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Coauthored Publications

Below are a number publications where the involvement of ICHEC staff members has lead to their inclusion as coauthors.

Title:There Is No 16-Clue Sudoku: Solving the Sudoku Minimum Number of Clues Problem via Hitting Set Enumeration
Authors:G. McGuire, B. Tugemann and G. Civario, 2014
Abstract: The sudoku minimum number of clues problem is the following question: what is the smallest number of clues that a sudoku puzzle can have? For several years it had been conjectured that the answer is 17. We have performed an exhaustive computer search for 16-clue sudoku puzzles, and did not find any, thus proving that the answer is indeed 17. In this article we describe our method and the actual search. As a part of this project we developed a novel way for enumerating hitting sets. The hitting set problem is computationally hard; it is one of Karp’s 21 classic NP-complete problems. A standard backtracking algorithm for finding hitting sets would not be fast enough to search for a 16-clue sudoku puzzle exhaustively, even at today’s supercomputer speeds. To make an exhaustive search possible, we designed an algorithm that allowed us to efficiently enumerate hitting sets of a suitable size.
ICHEC Project:
Publication:Experimental Mathematics, vol 23, issue 2, 12 June 2014
URL: http://www.tandfonline.com/doi/abs/10.1080/10586458.2013.870056#.VKwcz1esVBA
Status: Published

Title:The Markov chain tree theorem and the state reduction algorithm in commutative semirings
Authors:B. Benek Gursoy, S. Kirkland, O. Mason and S. Sergeev, 2014
Abstract: We extend the Markov Chain Tree Theorem to general commutative semirings, and we generalize the State Reduction Algorithm to general commutative semifields. This leads to a new universal algorithm, whose prototype is the State Reduction Algorithm which computes the Markov chain tree vector of a stochastic matrix.
ICHEC Project:
Publication:To appear in Linear Algebra Appl., doi:10.1016/j.laa.2014.06.028
URL: http://www.sciencedirect.com/science/article/pii/S0024379514003978
Keywords: Markov chain, Universal algorithm
Status: Accepted

Title:Collective Mind: Towards practical and collaborative auto-tuning
Authors:G. Fursin, R. Miceli, A. Lokhmotov, M. Gerndt, M. Baboulin, A. D. Malony, Z. Chamski, D. Novillo and D. Del Vento, 2014
Abstract: Empirical auto-tuning and machine learning techniques have been showing high potential to improve execution time, power consumption, code size, reliability and other important metrics of various applications for more than two decades. However, they are still far from widespread production use due to lack of native support for auto-tuning in an ever changing and complex software and hardware stack, large and multi-dimensional optimization spaces, excessively long exploration times, and lack of unified mechanisms for preserving and sharing of optimization knowledge and research material. We present a possible collaborative approach to solve above problems using Collective Mind knowledge management system. In contrast with previous cTuning framework, this modular infrastructure allows to preserve and share through the Internet the whole auto-tuning setups with all related artifacts and their software and hardware dependencies besides just performance data. It also allows to gradually structure, systematize and describe all available research material including tools, benchmarks, data sets, search strategies and machine learning models. Researchers can take advantage of shared components and data with extensible meta-description to quickly and collaboratively validate and improve existing auto-tuning and benchmarking techniques or prototype new ones. The community can now gradually learn and improve complex behavior of all existing computer systems while exposing behavior anomalies or model mispredictions to an interdisciplinary community in a reproducible way for further analysis. We present several practical, collaborative and model-driven auto-tuning scenarios. We also decided to release all material at http://c-mind.org/repo to set up an example for a collaborative and reproducible research as well as our new publication model in computer engineering where experimental results are continuously shared and validated by the community.
ICHEC Project:
Publication:Scientific Programming, IOS Press, 2014, Automatic Application Tuning for HPC Architectures, 22 (4), pp.309-329
URL: https://hal.inria.fr/hal-01054763
Status: Published

