Evaluating kernels on Xeon Phi to accelerate Gysela application

This work describes the challenges presented by porting parts ofthe Gysela code to the Intel Xeon Phi coprocessor, as well as techniques used for optimization, vectorization and tuning that can be applied to other applications. We evaluate the performance of somegeneric micro-benchmark on Phi versus Intel Sandy Bridge. Several interpolation kernels useful for the Gysela application are analyzed and the performance are shown. Some memory-bound and compute-bound kernels are accelerated by a factor 2 on the Phi device compared to Sandy architecture. Nevertheless, it is hard, if not impossible, to reach a large fraction of the peek performance on the Phi device,especially for real-life applications as Gysela. A collateral benefit of this optimization and tuning work is that the execution time of Gysela (using 4D advections) has decreased on a standard architecture such as Intel Sandy Bridge.Comment: submitted to ESAIM proceedings for CEMRACS 2014 summer school version reviewe

PoPe (Projection on Proper elements) for code control: verification, numerical convergence and reduced models. Application to plasma turbulence simulations

The Projection on Proper elements (PoPe) is a novel method of code control dedicated to 1) checking the correct implementation of models, 2) determining the convergence of numerical methods and 3) characterizing the residual errors of any given solution at very low cost. The basic idea is to establish a bijection between a simulation and a set of equations that generate it. Recovering equations is direct and relies on a statistical measure of the weight of the various operators. This method can be used in any dimensions and any regime, including chaotic ones. This method also provides a procedure to design reduced models and quantify the ratio costs to benefits. PoPe is applied to a kinetic and a fluid code of plasma turbulence

Matrix-Bound PAI-1 Supports Cell Blebbing via RhoA/ROCK1 Signaling

The microenvironment of a tumor can influence both the morphology and the behavior of cancer cells which, in turn, can rapidly adapt to environmental changes. Increasing evidence points to the involvement of amoeboid cell migration and thus of cell blebbing in the metastatic process; however, the cues that promote amoeboid cell behavior in physiological and pathological conditions have not yet been clearly identified. Plasminogen Activator Inhibitor type-1 (PAI-1) is found in high amount in the microenvironment of aggressive tumors and is considered as an independent marker of bad prognosis. Here we show by immunoblotting, activity assay and immunofluorescence that, in SW620 human colorectal cancer cells, matrix-associated PAI-1 plays a role in the cell behavior needed for amoeboid migration by maintaining cell blebbing, localizing PDK1 and ROCK1 at the cell membrane and maintaining the RhoA/ROCK1/MLC-P pathway activation. The results obtained by modeling PAI-1 deposition around tumors indicate that matrix-bound PAI-1 is heterogeneously distributed at the tumor periphery and that, at certain spots, the elevated concentrations of matrix-bound PAI-1 needed for cancer cells to undergo the mesenchymal-amoeboid transition can be observed. Matrix-bound PAI-1, as a matricellular protein, could thus represent one of the physiopathological requirements to support metastatic formation

PAI-1 and functional blockade of SNAI1 in breast cancer cell migration

12 pages, 5 figures.-- PMID: 19055748 [PubMed].-- et al.[Introduction]: Snail, a family of transcriptional repressors implicated in cell movement, has been correlated with tumour invasion. The Plasminogen Activation (PA) system, including urokinase plasminogen activator (uPA), its receptor and its inhibitor, plasminogen activator inhibitor type 1(PAI-1), also plays a key role in cancer invasion and metastasis, either through proteolytic degradation or by non-proteolytic modulation of cell adhesion and migration. Thus, Snail and the PA system are both over-expressed in cancer and influence this process. In this study we aimed to determine if the activity of SNAI1 (a member of the Snail family) is correlated with expression of the PA system components and how this correlation can influence tumoural cell migration.[Methods]: We compared the invasive breast cancer cell-line MDA-MB-231 expressing SNAI1 (MDA-mock) with its derived clone expressing a dominant-negative form of SNAI1 (SNAI1-DN). Expression of PA system mRNAs was analysed by cDNA microarrays and real-time quantitative RT-PCR. Wound healing assays were used to determine cell migration. PAI-1 distribution was assessed by immunostaining.[Results]: We demonstrated by both cDNA microarrays and realtime quantitative RT-PCR that the functional blockade of SNAI1 induces a significant decrease of PAI-1 and uPA transcripts. After performing an in vitro wound-healing assay, we observed that SNAI1-DN cells migrate more slowly than MDA-mock cells and in a more collective manner. The blockade of SNAI1 activity resulted in the redistribution of PAI-1 in SNAI1-DN cells decorating large lamellipodia, which are commonly found structures in these cells.[Conclusions]: In the absence of functional SNAI1, the expression of PAI-1 transcripts is decreased, although the protein is redistributed at the leading edge of migrating cells in a manner comparable with that seen in normal epithelial cells.This work was supported by the CNRS ACI Program "Complexité du vivant" (grant # 050009DR11) and by the Evry Genopole grant "Aide à l'acquisition d'équipement semi-lourd" 2007 and 2008.Peer reviewe

A posteriori error estimate in fluid simulations of turbulent edge plasmas for magnetic fusion in tokamak using the data mining iPoPe method

International audienceProgressing towards more reliable numerical solutions in the simulation of plasma for magnetic confinement fusion has become a critical issue for the success of the ITER operation. This requires developing rigorous and efficient methods of verification of the numerical simulations in any relevant flow regimes of the operation. The paper introduces a new formulation of the PoPe 1 method, namely the independent Projection on Proper elements method (iPoPe) to quantify the numerical error by performing a data-driven identification of the mathematical model from the simulation outputs. Based on a statistical postprocessing of the outputs database, the method provides a measure of the error by estimating the distance between the (numerical) effective and (analytical) theoretical weights of each operator implemented in the mathematical model. The efficiency of the present method is illustrated on turbulent edge plasma simulations based on a drift-reduced Braginskii fluid model in realistic magnetic geometries. Results show the effective order of the numerical method in these multiscale flow regimes as well as the values of the plasma parameters which can be safely simulated with respect to a given discretization. In this sense, the method goes one step further than the Method of Manufactured Solution (MMS 2-4), recently introduced in fusion, and provides an efficient verification procedure of the numerical simulations in any regimes, including turbulent ones that could be generalized to other scientific domains

Shear flow instabilities induced by trapped ion modes in collisionless temperature gradient turbulence

Équipe 107 : Physique des plasmas chaudsInternational audienceOne important issue in turbulence self-organization is the interplay between the Kelvin-Helmholtz (KH) instability and streamers and/or zonal flows. This question has been debated for a long time. The effects of the KH instability and its position in the sequence of events between streamers, turbulence, and zonal flows have been investigated with a reduced gyro-bounce averaged kinetic code devoted to study the primary ion temperature gradient (ITG) instability linked to trapped ion modes (TIM). In toroidal geometry, the specific dynamics of TIM linked to trapped particles becomes important when the frequency of ITG modes falls below the ion bounce frequency, allowing one to average on both the cyclotron and bounce motion fast time scales. This reduction of the number of degrees of freedom leads to a strong reduction of computer resources (memory and computation time). Bounce-averaged gyrokinetic code can be considered as a toy model able to describe basic structures of turbulent transport in tokamak devices. In particular, by means of this code, we have observed that the energy injected in the system by the TIM instability is exchanged between streamers and zonal flows by means of KH vortices that grow along these structures in the nonlinear phase. The energy transfer occurs throughout the relaxation phase of the streamer growth leading to a modification of the KH modes and to the generation of the zonal flows