Reproducible and User-Controlled Software Environments in HPC with Guix

Support teams of high-performance computing (HPC) systems often find themselves between a rock and a hard place: on one hand, they understandably administrate these large systems in a conservative way, but on the other hand, they try to satisfy their users by deploying up-to-date tool chains as well as libraries and scientific software. HPC system users often have no guarantee that they will be able to reproduce results at a later point in time, even on the same system-software may have been upgraded, removed, or recompiled under their feet, and they have little hope of being able to reproduce the same software environment elsewhere. We present GNU Guix and the functional package management paradigm and show how it can improve reproducibility and sharing among researchers with representative use cases.Comment: 2nd International Workshop on Reproducibility in Parallel Computing (RepPar), Aug 2015, Vienne, Austria. http://reppar.org

DEEP: a provenance-aware executable document system

The concept of executable documents is attracting growing interest from both academics and publishers since it is a promising technology for the dissemination of scientific results. Provenance is a kind of metadata that provides a rich description of the derivation history of data products starting from their original sources. It has been used in many different e-Science domains and has shown great potential in enabling reproducibility of scientific results. However, while both executable documents and provenance are aimed at enhancing the dissemination of scientific results, little has been done to explore the integration of both techniques. In this paper, we introduce the design and development of DEEP, an executable document environment that generates scientific results dynamically and interactively, and also records the provenance for these results in the document. In this system, provenance is exposed to users via an interface that provides them with an alternative way of navigating the executable document. In addition, we make use of the provenance to offer a document rollback facility to users and help to manage the system's dynamic resources

Full counting statistics of strongly non-Ohmic transport through single molecules

We study analytically the full counting statistics of charge transport through single molecules, strongly coupled to a weakly damped vibrational mode. The specifics of transport in this regime - a hierarchical sequence of avalanches of transferred charges, interrupted by "quiet" periods - make the counting statistics strongly non-Gaussian. We support our findings for the counting statistics as well as for the frequency-dependent noise power by numerical simulations, finding excellent agreement.Comment: 4+ pages, 2 figures; minor changes, version published in Phys. Rev. Let

Quasi-localization and quasi-mobility edge for light atoms mixed with heavy ones

A mixture of light and heavy atoms is considered. We study the kinetics of the light atoms, scattered by the heavy ones, the latter undergoing slow diffusive motion. In three-dimensional space we claim the existence of a crossover region (in energy), which separates the states of the light atoms with fast diffusion and the states with slow diffusion; the latter is determined by the dephasing time. For the two dimensional case we have a transition between weak localization, observed when the dephasing length is less than the localization length (calculated for static scatterers), and strong localization observed in the opposite case.Comment: LaTeX, 5 pages, 3 figures. The manuscript has been changed following the Referees' constructive criticism and is accepted for publication in EPJ

Quantum noise in current biased Josephson junction

Quantum fluctuations in a current biased Josephson junction, described in terms of the RCSJ-model, are considered. The fluctuations of the voltage and phase across the junction are assumed to be initiated by equilibrium current fluctuations in the shunting resistor. This corresponds to low enough temperatures, when fluctuations of the normal current in the junction itself can be neglected. We used the quantum Langevin equation in terms of random variables related to the limit cycle of the nonlinear Josephson oscillator. This allows to go beyond the perturbation theory and calculate the widths of the Josephson radiation lines

The effect of sampling effort and methodology on range size estimates of poorly-recorded species for IUCN Red List assessments

Geographic range size is the most commonly implemented criterion of species’ extinction risk used in IUCN Red List assessments, especially for poorly-recorded species. IUCN applies two contrasting range size measures to capture different facets of a species’ distribution: Extent of Occurrence (EOO; Criterion B1) is the area bounding all known occurrences and is a proxy for the spatial autocorrelation of risk, while the Area of Occupancy (AOO; Criterion B2) is the area occupied within this boundary and is related to population size at finer grains. Various methods have been proposed to measure both EOO and AOO. We evaluate the impact of applying four methods for each of Criterion B1 and of B2, as well as key parameter choices, on the Red List status of 227 poorly-recorded neotropical pteridophyte species. Between 2 and 100% of species would be considered threatened depending on methodology. The minimum convex polygon method of estimating EOO was relatively robust to sampling effort for all but the least-recorded species. The IUCN-recommended method for estimating AOO of summing occupied 2 × 2 km grid cells was very strongly correlated with the total number of records. It is likely that only a small fraction of species can be adequately assessed using this method, and we recommend caution applying the method to poorly-recorded species in particular, where models predicting occupancy in unsampled areas (e.g. species distribution models) may provide more accurate assessments. It is vital that methodological information is retained with assessments, and comparisons should only be made between assessments utilising equivalent methods