Title:Equilibrium and Rate Constants, and Reaction Mechanism of the HF Dissociation in the HF(H2O)7 Cluster by ab Initio Rare Event Simulations
Authors:A. M. Elena, S. Meloni and G. Ciccotti, 2013
Abstract: We perform restrained hybrid Monte Carlo (MC) simulations to compute the equilibrium constant of the dissociation reaction of HF in HF(H2O)7. We find that the HF is a stronger acid in the cluster than in the bulk, and its acidity is higher at lower T. The latter phenomenon has a vibrational entropic origin, resulting from a counterintuitive balance of intra- and intermolecular terms. We find also a temperature dependence of the reactions mechanism. At low T (≤225 K) the dissociation reaction follows a concerted path, with the H atoms belonging to the relevant hydrogen bond chain moving synchronously. At higher T (300 K), the first two hydrogen atoms move together, forming an intermediate metastable state having the structure of an eigen ion (H9O4+), and then the third hydrogen migrates completing the reaction. We also compute the dissociation rate constant, kRP. At very low T (≤75 K) kRP depends strongly on the temperature, whereas it gets almost constant at higher T’s. With respect to the bulk, the HF dissociation in the HF(H2O)7 is about 1 order of magnitude faster. This is due to a lower free energy barrier for the dissociation in the cluster.
ICHEC Project:
Publication:The Journal of Physical Chemistry A, vol 117, issue 49, pp 13039-13050, 2013/12/2
URL: http://pubs.acs.org/doi/abs/10.1021/jp406982h
Status: Published

Title:On the Markov Chain Tree Theorem in the Max Algebra
Authors:B. Benek Gursoy, S. Kirkland, O. Mason and S. Sergeev, 2013
Abstract: A max-algebraic analogue of the Markov Chain Tree Theorem is presented, and its connections with the classical Markov Chain Tree Theorem and the max-algebraic spectral theory are investigated.
ICHEC Project:
Publication:Electronic Journal of Linear Algebra 26 (2013) 15-27
URL: http://repository.uwyo.edu/ela/vol26/iss1/2/
Keywords: Markov chains, Stochastic matrices, Directed spanning trees, Max algebra, Kleene star
Status: Published

Title:The analytic hierarchy process, max algebra and multi-objective optimisation
Authors:B. Benek Gursoy, O. Mason and S. Sergeev, 2013
Abstract: The analytic hierarchy process (AHP) is widely used for decision making involving multiple criteria. Elsner and van den Driessche (2004, 2010) [10,11] introduced a max-algebraic approach to the single criterion AHP. We extend this to the multi-criteria AHP, by considering multi-objective generalisations of the single objective optimisation problem solved in these earlier papers. We relate the existence of globally optimal solutions to the commutativity properties of the associated matrices; we relate min–max optimal solutions to the generalised spectral radius; and we prove that Pareto optimal solutions are guaranteed to exist.
ICHEC Project:
Publication:Linear Algebra Appl. 438 (2013) 2911-2928.
URL: http://www.sciencedirect.com/science/article/pii/S0024379512008257
Keywords: Analytic hierarchy process (AHP); SR-matrix; Max algebra; Subeigenvector; Generalised spectral radius; Multi-objective optimization
Status: Published

Title:Wind Forecasting using HARMONIE with Bayes Model Averaging for Fine Tuning
Authors:M. Peters, E. O'Brien, A. McKinstry and A. Ralph, 2013
Abstract: Wind-speed forecasts for a wind-farm in southwest Ireland were made for over one year using the operational HARMONIE mesoscale weather forecast model, and Bayes Model Averaging (BMA) for statistical post-processing to remove systematic local bias. The deterministic forecasts alone generated mean absolute errors of 1.7−2.0 ms-1 out to 24hrs, when interpolated to the location of the met-mast. Application of BMA reduced these errors by about 15%, to 1.5−1.6 ms-1, on average. Forecast errors do not degrade significantly as forecast lead-time increases, at least out to 24 hours.
ICHEC Project:
Publication:Energy Procedia 40 (2013), 95-101
URL: http://www.sciencedirect.com/science/article/pii/S1876610213016068
Keywords: wind-farm; forecasting; HARMONIE; Bayes Model Averaging
Status: Published

