Barcelona Supercomputer Center

Barcelona, Spain

Barcelona Supercomputer Center

Barcelona, Spain
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Sharapov S.E.,Culham Center for Fusion Energy | Hellsten T.,Culham Center for Fusion Energy | Kiptily V.G.,Culham Center for Fusion Energy | Craciunescu T.,KTH Royal Institute of Technology | And 24 more authors.
Nuclear Fusion | Year: 2016

Dedicated fast ion D-D and D-3He fusion experiments were performed on JET with carbon wall (2008) and ITER-like wall (2014) for testing the upgraded neutron and energetic ion diagnostics of fusion products. Energy spectrum of D-D neutrons was the focus of the studies in pure deuterium plasmas. A significant broadening of the energy spectrum of neutrons born in D-D fast fusion was observed, and dependence of the maximum D and D-D neutron energies on plasma density was established. Diagnostics of charged products of aneutronic D-3He fusion reactions, 3.7 MeV alpha-particles similar to those in D-T fusion, and 14.6 MeV protons, were the focus of the studies in D-3He plasmas. Measurements of 16.4 MeV gamma-rays born in the weak secondary branch of D(3He, γ)5Li reaction were used for assessing D-3He fusion power. For achieving high yield of D-D and D-3He reactions at relatively low levels of input heating power, an acceleration of D beam up to the MeV energy range was used employing 3rd harmonic () ICRH technique. These results were compared to the techniques of D beam injection into D-3He mixture, and 3He-minority ICRH in D plasmas. © 2016 EURATOM.


Sanz-Navarro C.F.,Catalan Institute of Nanoscience and Nanotechnology | Grima R.,Barcelona Supercomputer Center | Garcia A.,CSIC - Institute of Materials Science | Bea E.A.,Barcelona Supercomputer Center | And 3 more authors.
Theoretical Chemistry Accounts | Year: 2011

We present the major features of a new implementation of a QM-MM method that uses the DFT code Siesta to treat the quantum mechanical subsystem and the AMBER force field to deal with the classical part. The computation of the electrostatic interaction has been completely revamped to treat periodic boundary conditions exactly, using a real-space grid that encompasses the whole system. Additionally, we present a new parallelization of the Siesta grid operations that provides near-perfect load balancing for all the relevant operations and achieves a much better scalability, which is important for efficient massive QM-MM calculations in which the grid can potentially be very large. © 2010 Springer-Verlag.


Alvanos M.,Barcelona Supercomputer Center | Alvanos M.,Polytechnic University of Catalonia | Alvanos M.,IBM | Farreras M.,Polytechnic University of Catalonia | And 4 more authors.
Proceedings of the International Conference on Supercomputing | Year: 2013

The goal of Partitioned Global Address Space (PGAS) languages is to improve programmer productivity in large scale parallel machines. However, PGAS programs may have many fine-grained shared accesses that lead to performance degradation. Manual code transformations or compiler optimizations are required to improve the performance of programs with fine-grained accesses. The downside of manual code transformations is the increased program complexity that hinders programmer productivity. On the other hand, most compiler optimizations of fine-grain accesses require knowledge of physical data mapping and the use of parallel loop constructs. This paper presents an optimization for the Unified Parallel C language that combines compile time (static) and runtime (dynamic) coalescing of shared data, without the knowledge of physical data mapping. Larger messages increase the network efficiency and static coalescing decreases the overhead of library calls. The performance evaluation uses two microbenchmarks and three benchmarks to obtain scaling and absolute performance numbers on up to 32768 cores of a Power 775 machine. Our results show that the compiler transformation results in speedups from 1.15X up to 21X compared with the baseline versions and that they achieve up to 63% the performance of the MPI versions. © 2013 ACM.


