PopSparse: Accelerated block sparse matrix multiplication on IPU

Reducing the computational cost of running large scale neural networks using sparsity has attracted great attention in the deep learning community. While much success has been achieved in reducing FLOP and parameter counts while maintaining acceptable task performance, achieving actual speed improvements has typically been much more difficult, particularly on general purpose accelerators (GPAs) such as NVIDIA GPUs using low precision number formats. In this work we introduce PopSparse, a library that enables fast sparse operations on Graphcore IPUs by leveraging both the unique hardware characteristics of IPUs as well as any block structure defined in the data. We target two different types of sparsity: static, where the sparsity pattern is fixed at compile-time; and dynamic, where it can change each time the model is run. We present benchmark results for matrix multiplication for both of these modes on IPU with a range of block sizes, matrix sizes and densities. Results indicate that the PopSparse implementations are faster than dense matrix multiplications on IPU at a range of sparsity levels with large matrix size and block size. Furthermore, static sparsity in general outperforms dynamic sparsity. While previous work on GPAs has shown speedups only for very high sparsity (typically 99\% and above), the present work demonstrates that our static sparse implementation outperforms equivalent dense calculations in FP16 at lower sparsity (around 90%). IPU code is available to view and run at ipu.dev/sparsity-benchmarks, GPU code will be made available shortly

Dependence on Dectin-1 Varies With Multiple Candida Species

This is the final version. Available from Frontiers Media via the DOI in this recordFour Candida spp. (albicans, glabrata, tropicalis, parapsilosis) cause >95% of invasive Candida infections. C. albicans elicits immune responses via pathogen recognition receptors including C-type lectin-like receptors (CLRs). The CLR, Dectin-1 is important for host immunity to C. albicans and C. glabrata, however, whether Dectin-1 is important for host defense against C. tropicalis or C. parapsilosis is unknown. Therefore, we compared the involvement of Dectin-1 in response to these four diverse Candida spp. We found that Dectin-1 mediates innate cytokine responses to these Candida spp. in a species- and cell-dependent manner. Dectin-1 KO mice succumbed to infection with highly virulent C. albicans while they mostly survived infection with less virulent Candida spp. However, Dectin-1 KO mice displayed increased fungal burden following infection with each Candida spp. Additionally, T cells from Dectin-1 KO mice displayed enhanced effector functions likely due to the inability of Dectin-1 KO mice to clear the infections. Together, these data indicate that Dectin-1 is important for host defense to multiple Candida spp., although the specific roles for Dectin-1 varies with different Candida spp.Wellcome TrustRoyal SocietyUK Dementia Research InstituteMRC Centre for Medical Mycolog

A new route to exposed thermal mass: Sound-absorbing poured concrete

This paper investigates the novel possibility of utilising the structural concrete floor slab as a means of providing additional mid- to low-frequency sound absorption through the addition of cavities on the ceiling side, formed using flexible formwork, acting as Helmholtz resonators. Mid- to low-frequency sound absorption in rooms is typically achieved through the use of perforated plasterboard or a suspended tile-in-grid system. Such an approach can separate the room from the thermal mass of the ceiling above, leading to higher peak temperatures or increased cooling load. Suspended ceilings can also increase the embodied energy of the building and limit the potential for stack effect ventilation by reducing room height. In this work, frequency-dependent absorption coefficients of perforated concrete samples were measured using an impedance tube test. The results were found to agree with a theoretical analysis, suggesting that it would be relatively easy to predict the performance of perforations of other depths and diameters including those targeted at absorbing higher frequencies. Practical application: The measurements indicate that such a slab could be used as a practical replacement for perforated plasterboard or a tile-in-grid system. This would allow the slab to be tuned to the building’s acoustic performance and structural requirements. The approach has the potential to: (1) reduce the embodied and operational energy of buildings; (2) improve thermal comfort and (3) create a better acoustic environment in situations where surface robustness or longevity is important, for example public stairwells, pathways under roads and metro stations. </jats:p

Dependence on Mincle and Dectin-2 Varies With Multiple Candida Species During Systemic Infection

