61 research outputs found
Interoperable job submission and management with GridSAM, JMEA, and UNICORE
Achieving interoperability between Grid infrastructures is required by all us-ers consuming computing time for projects spanning across Grid domain boundaries. Standards naturally evolve slowly and on Grid level only a few have been proposed and widely accepted so far, among them JSDL. This pa-per describes how GridSAM which supports JSDL in combination with JMEA can be used to submit jobs to a UNICORE infrastructure and hence how the number of Grid projects accessible via GridSAM can be increased right now
Accounting Facilities in the European Supercomputing Grid DEISA
Account management and resource usage monitoring are essential services for production Grids. The scope of a production Grid infrastructure, the heterogeneity of resources and services, the typical community usage profiles, and the depth of integration of the resource providers regarding operational procedures and policies imply specific requirements for accounting facilities. We present the accounting facilities currently used in production in the Distributed European Infra-structure for the Supercomputing Applications (DEISA). DEISA is a consortium of leading national supercomputing centres currently deploying and operating a persistent, production quality, distributed su-percomputing environment with continental scope. The DEISA accounting facilities gather information from the site-local batch systems and the distributed DEISA user administration system, and generate XML usage records conforming to the OGF usage record specification which are then stored locally in a XML data base at each DEISA site. The distributed accounting information can be fetched by clients such as users, project supervisors, site accounting managers and DEISA supervisors. The information is made available by site-local WSRF-compliant accounting information services that allow for a fine-grained setting of access rights. Each authorized client gets a specific view on the accounting information according to one of the following roles: a) a site accounting manager imports usage records of related home-site users from all DEISA sites for longterm archiving, b) a project supervisor retrieves information to assess the resource usage by his project partners, c) a DEISA supervisor (e.g. someone overlooking the usage on behalf of the DEISA executive committee) gets a report on the global usage of DEISA resources, and d) the user who can retrieve all the accounting information related to his own jobs. The privacy and integrity of the data provided and transferred from the accounting information service running at each site is guaranteed using X.509 certificates for mutual authentication and secure communication channels
A Federation of Language Archives Enabling Future eHumanities Scenarios
This paper describes the need for new infrastructures for future eScience scenarios in the humanities. Three projects working on different aspects of these infrastructures are examined in detail. The first project is trying to achieve a federation of archives, developing an integration layer at the level of localization, access to and referring to an archive’s raw data objects. The other two try to achieve interoperability at the level of semantic interpretation of linguistic data-types and tagging systems. The project’s different approaches to this problem show the trade-of between flexibility and the user’s workload. All three approaches give an impression about the necessary steps to come to an eHumanities scenario
Pure functions in C: A small keyword for automatic parallelization
© 2020, The Author(s). The need for parallel task execution has been steadily growing in recent years since manufacturers mainly improve processor performance by increasing the number of installed cores instead of scaling the processor’s frequency. To make use of this potential, an essential technique to increase the parallelism of a program is to parallelize loops. Several automatic loop nest parallelizers have been developed in the past such as PluTo. The main restriction of these tools is that the loops must be statically analyzable which, among other things, disallows function calls within the loops. In this article, we present a seemingly simple extension to the C programming language which marks functions without side-effects. These functions can then basically be ignored when the automatic parallelizer checks the parallelizability of loops. We integrated the approach into the GCC compiler toolchain and evaluated it by running several real-world applications. Our experiments show that the C extension helps to identify additional parallelization opportunities and, thus, to significantly increase the performance of applications
A new model for simulating colloidal dynamics
We present a new hybrid lattice-Boltzmann and Langevin molecular dynamics
scheme for simulating the dynamics of suspensions of spherical colloidal
particles. The solvent is modeled on the level of the lattice-Boltzmann method
while the molecular dynamics is done for the solute. The coupling between the
two is implemented through a frictional force acting both on the solvent and on
the solute, which depends on the relative velocity. A spherical colloidal
particle is represented by interaction sites at its surface. We demonstrate
that this scheme quantitatively reproduces the translational and rotational
diffusion of a neutral spherical particle in a liquid and show preliminary
results for a charged spherical particle. We argue that this method is
especially advantageous in the case of charged colloids.Comment: For a movie click on the link below Fig
Polyhedral vesicles
Polyhedral vesicles with a large bending modulus of the membrane such as the
gel phase lipid membrane were studied using a Brownian dynamics simulation. The
vesicles exhibit various polyhedral morphologies such as tetrahedron and cube
shapes. We clarified two types of line defects on the edges of the polyhedrons:
cracks of both monolayers at the spontaneous curvature of monolayer , and a crack of the inner monolayer at . Around the
latter defect, the inner monolayer curves positively. Our results suggested
that the polyhedral morphology is controlled by .Comment: 4 pages, 5 figure
Optimizing end-labeled free-solution electrophoresis by increasing the hydrodynamic friction of the drag-tag
We study the electrophoretic separation of polyelectrolytes of varying
lengths by means of end-labeled free-solution electrophoresis (ELFSE). A
coarse-grained molecular dynamics simulation model, using full electrostatic
interactions and a mesoscopic Lattice Boltzmann fluid to account for
hydrodynamic interactions, is used to characterize the drag coefficients of
different label types: linear and branched polymeric labels, as well as
transiently bound micelles.
