External Memory Pipelining Made Easy With TPIE

When handling large datasets that exceed the capacity of the main memory, movement of data between main memory and external memory (disk), rather than actual (CPU) computation time, is often the bottleneck in the computation. Since data is moved between disk and main memory in large contiguous blocks, this has led to the development of a large number of I/O-efficient algorithms that minimize the number of such block movements. TPIE is one of two major libraries that have been developed to support I/O-efficient algorithm implementations. TPIE provides an interface where list stream processing and sorting can be implemented in a simple and modular way without having to worry about memory management or block movement. However, if care is not taken, such streaming-based implementations can lead to practically inefficient algorithms since lists of data items are typically written to (and read from) disk between components. In this paper we present a major extension of the TPIE library that includes a pipelining framework that allows for practically efficient streaming-based implementations while minimizing I/O-overhead between streaming components. The framework pipelines streaming components to avoid I/Os between components, that is, it processes several components simultaneously while passing output from one component directly to the input of the next component in main memory. TPIE automatically determines which components to pipeline and performs the required main memory management, and the extension also includes support for parallelization of internal memory computation and progress tracking across an entire application. The extended library has already been used to evaluate I/O-efficient algorithms in the research literature and is heavily used in I/O-efficient commercial terrain processing applications by the Danish startup SCALGO

RAM-Efficient External Memory Sorting

In recent years a large number of problems have been considered in external memory models of computation, where the complexity measure is the number of blocks of data that are moved between slow external memory and fast internal memory (also called I/Os). In practice, however, internal memory time often dominates the total running time once I/O-efficiency has been obtained. In this paper we study algorithms for fundamental problems that are simultaneously I/O-efficient and internal memory efficient in the RAM model of computation.Comment: To appear in Proceedings of ISAAC 2013, getting the Best Paper Awar

Maintaining Contour Trees of Dynamic Terrains

We consider maintaining the contour tree $\mathbb{T}$ of a piecewise-linear triangulation $\mathbb{M}$ that is the graph of a time varying height function $h: \mathbb{R}^2 \rightarrow \mathbb{R}$. We carefully describe the combinatorial change in $\mathbb{T}$ that happen as $h$ varies over time and how these changes relate to topological changes in $\mathbb{M}$. We present a kinetic data structure that maintains the contour tree of $h$ over time. Our data structure maintains certificates that fail only when $h(v)=h(u)$ for two adjacent vertices $v$ and $u$ in $\mathbb{M}$, or when two saddle vertices lie on the same contour of $\mathbb{M}$. A certificate failure is handled in $O(\log(n))$ time. We also show how our data structure can be extended to handle a set of general update operations on $\mathbb{M}$ and how it can be applied to maintain topological persistence pairs of time varying functions

WH-questions in Estonian fathers’ child-directed speech with their 3 year-old children and their relation to children’s language development – pilot study

Uuringud on näidanud, et isa hoidjakeele komponendid ning täpsemalt just avatud küsimused võivad lapse kõne arengule soodustavalt mõjuda. Käesolevas pilootprojektis uuriti 8–perelises (16 lapsevanemat ja 8 3-aastast last) valimis 10-minutiliste vabamängu vestluste transkribeeringute põhjal seoseid isade hoidjakeele ning lapse kõne arengu (mõõdetud Reynell IV testi ning keskmise lausungi pikkusega [MLU]) vahel. Samuti võrreldi isade ja emade hoidjakeele komponente. Uuringuga leiti, et isade ja emade vahel statistiliselt olulisi erinevusi ei esinenud. Isade MLU ja avatud küsimuste osakaal küsimuste koguarvus seletasid osa Reynelli testi varieeruvusest. Kuigi isade avatud küsimuste osakaalu ning lapse kõne arengu näitajate vahel olulist korrelatsiooni ei esinenud, ennustas isade kõikide küsimuste osakaal lausungite koguarvus lapse MLUd isaga vestlemisel. Pilootuuringu põhjal soovitatakse edaspidistesse uurimustesse kaasata rohkem peresid ning uurida täpsemalt vanemate MLUde ning küsimuste seoseid laste keeletesti tulemustega

An event-based approach to validating solar wind speed predictions: high-speed enhancements in the Wang-Sheeley-Arge model

One of the primary goals of the Center for Integrated Space Weather Modeling (CISM) effort is to assess and improve prediction of the solar wind conditions in near‐Earth space, arising from both quasi‐steady and transient structures. We compare 8 years of L1 in situ observations to predictions of the solar wind speed made by the Wang‐Sheeley‐Arge (WSA) empirical model. The mean‐square error (MSE) between the observed and model predictions is used to reach a number of useful conclusions: there is no systematic lag in the WSA predictions, the MSE is found to be highest at solar minimum and lowest during the rise to solar maximum, and the optimal lead time for 1 AU solar wind speed predictions is found to be 3 days. However, MSE is shown to frequently be an inadequate “figure of merit” for assessing solar wind speed predictions. A complementary, event‐based analysis technique is developed in which high‐speed enhancements (HSEs) are systematically selected and associated from observed and model time series. WSA model is validated using comparisons of the number of hit, missed, and false HSEs, along with the timing and speed magnitude errors between the forecasted and observed events. Morphological differences between the different HSE populations are investigated to aid interpretation of the results and improvements to the model. Finally, by defining discrete events in the time series, model predictions from above and below the ecliptic plane can be used to estimate an uncertainty in the predicted HSE arrival times

The radial evolution of solar wind speeds

The WSA-ENLIL model predicts significant evolution of the solar wind speed. Along a flux tube the solar wind speed at 1.0 AU and beyond is found to be significantly altered from the solar wind speed in the outer corona at 0.1 AU, with most of the change occurring within a few tenths of an AU from the Sun. The evolution of the solar wind speed is most pronounced during solar minimum for solar wind with observed speeds at 1.0 AU between 400 and 500 km/s, while the fastest and slowest solar wind experiences little acceleration or deceleration. Solar wind ionic charge state observations made near 1.0 AU during solar minimum are found to be consistent with a large fraction of the intermediate-speed solar wind having been accelerated or decelerated from slower or faster speeds. This paper sets the groundwork for understanding the evolution of wind speed with distance, which is critical for interpreting the solar wind composition observations near Earth and throughout the inner heliosphere. We show from composition observations that the intermediate-speed solar wind (400-500 km/s) represents a mix of what was originally fast and slow solar wind, which implies a more bimodal solar wind in the corona than observed at 1.0 AU