Absolute value preconditioning for symmetric indefinite linear systems

We introduce a novel strategy for constructing symmetric positive definite (SPD) preconditioners for linear systems with symmetric indefinite matrices. The strategy, called absolute value preconditioning, is motivated by the observation that the preconditioned minimal residual method with the inverse of the absolute value of the matrix as a preconditioner converges to the exact solution of the system in at most two steps. Neither the exact absolute value of the matrix nor its exact inverse are computationally feasible to construct in general. However, we provide a practical example of an SPD preconditioner that is based on the suggested approach. In this example we consider a model problem with a shifted discrete negative Laplacian, and suggest a geometric multigrid (MG) preconditioner, where the inverse of the matrix absolute value appears only on the coarse grid, while operations on finer grids are based on the Laplacian. Our numerical tests demonstrate practical effectiveness of the new MG preconditioner, which leads to a robust iterative scheme with minimalist memory requirements

Физика пробоя жидких диэлектриков (История и современное состояние, вклад советских и российских ученых)

Дана краткая история развития учения об электрическом пробое диэлектрических жидкостей, совершенствования техники и методики исследования этого явления. Показано, что по целому ряду направлений советские (российские) ученые и, в частности, сотрудники Томского политехнического университета опережали зарубежных коллег и внесли определяющий вклад в понимание механизмов пробоя жидкостей. Представлены современные физические модели инициирования и развития разряда при импульсном воздействии напряжения

Building A High Performance Parallel File System Using Grid Datafarm and ROOT I/O

Sheer amount of petabyte scale data foreseen in the LHC experiments require a careful consideration of the persistency design and the system design in the world-wide distributed computing. Event parallelism of the HENP data analysis enables us to take maximum advantage of the high performance cluster computing and networking when we keep the parallelism both in the data processing phase, in the data management phase, and in the data transfer phase. A modular architecture of FADS/ Goofy, a versatile detector simulation framework for Geant4, enables an easy choice of plug-in facilities for persistency technologies such as Objectivity/DB and ROOT I/O. The framework is designed to work naturally with the parallel file system of Grid Datafarm (Gfarm). FADS/Goofy is proven to generate 10^6 Geant4-simulated Atlas Mockup events using a 512 CPU PC cluster. The data in ROOT I/O files is replicated using Gfarm file system. The histogram information is collected from the distributed ROOT files. During the data replication it has been demonstrated to achieve more than 2.3 Gbps data transfer rate between the PC clusters over seven participating PC clusters in the United States and in Japan.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 4 pages, PDF. PSN TUDT01

Distributed Management of Massive Data: an Efficient Fine-Grain Data Access Scheme

This paper addresses the problem of efficiently storing and accessing massive data blocks in a large-scale distributed environment, while providing efficient fine-grain access to data subsets. This issue is crucial in the context of applications in the field of databases, data mining and multimedia. We propose a data sharing service based on distributed, RAM-based storage of data, while leveraging a DHT-based, natively parallel metadata management scheme. As opposed to the most commonly used grid storage infrastructures that provide mechanisms for explicit data localization and transfer, we provide a transparent access model, where data are accessed through global identifiers. Our proposal has been validated through a prototype implementation whose preliminary evaluation provides promising results

The molecular and dusty composition of Betelgeuse's inner circumstellar environment

The study of the atmosphere of red supergiant stars in general and of Betelgeuse (alpha Orionis) in particular is of prime importance to understand dust formation and how mass is lost to the interstellar medium in evolved massive stars. A molecular shell, the MOLsphere (Tsuji, 2000a), in the atmosphere of Betelgeuse has been proposed to account for the near- and mid-infrared spectroscopic observations of Betelgeuse. The goal is to further test this hypothesis and to identify some of the molecules in this MOLsphere. We report on measurements taken with the mid-infrared two-telescope beam combiner of the VLTI, MIDI, operated between 7.5 and 13.5 $\mu$m. The data are compared to a simple geometric model of a photosphere surrounded by a warm absorbing and emitting shell. Physical characteristics of the shell are derived: size, temperature and optical depth. The chemical constituents are determined with an analysis consistent with available infrared spectra and interferometric data. We are able to account for the measured optical depth of the shell in the N band, the ISO-SWS spectrum and K and L band interferometric data with a shell whose inner and outer radii are given by the above range and with the following species: H2O, SiO and Al2O3. These results confirm the MOLsphere model. We bring evidence for more constituents and for the presence of species participating in the formation of dust grains in the atmosphere of the star, i.e. well below the distance at which the dust shell is detected. We believe these results bring key elements to the understanding of mass loss in Betelgeuse and red supergiants in general and bring support to the dust-driven scenario.Comment: 11 pages, 10 figures, accepted for publication in A&

Building Hierarchical Grid Storage Using the Gfarm Global File System and the JuxMem Grid Data-Sharing Service

International audienceAs more and more large-scale applications need to generate and process very large volumes of data, the need for adequate storage facilities is growing. It becomes crucial to efficiently and reliably store and retrieve large sets of data that may be shared at the global scale. Based on previous systems for global data sharing (global file systems, grid data-sharing services), this paper proposes a hierarchical approach for grid storage, which combines the access efficiency of RAM storage with the scalability and persistence of the global file system approach. Our proposal has been validated through a prototype that couples the Gfarm file system with the JuxMem data-sharing service. Experiments on the Grid'5000 testbed confirm the advantages of our approach

