Strategies for Energy-Efficient Resource Management of Hybrid Programming Models

Many scientific applications are programmed using hybrid programming models that use both message passing and shared memory, due to the increasing prevalence of large-scale systems with multicore, multisocket nodes. Previous work has shown that energy efficiency can be improved using software-controlled execution schemes that consider both the programming model and the power-aware execution capabilities of the system. However, such approaches have focused on identifying optimal resource utilization for one programming model, either shared memory or message passing, in isolation. The potential solution space, thus the challenge, increases substantially when optimizing hybrid models since the possible resource configurations increase exponentially. Nonetheless, with the accelerating adoption of hybrid programming models, we increasingly need improved energy efficiency in hybrid parallel applications on large-scale systems. In this work, we present new software-controlled execution schemes that consider the effects of dynamic concurrency throttling (DCT) and dynamic voltage and frequency scaling (DVFS) in the context of hybrid programming models. Specifically, we present predictive models and novel algorithms based on statistical analysis that anticipate application power and time requirements under different concurrency and frequency configurations. We apply our models and methods to the NPB MZ benchmarks and selected applications from the ASC Sequoia codes. Overall, we achieve substantial energy savings (8.74 percent on average and up to 13.8 percent) with some performance gain (up to 7.5 percent) or negligible performance loss.

Hepatocellular carcinoma and polymorphisms in carcinogen-metabolizing and DNA repair enzymes in a population with aflatoxin exposure and hepatitis B virus endemicity

High rates of hepatocellular carcinoma (HCC) in The Gambia, West Africa, are primarily due to a high prevalence of chronic hepatitis B virus infection and heavy aflatoxin exposure via groundnut consumption. We investigated genetic polymorphisms in carcinogen-metabolizing (GSTM1, GSTT1, HYL1*2) and DNA repair (XRCC1) enzymes in a hospital-based case-control study. Incident HCC cases (n = 216) were compared with frequency-matched controls (n = 408) with no clinically apparent liver disease. Although the prevalence of variant genotypes was generally low, in multivariable analysis (adjusting for demographic factors, hepatitis B virus, hepatitis C virus, and TP53 status), the GSTM1-null genotype [odds ratio (OR), 2.45; 95% confidence interval (95% CI), 1.21-4.95] and the heterozygote XRCC1-399 AG genotype (OR, 3.18; 95% CI, 1.35-7.51) were significantly associated with HCC. A weak association of the HYL1*2 polymorphism with HCC was observed but did not reach statistical significance. GSTT1 was not associated with HCC. The risk for HCC with null GSTM1 was most prominent among those with the highest groundnut consumption (OR, 4.67; 95% CI, 1.45-15.1) and was not evident among those with less than the mean groundnut intake (OR, 0.64; 95% Cl, 0.20-2.02). Among participants who had all three suspected aflatoxin-related high-risk genotypes [GSTM1 null, HLY1*2 (HY/HH), and XRCC1 (AG/GG)], a significant 15-fold increased risk of HCC was observed albeit with imprecise estimates (OR, 14.7; 95% CI, 1.27-169). Our findings suggest that genetic modulation of carcinogen metabolism and DNA repair can alter susceptibility to HCC and that these effects may be modified by environmental factors.

Genetic screening protocol for familial hypercholesterolemia which includes splicing defects gives an improved mutation detection rate

Familial hypercholesterolemia (FH) is a common single gene disorder, which predisposes to coronary artery disease. In a previous study, we have shown that in patients with definite FH around 20% had no identifiable gene defect after screening the entire exon coding area of the low density lipoprotein receptor (LDLR) and testing for the common Apolipoprotein B (ApoB) R3500Q mutation. In this study, we have extended the screen to additional families and have included the non-coding intron splice regions of the gene. In families with definite FH (tendon xanthoma present, n = 68) the improved genetic screening protocol increased the detection rate of mutations to 87%. This high detection rate greatly enhances the potential value of this test as part of a clinical screening program for FH. In contrast, the use of a limited screen in patients with possible FH (n = 130) resulted in a detection rate of 26%, but this is still of significant benefit in diagnosis of this genetic condition. We have also shown that 14% of LDLR defects are due to splice site mutations and that the most frequent splice mutation in our series (c.1845 + 11 c > g) is expressed at the RNA level. In addition, DNA samples from the patients in whom no LDLR or ApoB gene mutations were found, were sequenced for the NARC-1 gene. No mutations were identified which suggests that the role of NARC-1 in causing FH is minor. In a small proportion of families (

COMPUTATION OF SYNTHETIC SPECTRA FROM SIMULATIONS OF RELATIVISTIC SHOCKS

Particle-in-cell (PIC) simulations of relativistic shocks are in principle capable of predicting the spectra of photons that are radiated incoherently by the accelerated particles. The most direct method evaluates the spectrum using the fields given by the Lienard-Wiechart potentials. However, for relativistic particles this procedure is computationally expensive. Here we present an alternative method that uses the concept of the photon formation length. The algorithm is suitable for evaluating spectra both from particles moving in a specific realization of a turbulent electromagnetic field or from trajectories given as a finite, discrete time series by a PIC simulation. The main advantage of the method is that it identifies the intrinsic spectral features and filters out those that are artifacts of the limited time resolution and finite duration of input trajectories.

