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

Optical isolator for TE polarized light realized by adhesive bonding of Ce:YIG on silicon-on-insulator waveguide circuits

An optical isolator for transverse electric (TE) polarized light is demonstrated by adhesive bonding of a ferrimagnetic garnet die on top of a 380 nm thick silicon waveguide circuit. Polarization rotators are implemented in the arms of a nonreciprocal Mach-Zehnder interferometer to rotate the polarization to transverse magnetic in the nonreciprocal phase shifter regions. Calculation of the nonreciprocal phase shift (NRPS) as a function of bonding layer thickness experienced by the TM mode in the interferometer arms is presented, together with the simulation of the robustness of the polarization rotator. Experimentally, 32 dB isolation is measured at 1540.5 nm wavelength using a magnetic field transverse to the light propagation directions. This paves the way to the cointegration of laser diodes and optical isolators on a silicon photonics platform

Characterization of Mg2+ efflux from human, rat and chicken erythrocytes

AbstractNet Mg2+ efflux from Mg2+-loaded human, rat and chicken erythrocytes was measured in sucrose, NaCl and choline Cl medium. Thus, Na+-dependent (NaCl minus choline Cl) and Na+-independent Mg2+ efflux (in sucrose) were determined. Na+-dependent Mg2+ efflux amounted to 0.16, 8.9 and 1.57 mmol/l cells × 30 min, Na+-independent Mg2+ efflux amounted to 0.89, 1.55 and 0.37 mmol/l cells × 30 min for human, rat and chicken erythrocytes. Na+-dependent Mg2+ efflux was inhibited by quinidine. Na+-independent Mg2+ efflux was inhibited by SITS and Cl−. A small fraction of Na+-independent Mg2+ efflux (in choline Cl) was resistant to SITS and Cl−. Ca2+ loading increased Mg2+ efflux similar to K+ efflux (Gardos effect). This effect was differently expressed in human and chicken erythrocytes

Spectral induced polarization measurements for predicting the hydraulic conductivity in sandy aquifers

Field and laboratory spectral induced polarization (SIP) measurements are integrated to characterize the hydrogeological conditions at the Schillerslage test site in Germany. The phase images are capable of monitoring thin peat layers within the sandy aquifers. However, the field results show limitations of decreasing resolution with depth. In comparison with the field inversion results, the SIP laboratory measurements show a certain shift in SIP response due to different compaction and sorting of the samples. The SIP data are analyzed to derive an empirical relationship for predicting the hydraulic conductivity (K). In particular, two significant but weak correlations between individual real resistivities (ρ') and relaxation times (τ), based on a Debye decomposition (DD) model, with measured K are found for the upper groundwater aquifer. The maximum relaxation time (τmax) and logarithmically weighted average relaxation time (τlw) show a better relation with K values than the median value τ50. A combined power law relation between individual ρ' and τ with K is developed with an expression of A · (ρ')B · (τlw)C, where A, B and C are determined using a least-squares fit between the measured and predicted K. The suggested approach with the calculated coefficients of the first aquifer is applied for the second. Results show good correlation with the measured K indicating that the derived relationship is superior to single phase angle models as Börner or Slater models

Substrate rigidity deforms and polarizes active gels

We present a continuum model of the coupling between cells and substrate that accounts for some of the observed substrate-stiffness dependence of cell properties. The cell is modeled as an elastic active gel, adapting recently developed continuum theories of active viscoelastic fluids. The coupling to the substrate enters as a boundary condition that relates the cell's deformation field to local stress gradients. In the presence of activity, the coupling to the substrate yields spatially inhomogeneous contractile stresses and deformations in the cell and can enhance polarization, breaking the cell's front-rear symmetry.Comment: 6 pages, 4 figures, EPL forma