Eriksson J.,Uppsala University | Nocente M.,University of Milan Bicocca | Nocente M.,CNR Institute for Plasma Physics Piero Caldirola | Binda F.,Uppsala University | And 23 more authors.
Nuclear Fusion | Year: 2015

Observations made in a JET experiment aimed at accelerating deuterons to the MeV range by third harmonic radio-frequency (RF) heating coupled into a deuterium beam are reported. Measurements are based on a set of advanced neutron and gamma-ray spectrometers that, for the first time, observe the plasma simultaneously along vertical and oblique lines of sight. Parameters of the fast ion energy distribution, such as the high energy cut-off of the deuteron distribution function and the RF coupling constant, are determined from data within a uniform analysis framework for neutron and gamma-ray spectroscopy based on a one-dimensional model and by a consistency check among the individual measurement techniques. A systematic difference is seen between the two lines of sight and is interpreted to originate from the sensitivity of the oblique detectors to the pitch-angle structure of the distribution around the resonance, which is not correctly portrayed within the adopted one dimensional model. A framework to calculate neutron and gamma-ray emission from a spatially resolved, two-dimensional deuteron distribution specified by energy/pitch is thus developed and used for a first comparison with predictions from ab initio models of RF heating at multiple harmonics. The results presented in this paper are of relevance for the development of advanced diagnostic techniques for MeV range ions in high performance fusion plasmas, with applications to the experimental validation of RF heating codes and, more generally, to studies of the energy distribution of ions in the MeV range in high performance deuterium and deuterium-tritium plasmas. © 2015 EURATOM.


Cossins B.P.,Barcelona Supercomputer Center | Jacobson M.P.,University of California at San Francisco | Guallar V.,Barcelona Supercomputer Center
PLoS Computational Biology | Year: 2011

The cytosol is the major environment in all bacterial cells. The true physical and dynamical nature of the cytosol solution is not fully understood and here a modeling approach is applied. Using recent and detailed data on metabolite concentrations, we have created a molecular mechanical model of the prokaryotic cytosol environment of Escherichia coli, containing proteins, metabolites and monatomic ions. We use 200 ns molecular dynamics simulations to compute diffusion rates, the extent of contact between molecules and dielectric constants. Large metabolites spend ~80% of their time in contact with other molecules while small metabolites vary with some only spending 20% of time in contact. Large non-covalently interacting metabolite structures mediated by hydrogen-bonds, ionic and π stacking interactions are common and often associate with proteins. Mg2+ ions were prominent in NIMS and almost absent free in solution. K+ is generally not involved in NIMSs and populates the solvent fairly uniformly, hence its important role as an osmolyte. In simulations containing ubiquitin, to represent a protein component, metabolite diffusion was reduced owing to long lasting protein-metabolite interactions. Hence, it is likely that with larger proteins metabolites would diffuse even more slowly. The dielectric constant of these simulations was found to differ from that of pure water only through a large contribution from ubiquitin as metabolite and monatomic ion effects cancel. These findings suggest regions of influence specific to particular proteins affecting metabolite diffusion and electrostatics. Also some proteins may have a higher propensity for associations with metabolites owing to their larger electrostatic fields. We hope that future studies may be able to accurately predict how binding interactions differ in the cytosol relative to dilute aqueous solution. © 2011 Cossins et al.


Goel B.,Chalmers University of Technology | McKee S.A.,Chalmers University of Technology | Gioiosa R.,Barcelona Supercomputer Center | Singh K.,Cornell University | And 2 more authors.
2010 International Conference on Green Computing, Green Comp 2010 | Year: 2010

Performance, power, and temperature are now all first-order design constraints. Balancing power efficiency, thermal constraints, and performance requires some means to convey data about real-time power consumption and temperature to intelligent resource managers. Resource managers can use this information to meet performance goals, maintain power budgets, and obey thermal constraints. Unfortunately, obtaining the required machine introspection is challenging. Most current chips provide no support for per-core power monitoring, and when support exists, it is not exposed to software. We present a methodology for deriving per-core power models using sampled performance counter values and temperature sensor readings. We develop application- independent models for four different (four- to eight-core) platforms, validate their accuracy, and show how they can be used to guide scheduling decisions in power-aware resource managers. Model overhead is negligible, and estimations exhibit 1.1 %-5.2% per-suite median error on the NAS, SPEC OMP, and SPEC 2006 benchmarks (and 1.2%-4.4% overall). ©2010 IEEE.