RADIATIVE SIGNATURES OF RELATIVISTIC SHOCKS

Particle-in-cell simulations of relativistic, weakly magnetized collisionless shocks show that particles can gain energy by repeatedly crossing the shock front. This requires scattering off self-generated small length-scale magnetic fluctuations. The radiative signature of this first-order Fermi acceleration mechanism is important for models of both the prompt and afterglow emission in gamma-ray bursts and depends on the strength parameter a = lambda e/delta B/mc(2) of the fluctuations (lambda is the length scale and vertical bar delta B vertical bar is the magnitude of the fluctuations). For electrons (and positrons), acceleration saturates when the radiative losses produced by the scattering cannot be compensated by the energy gained on crossing the shock. We show that this sets an upper limit on both the electron Lorentz factor gamma <10(6) (n/1 cm(-3))(-1/6)(-1/6) and on the energy of the photons radiated during the scattering process h omega(max) <40Max(a, 1)(n/1 cm(-3))(1/6)(-1/6) eV, where n is the number density of the plasma and (gamma) over bar is the thermal Lorentz factor of the downstream plasma, provided a <a(crit) similar to 10(6). This rules out "jitter" radiation on self-excited fluctuations with a <I as a source of gamma rays, although high-energy photons might still be produced when the jitter photons are upscattered in an analog of the synchrotron self-Compton process. In fluctuations with a > 1, radiation is generated by the standard synchrotron mechanism, and the maximum photon energy rises linearly with a, until saturating at 70 MeV, when a = a(crit).

TWO-DIMENSIONAL PARTICLE-IN-CELL SIMULATIONS OF THE NONRESONANT, COSMIC-RAY-DRIVEN INSTABILITY IN SUPERNOVA REMNANT SHOCKS

In supernova remnants, the nonlinear amplification of magnetic fields upstream of collisionless shocks is essential for the acceleration of cosmic rays to the energy of the "knee" at 10(15.5) eV. A nonresonant instability driven by the cosmic ray current is thought to be responsible for this effect. We perform two-dimensional, particle-in-cell simulations of this instability. We observe an initial growth of circularly polarized nonpropagating magnetic waves as predicted in linear theory. It is demonstrated that in some cases the magnetic energy density in the growing waves can grow to at least 10 times its initial value. We find no evidence of competing modes, nor of significant modification by thermal effects. At late times, we observe saturation of the instability in the simulation, but the mechanism responsible is an artifact of the periodic boundary conditions and has no counterpart in the supernova-shock scenario.

A current-driven instability in parallel, relativistic shocks

Recently, Bell ( 2004 Mon. Not. R. Astron. Soc. 353 550) has reanalysed the problem of wave excitation by cosmic rays propagating in the pre-cursor region of a supernova remnant shock front. He pointed out a strong, non-resonant, current-driven instability that had been overlooked in the kinetic treatments by Achterberg ( 1983 Astron. Astrophys. 119 274) and McKenzie and Volk ( 1982 Astron. Astrophys. 116 191), and suggested that it is responsible for substantial amplification of the ambient magnetic field. Magnetic field amplification is also an important issue in the problem of the formation and structure of relativistic shock fronts, particularly in relation to models of gamma-ray bursts. We have therefore generalized the linear analysis to apply to this case, assuming a relativistic background plasma and a monoenergetic, unidirectional incoming proton beam. We find essentially the same non-resonant instability observed by Bell and show that also, under GRB conditions, it grows much faster than the resonant waves. We quantify the extent to which thermal effects in the background plasma limit the maximum growth rate.

LINEAR ACCELERATION EMISSION IN PULSAR MAGNETOSPHERES

Linear acceleration emission occurs when a charged particle is accelerated parallel to its velocity. We evaluate the spectral and angular distribution of this radiation for several special cases, including constant acceleration (hyperbolic motion) of finite duration. Based on these results, we find the following general properties of the emission from an electron in a linear accelerator that can be characterized by an electric field E acting over a distance L: (1) the spectrum extends to a cutoff frequency (h) over bar omega(c)/mc(2) approximate to L(E/E(Schw))(2)/(lambda) over bar (C), where E(Schw) = 1.3 x 10(18) V m(-1) is the Schwinger critical field and (lambda) over bar (C) = (h) over bar /mc = 3.86 x 10(-13) m is the Compton wavelength of the electron, (2) the total energy emitted by a particle traversing the accelerator is 4/3 alpha(f)(h) over bar omega(c) in accordance with the standard Larmor formula where alpha(f) is the fine-structure constant, and (3) the low frequency spectrum is flat for hyperbolic trajectories, but in general depends on the details of the accelerator. We also show that linear acceleration emission complements curvature radiation in the strongly magnetized pair formation regions in pulsar magnetospheres. It dominates when the length L of the accelerator is less than the formation length rho/gamma of curvature photons, where rho is the radius of curvature of the magnetic field lines and gamma the Lorentz factor of the emitting particle. In standard static models of pair creating regions linear acceleration emission is negligible, but it is important in more realistic dynamical models in which the accelerating field fluctuates on a short length scale.

The transport of cosmic rays in self-excited magnetic turbulence

The process of diffusive shock acceleration relies on the efficacy with which hydromagnetic waves can scatter charged particles in the precursor of a shock. The growth of self-generated waves is driven by both resonant and non-resonant processes. We perform high-resolution magnetohydrodynamic simulations of the non-resonant cosmic ray driven instability, in which the unstable waves are excited beyond the linear regime. In a snapshot of the resultant field, particle transport simulations are carried out. The use of a static snapshot of the field is reasonable given that the Larmor period for particles is typically very short relative to the instability growth time. The diffusion rate is found to be close to, or below, the Bohm limit for a range of energies. This provides the first explicit demonstration that self-excited turbulence reduces the diffusion coefficient and has important implications for cosmic-ray transport and acceleration in supernova remnants.