1,314 research outputs found
MPWide: a light-weight library for efficient message passing over wide area networks
We present MPWide, a light weight communication library which allows
efficient message passing over a distributed network. MPWide has been designed
to connect application running on distributed (super)computing resources, and
to maximize the communication performance on wide area networks for those
without administrative privileges. It can be used to provide message-passing
between application, move files, and make very fast connections in
client-server environments. MPWide has already been applied to enable
distributed cosmological simulations across up to four supercomputers on two
continents, and to couple two different bloodflow simulations to form a
multiscale simulation.Comment: accepted by the Journal Of Open Research Software, 13 pages, 4
figures, 1 tabl
The Rumsfeld paradox: some of the things we know that we don’t know about plant virus infection
Plant-infecting viruses cause significant crop losses around the world and the majority of emerging threats to crop production have a viral etiology. Significant progress has been made and continues to be made in understanding how viruses induce disease and overcome some forms of resistance–particularly resistance based on RNA silencing. However, it is still not clear how other antiviral mechanisms work, how viruses manage to exploit their hosts so successfully, or how viruses affect the interactions of susceptible plants with other organisms and if this is advantageous to the virus, the host, or both. In this article we explore these questions
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Aversion and attraction to harmful plant secondary compounds jointly shape the foraging ecology of a specialist herbivore.
Most herbivorous insect species are restricted to a narrow taxonomic range of host plant species. Herbivore species that feed on mustard plants and their relatives in the Brassicales have evolved highly efficient detoxification mechanisms that actually prevent toxic mustard oils from forming in the bodies of the animals. However, these mechanisms likely were not present during the initial stages of specialization on mustard plants ~100 million years ago. The herbivorous fly Scaptomyza nigrita (Drosophilidae) is a specialist on a single mustard species, bittercress (Cardamine cordifolia; Brassicaceae) and is in a fly lineage that evolved to feed on mustards only in the past 10-20 million years. In contrast to many mustard specialists, S. nigrita does not prevent formation of toxic breakdown products (mustard oils) arising from glucosinolates (GLS), the primary defensive compounds in mustard plants. Therefore, it is an appealing model for dissecting the early stages of host specialization. Because mustard oils actually form in the bodies of S. nigrita, we hypothesized that in lieu of a specialized detoxification mechanism, S. nigrita may mitigate exposure to high GLS levels within plant tissues using behavioral avoidance. Here, we report that jasmonic acid (JA) treatment increased GLS biosynthesis in bittercress, repelled adult female flies, and reduced larval growth. S. nigrita larval damage also induced foliar GLS, especially in apical leaves, which correspondingly displayed the least S. nigrita damage in controlled feeding trials and field surveys. Paradoxically, flies preferred to feed and oviposit on GLS-producing Arabidopsis thaliana despite larvae performing worse in these plants versus non-GLS-producing mutants. GLS may be feeding cues for S. nigrita despite their deterrent and defensive properties, which underscores the diverse relationship a mustard specialist has with its host when lacking a specialized means of mustard oil detoxification
Multivariate Methods for Monitoring Structural Change
Detection of structural change is a critical empirical activity, but continuous 'monitoring' of series, for structural changes in real time, raises well-known econometric issues that have been explored in a single series context. If multiple series co-break then it is possible that simultaneous examination of a set of series helps identify changes with higher probability or more rapidly than when series are examined on a case-by-case basis. Some asymptotic theory is developed for maximum and average CUSUM detection tests. Monte Carlo experiments suggest that these both provide an improvement in detection relative to a univariate detector over a wide range of experimental parameters, given a sufficiently large number of co-breaking series. This is robust to a cross-sectional correlation in the errors (a factor structure) and heterogeneity in the break dates. We apply the test to a panel of UK price indices.Monitoring, Structural change, Panel, CUSUM, Fluctuation test
The Living Application: a Self-Organising System for Complex Grid Tasks
We present the living application, a method to autonomously manage
applications on the grid. During its execution on the grid, the living
application makes choices on the resources to use in order to complete its
tasks. These choices can be based on the internal state, or on autonomously
acquired knowledge from external sensors. By giving limited user capabilities
to a living application, the living application is able to port itself from one
resource topology to another. The application performs these actions at
run-time without depending on users or external workflow tools. We demonstrate
this new concept in a special case of a living application: the living
simulation. Today, many simulations require a wide range of numerical solvers
and run most efficiently if specialized nodes are matched to the solvers. The
idea of the living simulation is that it decides itself which grid machines to
use based on the numerical solver currently in use. In this paper we apply the
living simulation to modelling the collision between two galaxies in a test
setup with two specialized computers. This simulation switces at run-time
between a GPU-enabled computer in the Netherlands and a GRAPE-enabled machine
that resides in the United States, using an oct-tree N-body code whenever it
runs in the Netherlands and a direct N-body solver in the United States.Comment: 26 pages, 3 figures, accepted by IJHPC
Simulating the universe on an intercontinental grid of supercomputers
Understanding the universe is hampered by the elusiveness of its most common
constituent, cold dark matter. Almost impossible to observe, dark matter can be
studied effectively by means of simulation and there is probably no other
research field where simulation has led to so much progress in the last decade.
Cosmological N-body simulations are an essential tool for evolving density
perturbations in the nonlinear regime. Simulating the formation of large-scale
structures in the universe, however, is still a challenge due to the enormous
dynamic range in spatial and temporal coordinates, and due to the enormous
computer resources required. The dynamic range is generally dealt with by the
hybridization of numerical techniques. We deal with the computational
requirements by connecting two supercomputers via an optical network and make
them operate as a single machine. This is challenging, if only for the fact
that the supercomputers of our choice are separated by half the planet, as one
is located in Amsterdam and the other is in Tokyo. The co-scheduling of the two
computers and the 'gridification' of the code enables us to achieve a 90%
efficiency for this distributed intercontinental supercomputer.Comment: Accepted for publication in IEEE Compute
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