Blocked All-Pairs Shortest Paths Algorithm on Intel Xeon Phi KNL Processor: A Case Study

Manycores are consolidating in HPC community as a way of improving performance while keeping power efficiency. Knights Landing is the recently released second generation of Intel Xeon Phi architecture. While optimizing applications on CPUs, GPUs and first Xeon Phi's has been largely studied in the last years, the new features in Knights Landing processors require the revision of programming and optimization techniques for these devices. In this work, we selected the Floyd-Warshall algorithm as a representative case study of graph and memory-bound applications. Starting from the default serial version, we show how data, thread and compiler level optimizations help the parallel implementation to reach 338 GFLOPS.Comment: Computer Science - CACIC 2017. Springer Communications in Computer and Information Science, vol 79

Computing CMB Anisotropy in Compact Hyperbolic Spaces

The measurements of CMB anisotropy have opened up a window for probing the global topology of the universe on length scales comparable to and beyond the Hubble radius. For compact topologies, the two main effects on the CMB are: (1) the breaking of statistical isotropy in characteristic patterns determined by the photon geodesic structure of the manifold and (2) an infrared cutoff in the power spectrum of perturbations imposed by the finite spatial extent. We present a completely general scheme using the regularized method of images for calculating CMB anisotropy in models with nontrivial topology, and apply it to the computationally challenging compact hyperbolic topologies. This new technique eliminates the need for the difficult task of spatial eigenmode decomposition on these spaces. We estimate a Bayesian probability for a selection of models by confronting the theoretical pixel-pixel temperature correlation function with the COBE-DMR data. Our results demonstrate that strong constraints on compactness arise: if the universe is small compared to the `horizon' size, correlations appear in the maps that are irreconcilable with the observations. If the universe is of comparable size, the likelihood function is very dependent upon orientation of the manifold wrt the sky. While most orientations may be strongly ruled out, it sometimes happens that for a specific orientation the predicted correlation patterns are preferred over the conventional infinite models.Comment: 15 pages, LaTeX (IOP style included), 3 color figures (GIF) in separate files. Minor revision to match the version accepted in Class. Quantum Grav.: Proc. of Topology and Cosmology, Cleveland, 1997. The paper can be also downloaded from http://www.cita.utoronto.ca/~pogosyan/cwru_proc.ps.g

Noncyclic covers of knot complements

Hempel has shown that the fundamental groups of knot complements are residually finite. This implies that every nontrivial knot must have a finite-sheeted, noncyclic cover. We give an explicit bound, $\Phi (c)$, such that if $K$ is a nontrivial knot in the three-sphere with a diagram with $c$ crossings and a particularly simple JSJ decomposition then the complement of $K$ has a finite-sheeted, noncyclic cover with at most $\Phi (c)$ sheets.Comment: 29 pages, 8 figures, from Ph.D. thesis at Columbia University; Acknowledgments added; Content correcte

Dimension of the Torelli group for Out(F_n)

Let T_n be the kernel of the natural map from Out(F_n) to GL(n,Z). We use combinatorial Morse theory to prove that T_n has an Eilenberg-MacLane space which is (2n-4)-dimensional and that H_{2n-4}(T_n,Z) is not finitely generated (n at least 3). In particular, this recovers the result of Krstic-McCool that T_3 is not finitely presented. We also give a new proof of the fact, due to Magnus, that T_n is finitely generated.Comment: 27 pages, 9 figure

Effects of Grade Control Structures on Fish Passage, Biological Assemblages and Hydraulic Environments in Western Iowa Streams: A Multidisciplinary Review

Land use changes and channelization of streams in the deep loess region of western Iowa have led to stream channel incision, altered flow regimes, increased sediment inputs, decreased habitat diversity and reduced lateral connectivity of streams and floodplains. Grade control structures (GCSs) are built in streams to prevent further erosion, protect infrastructure and reduce sediment loads. However, GCS can have a detrimental impact on fisheries and biological communities. We review three complementary biological and hydraulic studies on the effects of GCS in these streams. GCS with steep (≥1:4 rise : run) downstream slopes severely limited fish passage, but GCS with gentle slopes (≤1:15) allowed greater passage. Fish assemblages were dominated by species tolerant of degradation, and Index of Biotic Integrity (IBI) scores were indicative of fair or poor biotic integrity. More than 50% of fish species had truncated distributions. After modification of GCS to reduce slopes and permit increased passage, IBI scores increased and several species were detected further upstream than before modification. Total macroinvertebrate density, biomass and taxonomic diversity and abundance of ecologically sensitive taxa were greater at GCS than in reaches immediately upstream, downstream or ≥1 km from GCS. A hydraulic study confirmed results from fish passage studies; minimum depths and maximum current velocities at GCS with gentle slopes (≤1:15) were more likely to meet minimum criteria for catfish passage than GCS with steeper slopes. Multidisciplinary approaches such as ours will increase understanding of GCS-associated factors influencing fish passage, biological assemblage structure and other ecological relationships in streams