Spin effects in Bose-Glass phases

We study the mechanism of formation of Bose glass (BG) phases in the spin-1 Bose Hubbard model when diagonal disorder is introduced. To this aim, we analyze first the phase diagram in the zero-hopping limit, there disorder induces superposition between Mott insulator (MI) phases with different filling numbers. Then BG appears as a compressible but still insulating phase. The phase diagram for finite hopping is also calculated with the Gutzwiller approximation. The bosons' spin degree of freedom introduces another scattering channel in the two-body interaction modifying the stability of MI regions with respect to the action of disorder. This leads to some peculiar phenomena such as the creation of BG of singlets, for very strong spin correlation, or the disappearance of BG phase in some particular cases where fluctuations are not able to mix different MI regions

Decoherence in Disordered Conductors at Low Temperatures, the effect of Soft Local Excitations

The conduction electrons' dephasing rate, $\tau_{\phi}^{-1}$, is expected to vanish with the temperature. A very intriguing apparent saturation of this dephasing rate in several systems was recently reported at very low temperatures. The suggestion that this represents dephasing by zero-point fluctuations has generated both theoretical and experimental controversies. We start by proving that the dephasing rate must vanish at the $T\to 0$ limit, unless a large ground state degeneracy exists. This thermodynamic proof includes most systems of relevance and it is valid for any determination of $\tau_{\phi}$ from {\em linear} transport measurements. In fact, our experiments demonstrate unequivocally that indeed when strictly linear transport is used, the apparent low-temperature saturation of $\tau_{\phi}$ is eliminated. However, the conditions to be in the linear transport regime are more strict than hitherto expected. Another novel result of the experiments is that introducing heavy nonmagnetic impurities (gold) in our samples produces, even in linear transport, a shoulder in the dephasing rate at very low temperatures. We then show theoretically that low-lying local defects may produce a relatively large dephasing rate at low temperatures. However, as expected, this rate in fact vanishes when $T \to 0$, in agreement with our experimental observations.Comment: To appear in the proceedings of the Euresco Conference on Fundamental Problems of Mesoscopic Physics, Granada, September 2003, Kluwe

Relative and Absolute Risk to Guide the Management of Pulse Pressure, an Age-Related Cardiovascular Risk Factor

BACKGROUND Pulse pressure (PP) reflects the age-related stiffening of the central arteries, but no study addressed the management of the PP-related risk over the human lifespan. METHODS In 4663 young (18-49 years) and 7185 older adults (≥50 years), brachial PP was recorded over 24-hour. Total mortality and all major cardiovascular events combined (MACE) were co-primary endpoints. Cardiovascular death, coronary events and stroke were secondary endpoints. RESULTS In young adults (median follow-up, 14.1 years; mean PP, 45.1 mmHg), greater PP was not associated with absolute risk; the endpoint rates were ≤2.01 per 1000 person-years. The adjusted hazard ratios expressed per 10-mmHg PP increments were less than unity (P≤0.027) for MACE (0.67; 95% CI, 0.47-0.96) and cardiovascular death (0.33; 95% CI, 0.11-0.75). In older adults (median follow-up, 13.1 years; mean PP, 52.7 mmHg), the endpoint rates, expressing absolute risk, ranged from 22.5 to 45.4 per 1000 person-years and the adjusted hazard ratios, reflecting relative risk, from 1.09 to 1.54 (P3-fold from age 55 to 75 years, whereas absolute risk rose by a factor 3. CONCLUSIONS From 50 years onwards, the PP-related relative risk decreases, whereas absolute risk increases. From a lifecourse perspective, young adulthood provides a window of opportunity to manage risk factors and prevent target organ damage as forerunner of premature death and MACE. In older adults, treatment should address absolute risk, thereby extending life in years and qualit