Title:Failure modelling of trabecular bone using a non-linear combined damage and fracture voxel finite element approach
Authors:N. M. Harrison, P. McDonnell, L. Mullins, N. Wilson, D. O’Mahoney and P. E. McHugh, 2013
Abstract: Trabecular bone tissue failure can be considered as consisting of two stages: damage and fracture; however, most failure analyses of 3D high-resolution trabecular bone samples are confined to damage mechanisms only, that is, without fracture. This study aims to develop a computational model of trabecular bone consisting of an explicit representation of complete failure, incorporating damage criteria, fracture criteria, cohesive forces, asymmetry and large deformation capabilities. Following parameter studies on a test specimen, and experimental testing of bone sample to complete failure, the asymmetric critical tissue damage and fracture strains of ovine vertebral trabecular bone were calibrated and validated to be compression damage −1.16%, tension damage 0.69%, compression fracture −2.91% and tension fracture 1.98%. Ultimate strength and post–ultimate strength softening were captured by the computational model, and the failure of individual struts in bending and shear was also predicted. This modelling approach incorporated a cohesive parameter that provided a facility to calibrate ductile–brittle behaviour of bone tissue in this nonlinear geometric and non-linear constitutive property analyses tool. Finally, the full accumulation of tissue damage and tissue fracture has been monitored from range of small magnitude (normal daily loading) through to specimen yielding, ultimate strength and post–ultimate strength softening.
ICHEC Project:
Publication:Biomechanics and Modeling in Mechanobiology, vol 12, issue 2, pp 225-241, 2013
URL: http://link.springer.com/article/10.1007%2Fs10237-012-0394-7
Keywords: Trabecular · Damage · Cancellous · Fracture · Failure · Voxel · Finite element · Bone
Status: Published

Title:Enabling Smeagol on Xeon Phi: Lessons Learned
Authors:Alin M. Elena, Ivan Rungger, 2014
Abstract: The aim of the work is to port the quantum electron transport code Smeagol to the Intel Xeon Phi (MIC) based hybrid architecture. Smeagol is based on density functional theory, and utilises the non-equilibrium Green's function formalism (NEGF) to calculate the charge density at an applied bias voltage. We successfully ported Smeagol to run in native mode on the MIC, however for small systems the run-time on the host is always significantly shorter than the one on the MIC. It is not possible to run large systems on a single MIC due to memory limits. For large systems we adopt a different strategy for efficiently using this hybrid architecture: we propose to run most of the calculation on a number of host processors, distributed over a set of nodes, using MPI, and to port only the most time-consuming operations to the MIC for each host. This allows us to take advantage of the large memory on the host, which enables calculations for large systems. We show that in Smeagol the most time-consuming operation is the inversion required to obtain the Green's function within the NEGF formalism. Our results indicate that for sufficiently large systems our implementation of the recursive Green's functions (RGF) inversion algorithm can indeed run faster on the MIC plus host setup than on the host. This is also true for the whole Smeagol code utilised in such an offload mode.
ICHEC Project:
Publication:PRACE Whitepaper
URL: http://www.prace-ri.eu/IMG/pdf/wp134.pdf
Keywords: Xeon Phi, Smeagol
Status: Published

Title:An Analysis of State of the Art Tools for Preparing DL_POLY_4 for Exascale
Authors:B. Benek Gursoy and H. R. Nagel, 2014
Abstract: This whitepaper investigates the potential benefit of using the OpenACC directive-based programming tool for enabling DL_POLY_4 on GPUs. DL_POLY is a well-known general-purpose molecular dynamics simulation package, which has already been parallelised using MPI-2. DL_POLY_3 was accelerated using the CUDA framework by the Irish Centre for High-End Computing (ICHEC) in collaboration with Daresbury Laboratory. In this work, we have been inspired by the existing CUDA port to evaluate the effectiveness of OpenACC in further enabling DL_POLY_4 on the road to Exascale. We have been particularly concerned with investigating the benefits of OpenACC in terms of maintainability, programmability and portability issues that are becoming increasingly challenging as we advance to the Exascale era. The impact of the OpenACC port has been assessed in the context of a change in the reciprocal vector dimension for the calculation of SPME forces. Moreover, the interoperability of OpenACC with the existing CUDA port has been analysed.
ICHEC Project:
Publication:PRACE Whitepaper, 2014.
URL: www.prace-ri.eu/IMG/pdf/wp156.pdf
Status: Published

Title:Enabling the UCD-SPH code on the Xeon Phi
Authors:Christian Lalanne, Ashkan Rafiee, Denys Dutykh, Michael Lysaght, Frederic Dias, 2014
Abstract: This white-paper reports on our efforts to enable an SPH-based Fortran code on the Intel Xeon Phi. As a result of the work described here, the two most computationally intensive subroutines (rates and shepard_beta) of the UCD-SPH code were refactored and parallelised with OpenMP for the first time, enabling the code to be executed on multi-core and many-core shared memory systems. This parallelisation achieved speedups of up to 4.3x for the rates subroutine and 6.0x for the shepard_beta subroutine resulting in overall speedups of up to 4.2x on a 2 processor Sandy Bridge Xeon E5 machine. The code was subsequently enabled and refactored to execute in different modes on the Intel Xeon Phi co-processor achieving speedups of up to 2.8x for the rates subroutine and up to 3.8x for the shepard_beta subroutine producing overall speedups of up to 2.7x compared to the original unoptimised code. To explore the capabilities of auto-vectorisation the shepard_beta subroutine was refactored which results in speedups of up to 6.4x for the shepard_beta subroutine relative to the original unoptimised version of the shepard_beta subroutine. The development and testing phases of the project were carried out on the PRACE EURORA machine.
ICHEC Project:
Publication:White paper 131 for the PRACE project, First Implementation Phase, Work Package 7, February 2014
URL: http://www.prace-ri.eu/IMG/pdf/wp131.pdf
Status: Published