FUNDING SO was supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (Grant No. 099953/Z/12/Z) and by a Wellcome Trust Cross-Disciplinary Award. NG acknowledges Wellcome Trust support of a Senior Investigator (101873/Z/13/Z), Collaborative (200208/A/15/Z) and Strategic Awards (097377/Z11/Z) and the MRC Centre for Medical Mycology (MR/N006364/2). PT was funded by a Wellcome Trust Investigator Award (107964/Z/15/Z) and the UK Dementia Research Institute. ACKNOWLEDGMENTS We wish to acknowledge the NIH-sponsored Mutant Mouse Regional Resource Center (MMRRC) National System as the source of genetically altered mice (C57BL/6-Clec4et m1. 1C fg /Mmucd 031936-UCD) for use in this study. The mice were produced and deposited to the MMRRC by the Consortium for Functional Glycomics supported by the National Institute of General Medical Sciences (GM62116). We also thank the Microscopy and Histology Core Facility at the University of Aberdeen for expert assistance with TEM.Peer reviewedPublisher PD

Stronger or longer: Discriminating between Hawaiian and Strombolian eruption styles

The weakest explosive volcanic eruptions globally, Strombolian explosions and Hawaiian fountaining, are also the most common. Yet, despite over a hundred years of observations, no classifications have offered a convincing, quantitative way of demarcating these two styles. New observations show that the two styles are distinct in their eruptive time scale, with the duration of Hawaiian fountaining exceeding Strombolian explosions by ∼300–10,000 s. This reflects the underlying process of whether shallow-exsolved gas remains trapped in the erupting magma or is decoupled from it. We propose here a classification scheme based on the duration of events (brief explosions versus prolonged fountains) with a cutoff at 300 s that separates transient Strombolian explosions from sustained Hawaiian fountains.The authors wish to acknowledge grants from NSF (EAR-0409303, 0810332, 1145159, 1427357) and ARRA (113153 via the Hawaiian Volcano Observatory), which funded this research.This is the accepted manuscript. The final version is available at http://dx.doi.org/10.1130/G37423.

A theoretical investigation of the low lying electronic structure of poly(p-phenylene vinylene)

The two-state molecular orbital model of the one-dimensional phenyl-based semiconductors is applied to poly(p-phenylene vinylene). The energies of the low-lying excited states are calculated using the density matrix renormalization group method. Calculations of both the exciton size and the charge gap show that there are both Bu and Ag excitonic levels below the band threshold. The energy of the 1Bu exciton extrapolates to 2.60 eV in the limit of infinite polymers, while the energy of the 2Ag exciton extrapolates to 2.94 eV. The calculated binding energy of the 1Bu exciton is 0.9 eV for a 13 phenylene unit chain and 0.6 eV for an infinite polymer. This is expected to decrease due to solvation effects. The lowest triplet state is calculated to be at ca. 1.6 eV, with the triplet-triplet gap being ca. 1.6 eV. A comparison between theory, and two-photon absorption and electroabsorption is made, leading to a consistent picture of the essential states responsible for most of the third-order nonlinear optical properties. An interpretation of the experimental nonlinear optical spectroscopies suggests an energy difference of ca. 0.4 eV between the vertical energy and ca. 0.8 eV between the relaxed energy, of the 1Bu exciton and the band gap, respectively.Comment: LaTeX, 19 pages, 7 eps figures included using epsf. To appear in Physical Review B, 199

Impacts of organic and conventional crop management on diversity and activity of free-living nitrogen fixing bacteria and total bacteria are subsidiary to temporal effects

A three year field study (2007-2009) of the diversity and numbers of the total and metabolically active free-living diazotophic bacteria and total bacterial communities in organic and conventionally managed agricultural soil was conducted at the Nafferton Factorial Systems Comparison (NFSC) study, in northeast England. The result demonstrated that there was no consistent effect of either organic or conventional soil management across the three years on the diversity or quantity of either diazotrophic or total bacterial communities. However, ordination analyses carried out on data from each individual year showed that factors associated with the different fertility management measures including availability of nitrogen species, organic carbon and pH, did exert significant effects on the structure of both diazotrophic and total bacterial communities. It appeared that the dominant drivers of qualitative and quantitative changes in both communities were annual and seasonal effects. Moreover, regression analyses showed activity of both communities was significantly affected by soil temperature and climatic conditions. The diazotrophic community showed no significant change in diversity across the three years, however, the total bacterial community significantly increased in diversity year on year. Diversity was always greatest during March for both diazotrophic and total bacterial communities. Quantitative analyses using qPCR of each community indicated that metabolically active diazotrophs were highest in year 1 but the population significantly declined in year 2 before recovering somewhat in the final year. The total bacterial population in contrast increased significantly each year. Seasonal effects were less consistent in this quantitative study