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

Sulfur cycling in freshwater sediments

Organic sulfur containing compounds represent greater than 80% of the total sulfur in sediments of eutrophic freshwater lakes. Although sedimentary sulfur is predominantly in the form of organic compounds, more sulfur is transformed by sulfate reduction than by any other process. Rates of sulfate reduction in these sediments average 7 mmol/sq m/day. This rate is 19 times greater than the net rate of production of inorganic sulfur from organic compounds on an annual basis

Isochoric, isobaric and ultrafast conductivities of aluminum, lithium and carbon in the warm dense matter (WDM) regime

We study the conductivities $\sigma$ of (i) the equilibrium isochoric state ($\sigma_{\rm is}$), (ii) the equilibrium isobaric state ($\sigma_{\rm ib}$), and also the (iii) non-equilibrium ultrafast matter (UFM) state ($\sigma_{\rm uf}$) with the ion temperature $T_i$ less than the the electron temperature $T_e$. Aluminum, lithium and carbon are considered, being increasingly complex warm dense matter (WDM) systems, with carbon having transient covalent bonds. First-principles calculations, i.e., neutral-pseudoatom (NPA) calculations and density-functional theory (DFT) with molecular-dynamics (MD) simulations, are compared where possible with experimental data to characterize $\sigma_{\rm ic}, \sigma_{\rm ib}$ and $\sigma_{\rm uf}$. The NPA $\sigma_{\rm ib}$ are closest to the available experimental data when compared to results from DFT+MD, where simulations of about 64-125 atoms are typically used. The published conductivities for Li are reviewed and the value at a temperature of 4.5 eV is examined using supporting X-ray Thomson scattering calculations. A physical picture of the variations of $\sigma$ with temperature and density applicable to these materials is given. The insensitivity of $\sigma$ to $T_e$ below 10 eV for carbon, compared to Al and Li, is clarified.Comment: 10 figure

Two-temperature pair potentials and phonon spectra for simple metals in the warm dense matter regime

We develop ion-ion pair potentials for Al, Na and K for densities and temperatures relevant to the warm-dense-matter (WDM) regime. Furthermore, we emphasize non-equilibrium states where the ion temperature $T_i$ differs from the electron temperature $T_e$. This work focuses mainly on ultra-fast laser-metal interactions where the energy of the laser is almost exclusively transferred to the electron sub-system over femtosecond time scales. This results in a two-temperature system with $T_e>T_i$ and with the ions still at the initial room temperature $T_i=T_r$. First-principles calculations, such as density functional theory (DFT) or quantum Monte Carlo, are as yet not fully feasible for WDM conditions due to lack of finite-$T$ features, e.g. pseudopotentials, and extensive CPU time requirements. Simpler methods are needed to study these highly complex systems. We propose to use two-temperature pair potentials $U_{ii}(r, T_i,T_e)$ constructed from linear-response theory using the non-linear electron density $n(\mathbf{r})$ obtained from finite-$T$ DFT with a single ion immersed in the appropriate electron fluid. We compute equilibrium phonon spectra at $T_r$ which are found to be in very good agreement with experiments. This gives credibility to our non-equilibrium phonon dispersion relations which are important in determining thermophysical properties, stability, energy-relaxation mechanisms and transport coefficients.Comment: International Conf. on Strongly-Coupled Coulombo Systems (SCCS) 201

Modelling the atomic structure of very high-density amorphous ice

The structure of very high-density amorphous (VHDA) ice has been modelled by positionally disordering three crystalline phases, namely ice IV, VI and XII. These phases were chosen because only they are stable or metastable in the region of the ice phase diagram where VHDA ice is formed, and their densities are comparable to that of VHDA ice. An excellent fit to the medium range of the experimentally observed pair-correlation function g(r) of VHDA ice was obtained by introducing disorder into the positions of the H2O molecules, as well as small amounts of molecular rotational disorder, disorder in the O--H bond lengths and disorder in the H--O--H bond angles. The low-k behaviour of the experimental structure factor, S(k), is also very well reproduced by this disordered-crystal model. The fraction of each phase present in the best-fit disordered model is very close to that observed in the probable crystallization products of VHDA ice. In particular, only negligible amounts of ice IV are predicted, in accordance with experimental observation.Comment: 4 pages, 3 figures, 1 table, v2: changes made in response to referees' comments, the justification for using certain ice phases is improved, and ice IV is now disordered as wel

Assessment of deep cryogenic heat-treatment impact on the microstructure and surface chemistry of austenitic stainless steel

This systematic study deals with the influence of deep cryogenic treatment (DCT) on microstructure and surface properties of austenitic stainless steel AISI 304 L on different length scales and in the surface region. The study incorporates different analysis techniques, such as light microscopy, scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), electron backscatter diffraction (EBSD), high-resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ions mass spectrometry (ToF-SIMS). DCT modifies the microstructure of treated samples through promoted precipitation of Cr7C3 carbides, induced twinning and α-martensite formation. Additionally, XPS/AR-XPS and ToF-SIMS results also provide evidence of modified oxidation dynamics of DCT samples compared to conventionally heat-treated samples with increase of the Fe-oxide fraction and lower Cr-oxide fraction in the surface oxide layer. An evaluation of oxidation states and ions distribution within the surface layer of deep cryogenically heat-treated stainless steel AISI 304 L is conducted with XPS/ToF-SIMS. These results are correlated with the microstructural changes and nitrogen diffusivity induced by DCT, which are associated with modified oxidation behaviour of AISI 304 L. These results provide further understanding of DCT dynamic on the overall microstructure and the corresponding surface behaviour

Sulfur reduction in sediments of marine and evaporite environments

Transformations of sulfur in sediments of ponds ranging in salinities from that of normal seawater to those of brines saturated with sodium chloride were examined. The chemistry of the sediment and pore waters were focused on with emphasis on the fate of sulfate reduction. The effects of increasing salinity on both forms of sulfur and microbial activity were determined. A unique set of chemical profiles and sulfate-reducing activity was found for the sediments of each of the sites examined. The quantity of organic matter in the salt pond sediments was significantly greater than that occurring in the adjacent intertidal site. The total quantitative and qualitative distribution of volatile fatty acids was also greater in the salt ponds. Volatile fatty acids increased with salinity