Title:Scaling Coupled Climate Models to Exascale: OpenACC-enabled EC-Earth3, Earth System Model
Authors:P. Nolan and A. McKinstry, 2014
Abstract: Climate change due to increasing anthropogenic greenhouse gases and land surface change is currently one of the most relevant environmental concerns. It threatens ecosystems and human societies. However, its impact on the economy and our living standards depends largely on our ability to anticipate its effects and take appropriate action. Earth System Models (ESMs), such as EC-Earth, can be used to provide society with information on the future climate. EC-Earth3 generates reliable predictions and projections of global climate change, which are a prerequisite to support the development of national adaptation and mitigation strategies. This project investigates methods to enhance the parallel capabilities of EC-Earth3 by offloading bottleneck routines to GPUs and Intel Xeon Phi coprocessors. To gain a full understanding of climate change at a regional scale will require EC-Earth3 to be run at a much higher spatial resolution (T3999 ~5km) than is currently feasible. It is envisaged that the work outlined in this project will provide climate scientists with valuable data for simulations planned for future exascale systems.
ICHEC Project:
Publication:PRACE Whitepaper, 2014
URL: http://www.prace-ri.eu/IMG/pdf/wp166.pdf
Status: Published

Title:Performance Improvement in Kernels by Guiding Compiler Auto-Vectorization Heuristics
Authors:W. Killian, R. Miceli, E. Park, M. Alvarez Vega and J. Cavazos, 2014
Abstract: Vectorization support in hardware continues to expand and grow as we still continue on superscalar architectures. Unfortunately, compilers are not always able to generate optimal code for the hardware; detecting and generating vectorized code is extremely complex. Programmers can use a number of tools to aid in development and tuning, but most of these tools require expert or domain-specific knowledge to use. In this work we aim to provide techniques for determining the best way to optimize certain codes, with an end goal of guiding the compiler into generating optimized code without requiring expert knowledge from the developer. Initially, we study how to combine vectorization reports with iterative compilation and code generation and summarize our insights and patterns on how the compiler vectorizes code. Our utilities for iterative compilation and code generation can be further used by non-experts in the generation and analysis of programs. Finally, we leverage the obtained knowledge to design a Support Vector Machine classifier to predict the speedup of a program given a sequence of optimization. We show that our classifier is able to predict the speedup of 56% of the inputs within 15% overprediction and 50% underprediction, with 82% of these accurate within 15% both ways.
ICHEC Project:
Publication:PRACE Whitepaper, 2014
URL: www.prace-ri.eu/IMG/pdf/WP183.pdf
Status: Published

Title:Investigating Performance Benefits from OpenACC Kernel Directives
Authors:Benjamin Eagan, Gilles Civario, Renato Miceli, 2014
Abstract: OpenACC is a high-level programming model that uses directives for offloading computation to accelerators. This paper explores the benefit of using OpenACC performance tuning directives to manually specify GPU scheduling, versus the scheduling OpenACC applies by default. We performed manual scheduling using gang and vector clauses in a directive, and applied to matrix-matrix multiply and Classical Gram-Schmidt orthonormalisation test cases. We then tested using the NVIDIA M2090 and K20 GPGPUs, in conjunction with both the PGI and CAPS implementations of OpenACC. The speedup realised by tuning the gang and vector values ranged from 1.0 to 3.1 in the test cases examined. This shows that the gang and vector values have a large impact on performance, and in some cases the compilers are able to automatically select ideal gang and vector values.
ICHEC Project:
Publication:Proc. of the 2013 International Conference on Parallel Computing (ParCo 2013). Parallel Computing: Accelerating Computational Science and Engineering (CSE), Advances in Parallel Computing, IOS Press. Munich, Germany. vol 25, p 616-625. March 2014
URL: http://dx.doi.org/10.3233/978-1-61499-381-0-616
Keywords: OpenACC; GPGPU Computing; Software Tuning
Status: Published

