Throughput constrained parallelism reduction in cyclo-static dataflow applications

International audienceThis paper deals with semantics-preserving parallelism reduction methods for cyclo-static dataflow applications. Parallelism reduction is the process of equivalent actors fusioning. The principal objectives of parallelism reduction are to decrease the memory footprint of an application and to increase its execution performance. We focus on parallelism reduction methodologies constrained by application throughput. A generic parallelism reduction methodology is introduced. Experimental results are provided for asserting the performance of the proposed method

Generating Code and Memory Buffers to Reorganize Data on Many-core Architectures

International audienceThe dataflow programming model has shown to be a relevant approach to efficiently run mas-sively parallel applications over many-core architectures. In this model, some particular builtin agents are in charge of data reorganizations between user agents. Such agents can Split, Join and Duplicate data onto their communication ports. They are widely used in signal processing for example. These system agents, and their associated implementations, are of major impor-tance when it comes to performance, because they can stand on the critical path (think about Amdhal's law). Furthermore, a particular data reorganization can be expressed by the devel-oper in several ways that may lead to inefficient solutions (mostly unneeded data copies and transfers). In this paper, we propose several strategies to manage data reorganization at compile time, with a focus on indexed accesses to shared buffers to avoid data copies. These strategies are complementary: they ensure correctness for each system agent configuration, as well as performance when possible. They have been implemented within the Sigma-C industry-grade compilation toolchain and evaluated over the Kalray MPPA 256-core processor

SiF4 anomalous behaviour reassessed

The Si 1s−1, Si 2s−1, and Si 2p−1 photoelectron spectra of the SiX4 molecules with X = F, Cl, Br, CH3 were measured. From these spectra the Si 1s−1 and Si 2s−1 lifetime broadenings were determined, revealing a significantly larger value for the Si 2s−1 core hole of SiF4 than for the same core hole of the other molecules of the sequence. This finding is in line with the results of the Si 2p−1 core holes of a number of SiX4 molecules, with an exceptionally large broadening for SiF4. For the Si 2s−1 core hole of SiF4 the difference to the other SiX4 molecules can be explained in terms of Interatomic Coulomb Decay (ICD)-like processes. For the Si 2p−1 core hole of SiF4 the estimated values for the sum of the Intraatomic Auger Electron Decay (IAED) and ICD-like processes are too small to explain the observed linewidth. However, the results of the given discussion render for SiF4 significant contributions from Electron Transfer Mediated Decay (ETMD)-like processes at least plausible. On the grounds of our results, some more molecular systems in which similar processes can be observed are identified

Collaborative analysis of multi-gigapixel imaging data using Cytomine

Motivation: Collaborative analysis of massive imaging datasets is essential to enable scientific discoveries. Results: We developed Cytomine to foster active and distributed collaboration of multidisciplinary teams for large-scale image-based studies. It uses web development methodologies and machine learning in order to readily organize, explore, share and analyze (semantically and quantitatively) multi-gigapixel imaging data over the internet. We illustrate how it has been used in several biomedical applications

C-terminal amino acids are essential for human heat shock protein 70 dimerization

The human inducible heat shock protein 70 (hHsp70), which is involved in several major pathologies, including neurodegenerative disorders and cancer, is a key molecular chaperone and contributes to the proper protein folding and maintenance of a large number of protein structures. Despite its role in disease, the current structural knowledge of hHsp70 is almost exclusively based on its Escherichia coli homolog, DnaK, even though these two proteins only share ~50 % amino acid identity. For the first time, we describe a complete heterologous production and purification strategy that allowed us to obtain a large amount of soluble, full-length, and non-tagged hHsp70. The protein displayed both an ATPase and a refolding activity when combined to the human Hsp40. Multi-angle light scattering and bio-layer interferometry analyses demonstrated the ability of hHsp70 to homodimerize. The role of the C-terminal part of hHsp70 was identified and confirmed by a study of a truncated version of hHsp70 that could neither dimerize nor present refolding activity

Argon 1s(-2) Auger hypersatellites

The 1s(-2) Auger hypersatellite spectrum of argon is studied experimentally and theoretically. In total, three transitions to the final states 1s(-1)2p(-2)(S-2(e),D-2(e)) and 1s(-1)2s(-1)(S-1)2p(-1)(P-2(o)) are experimentally observed. The lifetime broadening of the 1s(-2) -> 1s(-1)2p(-2)(S-2(e),D-2(e)) states is determined to be 2.1(4) eV. For the used photon energy of h nu = 7500 eV a KK/K ionisation ratio of 2.5(3) x 10(-4) is derived. Generally, a good agreement between the experimental and present theoretical energy positions, linewidths, and intensities is obtained

Electron spectroscopy and dynamics of HBr around the Br 1s-1 threshold

A comprehensive electron spectroscopic study combined with partial electron yield measurements around the Br 1s ionization threshold of HBr at approximately equal to 13.482 keV is reported. In detail, the Br 1s(-1) X-ray absorption spectrum, the 1s(-1) photoelectron spectrum as well as the normal and resonant KLL Auger spectra are presented. Moreover, the L-shell Auger spectra measured with photon energies below and above the Br 1s(-1) ionization energy as well as on top of the Br 1s(-1)sigma* resonance are shown. The latter two Auger spectra represent the second step of the decay cascade subsequent to producing a Br 1s(-1) core hole. The measurements provide information on the electron and nuclear dynamics of deep core-excited states of HBr on the femtosecond timescale. From the different spectra the lifetime broadening of the Br 1s(-1) single core-hole state as well as of the Br(2s(-2),2s(-1)2p(-1),2p(-2)) double core-hole states are extracted and discussed. The slope of the strongly dissociative HBr 2p(-2)sigma* potential energy curve is found to be about -13.60 eV angstrom(-1). The interpretation of the experimental data, and in particular the assignment of the spectral features in the KLL and L-shell Auger spectra, is supported by relativistic calculations for HBr molecule and atomic Br