Partition Around Medoids Clustering on the Intel Xeon Phi Many-Core Coprocessor

Abstract. The paper touches upon the problem of implementation Partition Around Medoids (PAM) clustering algorithm for the Intel Many Integrated Core architecture. PAM is a form of well-known k-Medoids clustering algorithm and is applied in various subject domains, e.g. bioinformatics, text analysis, intelligent transportation systems, etc. An optimized version of PAM for the Intel Xeon Phi coprocessor is introduced where OpenMP parallelizing technology, loop vectorization, tiling technique and efficient distance matrix computation for Euclidean metric are used. Experimental results for different data sets confirm the efficiency of the proposed algorithm

First results from the LUCID-Timepix spacecraft payload onboard the TechDemoSat-1 satellite in Low Earth Orbit

The Langton Ultimate Cosmic ray Intensity Detector (LUCID) is a payload onboard the satellite TechDemoSat-1, used to study the radiation environment in Low Earth Orbit ($\sim$635km). LUCID operated from 2014 to 2017, collecting over 2.1 million frames of radiation data from its five Timepix detectors on board. LUCID is one of the first uses of the Timepix detector technology in open space, with the data providing useful insight into the performance of this technology in new environments. It provides high-sensitivity imaging measurements of the mixed radiation field, with a wide dynamic range in terms of spectral response, particle type and direction. The data has been analysed using computing resources provided by GridPP, with a new machine learning algorithm that uses the Tensorflow framework. This algorithm provides a new approach to processing Medipix data, using a training set of human labelled tracks, providing greater particle classification accuracy than other algorithms. For managing the LUCID data, we have developed an online platform called Timepix Analysis Platform at School (TAPAS). This provides a swift and simple way for users to analyse data that they collect using Timepix detectors from both LUCID and other experiments. We also present some possible future uses of the LUCID data and Medipix detectors in space.Comment: Accepted for publication in Advances in Space Researc

Jet analysis by Deterministic Annealing

We perform a comparison of two jet clusterization algorithms. The first one is the standard Durham algorithm and the second one is a global optimization scheme, Deterministic Annealing, often used in clusterization problems, and adapted to the problem of jet identification in particle production by high energy collisions; in particular we study hadronic jets in WW production by high energy electron positron scattering. Our results are as follows. First, we find that the two procedures give basically the same output as far as the particle clusterization is concerned. Second, we find that the increase of CPU time with the particle multiplicity is much faster for the Durham jet clustering algorithm in comparison with Deterministic Annealing. Since this result follows from the higher computational complexity of the Durham scheme, it should not depend on the particular process studied here and might be significant for jet physics at LHC as well.Comment: 15 pages, 4 figure

Mixing multi-core CPUs and GPUs for scientific simulation software

Recent technological and economic developments have led to widespread availability of multi-core CPUs and specialist accelerator processors such as graphical processing units (GPUs). The accelerated computational performance possible from these devices can be very high for some applications paradigms. Software languages and systems such as NVIDIA's CUDA and Khronos consortium's open compute language (OpenCL) support a number of individual parallel application programming paradigms. To scale up the performance of some complex systems simulations, a hybrid of multi-core CPUs for coarse-grained parallelism and very many core GPUs for data parallelism is necessary. We describe our use of hybrid applica- tions using threading approaches and multi-core CPUs to control independent GPU devices. We present speed-up data and discuss multi-threading software issues for the applications level programmer and o er some suggested areas for language development and integration between coarse-grained and ne-grained multi-thread systems. We discuss results from three common simulation algorithmic areas including: partial di erential equations; graph cluster metric calculations and random number generation. We report on programming experiences and selected performance for these algorithms on: single and multiple GPUs; multi-core CPUs; a CellBE; and using OpenCL. We discuss programmer usability issues and the outlook and trends in multi-core programming for scienti c applications developers

UHECR besides CenA: hints of galactic sources

Ultra High Energy Cosmic Rays, UHECR, maybe protons, as most still believe and claim, or nuclei; in particular lightest nuclei as we advocated recently. The first (Auger Collaboration) nucleon proposal (2007)[2] foresaw to trace clearly the UHECR GZK Universe reaching far (up to 100 Mpc) Super-Galactic-Plane, with little angular dispersion. On the contrary Lightest Nuclei model (2008)[3], inspired by observed composition and by nearest CenA clustering (almost a quarter of the AUGER events) explains a modest and narrow (few Mpc) Universe view, as well as the puzzling Virgo absence: lightest nuclei offer a fragile (and therefore very nearby) blurred Astronomy. Here we address to a part of the remaining scattered events in the new up-dated Auger map (March 2009-ICRC09). We found within rarest clustering the surprising imprint of a few galactic sources, a partial component of UHECR sources. In particular we recognize a first trace of Vela, brightest gamma and radio galactic source, and smeared sources along Galactic Plane and Center. The clustering may imply additional tails of fragments (by nuclei photo-dissociation) at half energies. The UHECR light-nuclei fragility and opacity may also reflect into a train of secondaries as gamma and neutrinos UHE events at tens-hundred PeVs. These UHE neutrinos might be detectable in a coming future within nearest AUGER and Array Fluorescence Telescope views,(few km distances) by fast fluorescence flashing of horizontal up-going tau Air-showers.Comment: 3 pages, 6 figures + 1 original Map figure (from public web service SCINEGHE Oct. 2009: Daniele Martello for AUGER Collab: http://agenda.infn.it/conferenceOtherViews.py?view=standard&confId=1369, Talk n.21

Control Infrastructure for a Pulsed Ion Accelerator

We report on updates to the accelerator controls for the Neutralized Drift Compression Experiment II, a pulsed induction-type accelerator for heavy ions. The control infrastructure is built around a LabVIEW interface combined with an Apache Cassandra backend for data archiving. Recent upgrades added the storing and retrieving of device settings into the database, as well as ZeroMQ as a message broker that replaces LabVIEW's shared variables. Converting to ZeroMQ also allows easy access via other programming languages, such as Python

UHECR Acceleration in Dark Matter Filaments of Cosmological Structure Formation

A mechanism for proton acceleration to ~10^21eV is suggested. It may operate in accretion flows onto thin dark matter filaments of cosmic structure formation. The flow compresses the ambient magnetic field to strongly increase and align it with the filament. Particles begin the acceleration by the ExB drift with the accretion flow. The energy gain in the drift regime is limited by the conservation of the adiabatic invariant p_perp^2/B. Upon approaching the filament, the drift turns into the gyro-motion around the filament so that the particle moves parallel to the azimuthal electric field. In this 'betatron' regime the acceleration speeds up to rapidly reach the electrodynamic limit $cp_{max}=eBR$ for an accelerator with magnetic field $B$ and the orbit radius $R$ (Larmor radius). The periodic orbit becomes unstable and the particle slings out of the filament to the region of a weak (uncompressed) magnetic field, which terminates the acceleration. The mechanism requires pre-acceleration that is likely to occur in structure formation shocks upstream or nearby the filament accretion flow. Previous studies identify such shocks as efficient proton accelerators to a firm upper limit ~10^19.5 eV placed by the catastrophic photo-pion losses. The present mechanism combines explosive energy gain in its final (betatron) phase with prompt particle release from the region of strong magnetic field. It is this combination that allows protons to overcome both the photo-pion and the synchrotron-Compton losses and therefore attain energy 10^21 eV. A requirement on accelerator to reach a given E_max placed by the accelerator energy dissipation \propto E_{max}^{2}/Z_0 due to the finite vacuum impedance Z_0 is circumvented by the cyclic operation of the accelerator.Comment: 34 pages, 10 figures, to be published in JCA