00540nas a2200145   4500008004100000245010800041210006900149653002100218653003300239100002100272700002100293700002200314700002100336856003700357       2020                        eng d00aMicroROM: An Efficient and Accurate Reduced Order Method to Solve Many-Query Problems in Micro-Motility0 aMicroROM An Efficient and Accurate Reduced Order Method to Solve10aFOS: Mathematics10aNumerical Analysis (math.NA)1 aGiuliani, Nicola1 aHess, Martin, W.1 aDeSimone, Antonio1 aRozza, Gianluigi  uhttps://arxiv.org/abs/2006.1383602204nas a2200229   4500008004100000022001400041245009200055210006900147300001400216490000800230520153700238653000801775653001801783653000801801653001501809653000801824653002501832653001701857653000801874100002101882856007101903       2019                        eng d  a0010-465500aBlackNUFFT: Modular customizable black box hybrid parallelization of type 3 NUFFT in 3D0 aBlackNUFFT Modular customizable black box hybrid parallelization  a324 - 3350 v2353 a<p>Many applications benefit from an efficient Discrete Fourier Transform (DFT) between arbitrarily spaced points. The Non Uniform Fast Fourier Transform reduces the computational cost of such operation from O(N2) to O(NlogN) exploiting gridding algorithms and a standard Fast Fourier Transform on an equi-spaced grid. The parallelization of the NUFFT of type 3 (between arbitrary points in space and frequency) still poses some challenges: we present a novel and flexible hybrid parallelization in a MPI-multithreaded environment exploiting existing HPC libraries on modern architectures. To ensure the reliability of the developed library, we exploit continuous integration strategies using Travis CI. We present performance analyses to prove the effectiveness of our implementation, possible extensions to the existing library, and an application of NUFFT type 3 to MRI image processing. Program summary Program Title: BlackNUFFT Program Files doi: http://dx.doi.org/10.17632/vxfj6x2p8x.1 Licensing provisions: LGPL Programming language: C++ External routines/libraries: deal.II , FFTW, PFFT Nature of problem: Provide a modular and extensible implementation of a parallel Non Uniform Fast Fourier Transform of type 3. Solution method: Use of hybrid shared distributed memory paradigm to achieve high level of efficiency. We exploit existing HPC library following best practices in scientific computing (as continuous integration via TravisCI) to reach higher complexities and guarantee the accuracy of the solution proposed.</p>10aC++10aExtensibility10aFFT10aModularity10aMPI10aMRI image processing10aNUFFT type 310aTBB1 aGiuliani, Nicola  uhttp://www.sciencedirect.com/science/article/pii/S001046551830353900536nas a2200145   4500008004100000245007700041210006900118300001400187490000600201100002100207700002100228700002200249700001700271856010200288       2018                        eng d00adeal2lkit: A toolkit library for high performance programming in deal.II0 adeal2lkit A toolkit library for high performance programming in   a318–3270 v71 aSartori, Alberto1 aGiuliani, Nicola1 aBardelloni, Mauro1 aHeltai, Luca  uhttps://math.sissa.it/publication/deal2lkit-toolkit-library-high-performance-programming-dealii-000509nas a2200133   4500008004100000245012700041210006900168300001400237490000600251100002100257700001700278700002200295856005800317       2018                        eng d00aPredicting and Optimizing Microswimmer Performance from the Hydrodynamics of Its Components: The Relevance of Interactions0 aPredicting and Optimizing Microswimmer Performance from the Hydr  a410–4240 v51 aGiuliani, Nicola1 aHeltai, Luca1 aDeSimone, Antonio  uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6094362/00570nas a2200133   4500008004100000245012000041210007000161300001200231490000800243100002100251700001700272700001700289856013000306       2018                        eng d00aπ-BEM : A flexible parallel implementation for adaptive , geometry aware , and high order boundary element methods0 aπBEM A flexible parallel implementation for adaptive geometry aw  a39–580 v1211 aGiuliani, Nicola1 aMola, Andrea1 aHeltai, Luca  uhttps://math.sissa.it/publication/%CF%80-bem-flexible-parallel-implementation-adaptive-geometry-aware-and-high-order-boundary01640nas a2200145   4500008004100000245007700041210006900118260001000187520116500197100002101362700002101383700002201404700001701426856005101443       2015                        en  d00aDeal2lkit: a Toolkit Library for High Performance Programming in deal.II0 aDeal2lkit a Toolkit Library for High Performance Programming in   bSISSA3 aWe present version 1.0.0 of the deal2lkit (deal.II ToolKit) library. deal2lkit is a collection of modules and classes for the general purpose finite element library deal.II. Its principal aim is to provide a high level interface, controlled via parameter files, for those steps  that are common in all finite element programs: mesh generation, selection of the finite element type, application of boundary conditions and many others. Each module can be used as a building block independently on the others, and can be integrated in existing finite element codes based on deal.II, drastically reducing the size of programs, rendering their use automatically parametrised, and reducing the overall time-to-market of finite element
programming. Moreover, deal2lkit features interfaces with the SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers) and ASSIMP (Open Asset Import Library) libraries. Some examples are provided which show the aim and scopes of deal2lkit. The deal2lkit library is released under the GNU Lesser General Public License (LGPL) and can be retrieved from the deal2lkit repository https://github.com/mathLab/deal2lkit.1 aSartori, Alberto1 aGiuliani, Nicola1 aBardelloni, Mauro1 aHeltai, Luca  uhttp://urania.sissa.it/xmlui/handle/1963/3500601899nas a2200133   4500008004300000245010100043210006900144520142800213100002101641700001701662700001701679700001801696856005101714       2015                        en_Ud  00aFEM SUPG stabilisation of mixed isoparametric BEMs: application to linearised free surface flows0 aFEM SUPG stabilisation of mixed isoparametric BEMs application t3 a<p>In finite element formulations, transport dominated problems are often stabilised through the Streamline-Upwind-Petrov–Galerkin (SUPG) method. Its application is straightforward when the problem at hand is solved using Galerkin methods. Applications of boundary integral formulations often resort to collocation techniques which are computationally more tractable. In this framework, the Galerkin method and the stabilisation may still be used to successfully apply boundary conditions and resolve instabilities that are frequently observed in transport dominated problems. We apply this technique to an adaptive collocation boundary element method for the solution of stationary potential flows, where we solve a mixed Poisson problem in boundary integral form, with the addition of linearised free surface boundary conditions. We use a mixed boundary element formulation to allow for different finite dimensional spaces describing the flow potential and its normal derivative, and we validate our method simulating the flow around both a submerged body and a surface piercing body. The coupling of mixed surface finite elements and strongly consistent stabilisation techniques with boundary elements opens up the possibility to use non conformal unstructured grids with local refinement, without introducing the inconsistencies of other stabilisation techniques based on up-winding and finite difference schemes.</p>1 aGiuliani, Nicola1 aMola, Andrea1 aHeltai, Luca1 aFormaggia, L.  uhttp://urania.sissa.it/xmlui/handle/1963/34466