Improving Performance of Iterative Methods by Lossy Checkponting

Iterative methods are commonly used approaches to solve large, sparse linear systems, which are fundamental operations for many modern scientific simulations. When the large-scale iterative methods are running with a large number of ranks in parallel, they have to checkpoint the dynamic variables periodically in case of unavoidable fail-stop errors, requiring fast I/O systems and large storage space. To this end, significantly reducing the checkpointing overhead is critical to improving the overall performance of iterative methods. Our contribution is fourfold. (1) We propose a novel lossy checkpointing scheme that can significantly improve the checkpointing performance of iterative methods by leveraging lossy compressors. (2) We formulate a lossy checkpointing performance model and derive theoretically an upper bound for the extra number of iterations caused by the distortion of data in lossy checkpoints, in order to guarantee the performance improvement under the lossy checkpointing scheme. (3) We analyze the impact of lossy checkpointing (i.e., extra number of iterations caused by lossy checkpointing files) for multiple types of iterative methods. (4)We evaluate the lossy checkpointing scheme with optimal checkpointing intervals on a high-performance computing environment with 2,048 cores, using a well-known scientific computation package PETSc and a state-of-the-art checkpoint/restart toolkit. Experiments show that our optimized lossy checkpointing scheme can significantly reduce the fault tolerance overhead for iterative methods by 23%~70% compared with traditional checkpointing and 20%~58% compared with lossless-compressed checkpointing, in the presence of system failures.Comment: 14 pages, 10 figures, HPDC'1

Nutrition in cancer prevention: an integrated approach

There is considerable evidence that the war on cancer is not being won. There is, however, strong evidence that a substantial fraction of cancer can be prevented by using existing nutritional knowledge. In this paper we discuss strategies for reducing cancer incidence by implementing this knowledge. The most obvious route for persuading large numbers to change their diets is by individual counseling in a health-care setting, public education campaigns and interventions at the worksite. However, such health promotion actions have met with only limited success. For efforts to change population diets to be successful, a vital component must include changes in government policies. Examples of the tools that need to be employed are restrictions on advertising and marketing. Effective action will likely require an economic dimension, namely the employment of taxation and subsidies, for instance, by taxing unhealthy food choices and by subsidizing fruit and vegetables

Low zinc status and absorption exist in infants with jejunostomies or ileostomies which persists after intestinal repair.

There is very little data regarding trace mineral nutrition in infants with small intestinal ostomies. Here we evaluated 14 infants with jejunal or ileal ostomies to measure their zinc absorption and retention and biochemical zinc and copper status. Zinc absorption was measured using a dual-tracer stable isotope technique at two different time points when possible. The first study was conducted when the subject was receiving maximal tolerated feeds enterally while the ostomy remained in place. A second study was performed as soon as feasible after full feeds were achieved after intestinal repair. We found biochemical evidence of deficiencies of both zinc and copper in infants with small intestinal ostomies at both time points. Fractional zinc absorption with an ostomy in place was 10.9% ± 5.3%. After reanastamosis, fractional zinc absorption was 9.4% ± 5.7%. Net zinc balance was negative prior to reanastamosis. In conclusion, our data demonstrate that infants with a jejunostomy or ileostomy are at high risk for zinc and copper deficiency before and after intestinal reanastamosis. Additional supplementation, especially of zinc, should be considered during this time period

Full sphere hydrodynamic and dynamo benchmarks

Convection in planetary cores can generate fluid flow and magnetic fields, and a number of sophisticated codes exist to simulate the dynamic behaviour of such systems. We report on the first community activity to compare numerical results of computer codes designed to calculate fluid flow within a whole sphere. The flows are incompressible and rapidly rotating and the forcing of the flow is either due to thermal convection or due to moving boundaries. All problems defined have solutions that allow easy comparison, since they are either steady, slowly drifting or perfectly periodic. The first two benchmarks are defined based on uniform internal heating within the sphere under the Boussinesq approximation with boundary conditions that are uniform in temperature and stress-free for the flow. Benchmark 1 is purely hydrodynamic, and has a drifting solution. Benchmark 2 is a magnetohydrodynamic benchmark that can generate oscillatory, purely periodic, flows and magnetic fields. In contrast, Benchmark 3 is a hydrodynamic rotating bubble benchmark using no slip boundary conditions that has a stationary solution. Results from a variety of types of code are reported, including codes that are fully spectral (based on spherical harmonic expansions in angular coordinates and polynomial expansions in radius), mixed spectral and finite difference, finite volume, finite element and also a mixed Fourier–finite element code. There is good agreement between codes. It is found that in Benchmarks 1 and 2, the approximation of a whole sphere problem by a domain that is a spherical shell (a sphere possessing an inner core) does not represent an adequate approximation to the system, since the results differ from whole sphere results

Black Hole-Neutron Star Binaries in General Relativity: Quasiequilibrium Formulation

We present a new numerical method for the construction of quasiequilibrium models of black hole-neutron star binaries. We solve the constraint equations of general relativity, decomposed in the conformal thin-sandwich formalism, together with the Euler equation for the neutron star matter. We take the system to be stationary in a corotating frame and thereby assume the presence of a helical Killing vector. We solve these coupled equations in the background metric of a Kerr-Schild black hole, which accounts for the neutron star's black hole companion. In this paper we adopt a polytropic equation of state for the neutron star matter and assume large black hole--to--neutron star mass ratios. These simplifications allow us to focus on the construction of quasiequilibrium neutron star models in the presence of strong-field, black hole companions. We summarize the results of several code tests, compare with Newtonian models, and locate the onset of tidal disruption in a fully relativistic framework.Comment: 17 pages, 7 figures; added discussion, tables; PRD in pres