Title:Gene Expression and epigenetic discovery screen reveal methylation of SFRP2 in prostate cancer
Authors:Perry A., O'Hurley G., Raheem O.A., Brennan K., Wong S., O'Grady A., Kennedy A.-M., Marignol L., Murphy T.M., Sullivan L., Barrett C., Loftus B., Thornhill J., Hewitt S.M., Lawler M., Kay E., Lynch T. and Hollywood D., 2013
Abstract: Aberrant activation of Wnts is common in human cancers, including prostate. Hypermethylation associated transcriptional silencing of Wnt antagonist genes SFRPs (Secreted Frizzled-Related Proteins) is a frequent oncogenic event. The significance of this is not known in prostate cancer. The objectives of this study were to (1) profile Wnt signaling related gene expression and (2) investigate methylation of Wnt antagonist genes in prostate cancer. Using TaqMan Low Density Arrays, we identified 15 Wnt signaling related genes with significantly altered expression in prostate cancer; the majority of which were upregulated in tumors. Notably, histologically benign tissue from men with prostate cancer appeared more similar to tumor (r=0.76) than to benign prostatic hyperplasia (BPH) (r=0.57) (P<0.001). Overall, the expression profile was highly similar between tumors of high (≥7) and low (≤6) Gleason scores. Pharmacological demethylation of PC-3 cells with 5-Aza-CdR reactivated 39 genes (≥2-fold); 40% of which inhibit Wnt signaling. Methylation frequencies in prostate cancer were 10% (2/20) (SFRP1), 64.86% (48/74) (SFRP2), 0% (0/20) (SFRP4) and 60% (12/20) (SFRP5). SFRP2 methylation was detected at significantly lower frequencies in high-grade prostatic intraepithelial neoplasia (HGPIN) (30%, 6/20), P=0.0096), tumor adjacent benign areas (8.82%, 7/69 P<0.0001) and BPH (11.43% (4/35), P<0.0001). The quantitative level of SFRP2 methylation (normalised index of methylation, NIM) was also significantly higher in tumors (116) than in the other samples (HGPIN=7.45, HB=0.47 and BPH=0.12). We show that SFRP2 hypermethylation is a common event in prostate cancer. SFRP2 methylation in combination with other epigenetic markers may be a useful biomarker of prostate cancer.
ICHEC Project:
Publication:International Journal of Cancer (2013) 132:1771-1780.
URL: http://dx.doi.org/10.1002/ijc.27798
Keywords: SFRP2; Prostate cancer; Hypermethylation; Wnt signaling
Status: Published

Title:Integrated Virtual Screening for the Identification of Novel and Selective Peroxisome Proliferator-Activated Receptor (PPAR) Scaffolds
Authors:Daniel K. Nevin, Martin B. Peters, Giorgio Carta, Darren Fayne, and David G. Lloyd, 2012
Abstract: We describe a fully customizable and integrated target-specific “tiered” virtual screening approach tailored to identifying and characterizing novel peroxisome proliferator activated receptor γ (PPARγ) scaffolds. Built on structure- and ligand-based computational techniques, a consensus protocol was developed for use in the virtual screening of chemical databases, focused toward retrieval of novel bioactive chemical scaffolds for PPARγ. Consequent from application, three novel PPAR scaffolds displaying distinct chemotypes have been identified, namely, 5-(4-(benzyloxy)-3-chlorobenzylidene)dihydro-2-thioxopyrimidine-4,6(1H,5H)-dione (MDG 548), 3-((4-bromophenoxy)methyl)-N-(4-nitro-1H-pyrazol-1-yl)benzamide (MDG 559), and ethyl 2-[3-hydroxy-5-(5-methyl-2-furyl)-2-oxo-4-(2-thienylcarbonyl)-2,5-dihydro-1H-pyrrol-1-yl]-4-methyl-1,3-thiazole-5-carboxylate (MDG 582). Fluorescence polarization(FP) and time resolved fluorescence resonance energy transfer (TR-FRET) show that these compounds display high affinity competitive binding to the PPARγ-LBD (EC50 of 215 nM to 5.45 μM). Consequent characterization by a TR-FRET activation reporter assay demonstrated agonism of PPARγ by all three compounds (EC50 of 467–594nM). Additionally, differential PPAR isotype specificity was demonstrated through assay against PPARα and PPARδ subtypes. This work showcases the ability of target specific “tiered screen” protocols to successfully identify novel scaffolds of individual receptor subtypes with greater efficacy than isolated screening methods.
ICHEC Project:PPARgamma Tiered Virtual Screening- Development of an Improved Post-Hit Scoring Process
Publication:J. Med. Chem., Article ASAP, May 14, 2012
URL: http://pubs.acs.org/doi/abs/10.1021/jm300068n
Keywords: Virtual Screening;drug discovery;workflows
Status: Published

