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Amsterdam-Zuidoost, Netherlands

Moghaddam F.A.,VU University Amsterdam | Geenen T.,SURFsara | Lago P.,VU University Amsterdam | Grosso P.,VU University Amsterdam
2015 Sustainable Internet and ICT for Sustainability, SustainIT 2015

The growth of power consumption in ICT infrastructures emphasizes the importance of monitoring their usage and finding available room for improvement. Users can choose among several existing tools to determine the energy profile of a running application in order to provide more sustainable software. We conducted a field study in the SURFsara data center and we experimented with the tools available, assessing them in light of their informative power. We derived some recommendations for ICT users and infrastructure operators that highlight the relation between the intended use of the profile and the easiness of running a specific tool. We categorize users in two types: the generic user, who is interested in summary statistical results on power measurements and the software developer that intends to delve in the code details in order to reprogram the application more efficiently. We concluded that SLURM and Score-P are suitable for both types of users when their requirements are thoroughly studied and taken into account. © 2015 IFIP. Source

Hillebrand B.,University Utrecht | Thieulot C.,University Utrecht | Thieulot C.,University of Oslo | Geenen T.,SURFsara | And 3 more authors.
Solid Earth

The level set method allows for tracking material surfaces in 2-D and 3-D flow modeling and is well suited for applications of multi-material flow modeling. The level set method utilizes smooth level set functions to define material interfaces, which makes the method stable and free of oscillations that are typically observed in case step-like functions parameterize interfaces. By design the level set function is a signed distance function and gives for each point in the domain the exact distance to the interface as well as on which side it is located. In this paper we present four benchmarks which show the validity, accuracy and simplicity of using the level set method for multi-material flow modeling. The benchmarks are simplified setups of dynamical geophysical processes such as the Rayleigh-Taylor instability, post-glacial rebound, subduction and slab detachment. We also demonstrate the benefit of using the level set method for modeling a free surface with the sticky air approach. Our results show that the level set method allows for accurate material flow modeling and that the combination with the sticky air approach works well in mimicking Earth's free surface. Since the level set method tracks material interfaces instead of materials themselves, it has the advantage that the location of these interfaces is accurately known and that it represents a viable alternative to the more commonly used tracer method. © 2014 Author(s). Source

Genseberger M.,Deltares | Donners J.,SURFsara
Procedia Computer Science

In the Netherlands, for coastal and inland water applications, wave modelling with SWAN has become a main ingredient. However, computational times are relatively high. Therefore we investigated the parallel efficiency of the current MPI and OpenMP versions of SWAN. The MPI version is not that efficient as the OpenMP version within a single node. Therefore, in this paper we propose a hybrid version of SWAN. It combines the efficiency of the current OpenMP version on shared memory with the capability of the current MPI version to distribute memory over nodes. We describe the numerical algorithm. With initial numerical experiments we show the potential of this hybrid version. Parallel I/O, further optimization, and behavior for larger number of nodes will be subject of future research. © The Authors. Published by Elsevier B.V. Source

Makkes M.X.,University of Amsterdam | Makkes M.X.,TNO | Taal A.,University of Amsterdam | Osseyran A.,SURFsara | Grosso P.,University of Amsterdam
Journal of Cloud Computing

Cloud computing gives users much freedom on where they host their computation and storage. However the CO2 emission of a job depends on the location and the energy efficiency of the data centers where it is run. We developed a decision framework that determines to move computation with accompanying data from a local to a greener remote data center for a lower CO2 emissions. The model underlying the framework accounts for the energy consumption at the local and remote sites, as well as of networks among them. We showed that the type of network connecting the two sites has a significant impact on the total CO2 emission. Furthermore, the task's complexity is a factor in deciding when and where to move computation. © 2013 Makkes et al. Source

Francioli L.C.,University Utrecht | Menelaou A.,University Utrecht | Pulit S.L.,University Utrecht | Van Dijk F.,University of Groningen | And 93 more authors.
Nature Genetics

Whole-genome sequencing enables complete characterization of genetic variation, but geographic clustering of rare alleles demands many diverse populations be studied. Here we describe the Genome of the Netherlands (GoNL) Project, in which we sequenced the whole genomes of 250 Dutch parent-offspring families and constructed a haplotype map of 20.4 million single-nucleotide variants and 1.2 million insertions and deletions. The intermediate coverage (∼13×) and trio design enabled extensive characterization of structural variation, including midsize events (30-500 bp) previously poorly catalogued and de novo mutations. We demonstrate that the quality of the haplotypes boosts imputation accuracy in independent samples, especially for lower frequency alleles. Population genetic analyses demonstrate fine-scale structure across the country and support multiple ancient migrations, consistent with historical changes in sea level and flooding. The GoNL Project illustrates how single-population whole-genome sequencing can provide detailed characterization of genetic variation and may guide the design of future population studies. © 2014 Nature America, Inc. Source

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