SHAPE 3rd Call

On this page you will find details of the projects awarded under the SHAPE 3rd Call.

Project Title: MARS (Matrix of RNA-Seq)

SME: ACOBIOM, France

Description
RNA-Seq approach is used in a wide variety of applications. These include identifying diseaserelated genes, analysing the effects of drugs on tissues, and providing insight into disease pathways. The RNA-Seq is widely used to characterise gene expression patterns associated with tumor formation. Since RNA-Seq provides absolute values and does not require any calibration with arbitrary standards, results can be compared at any time with other data, even raised by independent laboratories. Once collected, these data can be digitalised and then easily and reliably compared in silico with the growing library of RNA-Seq databases generated for normal and pathological situations in other laboratories around the world (Human: ~27000 libraries and Mouse: ~42000 libraries. Average size of a library: 1.7GB. Total size: 120TB). We intend to compare and search the specificity of our blood gene expression signatures (eg. the masitinib in pancreas) against already existing data in different tissues or pathologies, in Human and Mouse Omic data.

White Paper

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Project Title: High level optimization in aerodynamic design

SME: Airinnova AB, Sweden

Description
The company is developing computational solutions for aerodynamic shape optimization, which is an important task in aircraft design. The goal is to design a lighter, greener, and quieter airplane by reducing drag especially in high speed. Aerodynamic shape optimization for reduced drag requires a large number of CFD solutions, and computational power is a limiting factor. Current ideas for surrogate modelling are being developed to improve computational efficiency.

The company has been discussing the project with SNIC-KTH and the work plan was developed by Airinnova and SNIC-KTH together.

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Project Title: DemocraSIM: DEMOCRatic Air quaility SIMulation

SME: AmpliSIM, France

Description
DemocraSIM aims to bring numerical simulation as a commodity to users concerned about air quality, filling a gap between HPC simulation production and non-academic community of potential users.

DemocraSIM idea popped to our mind when we saw what people did when Fukushima hazard occurred: crowd-sourced data of radioactivity measurements displayed on a single web map (see http://safecast.org/tilemap/ for the map and http://blog.safecast.org/history/ for the history). The question that we ask ourselves was: why can people do their own measurement of radioactivity, and share them, while they can not do this for simulations of the event?

DemocraSIM will provide a web service allowing individual people or organization to:
– Perform relevant air quality simulation for impact assessment or in case of hazard
– Share them using state of the art visualization tools and data analytics
– Improve and validate them using expertise from the community.

The technology and the data are out there: web maps, mature models, input data (meteorology, topography). And most of them are even available either open source or free.

The DemocraSIM SHAPE project will allow AmpliSIM to tackle technological locks on the use of urgent-computing, advanced visualization and data-analytics with PRACE HPC experts, before being able to launch an industrial solution on a private HPC-cloud (such as Fortissimo platform). It will also allow PRACE HPC expert to address these issues on “real cases”, with potential reuse on academic cases of urgent-computing.

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Project Title: SUNSTAR: Simulation of UNSteady Turbulent flows for the AeRospace industry

SME: ANEMOS SRL, Italy

Description
The proposed project aims at improving robustness and performance of our in-house software for the simulation and the analysis of complex turbulent flows relevant to the aerospace industry on the HPC systems provided by PRACE. The kernel of this software is an immersedboundary-based, compressible, massively parallel flow solver, incorporating state-of-the-art numerical methods and advanced features for the simulation of supersonic flows in complex configurations.

The code was born as an academic code developed for the BlueGene architecture. The engineering of the code for industrial applications and the dismissal of the BG architecture by IBM requires the investigation of how to port the code to more modern computer architectures while maintaining (and possibly increasing) parallel efficiency, while conserving numerical consistency. To achieve this goal, the support of PRACE experts is of invaluable importance.

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Project Title: Numerical simulation of accidental fires with a spillage of oil in large buildings

SME: BAC Engineering Consultancy Group, Spain

Description
The objective of the project is to develop a fire engineering analysis (Performance-Based design) of the steel structure buildings that belong to the ITER (International Thermonuclear Experimental Reactor) industrial complex in Cadarache (France), which is devoted to research in the field of Nuclear Fusion. In particular, the project will focus on the building that hosts the cryogenic system of the Tokamak.

This building is characterized by its large size, approximately 75m long, 45m wide and 20m high. The building hosts a large number of helium and nitrogen compressors, as well as the charcoal filter system, that is necessary for the cryogenic system.

It is intended to carry out numeric simulations of the accidental fires that can take place inside of the building, some of them as complex as the combination of a liquid combustible spillage added to an oil cloud due to the breakage of a high pressure pipe.

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Project Title: Large scale aero-acoustics applications using open source CFD

SME: Creo Dynamics AB, Sweden

Description
The proposed project aims to demonstrate how aero-acoustics simulation processes based entirely on open source CFD software can be tailored and deployed in parallel at large scale to produce robust and efficient results for real life applications. The chosen test case should be of high industrial relevance; e.g. the prediction of the unsteady aerodynamics flow field (and acoustics) around a road car.

Results from the project should be made public to showcase the technology and encourage new users to adopt and invest in high performance computing (HPC) and open source software.

The envisaged CFD methodology is expected to deliver simulation accuracy in-line with current industry best practices at a considerably lower cost.

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Project Title: Pressure drop simulation for a compressed gas closed system

SME: FDD Engitec S.L., Spain

Description
The objective of the project is to calculate by simulation, the pressure drop of a firefighting pressure regulated discharge valve for inert gas agent.

For doing that, it is needed to simulate the discharge of a pressurized closed canister through the valve according to the below listed:
– Initial pressure into the canister: 300 bar / 200 bar
– Final pressure into the canister: 0 bar
– Volume of canister: 80 litres and 140 litres
– In the canister there is just one outlet where the valve is installed
– The valve itself can regulate the outlet discharge pressure to a fix value during the discharge by internal mechanical devices
– Outlet discharge pressure: 60 bar / 40 bar

Goals of the project:
– To determine the pressure drop of the valve
– To determine the functioning of the outlet pressure regulation system of the valve
– Assure the quantity of gas that can be discharge across the valve in one minute and in two minutes when:
— The initial pressure is 300 bar and the outlet discharge pressure is 60 bar
— The initial pressure is 200 bar and the outlet discharge pressure is 40 bar

This project will be done in collaboration with the Barcelona Supercomputing Center (BSC).

The code to be used to perform the numerical simulations is Alya, a multi-physics code developed at BSC. The code will be adapted to solve this application problem.

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Project Title: HPC methodologies for PharmScreen

SME: Pharmacelera, Spain

Description
PharmScreen, our software tool for ligand-based drug design, is able to find more relevant molecules than the software from the competition. However, we have not been able to fully explore its potential due to its significant computing requirements and we have started exploring mechanisms to reduce its execution time. Hence, the proposed project aims at applying HPC methodologies to PharmScreen in order to improve its performance / accuracy. In particular, the project has four different goals:
– Define a parallelisation strategy for PharmScreen using a combination of traditional CPUs, GPUs and highly parallel vector machines and setting up an appropriate testing methodology for such a HPC solution.
– Implement a first parallel version of PharmScreen beyond OpenMP (currently available).
– Explore HPC alternatives for the PharmaBox and PharmaBlade platforms.
– Assess the performance and accuracy of PharmScreen by doing a sensitivity analysis of its different parameters.

White Paper

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