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

The Epicurean Parasite: Horace, Satires 1.1-3

We have learned a great deal in recent years about reading Horace\u27s satires; there is now widespread agreement that the speaker of the satires is himself a character within them, a persona. Such a persona may be most effective when it has obvious connections with its creator, but that fact does not preclude the exaggeration of reality, or even its complete inversion. For Horace the implications of this approach are exciting: instead of a poet discoursing with cheerful earnestness on morality, on poetry and on his daily life, we have a fictional character, whom we do not have to take seriously at all.The three diatribe satires present us with a character so absurd that they have been taken, I think rightly, as parodies. Although the poems were once appreciated as effective moralising sermons, even their admirers found it hard to justify the lack of intellectual coherence, to say nothing of the astonishing vulgarity of the second satire. As parodies, however, the poems are wonderfully successful. The speaker trots out a series of banalities: ‘people should be content with who they are’; ‘people should not go to extremes’; ‘people should be consistent’. But he invariably gets distracted, goes off on tangential rants, and makes a fool of himself. The moralist of the first three satires is, to put it bluntly, a jerk

Touring as a Peircean habit

The Peircean sign contains three parts: object, representamen (image) and interpretant (interpretation). Interpretation in the Peircean system draws heavily upon the accumulated knowledge that an individual has built up over time. Interpretation might be thoughtful, but more often it is an embodied habit. The Peircean notion of habit inherently relates to the performative and is sufficiently general to incorporate emotionality

A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals

AbstractCells perceive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate particular phenotypic responses. Here, we employ both single and mixed cell type populations, pre-programmed with engineered modular cell signalling and sensing circuits, as processing units to detect and integrate multiple environmental signals. Based on an engineered modular genetic AND logic gate, we report the construction of a set of scalable synthetic microbe-based biosensors comprising exchangeable sensory, signal processing and actuation modules. These cellular biosensors were engineered using distinct signalling sensory modules to precisely identify various chemical signals, and combinations thereof, with a quantitative fluorescent output. The genetic logic gate used can function as a biological filter and an amplifier to enhance the sensing selectivity and sensitivity of cell-based biosensors. In particular, an Escherichia coli consortium-based biosensor has been constructed that can detect and integrate three environmental signals (arsenic, mercury and copper ion levels) via either its native two-component signal transduction pathways or synthetic signalling sensors derived from other bacteria in combination with a cell-cell communication module. We demonstrate how a modular cell-based biosensor can be engineered predictably using exchangeable synthetic gene circuit modules to sense and integrate multiple-input signals. This study illustrates some of the key practical design principles required for the future application of these biosensors in broad environmental and healthcare areas

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

Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020

The inaugural “Microbiome for Mars” virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duration human space travel. The conference focused on surveying current microbiome research, future endeavors, and how this growing field could broadly impact human health and space exploration. This report summarizes each speaker’s presentation in the order presented at the workshop

ParaHaplo 2.0: a program package for haplotype-estimation and haplotype-based whole-genome association study using parallel computing

<p>Abstract</p> <p>Background</p> <p>The use of haplotype-based association tests can improve the power of genome-wide association studies. Since the observed genotypes are unordered pairs of alleles, haplotype phase must be inferred. However, estimating haplotype phase is time consuming. When millions of single-nucleotide polymorphisms (SNPs) are analyzed in genome-wide association study, faster methods for haplotype estimation are required.</p> <p>Methods</p> <p>We developed a program package for parallel computation of haplotype estimation. Our program package, ParaHaplo 2.0, is intended for use in workstation clusters using the Intel Message Passing Interface (MPI). We compared the performance of our algorithm to that of the regular permutation test on both Japanese in Tokyo, Japan and Han Chinese in Beijing, China of the HapMap dataset.</p> <p>Results</p> <p>Parallel version of ParaHaplo 2.0 can estimate haplotypes 100 times faster than a non-parallel version of the ParaHaplo.</p> <p>Conclusion</p> <p>ParaHaplo 2.0 is an invaluable tool for conducting haplotype-based genome-wide association studies (GWAS). The need for fast haplotype estimation using parallel computing will become increasingly important as the data sizes of such projects continue to increase. The executable binaries and program sources of ParaHaplo are available at the following address: <url>http://en.sourceforge.jp/projects/parallelgwas/releases/</url></p