MERIC and RADAR generator: tools for energy evaluation and runtime tuning of HPC applications

This paper introduces two tools for manual energy evaluation and runtime tuning developed at IT4Innovations in the READEX project. The MERIC library can be used for manual instrumentation and analysis of any application from the energy and time consumption point of view. Besides tracing, MERIC can also change environment and hardware parameters during the application runtime, which leads to energy savings. MERIC stores large amounts of data, which are difficult to read by a human. The RADAR generator analyses the MERIC output files to find the best settings of evaluated parameters for each instrumented region. It generates a Open image in new window report and a MERIC configuration file for application production runs

Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes

<p>Abstract</p> <p>Background</p> <p>Annelida is one of the major protostome phyla, whose deep phylogeny is very poorly understood. Recent molecular phylogenies show that Annelida may include groups once considered separate phyla (Pogonophora, Echiurida, and Sipunculida) and that Clitellata are derived polychaetes. SThe "total-evidence" analyses combining morphological and molecular characters have been published for a few annelid taxa. No attempt has yet been made to analyse simultaneously morphological and molecular information concerning the Annelida as a whole.</p> <p>Results</p> <p>Phylogenetic relationships within Annelida were analysed on the basis of 93 morphological characters and sequences of six genes (<it>18S</it>, <it>28S</it>, and <it>16S rRNA</it>, <it>EF1α</it>, <it>H3</it>, <it>COI</it>), altogether, 87 terminals of all annelid "families" and 3,903 informative characters, by Bayesian and maximum-parsimony methods. The analysis of the combined dataset yields the following scheme of relationships: Phyllodocida and Eunicida are monophyletic groups, together probably forming monophyletic Aciculata (incl. Orbiniidae and Parergodrilidae that form a sister group of the Eunicida). The traditional "Scolecida" and "Canalipalpata" are both polyphyletic, forming instead two clades: one including Cirratuliformia and the "sabelloid-spionoid clade" (incl. <it>Sternaspis</it>, Sabellidae-Serpulidae, Sabellariidae, Spionida s.str.), the other ("terebelloid-capitelloid clade") including Terebelliformia, Arenicolidae-Maldanidae, and Capitellidae-Echiurida. The Clitellata and "clitellate-like polychaetes" (Aeolosomatidae, Potamodrilidae, <it>Hrabeiella</it>) form a monophyletic group. The position of the remaining annelid groups is uncertain – the most problematic taxa are the Opheliidae-Scalibregmatidae clade, the Amphinomida-<it>Aberranta </it>clade, <it>Apistobranchus</it>, Chaetopteridae, Myzostomida, the Sipunculida-Dinophilidae clade, and the "core Archiannelida" (= Protodrilidae, Nerillidae, Polygordiidae, Saccocirridae).</p> <p>Conclusion</p> <p>The combined ("total-evidence") phylogenetic analysis provides a modified view of annelid evolution, with several higher-level taxa, i.e. Phyllodocida, Eunicida, orbinioid-parergodrilid clade (OPC), Cirratuliformia, sabelloid-spionoid clade (SSC), terebelloid-capitelloid clade (TCC), and "Clitellatomorpha". Two unorthodox clades, the "core Archiannelida" and Sipunculida-Dinophilidae, are proposed. Although the deep-level evolutionary relationships of Annelida remain poorly understood, we propose the monophyly of the Aciculata, sister-group relationships between the Eunicida and OPC, between the Cirratuliformia and SSC, and possibly also between the "Clitellatomorpha" and Oweniidae-Pogonophora clades.</p

Procjena onečiščenja podzemnih voda na području bivšeg vojnog aerodroma

The analysis of groundwater contamination at the former military airport, due to fuel tanks leakage and other accidental spills, mainly involving polycyclic aromatic hydrocarbons (PAH), is presented in the paper. It was observed by modelling that, after termination of pumping, the contaminant by-passes the slurry wall around its edges and proceeds towards the withdrawal area. The modelling showed that the water contamination hazard is quite low, which is mainly due to pollutant deterioration (decay) and sorption. Systematic and long-term groundwater quality monitoring is recommended once pumping at the barrier is stopped.Rad se bavi analizom onečiščenja podzemnih voda na području bivšeg vojnog aerodroma uzrokovanog curenjem goriva iz spremnika te drugim slučajnimi izlijevnjemonečiščivača, uglavnom policikličkih arometskih ugljikovodika (PAH). Modeliranjem je zamiječeno da nakon prestanka crpljenja zagadivač zaobilazi brtveni zid oko njegovih rubova te se natavlja kretati prema području gdje se zahvača voda. Ovim modelom zaključeno je da postoji niska razina opasnosti od zagadenja, uglavnom zbog utjecaja raspada (razhradnje) zagadivača te sorpcije. Preporučeno je dugoročno i sustavno pračenje kvalitete podzemnih voda nakon prestanka crpljenja vode

Dam Break Modeling in a Cascade of Small EarthenDams: Case Study of the Cizina River in the Czech Republic