Blanco R.,Yahoo! | Bortnikov E.,Yahoo! | Junqueira F.,Yahoo! | Lempel R.,Yahoo! | And 2 more authors.
Proceedings of the 19th International Conference on World Wide Web, WWW '10 | Year: 2010

A Web search engine must update its index periodically to incorporate changes to the Web, and we argue in this work that index updates fundamentally impact the design of search engine result caches. Index updates lead to the problem of cache invalidation: invalidating cached entries of queries whose results have changed. To enable efficient invalidation of cached results, we propose a framework for developing invalidation predictors and some concrete predictors. Evaluation using Wikipedia documents and a query log from Yahoo shows that selective invalidation of cached search results can lower the number of query re-evaluations by as much as 30% compared to a baseline time-to-live scheme, while returning results of similar freshness. © 2010 Copyright is held by the author/owner(s).


Sanjuan G.,Autonomous University of Barcelona | Tena C.,Barcelona Supercomputer Center | Margalef T.,Autonomous University of Barcelona | Cortes A.,Autonomous University of Barcelona
Journal of Supercomputing | Year: 2016

Wind field calculation is a critical issue in reaching accurate forest fire propagation predictions. However, when the involved terrain map is large, the amount of memory and the execution time can prevent them from being useful in an operational environment. Wind field calculation involves sparse matrices that are usually stored in CSR storage format. This storage format can cause sparse matrix-vector multiplications to create a bottleneck due to the number of cache misses involved. Moreover, the matrices involved are extremely sparse and follow a very well-defined pattern. Therefore, a new storage system has been designed to reduce memory requirements and cache misses in this particular sparse matrix-vector multiplication. Sparse matrix-vector multiplication has been implemented using this new storage format and taking advantage of the inherent parallelism of the operation. The new method has been implemented in OpenMP, MPI and CUDA and has been tested on different hardware configurations. The results are very promising and the execution time and memory requirements are significantly reduced. © 2016 The Author(s)


PubMed | Barcelona Supercomputer Center
Type: Journal Article | Journal: PLoS computational biology | Year: 2011

The cytosol is the major environment in all bacterial cells. The true physical and dynamical nature of the cytosol solution is not fully understood and here a modeling approach is applied. Using recent and detailed data on metabolite concentrations, we have created a molecular mechanical model of the prokaryotic cytosol environment of Escherichia coli, containing proteins, metabolites and monatomic ions. We use 200 ns molecular dynamics simulations to compute diffusion rates, the extent of contact between molecules and dielectric constants. Large metabolites spend 80% of their time in contact with other molecules while small metabolites vary with some only spending 20% of time in contact. Large non-covalently interacting metabolite structures mediated by hydrogen-bonds, ionic and stacking interactions are common and often associate with proteins. Mg(2+) ions were prominent in NIMS and almost absent free in solution. (+) is generally not involved in NIMSs and populates the solvent fairly uniformly, hence its important role as an osmolyte. In simulations containing ubiquitin, to represent a protein component, metabolite diffusion was reduced owing to long lasting protein-metabolite interactions. Hence, it is likely that with larger proteins metabolites would diffuse even more slowly. The dielectric constant of these simulations was found to differ from that of pure water only through a large contribution from ubiquitin as metabolite and monatomic ion effects cancel. These findings suggest regions of influence specific to particular proteins affecting metabolite diffusion and electrostatics. Also some proteins may have a higher propensity for associations with metabolites owing to their larger electrostatic fields. We hope that future studies may be able to accurately predict how binding interactions differ in the cytosol relative to dilute aqueous solution.

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