The European Integrated Tokamak Modelling Effort:Achievements and First Physics Results

This article compares both new and commonly used boundary conditions for generating pressure-driven water flows through carbon nanotubes in molecular dynamics simulations. Three systems are considered: (1) a finite carbon nanotube membrane with streamwise periodicity and ‘gravity’-type Gaussian forcing, (2) a non-periodic finite carbon nanotube membrane with reservoir pressure control, and (3) an infinite carbon nanotube with periodicity and ‘gravity’-type uniform forcing. Comparison between these focuses on the flow behaviour, in particular the mass flow rate and pressure gradient along the carbon nanotube, as well as the radial distribution of water density inside the carbon nanotube. Similar flow behaviour is observed in both membrane systems, with the level of user input required for such simulations found to be largely dependent on the state controllers selected for use in the reservoirs. While System 1 is simple to implement in common molecular dynamics codes, System 2 is more complicated, and the selection of control parameters is less straightforward. A large pressure difference is required between the water reservoirs in these systems to compensate for large pressure losses sustained at the entrance and exit of the nanotube. Despite a simple set-up and a dramatic increase in computational efficiency, the infinite length carbon nanotube in System 3 does not account for these significant inlet and outlet effects, meaning that a much smaller pressure gradient is required to achieve a specified mass flow rate. The infinite tube set-up also restricts natural flow development along the carbon nanotube due to the explicit control of the fluid. Observation of radial density profiles suggests that this results in over-constraint of the water molecules in the tube

Approaches to distributed execution of scientific workflows in Kepler

et al.The Kepler scientific workflow system enables creation, execution and sharing of workflows across a broad range of scientific and engineering disciplines while also facilitating remote and distributed execution of workflows. In this paper, we present and compare different approaches to distributed execution of workflows using the Kepler environment, including a distributed data-parallel framework using Hadoop and Stratosphere, and Cloud and Grid execution using Serpens, Nimrod/K and Globus actors. We also present real-life applications in computational chemistry, bioinformatics and computational physics to demonstrate the usage of different distributed computing capabilities of Kepler in executable workflows. We further analyze the differences of each approach and provide a guidance for their applications.The research leading to these results has received funding from different projects and funding schema, including: the European Community’s Seventh Framework Programme under grant agreement RI-261323 (EGI-InsPIRE), the European Communities under the contracts of Association between EURATOM and CEA, IPPLM, carried out within the framework of the Task Force on Integrated Tokamak Modeling of the EFDA, the Polish project PLGrid Plus under the contract POIG 02.03.00-00-096/10, NSF ABI Award DBI-1062565 for bioKepler, partial financial support from the Spanish Ministerio de Economia y Competitividad AYA 2010-21766-C03-01 and Consolider Ingenio 2010 CSD2010-00064 projects, and from the Juan de la Cierva programme.Peer Reviewe

High Performance Computing tools for the Integrated Tokamak Modelling project

6 páginas, 6 figuras, 2 tablas.-- European Task Force on Integrated Tokamak Modelling Activity: et al.Fusion Modelling and Simulation are very challenging and the High Performance Computing issues are addressed here. Toolset for jobs launching and scheduling, data communication and visualization have been developed by the EUFORIA project and used with a plasma edge simulation code.This work, supported by the European Communities under the contract of Association between EURATOM and several Associations, was carried out within the framework of the European Fusion Development Agreement. The research leading to these results has also received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement n◦211804 (EUFORIA).Peer reviewe

Gateway: New high performance computing facility for EFDA task force on integrated Tokamak modelling

The EFDA task force on Integrated Tokamak Modelling (ITM-TF) is providing the EU fusion community with a complete and flexible suite of reliable software tools and codes able to simulate the next ITER and DEMO plasma discharges. EFDA has launched the Gateway project as the first computing facility to be jointly used by EU fusion associations. The Gateway has been designed to allow the ITM-TF members to work together on a common platform and share their codes, developments tools and technologies as well as to make able the inter-operation with tera-scale supercomputer facilities. Technically the Gateway is a rather small high computing facility in operation since 2008, with 1 Teraflops of theoretical peak and 100 Terabytes shared storage area for experimental and simulation data. This paper describes the information technologies involved in the Gateway facility, particularly as regards the low latency interconnect network for multi-core platform as well as fast I/O solutions implemented with storage over Infiniband and high performance parallel file systems. The solutions adopted on the Gateway facility had undergone to specific benchmarks showing excellent performances in typical fusion data handling issues. Finally the interoperability between Gateway and ENEA CRESCO supercomputer will be described showing the access solutions that allow the exploitation of tera-scale supercomputer facilities