Best practices for HPM-assisted performance engineering on modern multicore processors

Many tools and libraries employ hardware performance monitoring (HPM) on modern processors, and using this data for performance assessment and as a starting point for code optimizations is very popular. However, such data is only useful if it is interpreted with care, and if the right metrics are chosen for the right purpose. We demonstrate the sensible use of hardware performance counters in the context of a structured performance engineering approach for applications in computational science. Typical performance patterns and their respective metric signatures are defined, and some of them are illustrated using case studies. Although these generic concepts do not depend on specific tools or environments, we restrict ourselves to modern x86-based multicore processors and use the likwid-perfctr tool under the Linux OS.Comment: 10 pages, 2 figure

Editorial: Exercise as a Countermeasure to Human Aging, Volume II

Tis impossible to be sure of anything but death and taxes (Christopher Bullock in the Cobbler of Preston, 1716). We are inclined to agree with Bullock concerning the certainly of death and in this context, aging is ubiquitous amongst humans which results in a deterioration of physiological function and an inevitable march towards death. However, physical activity and exercise are known to exert positive effects on health and wider physiological function via multiple complex and interacting mechanisms (that have not yet been completely defined). In volume II of this Research Topic, 10 articles covered the interplay between exercise and aging, utilizing approaches that spanned molecular, physiological, and population scale approaches, in both healthy older populations and certain disease subsets. This work builds on our previous work Exercise as a Countermeasure to Human Aging, Volume I and it is a pleasure to note continued progress in this field, and the range of methodological approaches authors have used

Radiative transfer modelling of parsec-scale dusty warped discs

Warped discs have been found on (sub-)parsec scale in some nearby Seyfert nuclei, identified by their maser emission. Using dust radiative transfer simulations we explore their observational signatures in the infrared in order to find out whether they can partly replace the molecular torus. Strong variations of the brightness distributions are found, depending on the orientation of the warp with respect to the line of sight. Whereas images at short wavelengths typically show a disc-like and a point source component, the warp itself only becomes visible at far-infrared wavelengths. A similar variety is visible in the shapes of the spectral energy distributions. Especially for close to edge-on views, the models show silicate feature strengths ranging from deep absorption to strong emission for variations of the lines of sight towards the warp. To test the applicability of our model, we use the case of the Circinus galaxy, where infrared interferometry has revealed a highly elongated emission component matching a warped maser disc in orientation and size. Our model is for the first time able to present a physical explanation for the observed dust morphology as coming from the AGN heated dust. As opposed to available torus models, a warped disc morphology produces a variety of silicate feature shapes for grazing lines of sight, close to an edge-on view. This could be an attractive alternative to a claimed change of the dust composition for the case of the nearby Seyfert 2 galaxy NGC 1068, which harbours a warped maser disc as well.Comment: accepted by MNRA

The life cycle of starbursting circumnuclear gas discs

High-resolution observations from the sub-mm to the optical wavelength regime resolve the central few 100pc region of nearby galaxies in great detail. They reveal a large diversity of features: thick gas and stellar discs, nuclear starbursts, in- and outflows, central activity, jet interaction, etc. Concentrating on the role circumnuclear discs play in the life cycles of galactic nuclei, we employ 3D adaptive mesh refinement hydrodynamical simulations with the RAMSES code to self-consistently trace the evolution from a quasi-stable gas disc, undergoing gravitational (Toomre) instability, the formation of clumps and stars and the disc's subsequent, partial dispersal via stellar feedback. Our approach builds upon the observational finding that many nearby Seyfert galaxies have undergone intense nuclear starbursts in their recent past and in many nearby sources star formation is concentrated in a handful of clumps on a few 100pc distant from the galactic centre. We show that such observations can be understood as the result of gravitational instabilities in dense circumnuclear discs. By comparing these simulations to available integral field unit observations of a sample of nearby galactic nuclei, we find consistent gas and stellar masses, kinematics, star formation and outflow properties. Important ingredients in the simulations are the self-consistent treatment of star formation and the dynamical evolution of the stellar distribution as well as the modelling of a delay time distribution for the supernova feedback. The knowledge of the resulting simulated density structure and kinematics on pc scale is vital for understanding inflow and feedback processes towards galactic scales.Comment: accepted by MNRA

The dusty torus in the Circinus galaxy: a dense disk and the torus funnel

(Abridged) With infrared interferometry it is possible to resolve the nuclear dust distributions that are commonly associated with the dusty torus in active galactic nuclei (AGN). The Circinus galaxy hosts the closest Seyfert 2 nucleus and previous interferometric observations have shown that its nuclear dust emission is well resolved. To better constrain the dust morphology in this active nucleus, extensive new observations were carried out with MIDI at the Very Large Telescope Interferometer. The emission is distributed in two distinct components: a disk-like emission component with a size of ~ 0.2 $\times$ 1.1 pc and an extended component with a size of ~ 0.8 $\times$ 1.9 pc. The disk-like component is elongated along PA ~ 46{\deg} and oriented perpendicular to the ionisation cone and outflow. The extended component is elongated along PA ~ 107{\deg}, roughly perpendicular to the disk component and thus in polar direction. It is interpreted as emission from the inner funnel of an extended dust distribution and shows a strong increase in the extinction towards the south-east. We find no evidence of an increase in the temperature of the dust towards the centre. From this we infer that most of the near-infrared emission probably comes from parsec scales as well. We further argue that the disk component alone is not sufficient to provide the necessary obscuration and collimation of the ionising radiation and outflow. The material responsible for this must instead be located on scales of ~ 1 pc, surrounding the disk. The clear separation of the dust emission into a disk-like emitter and a polar elongated source will require an adaptation of our current understanding of the dust emission in AGN. The lack of any evidence of an increase in the dust temperature towards the centre poses a challenge for the picture of a centrally heated dust distribution.Comment: 30 pages, 12 figures; A&A in pres

The complexity of parsec-scaled dusty tori in AGN

Warm gas and dust surround the innermost regions of active galactic nuclei (AGN). They provide the material for accretion onto the super-massive black hole and they are held responsible for the orientation-dependent obscuration of the central engine. The AGN-heated dust distributions turn out to be very compact with sizes on scales of about a parsec in the mid-infrared. Only infrared interferometry currently provides the necessary angular resolution to directly study the physical properties of this dust. Size estimates for the dust distributions derived from interferometric observations can be used to construct a size--luminosity relation for the dust distributions. The large scatter about this relation suggests significant differences between the dust tori in the individual galaxies, even for nuclei of the same class of objects and with similar luminosities. This questions the simple picture of the same dusty doughnut in all AGN. The Circinus galaxy is the closest Seyfert 2 galaxy. Because its mid-infrared emission is well resolved interferometrically, it is a prime target for detailed studies of its nuclear dust distribution. An extensive new interferometric data set was obtained for this galaxy. It shows that the dust emission comes from a very dense, disk-like structure which is surrounded by a geometrically thick, similarly warm dust distribution as well as significant amounts of warm dust within the ionisation cone.Comment: 8 pages, 3 figures, to appear in the proceedings of the conference "The central kiloparsec in Galactic Nuclei: Astronomy at High Angular Resolution 2011", open access Journal of Physics: Conference Series (JPCS), published by IOP Publishin