Training Week at Edinburgh

“Hey, thought this might be of interest…” A one line email with a link from my supervisor this spring. The website was of course,, and I did in fact, find it of interest. The opportunity to work in a

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Students participating in PRACE Summer of HPC 2018

The 23 projects for the Summer of HPC 2018 will start with the selected students listed at the application page. The programme will start with the training week at EPCC in Edinburgh and then continue directly at 11 PRACE hosting

PRACE Summer of HPC 2018 opens applications

Early-stage postgraduate and late-stage undergraduate students are invited to apply for the PRACE Summer of HPC 2018 programme, to be held in July & August 2018. Consisting of a training week and two months on placement at top HPC centres

Visualization schema for HPC data

Project reference: 1823 ParaView is ubiquitously used in HPC to provide insight to complex data structures often stored in custom data formats that require transformation before they can be visualised. Furthermore, information is dispersed at many places and one needs

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Hybrid-parallel Convolutional Neural Network training

Project reference: 1820 There is a lot of research around scaling out convolutional neural networks to a large number of compute nodes, as the computational requirements when training complex networks on large-scale datasets become prohibitive. However, most if not all

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Big Data clustering with RHadoop

Project reference: 1822 The project will consist of: Getting to know Hadoop and RHadoop; Creating and storing big data files (BD); Preparing BD for clustering task; Writing RHadoop code for performing clustering tasks with two clustering algorithms (e.g., k-means and

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Large scale accelerator enabled quantum simulator

Project reference: 1821 Although the topic of creating a scalable, efficient, quantum simulator has been actively pursued by multiple entities in the past years, due to the complexity of the solution required (for example multiple types of gates and formalisms)

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One kernel to rule them all

Project reference: 1819 Today’s multi-core, many-core and accelerator hardware provides a tremendous amount of floating point operations (FLOPs). However, CPU and GPU FLOPs cannot be harvested in the same manner. While the CPU is designed to minimize the latency of

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GraPhine meets CudeCD

Project reference: 1818 Simulations of classical or quantum field theories often rely on a lattice discretized version of the underlying theory. For example, simulations of Lattice Quantum Chromodynamics (QCD, the theory of quarks and gluons) are used to study properties

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Improving existing genomic tools for HPC infrastructure

Project reference: 1817 Since the emergence of the Next-Generation Sequencing technologies the number of genomics projects has risen exponentially. Human population genomics is an exciting field for research with significant outputs into clinical medicine. While there was just one human

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High-level Visualizations of Performance Data

Project reference: 1816 In the world of parallel programs, performance plays one of the key roles. There are mature tools (e.g. Scalasca) that enable to inspect the performance of an application, do analysis, and based on this, judge its performance.

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Investigating the effect of the oncogenic mutation E545K of the PI3Ka protein with enhanced sampling MD simulations

Project reference: 1815 The PI3Ka protein is the most commonly mutated kinase in human malignancies. One of the most common mutations is located in amino acid E545K, where a glutamic acid is replaced by lysine. It has been recently proposed

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High throughput Virtual Screening to discover novel drug candidates

Project reference: 1814 Structure-based drug discovery (SBDD) is becoming an essential tool in assisting fast and cost-efficient lead discovery and optimization. The application of rational, structure-based drug design is proven to be more efficient than the traditional way of drug

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Parallel Computing Demonstrations on Wee ARCHIE

Project reference: 1813 EPCC has developed a small, portable Raspberry-pi based cluster which is taken to schools, science festivals etc. to illustrate how parallel computers work. It is called “Wee ARCHIE” (in fact there are two versions in existence) because

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An alert system analysing data from environmental sensors

Project reference: 1811 The objective of the project will be to improve a data-hub framework (using Apache Kafka, Apache Spark, Elastic Search and Kibana) to collect and to monitor real time environmental data (air composition, groundwater quality, and seismicity data,

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Scheduling on Novel and Advanced Hardware

Project reference: 1812 The aim of this project is to explore the effects of upcoming novel hardware, such as NVRAM, on HPC job scheduling. By adapting a workload simulator that is being developed at EPCC to model new hardware, and by using traces

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Web Visualization and Data Analysis of energy Load of an HPC system

Project reference: 1810 Energy Efficiency is one of the timeliest problems in managing HPC facilities. Clearly this problem involves many technological issues, including, web visualization, interaction with HPC systems and schedulers, big data analysis, virtual machines manipulations, and authentication protocols. Our

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In Situ/Web Visualization of CFD Data Using OpenFOAM

Project reference: 1809 Visualization of cavitation is currently a very interesting topic. In the project, results from previous HPC simulations will be provided as a base to develop a visualization strategy based on advanced open-source tools. Starting from an already

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Machine learning from the HPC perspective

Project reference: 1808 This project is, to a large extent, a continuation of the last year’s SoHPC effort, where we demonstrated a notable increase of the efficiency of popular machine learning algorithms, such as K-means, when implemented using C/C++ and

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Electronic structure of nanotubes by utilizing the helical symmetry properties: The code parallelization

Project reference: 1807 In calculations of nanotubes methods prevailing are based on a one-dimensional translational symmetry using a huge unit cell. A pseudo two-dimensional approach, when the inherent helical symmetry of general chirality nanotubes is exploited and has been limited

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Multithreading the Multigrid Solver for lattice QCD

Project reference: 1806 This project will involve optimising lattice Quantum Chromodynamics (lattice QCD) codes, which currently run on PRACE Tier-0 and other European Peta-scale supercomputers. Lattice QCD is a method to study Quantum Chromodynamics, the theory which describes how quarks

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Enabling lattice QCD simulations on GPUs

Project reference: 1805 Lattice Quantum Chromodynamics (lattice QCD) can solve and predict physics in the low energy regime of particle physics where analytical methods such as perturbation theory are not applicable. Realistic simulations of QCD are carried out using Markov

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Dynamic management of resources simulator

Project reference: 1803 In this project we want to introduce the student to the field of malleability of scientific applications. We understand malleability as the capacity of a multi-process job to be resized on-the-fly, in other words, to change the

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Automatic Frequency Scaling for Embedded Co-processor Acceleration

Project reference: 1802 Energy minimization is critical in current and future computing platforms in fields such as HPC and embedded systems. While for the former it is a requirement to achieve exascale systems, the latter usually features strong power and/or

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Get more throughput, resize me! A case of study: LAMMPS malleable

Project reference: 1804 This project is based on LAMMPS, a classical molecular dynamics code, used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in

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