A spherical shell numerical dynamo benchmark with pseudo vacuum magnetic boundary conditions

It is frequently considered that many planetary magnetic fields originate as a result of convection within planetary cores. Buoyancy forces responsible for driving the convection generate a fluid flow that is able to induce magnetic fields; numerous sophisticated computer codes are able to simulate the dynamic behaviour of such systems. This paper reports the results of a community activity aimed at comparing numerical results of several different types of computer codes that are capable of solving the equations of momentum transfer, magnetic field generation and heat transfer in the setting of a spherical shell, namely a sphere containing an inner core. The electrically conducting fluid is incompressible and rapidly rotating and the forcing of the flow is thermal convection under the Boussinesq approximation. We follow the original specifications and results reported in Harder & Hansen to construct a specific benchmark in which the boundaries of the fluid are taken to be impenetrable, non-slip and isothermal, with the added boundary condition for the magnetic field <b>B</b> that the field must be entirely radial there; this type of boundary condition for <b>B</b> is frequently referred to as ‘pseudo-vacuum’. This latter condition should be compared with the more frequently used insulating boundary condition. This benchmark is so-defined in order that computer codes based on local methods, such as finite element, finite volume or finite differences, can handle the boundary condition with ease. The defined benchmark, governed by specific choices of the Roberts, magnetic Rossby, Rayleigh and Ekman numbers, possesses a simple solution that is steady in an azimuthally drifting frame of reference, thus allowing easy comparison among results. Results from a variety of types of code are reported, including codes that are fully spectral (based on spherical harmonic expansions in angular coordinates and polynomial expansions in radius), mixed spectral and finite difference, finite volume, finite element and also a mixed Fourier-finite element code. There is good agreement among codes

Head-on collisions of binary white dwarf--neutron stars: Simulations in full general relativity

We simulate head-on collisions from rest at large separation of binary white dwarf -- neutron stars (WDNSs) in full general relativity. Our study serves as a prelude to our analysis of the circular binary WDNS problem. We focus on compact binaries whose total mass exceeds the maximum mass that a cold degenerate star can support, and our goal is to determine the fate of such systems. A fully general relativistic hydrodynamic computation of a realistic WDNS head-on collision is prohibitive due to the large range of dynamical time scales and length scales involved. For this reason, we construct an equation of state (EOS) which captures the main physical features of NSs while, at the same time, scales down the size of WDs. We call these scaled-down WD models "pseudo-WDs (pWDs)". Using pWDs, we can study these systems via a sequence of simulations where the size of the pWD gradually increases toward the realistic case. We perform two sets of simulations; One set studies the effects of the NS mass on the final outcome, when the pWD is kept fixed. The other set studies the effect of the pWD compaction on the final outcome, when the pWD mass and the NS are kept fixed. All simulations show that 14%-18% of the initial total rest mass escapes to infinity. All remnant masses still exceed the maximum rest mass that our cold EOS can support (1.92 solar masses), but no case leads to prompt collapse to a black hole. This outcome arises because the final configurations are hot. All cases settle into spherical, quasiequilibrium configurations consisting of a cold NS core surrounded by a hot mantle, resembling Thorne-Zytkow objects. Extrapolating our results to realistic WD compactions, we predict that the likely outcome of a head-on collision of a realistic, massive WDNS system will be the formation of a quasiequilibrium Thorne-Zytkow-like object.Comment: 24 pages, 14 figures, matches PRD published version, tests of HRSC schemes with piecewise polytropes adde

How universal is the fractional-quantum-Hall edge Luttinger liquid?

This article reports on our microscopic investigations of the edge of the fractional quantum Hall state at filling factor $\nu=1/3$. We show that the interaction dependence of the wave function is well described in an approximation that includes mixing with higher composite-fermion Landau levels in the lowest order. We then proceed to calculate the equal time edge Green function, which provides evidence that the Luttinger exponent characterizing the decay of the Green function at long distances is interaction dependent. The relevance of this result to tunneling experiments is discussed.Comment: 5 page

Extended Lifetime in Computational Evolution of Isolated Black Holes

Solving the 4-d Einstein equations as evolution in time requires solving equations of two types: the four elliptic initial data (constraint) equations, followed by the six second order evolution equations. Analytically the constraint equations remain solved under the action of the evolution, and one approach is to simply monitor them ({\it unconstrained} evolution). The problem of the 3-d computational simulation of even a single isolated vacuum black hole has proven to be remarkably difficult. Recently, we have become aware of two publications that describe very long term evolution, at least for single isolated black holes. An essential feature in each of these results is {\it constraint subtraction}. Additionally, each of these approaches is based on what we call "modern," hyperbolic formulations of the Einstein equations. It is generally assumed, based on computational experience, that the use of such modern formulations is essential for long-term black hole stability. We report here on comparable lifetime results based on the much simpler ("traditional") $\dot g$ - $\dot K$ formulation. We have also carried out a series of {\it constrained} 3-d evolutions of single isolated black holes. We find that constraint solution can produce substantially stabilized long-term single hole evolutions. However, we have found that for large domains, neither constraint-subtracted nor constrained $\dot g$ - $\dot K$ evolutions carried out in Cartesian coordinates admit arbitrarily long-lived simulations. The failure appears to arise from features at the inner excision boundary; the behavior does generally improve with resolution.Comment: 20 pages, 6 figure