Title:A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags
Authors:Tyson T., O'Mahony Zamora G., Wong S., Skelton M., Daly B., Jones J.T., Mulvihill E.D., Elsworth B., Phillips M., Blaxter M. and Burnell A.M., 2012
Abstract:

Background:
Some organisms can survive extreme desiccation by entering into a state of suspended animation known as anhydrobiosis. Panagrolaimus superbus is a free-living anhydrobiotic nematode that can survive rapid environmental desiccation. The mechanisms that P. superbus uses to combat the potentially lethal effects of cellular dehydration may include the constitutive and inducible expression of protective molecules, along with behavioural and/or morphological adaptations that slow the rate of cellular water loss. In addition, inducible repair and revival programmes may also be required for successful rehydration and recovery from anhydrobiosis.

Results
To identify constitutively expressed candidate anhydrobiotic genes we obtained 9,216 ESTs from an unstressed mixed stage population of P. superbus. We derived 4,009 unigenes from these ESTs. These unigene annotations and sequences can be accessed at http://www.nematodes.org/nembase4/species_info.php?species=PSC. We manually annotated a set of 187 constitutively expressed candidate anhydrobiotic genes from P. superbus. Notable among those is a putative lineage expansion of the lea (late embryogenesis abundant) gene family. The most abundantly expressed sequence was a member of the nematode specific sxp/ral-2 family that is highly expressed in parasitic nematodes and secreted onto the surface of the nematodes' cuticles. There were 2,059 novel unigenes (51.7% of the total), 149 of which are predicted to encode intrinsically disordered proteins lacking a fixed tertiary structure. One unigene may encode an exo-beta-1,3-glucanase (GHF5 family), most similar to a sequence from Phytophthora infestans. GHF5 enzymes have been reported from several species of plant parasitic nematodes, with horizontal gene transfer (HGT) from bacteria proposed to explain their evolutionary origin. This P. superbus sequence represents another possible HGT event within the Nematoda. The expression of five of the 19 putative stress response genes tested was upregulated in response to desiccation. These were the antioxidants glutathione peroxidase, dj-1 and 1-Cys peroxiredoxin, an shsp sequence and an lea gene.

Conclusions
P. superbus appears to utilise a strategy of combined constitutive and inducible gene expression in preparation for entry into anhydrobiosis. The apparent lineage expansion of lea genes, together with their constitutive and inducible expression, suggests that LEA3 proteins are important components of the anhydrobiotic protection repertoire of P. superbus.

ICHEC Project:Transcriptomic and Genomic Analyses of the Nematode Panagrolaimus superbus
Publication:BMC Research Notes (2012) 5:68
URL: http://dx.doi.org/10.1186/1756-0500-5-68
Status: Published

Title:Transitioning a message passing interface wavefront sensor model to a graphics processor environment
Authors:Michael T. Browne, Renato Miceli, 2011
Abstract: Previous work produced a parallel and moderately scalable wavefront sensor model as part of a larger integrated telescope model. This relied on traditional high performance computing (HPC) techniques using optimised C and MPI based parallelism to marry maximum performance with the productive high-level modelling environment of MATLAB. In the intervening period the computational power and flexibility offered by graphics processors (GPUs) has increased dramatically. This presents both new options in terms of the level of hardware required to perform simulations and also new capabilities in terms of the scope of such simulations. We present a discussion of the currently available approaches and test case performance results based on a port to a GPU platform.
ICHEC Project:
Publication:Integrated Modeling of Complex Optomechanical Systems, Proceedings Vol. 8336, DOI: 10.1117/12.915921
URL: http://dx.doi.org/10.1117/12.915921
Keywords: GPU MATLAB Wavefront sensor
Status: Published

