In the simulation of complex multi-scale flows arising in weather and climate modelling, one of the biggest challenges is to satisfy strict service requirements in terms of time to solution and to ...satisfy budgetary constraints in terms of energy to solution, without compromising the accuracy and stability of the application. These simulations require algorithms that minimise the energy footprint along with the time required to produce a solution, maintain the physically required level of accuracy, are numerically stable, and are resilient in case of hardware failure.
What designs for coming supercomputers? Vigouroux, Xavier
2013 Design, Automation & Test in Europe Conference & Exhibition (DATE),
2013-March
Conference Proceeding
Summary form only given. The paper introduces a new pulsed measurement system for the characterization of thermal and charge trapping effects in compound semiconductor III-V FETs. Minimization of ...reflections are obtained by pulse generation in a 50 Ω environment and separation between DC and AC path guarantees no variations of the average voltage values of pulses. Both GaAs- and GaN-based FETs are characterized and some differences between the two technologies are outlined as far as the charge trapping behaviour is concerned.
•A framework to perform inverse docking was developed.•Different strategies to distribute the docking procedure were implemented.•Validation with experimental complex have been done.•A docking test ...of one ligand versus 100 proteins was performed.•A better conformational sampling is processed than current methods.
Molecular docking is a widely used computational technique that allows studying structure-based interactions complexes between biological objects at the molecular scale. The purpose of the current work is to develop a set of tools that allows performing inverse docking, i.e., to test at a large scale a chemical ligand on a large dataset of proteins, which has several applications on the field of drug research. We developed different strategies to parallelize/distribute the docking procedure, as a way to efficiently exploit the computational performance of multi-core and multi-machine (cluster) environments. The experiments conducted to compare these different strategies encourage the search for decomposing strategies since it improves the execution of inverse docking.
What designs for coming supercomputers? Vigouroux, Xavier
Proceedings of the Conference on Design, Automation and Test in Europe,
03/2013
Conference Proceeding
The next grail sought by HPC community is the exascale, 100 times the current scale. This target will not be reached easily as many challenges are uprising. The first challenge, the Energy ...consumption, has become a strict constraint now with a limit set to 20MW (twice as the current top supercomputers). Multiplying the computing elements will imply to drastically reduce the power consumption of each of them. The second challenge will be to keep it cool as: first the overall power envelope, 20MW, include the energy for cooling and second, because 20MW will be turned into heat by joule effect. And the operating temperature of electronic must be bounded otherwise, the leakage (and thus the power consumption) increases and the reliability decreases. This brings us to a third challenge regarding the reliability of the machine, the number of components will be tremendous, thus, the probability of having failing ones will increase. It has to be managed in such a way that applications will not be impacted by the failures. Finally, The last challenge is related to the software stack of these supercomputers, how will we manage billions of threads, how will we debug it,... New paradigms are currently being studied, for instance Bag of tasks, that try to tackle these aspects. These are the challenges we have to solve!! In this presentation, brightened up with insight into Bull roadmap, we present a possible future.
This document is one of the deliverable reports created for the ESCAPE project. ESCAPE stands for Energy-efficient Scalable Algorithms for Weather Prediction at Exascale. The project develops ...world-class, extreme-scale computing capabilities for European operational numerical weather prediction and future climate models. This is done by identifying Weather & Climate dwarfs which are key patterns in terms of computation and communication (in the spirit of the Berkeley dwarfs). These dwarfs are then optimised for different hardware architectures (single and multi-node) and alternative algorithms are explored. Performance portability is addressed through the use of domain specific languages. Here we summarize the work performed on optimizations of the dwarfs on CPUs, Xeon Phi, GPUs and on the Optalysys optical processor. We limit ourselves to a subset of the dwarf configurations and to problem sizes small enough to execute on a single node. Also, we use time-to-solution as the main performance metric. Multi-node optimizations of the dwarfs and energy-specific optimizations are beyond the scope of this report and will be described in Deliverable D3.4. To cover the important algorithmic motifs we picked dwarfs related to the dynamical core as well as column physics. Specifically, we focused on the formulation relevant to spectral codes like ECMWF's IFS code. The main findings of this report are: (a) Acceleration of 1.1x - 2.5x of the dwarfs on CPU based systems using compiler directives, (b) order of magnitude acceleration of the dwarfs on GPUs (23x for spectral transform, 9x for MPDATA) using data locality optimizations and (c) demonstrated feasibility of a spectral transform in a purely optical fashion.
PDF