Bouncing inflation in nonlinear R2+R4R^2+R^4 gravitational model

We study a gravitational model with curvature-squared $R^2$ and curvature-quartic $R^4$ nonlinearities. The effective scalar degree of freedom $\phi$ (scalaron) has a multi-valued potential $U(\phi)$ consisting of a number of branches. These branches are fitted with each other in the branching and monotonic points. In the case of four-dimensional space-time, we show that the monotonic points are penetrable for scalaron while in the vicinity of the branching points scalaron has the bouncing behavior and cannot cross these points. Moreover, there are branching points where scalaron bounces an infinite number of times with decreasing amplitude and the Universe asymptotically approaches the de Sitter stage. Such accelerating behavior we call bouncing inflation. For this accelerating expansion there is no need for original potential $U(\phi)$ to have a minimum or to check the slow-roll conditions. A necessary condition for such inflation is the existence of the branching points. This is a new type of inflation. We show that bouncing inflation takes place both in the Einstein and Brans-Dicke frames.Comment: RevTex 13 pages, 13 figures, a few comments and references adde

Hydraulic properties at the North Sea island of Borkum derived from joint inversion of magnetic resonance and electrical resistivity soundings

For reliably predicting the impact of climate changes on salt/freshwater systems below barrier islands, a long-term hydraulic modelling is inevitable. As input we need the parameters porosity, salinity and hydraulic conductivity at the catchment scale, preferably non-invasively acquired with geophysical methods. We present a methodology to retrieve the searched parameters and a lithological interpretation by the joint analysis of magnetic resonance soundings (MRS) and vertical electric soundings (VES). Both data sets are jointly inverted for resistivity, water content and decay time using a joint inversion scheme. Coupling is accomplished by common layer thicknesses. <br><br> We show the results of three soundings measured on the eastern part of the North Sea island of Borkum. Pumping test data is used to calibrate the petrophysical relationship for the local conditions in order to estimate permeability from nuclear magnetic resonance (NMR) data. Salinity is retrieved from water content and resistivity using a modified Archie equation calibrated by local samples. As a result we are able to predict porosity, salinity and hydraulic conductivities of the aquifers, including their uncertainties. <br><br> The joint inversion significantly improves the reliability of the results. Verification is given by comparison with a borehole. A sounding in the flooding area demonstrates that only the combined inversion provides a correct subsurface model. Thanks to the joint application, we are able to distinguish fluid conductivity from lithology and provide reliable hydraulic parameters as shown by uncertainty analysis. <br><br> These findings can finally be used to build groundwater flow models for simulating climate changes. This includes the improved geometry and lithological attribution, and also the parameters and their uncertainties

Hydraulic properties at the North Sea island of Borkum derived from joint inversion of magnetic resonance and electrical resistivity soundings

For reliably predicting the impact of climate changes on salt/freshwater systems below barrier islands, a long-term hydraulic modelling is inevitable. As input we need the parameters porosity, salinity and hydraulic conductivity at the catchment scale, preferably non-invasively acquired with geophysical methods. We present a methodology to retrieve the searched parameters and a lithological interpretation by the joint analysis of magnetic resonance soundings (MRS) and vertical electric soundings (VES). Both data sets are jointly inverted for resistivity, water content and decay time using a joint inversion scheme. Coupling is accomplished by common layer thicknesses. We show the results of three soundings measured on the eastern part of the North Sea island of Borkum. Pumping test data is used to calibrate the petrophysical relationship for the local conditions in order to estimate permeability from nuclear magnetic resonance (NMR) data. Salinity is retrieved from water content and resistivity using a modified Archie equation calibrated by local samples. As a result we are able to predict porosity, salinity and hydraulic conductivities of the aquifers, including their uncertainties. The joint inversion significantly improves the reliability of the results. Verification is given by comparison with a borehole. A sounding in the flooding area demonstrates that only the combined inversion provides a correct subsurface model. Thanks to the joint application, we are able to distinguish fluid conductivity from lithology and provide reliable hydraulic parameters as shown by uncertainty analysis. These findings can finally be used to build groundwater flow models for simulating climate changes. This includes the improved geometry and lithological attribution, and also the parameters and their uncertainties. © Author(s) 2012