute Ontario and WestGrid, leads the acceleration of research innovation by deploying state-of-the-art advanced research computing (ARC) systems, storage and software solutions. Together they provide essential ARC services and infrastructure for Canadian researchers and their collaborators in all academic and industrial sectors. The Partnership for Advanced Computing in Europe (PRACE) is an international non-profit association with its seat in Brussels. The PRACE Research Infrastructure provides a persistent world-class high performance computing service for scientists and researchers from academia and industry in Europe. The computer systems and their operations accessible through PRACE are provided by 4 PRACE members (BSC representing Spain, CINECA representing Italy, GCS representing Germany and GENCI representing France). RIKEN is one of Japan’s largest research organizations with institutes and centers in locations throughout Japan. The Advanced Institute for Computational Science (AICS) strives to create an international center of excellence dedicated to generating world-leading results through the use of its world-class supercomputer ”K computer.” It serves as the core of the “innovative high-performance computer infrastructure” project promoted by the Ministry of Education, Culture, Sports, Science and Technology. The Extreme Science and Engineering Discovery Environment (XSEDE) is the most advanced, powerful and robust collection of integrated digital resources and services in the world. It is a single virtual system that scientists can use to interactively share computing resources, data and expertise. XSEDE accelerates scientific discovery by enhancing the productivity of researchers, engineers and scholars by deepening and extending the use of XSEDE¹s ecosystem of advanced digital services and by advancing and sustaining the XSEDE advanced digital infrastructure. XSEDE is a five-year, $121-million project and is supported by the National Science Foundation.

Azadi S.,International School for Advanced Studies | Cavazzoni C.,CINECA | Sorella S.,International School for Advanced Studies | Sorella S.,CNR Institute of Materials
Physical Review B - Condensed Matter and Materials Physics | Year: 2010

We introduce a method for solving a self-consistent electronic calculation within localized atomic orbitals that allows us to converge to the complete basis set (CBS) limit in a stable, controlled, and systematic way. We compare our results with the ones obtained with a standard quantum chemistry package for the simple benzene molecule. We find perfect agreement for small basis set and show that, within our scheme, it is possible to work with a very large basis in an efficient and stable way. Therefore we can avoid to introduce any extrapolation to reach the CBS limit. In our study we have also carried out variational Monte Carlo and lattice regularized diffusion Monte Carlo with a standard many-body wave function defined by the product of a Slater determinant and a Jastrow factor. Once the Jastrow factor is optimized by keeping fixed the Slater determinant provided by our scheme, we obtain a very good description of the atomization energy of the benzene molecule only when the basis of atomic orbitals is large enough and close to the CBS limit, yielding the lowest variational energies. © 2010 The American Physical Society. Source

Baftizadeh F.,International School for Advanced Studies | Biarnes X.,Ramon Llull University | Pietrucci F.,Ecole Polytechnique Federale de Lausanne | Affinito F.,CINECA | Laio A.,International School for Advanced Studies
Journal of the American Chemical Society | Year: 2012

Starting from a disordered aggregate, we have simulated the formation of ordered amyloid-like beta structures in a system formed by 18 polyvaline chains in explicit solvent, employing molecular dynamics accelerated by bias-exchange metadynamics. We exploited 8 different collective variables to compute the free energy of hundreds of putative aggregate structures, with variable content of parallel and antiparallel β-sheets and different packing among the sheets. This allowed characterizing in detail a possible nucleation pathway for the formation of amyloid fibrils: first the system forms a relatively large ordered nucleus of antiparallel β-sheets, and then a few parallel sheets start appearing. The relevant nucleation process culminates at this point: when a sufficient number of parallel sheets is formed, the free energy starts to decrease toward a new minimum in which this structure is predominant. The complex nucleation pathway we found cannot be described within classical nucleation theory, namely employing a unique simple reaction coordinate like the total content of β-sheets. © 2012 American Chemical Society. Source

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