Title:The Eyjafjallajökull ash plume – Part 2: Simulating ash cloud dispersion with REMOTE
Authors:C. O'Dowd, S. Varghese, D. Martin, R. Flanagan, A. McKinstry, D. Ceburnis, J. Ovadnevaite, G. Martucci, J. Bialek, C. Monahan, H. Berresheim, A. Vaishya, T. Grigas, Z. McGraw, S.G. Jennings, B. Langmann, T. Semmler, R. McGrath, 2011
Abstract: The recent eruption of Iceland's Eyjafjallajökull volcano caused extensive disruption across Europe. In this paper, we describe the volcanic ash parameterisation incorporated in the regional climate model (REMOTE) for forecasting volcanic ash dispersion. We investigate model sensitivity to emission parameters including eruption column height and vertical release distribution. Model results over a number of key ash incursion events are assessed in terms of agreement with both ground based measurements and retrieved LIDAR data at a number of European sites.
ICHEC Project:
Publication:DOI:10.1016/j.atmosenv.2011.10.037
URL: http://www.sciencedirect.com/science/article/pii/S1352231011011113
Keywords: Volcano, Ash, REMOTE, Eyjafjallajokull; Volcanic ash; Dispersion; Modelling
Status: Published

Title:The impact of Arctic sea ice on the Arctic energy budget and on the climate of the Northern mid- latitudes
Authors:Tido Semmler, Raymond McGrath, Shiyu Wang, 2012
Abstract: The atmospheric general circulation model EC-EARTH-IFS has been applied to investigate the influence of both a reduced and a removed Arctic sea ice cover and therefore a reduced meridional temperature gradient on the climate of the Northern mid-latitudes. Three 40-year simulations driven by original and modified ERA-40 sea surface temperatures and sea ice distributions have been performed at T255L62 resolution, corresponding to about 50 km horizontal resolution. Simulated changes between sensitivity and reference experiments are most pronounced over the Arctic itself where the reduced or removed sea ice leads to strongly increased upward heat and longwave radiation fluxes and precipitation in winter. In summer, the most pronounced change is the stronger absorption of shortwave radiation which is enhanced by optically thinner clouds. Averaged over the year and over the area north of 70° N, the negative energy imbalance at the top of the atmosphere decreases by about 10 W/m2 in both sensitivity experiments. The energy transport across 70° N is reduced as a result of the decreased temperature gradient. Changes are not restricted to the Arctic. A weaker pressure gradient, less extreme cold events and less precipitation are simulated in sub-Arctic and Northern mid- latitude regions in winter
ICHEC Project:Simulating the Global Climate with the EC-EARTH Coupled Atmosphere-Ocean-Ice Model
URL: http://ecearth.knmi.nl/Semmleretal.pdf
Keywords: climate, EC-EARTH
Status: Submitted

Title:EC-EARTH: A seamless earth system prediction approach in action
Authors:Hazeleger, W., Severijns, C., Semmler, T., Stefanescu, S., Yang, S., Wang, X., Wyser, K., Baldasano, J. M., Bintanja, R., Bougeault, P., Caballero, R., Dutra, E., Ekman, A. M. L., Christensen, J. H., van den Hurk, B., Jimenez, P., Jones, C., Kallberg, P., Koenigk, T., McGrath, R., Miranda, P., van Noije, T., Parodi, J. A., Schmith, T., Selten, F., Storelvmo, T., Sterl, A., Tapamo, H., Vancoppenolle, M., Viterbo, P., and Willen, U., 2010
ICHEC Project:Simulating the Global Climate with the EC-EARTH Coupled Atmosphere-Ocean-Ice Model
Publication:Bulletin of the American Meteorological Society,
URL: http://www.ametsoc.org/PUBS/bams/
Status: Published

Title:A prediction of cell differentiation and proliferation within a collagen-glycosaminoglycan scaffold subjected to mechanical strain and perfusive fluid flow
Authors:AJF Stops, KB Heraty, M Browne, FJ O’Brien, PE McHugh, 2010
Abstract: scaffold strain magnitudes and inlet fluid velocities to specific cell responses are thus far underdeveloped. This investigation attempted to simulate cell responses in a collagen–glycosaminoglycan (CG) scaffold within a bioreactor. CG scaffold deformation was simulated using μ-computed tomography (CT) and an in-house finite element solver (FEEBE/linear). Similarly, the internal fluid velocities were simulated using the afore-mentioned μCT dataset with a computational fluid dynamics solver (ANSYS/CFX). From the ensuing cell-level mechanics, albeit octahedral shear strain or fluid velocity, the proliferation and differentiation of the representative cells were predicted from deterministic functions. Cell proliferation patterns concurred with previous experiments. MSC differentiation was dependent on the level of CG scaffold strain and the inlet fluid velocity. Furthermore, MSC differentiation patterns indicated that specific combinations of scaffold strains and inlet fluid flows cause phenotype assemblies dominated by single cell types. Further to typical laboratory procedures, this predictive methodology demonstrated loading-specific differentiation lineages and proliferation patterns. It is hoped these results will enhance in-vitro tissue engineering procedures by providing a platform from which the scaffold loading applications can be tailored to suit the desired tissue.
ICHEC Project:A FINITE ELEMENT ANALYSIS OF THE MICROSCALE FORCES THAT DRIVE CELL-DERIVED TISSUE FORMATION: A TISSUE ENGINEERING SOLUTION
Publication:Journal of Biomechanics, vol. 43, pp. 618-626, DOI: 10.1016/j.jbiomech.2009.10.037
URL: http://www.jbiomech.com/
Keywords: Collagen–glycosaminoglycan scaffold, Perfusion bioreactor, Tissue engineering
Status: Published