Augmenting forearm crutches with wireless sensors for lower limb rehabilitation

Forearm crutches are frequently used in the rehabilitation of an injury to the lower limb. The recovery rate is improved if the patient correctly applies a certain fraction of their body weight (specified by a clinician) through the axis of the crutch, referred to as partial weight bearing (PWB). Incorrect weight bearing has been shown to result in an extended recovery period or even cause further damage to the limb. There is currently no minimally invasive tool for long-term monitoring of a patient's PWB in a home environment. This paper describes the research and development of an instrumented forearm crutch that has been developed to wirelessly and autonomously monitor a patient's weight bearing over the full period of their recovery, including its potential use in a home environment. A pair of standard forearm crutches are augmented with low-cost off-the-shelf wireless sensor nodes and electronic components to provide indicative measurements of the applied weight, crutch tilt and hand position on the grip. Data are wirelessly transmitted between crutches and to a remote computer (where they are processed and visualized in LabVIEW), and the patient receives biofeedback by means of an audible signal when they put too much or too little weight through the crutch. The initial results obtained highlight the capability of the instrumented crutch to support physiotherapists and patients in monitoring usage

High performance checksum computation for fault-tolerant MPI over InfiniBand

International audienceWith the increase of the number of nodes in clusters, the probability of failures and unusual events increases. In this paper, we present checksum mechanisms to detect data corruption. We study the impact of checksums on network communication performance and we propose a mechanism to amortize their cost on InfiniBand. We have implemented our mechanisms in the NEWMADELEINE communication library. Our evaluation shows that our mechanisms to ensure message integrity do not impact noticeably the application performance, which is an improvement over the state of the art MPI implementations

Reshaping Curriculum to Enhance the Relevance of Literary Competence in Children's Education06

Twenty-first century learners face a multi-literacy landscape as they strive to acquire the cognitive skills needed for independent learning, apply linguistic skills to other knowledge base, and become computer literate. This article envisions a combination of skill sets and knowledge bases as the foundation of a literary competence-based curriculum. Such a curriculum would have the goal of enhancing young learners"critical thinking abilities; this would also help them take charge of the cognitive,linguistic, and sociocultural dimensions of written and spoken language in order to make learning transferable and applicable to the real world

Haplotype Structure of FSHB, the Beta-Subunit Gene for Fertility-Associated Follicle-Stimulating Hormone: Possible Influence of Balancing Selection

Follicle-stimulating hormone (FSH) is essential for human reproduction. The unique functions of this hormone are provided by the FSH receptor-binding beta-subunit encoded by the FSHB gene. Resequencing and genotyping of FSHB in three European, two Asian and one African population, as well as in the great apes (chimpanzee, gorilla, orangutan), revealed low diversity and significant excess of polymorphisms with intermediate frequency alleles. Statistical tests for FSHB showed deviations from neutrality in all populations suggesting a possible effect of balancing selection. Two core haplotypes were identified (carried by 76-96.6% of each population's sample), the sequences of which are clearly separated from each other. As fertility most directly affects an organism's fitness, the carriers of these haplotypes have apparently had more success in human history to contribute to the next generation. There is a preliminary observation suggesting that the second most frequent FSHB haplotype may be associated with rapid conception success in females. Interestingly, the same haplotype is related to an ancestral FSHB variant shared with the ancestor of the great apes. The determination of the functional consequence of the two core FSHB variants may have implications for understanding and regulating human fertility, as well as in assisting infertility treatments

Blocked All-Pairs Shortest Paths Algorithm on Intel Xeon Phi KNL Processor: A Case Study

Manycores are consolidating in HPC community as a way of improving performance while keeping power efficiency. Knights Landing is the recently released second generation of Intel Xeon Phi architec- ture.While optimizing applications on CPUs, GPUs and first Xeon Phi’s has been largely studied in the last years, the new features in Knights Landing processors require the revision of programming and optimization techniques for these devices. In this work, we selected the Floyd-Warshall algorithm as a representative case study of graph and memory-bound ap- plications. Starting from the default serial version, we show how data, thread and compiler level optimizations help the parallel implementation to reach 338 GFLOPS