Parameter identification problems in the modelling of cell motility

We present a novel parameter identification algorithm for the estimation of parameters in models of cell motility using imaging data of migrating cells. Two alternative formulations of the objective functional that measures the difference between the computed and observed data are proposed and the parameter identification problem is formulated as a minimisation problem of nonlinear least squares type. A Levenberg–Marquardt based optimisation method is applied to the solution of the minimisation problem and the details of the implementation are discussed. A number of numerical experiments are presented which illustrate the robustness of the algorithm to parameter identification in the presence of large deformations and noisy data and parameter identification in three dimensional models of cell motility. An application to experimental data is also presented in which we seek to identify parameters in a model for the monopolar growth of fission yeast cells using experimental imaging data. Our numerical tests allow us to compare the method with the two different formulations of the objective functional and we conclude that the results with both objective functionals seem to agree

The coordination of cell growth during fission yeast mating requires Ras1-GTP hydrolysis

The spatial and temporal control of polarity is fundamental to the survival of all organisms. Cells define their polarity using highly conserved mechanisms that frequently rely upon the action of small GTPases, such as Ras and Cdc42. Schizosaccharomyces pombe is an ideal system with which to study the control of cell polarity since it grows from defined tips using Cdc42-mediated actin remodeling. Here we have investigated the importance of Ras1-GTPase activity for the coordination of polarized cell growth during fission yeast mating. Following pheromone stimulation, Ras1 regulates both a MAPK cascade and the activity of Cdc42 to enable uni-directional cell growth towards a potential mating partner. Like all GTPases, when bound to GTP, Ras1 adopts an active conformation returning to an inactive state upon GTP-hydrolysis, a process accelerated through interaction with negative regulators such as GAPs. Here we show that, at low levels of pheromone stimulation, loss of negative regulation of Ras1 increases signal transduction via the MAPK cascade. However, at the higher concentrations observed during mating, hyperactive Ras1 mutations promote cell death. We demonstrate that these cells die due to their failure to coordinate active Cdc42 into a single growth zone resulting in disorganized actin deposition and unsustainable elongation from multiple tips. These results provide a striking demonstration that the deactivation stage of Ras signaling is fundamentally important in modulating cell polarity

Reconstructing extreme AMOC events through nudging of the ocean surface: a perfect model approach

While the Atlantic Meridional Overturning Circulation (AMOC) is thought to be a crucial component of the North Atlantic climate, past changes in its strength are challenging to quantify, and only limited information is available. In this study, we use a perfect model approach with the IPSL-CM5A-LR model to assess the performance of several surface nudging techniques in reconstructing the variability of the AMOC. Special attention is given to the reproducibility of an extreme positive AMOC peak from a preindustrial control simulation. Nudging includes standard relaxation techniques towards the sea surface temperature and salinity anomalies of this target control simulation, and/or the prescription of the wind-stress fields. Surface nudging approaches using standard fixed restoring terms succeed in reproducing most of the target AMOC variability, including the timing of the extreme event, but systematically underestimate its amplitude. A detailed analysis of the AMOC variability mechanisms reveals that the underestimation of the extreme AMOC maximum comes from a deficit in the formation of the dense water masses in the main convection region, located south of Iceland in the model. This issue is largely corrected after introducing a novel surface nudging approach, which uses a varying restoring coefficient that is proportional to the simulated mixed layer depth, which, in essence, keeps the restoring time scale constant. This new technique substantially improves water mass transformation in the regions of convection, and in particular, the formation of the densest waters, which are key for the representation of the AMOC extreme. It is therefore a promising strategy that may help to better constrain the AMOC variability and other ocean features in the models. As this restoring technique only uses surface data, for which better and longer observations are available, it opens up opportunities for improved reconstructions of the AMOC over the last few decades

Seasonal-to-decadal predictions with the ensemble Kalman filter and the Norwegian Earth System Model: a twin experiment

Here, we firstly demonstrate the potential of an advanced flow dependent data assimilation method for performing seasonal-to-decadal prediction and secondly, reassess the use of sea surface temperature (SST) for initialisation of these forecasts. We use the Norwegian Climate Prediction Model (NorCPM), which is based on the Norwegian Earth System Model (NorESM) and uses the deterministic ensemble Kalman filter to assimilate observations. NorESM is a fully coupled system based on the Community Earth System Model version 1, which includes an ocean, an atmosphere, a sea ice and a land model. A numerically efficient coarse resolution version of NorESM is used. We employ a twin experiment methodology to provide an upper estimate of predictability in our model framework (i.e. without considering model bias) of NorCPM that assimilates synthetic monthly SST data (EnKF-SST). The accuracy of EnKF-SST is compared to an unconstrained ensemble run (FREE) and ensemble predictions made with near perfect (i.e. microscopic SST perturbation) initial conditions (PERFECT). We perform 10 cycles, each consisting of a 10-yr assimilation phase, followed by a 10-yr prediction. The results indicate that EnKF-SST improves sea level, ice concentration, 2 m atmospheric temperature, precipitation and 3-D hydrography compared to FREE. Improvements for the hydrography are largest near the surface and are retained for longer periods at depth. Benefits in salinity are retained for longer periods compared to temperature. Near-surface improvements are largest in the tropics, while improvements at intermediate depths are found in regions of large-scale currents, regions of deep convection, and at the Mediterranean Sea outflow. However, the benefits are often small compared to PERFECT, in particular, at depth suggesting that more observations should be assimilated in addition to SST. The EnKF-SST system is also tested for standard ocean circulation indices and demonstrates decadal predictability for Atlantic overturning and sub-polar gyre circulations, and heat content in the Nordic Seas. The system beats persistence forecast and shows skill for heat content in the Nordic Seas that is close to PERFECT