Title:Dispersion analysis and computational efficiency of elastic lattice methods for seismic wave propagation
Authors:O'Brien G.S., Bean C.J. and Tapamo H., 2009
Abstract: Discrete particle methods or elastic lattice methods represent a 3D elastic solid by a series of interconnected springs arranged on a regular lattice. Generally, these methods only consider nearest neighbour interactions, i.e. they are first-order in space. These interconnected springs interacted through a force term (Hooke's Law for an elastic body), which when viewed on a macroscopic scale provide a numerical solution for the elastodynamic wave equations. Along with solving the elastodynamic wave equations these schemes are capable of simulating elastic static deformation. However, as these methods rely on nearest neighbour interactions they suffer from more pronounced numerical dispersion than traditional continuum methods. By including a new force term, the numerical dispersion can be reduced while keeping the flexibility of the nearest neighbour interaction rule. We present results of simulations where the additional force term reduces the numerical dispersion and increases the accuracy of the elastic lattice method solution. The computational efficiency and parallel scaling of this method on multiple processors is compared with a finite-difference solution to assess the computational cost of using this approach for simulating seismic wave propagation. We also show the applicability of this method to modelling seismic propagation in a complex Earth model.
ICHEC Project:Seismic source modelling and wave propagation in volcanoes
Publication:Computers & Geosciences (2009) 35:1768-1775
URL: http://dx.doi.org/10.1016/j.cageo.2008.12.004
Keywords: Computational seismic wave propagation; Discrete particle method; Elastic lattice method; Numerical seismic dispersion
Status: Published

Title:Spectrum of the non-abelian phase in Kitaev’s honeycomb lattice model
Authors:Lahtinen V., Kells G., Carollo A., Stitt T., Vala J. and Pachos J.K., 2008
Abstract: The spectral properties of Kitaev's honeycomb lattice model are investigated both analytically and numerically with the focus on the non-abelian phase of the model. After summarizing the fermionization technique which maps spins into free Majorana fermions, we evaluate the spectrum of sparse vortex configurations and derive the interaction between two vortices as a function of their separation. We consider the effect vortices can have on the fermionic spectrum as well as on the phase transition between the abelian and non-abelian phases. We explicitly demonstrate the 2n-fold ground state degeneracy in the presence of 2n well separated vortices and the lifting of the degeneracy due to their short-range interactions. The calculations are performed on an infinite lattice. In addition to the analytic treatment, a numerical study of finite size systems is performed which is in exact agreement with the theoretical considerations. The general spectral properties of the non-abelian phase are considered for various finite toroidal systems.
ICHEC Project:Topological phases in quantum lattice systems
Publication:Annals of Physics (2008) 323:2286-2310
URL: http://dx.doi.org/10.1016/j.aop.2007.12.009
Keywords: Topological models; Non-abelian vortices; Kitaev's model
Status: Published

Title:Shoreline approximation for unstructured mesh generation
Authors:G.J. Gorman, D. Piggott, and C.C. Pain, 2007
Abstract: A new method for approximating shorelines (polygons and polylines) is presented. The algorithm differs from commonly used Douglas-Peucker type algorithms as the method can approximate to some feature error given the constraint that edge lengths must satisfy some minimum edge length criteria. This constraint is necessary for the shoreline approximation to be useful for unstructured mesh generation for ocean modelling. In addition the method applies local optimisations to iteratively improve the shoreline approximation. Applications of the method are presented.
ICHEC Project:Parallel unstructured adaptive mesh method for three-dimensional range-of-scale ocean modelling
Publication:Computers & Geosciences, to appear
Keywords: simplification; shoreline; mesh generation; ocean modelling
Status: Accepted