It is specifically shown that the label's drag coefficient is determined by
its hydrodynamic size, and that the drag per label monomer is largest for
linear labels. However, the addition of side chains to a linear label offers
the possibility to increase the hydrodynamic size, and therefore the label
efficiency, without having to increase the linear length of the label, thereby
simplifying synthesis. The third class of labels investigated, transiently
bound micelles, seems very promising for the usage in ELFSE, as they provide a
significant higher hydrodynamic drag than the other label types.
The results are compared to theoretical predictions, and we investigate how
the efficiency of the ELFSE method can be improved by using smartly designed
drag-tags.Comment: 32 pages, 11 figures, submitted to Macromolecule
Shear induced instabilities in layered liquids
Motivated by the experimentally observed shear-induced destabilization and
reorientation of smectic A like systems, we consider an extended formulation of
smectic A hydrodynamics. We include both, the smectic layering (via the layer
displacement u and the layer normal p) and the director n of the underlying
nematic order in our macroscopic hydrodynamic description and allow both
directions to differ in non equilibrium situations. In an homeotropically
aligned sample the nematic director does couple to an applied simple shear,
whereas the smectic layering stays unchanged. This difference leads to a finite
(but usually small) angle between n and p, which we find to be equivalent to an
effective dilatation of the layers. This effective dilatation leads, above a
certain threshold, to an undulation instability of the layers. We generalize
our earlier approach [Rheol. Acta, vol.39(3), 15] and include the cross
couplings with the velocity field and the order parameters for orientational
and positional order and show how the order parameters interact with the
undulation instability. We explore the influence of various material parameters
on the instability. Comparing our results to recent experiments and molecular
dynamic simulations, we find a good qualitative agreement.Comment: 15 pages, 12 figures, accepted for publication in PR
Lattice Boltzmann simulations of soft matter systems
This article concerns numerical simulations of the dynamics of particles
immersed in a continuum solvent. As prototypical systems, we consider colloidal
dispersions of spherical particles and solutions of uncharged polymers. After a
brief explanation of the concept of hydrodynamic interactions, we give a
general overview over the various simulation methods that have been developed
to cope with the resulting computational problems. We then focus on the
approach we have developed, which couples a system of particles to a lattice
Boltzmann model representing the solvent degrees of freedom. The standard D3Q19
lattice Boltzmann model is derived and explained in depth, followed by a
detailed discussion of complementary methods for the coupling of solvent and
solute. Colloidal dispersions are best described in terms of extended particles
with appropriate boundary conditions at the surfaces, while particles with
internal degrees of freedom are easier to simulate as an arrangement of mass
points with frictional coupling to the solvent. In both cases, particular care
has been taken to simulate thermal fluctuations in a consistent way. The
usefulness of this methodology is illustrated by studies from our own research,
where the dynamics of colloidal and polymeric systems has been investigated in
both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures,
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