Failures of small dams can pose a serious threat to people and property even if the size of the schemes is relatively low. In many cases, small dams are situated in a cascade along streams, meaning that the failure of the uppermost dam may cause the dams downstream to fail. In this paper, a cascade of three small reservoirs, Lichnov II (14.6 m high), Lichnov III (10 m high), and Pochen (8.5 m high), is the subject of the dam break analyses carried out via various methods such as empirical formulae, analogy, and hydraulic modeling. The dam-break flood routing was simulated using a shallow water flow hydraulic model. The simulations confirm that the attenuation effect of the peak discharge is governed by the flood volume, slope, and morphology of the floodplain and increases with the distance from the breached dam following an approximately exponential trend. When estimating peak discharge, empirical formulae derived for a single dam break should be applied carefully as they may underestimate the peak outflow by up to 10% in the case of a dam cascade. The attenuation volume of small reservoirs is small when compared to the flood volume, meaning that the attenuation of the peak discharge usually varies between 5–10%.Poruchy malých hrází mohou představovat vážné ohrožení lidí a majetku, i když je velikost nádrží relativně nízká. V mnoha případech jsou malé nádrže umístěny v kaskádě podél toků, což znamená, že selhání horní hráze může způsobit selhání hrází po proudu. V tomto článku je uvedena kaskáda tří malých nádrží, Lichnov II (14,6 m vysoká), Lichnov III (10 m vysoká) a Pocheň (8,5 m vysoká). Analýza porušení jednotlivých přehrad byla prováděna pomocí různých metod, jako jsou empirické vzorce, analogie a hydraulické modelování. Proudění pod hrází bylo simulováno pomocí hydraulického modelu mělkého toku. Simulace potvrzují, že útlumový efekt kulminačního průtoku je ovlivněn objemem povodně, sklonem a morfologií nivy a se zvyšující se vzdáleností od porušené hráze stoupá útlumový efekt podle přibližně pomocí exponenciálního trendu. Při odhadu kulminačního průtoku by měly být použity empirické vzorce odvozené pro jednotlivá porušení hrází, protože v případě kaskády přehrad mohou podceňovat kulminační průtok až o 10%. Útlumový objem malých nádrží je ve srovnání s objemem povodní malý, což znamená, že útlum kulminačního průtoku nádrží se obvykle pohybuje mezi 5–10%

The energy consumption optimization of the BLAS routines

The paper deals with the energy consumption evaluation of selected Sparse and Dense BLAS Level 1, 2 and 3 routines. Authors employed AXPY, Sparse Matrix-Vector, Sparse Matrix-Matrix, Dense Matrix-Vector, Dense Matrix-Matrix and Sparse Matrix-Dense Matrix multiplication routines from Intel Math Kernel Library (MKL). The measured characteristics illustrate the different energy consumption of BLAS routines, as some operations are memory-bounded and others are compute-bounded. Based on their recommendations one can explore dynamic frequency switching to achieve significant energy savings up to 23%

Domain knowledge specification for energy tuning

To overcome the challenges of energy consumption of HPC systems, the European Union Horizon 2020 READEX (Runtime Exploitation of Application Dynamism for Energy-efficient Exascale computing) project uses an online auto-tuning approach to improve energy efficiency of HPC applications. The READEX methodology pre-computes optimal system configurations at design-time, such as the CPU frequency, for instances of program regions and switches at runtime to the configuration given in the tuning model when the region is executed. READEX goes beyond previous approaches by exploiting dynamic changes of a region's characteristics by leveraging region and characteristic specific system configurations. While the tool suite supports an automatic approach, specifying domain knowledge such as the structure and characteristics of the application and application tuning parameters can significantly help to create a more refined tuning model. This paper presents the means available for an application expert to provide domain knowledge and presents tuning results for some benchmarks.Web of Science316art. no. E465

Toward highly parallel loading of unstructured meshes

This paper presents an algorithm for highly-parallel loading and processing of unstructured mesh databases in a dis tributed memory environment of large HPC clusters without collecting data into a single process. The algorithm is proved effective, having linear speedup in the large dataset limit. Demonstrated on Ansys CDB, EnSight, VTK Legacy, and XDMF databases, we show that it is possible to efficiently reconstruct meshes with 800 million nodes and 500 million elements in several seconds on thousands of processors, even from databases that were not designed to be read in parallel. The algorithm is implemented in our MESIO library that can be used as (i) an efficient parallel loader (e.g. for numerical physical solvers) or as (ii) a high performing parallel converter between mesh databases.Web of Science166art. no. 10310

GPU accelerated path tracing of massive scenes

This article presents a solution to path tracing of massive scenes on multiple GPUs. Our approach analyzes the memory access pattern of a path tracer and defines how the scene data should be distributed across up to 16 CPUs with minimal effect on performance. The key concept is that the parts of the scene that have the highest amount of memory accesses are replicated on all GPUs. We propose two methods for maximizing the performance of path tracing when working with partially distributed scene data. Both methods work on the memory management level and therefore path tracer data structures do not have to be redesigned, making our approach applicable to other path tracers with only minor changes in their code. As a proof of concept, we have enhanced the open-source Blender Cycles path tracer. The approach was validated on scenes of sizes up to 169 GB. We show that only 1 5% of the scene data needs to be replicated to all machines for such large scenes. On smaller scenes we have verified that the performance is very close to rendering a fully replicated scene. In terms of scalability we have achieved a parallel efficiency of over 94% using up to 16 GPUs.Web of Science402art. no. 1

Суброгация

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Глобализация, региональная интеграция и экономическое развитие

The paper deals with the energy consumption evaluation of the Finite Element Tearing and Interconnect (FETI) based solvers of linear systems, which is an established method for solving real-world engineering problems. Authors evaluated the effect of the CPU frequency on the energy consumption of the FETI solver using a linear elasticity 3D cube synthetic benchmark. In this problem, the effect of frequency tuning on the energy consumption of the essential processing kernels of the FETI method was evaluated. The paper provides results for two types of frequency tuning: (1) static tuning and (2) dynamic tuning. For static tuning experiments, the frequency is set before execution and kept constant during the runtime. For dynamic tuning, the frequency is changed during the program execution to adapt the system to the actual needs of the application. The paper shows that static tuning brings up 12% energy savings when compared to default CPU settings (the highest clock rate). The dynamic tuning improves this further by up to 3%