Scalable Computing: Practice and Experience <p>&nbsp;<strong>Welcome to SCPE</strong></p> <p><span style="text-decoration: underline;"><em>Topics of interest</em></span>.&nbsp;The area of scalable computing has matured and reached a point where new issues and trends require a professional forum. SCPE provides this avenue by publishing original refereed papers that address the present as well as the future of parallel and distributed computing. The journal focus on algorithm development, implementation and execution on parallel and distributed architectures, as well on application of parallel and distributed computing to the solution of real-life problems.</p> <p><span style="text-decoration: underline;"><em>Electronic journal</em></span>.&nbsp;SCPE provides immediate open access to its content following the principle that making research freely available to the public supports a greater global exchange of knowledge. &nbsp;We invite you to have a look to the open content of the volumes and to consider to interact with this publication willing to promote your results and achievements. Publication or access fees are not requested.</p> <p><span style="text-decoration: underline;"><em>Special calls for papers</em></span><em>&nbsp;</em>. SCPE editorial board welcomes initiatives to publish <a title="Special Issues" href="/index.php/scpe/pages/view/CallSpecialIssue">special issues</a> on topics aligned with the SCPE ones.</p> <p><span style="text-decoration: underline;"><em>History</em></span><em>&nbsp;</em>. The journal has evolve with the community that it represents.&nbsp;Initiated in 1998 under the name of Parallel and Distributed Computing Practices (PDCP) journal, first 5 volumes have been published by Nova Science Publishers.&nbsp;Next 4 volumes were sustained by published by Warsaw School of Social Psychology, Poland, only as electronic journal, as an expression of the current tendencies in digital libraries.&nbsp;The electronic journal is currently published by West University of Timisoara, Romania, with the support of highly-devoted international editorial team.More information about changes that took place can be found in the Editorial published in <a href="/index.php/scpe/issue/view/56" target="_self">SCPE 6(1)</a> and <a href="/index.php/scpe/issue/view/79">SCPE 9(4)</a>.</p> <p><span style="text-decoration: underline;"><em>Indexing. </em></span>The journal is indexed by several organizations (see a complete list <a title="Journal Indexing" href="/index.php/scpe/pages/view/JournalIndexing">here</a>). Current impact factors are the followings:</p> <ul> <li class="show">in 2016,&nbsp;<a title="Journal Metrics" href="">SNIP</a>&nbsp;(Scopus Source Normalized Impact per Paper)&nbsp; was 0.581,&nbsp;<a title="SCPE's SJR" href=";tip=sid&amp;clean=0">SJR</a> (Scimago Journal Ranking) was 0.211 (Q3 of quality) and was classified no. <a href="">88 from 191 journals (54% percentile) </a>&nbsp;in Computer Science in Scopus</li> <li class="show">in 2015,&nbsp;<a href="">Global impact factor</a> was 0.876 and&nbsp;<a title="ICV" href="" target="_blank" rel="noopener">ICV</a>&nbsp;(Index Copernicus Value)&nbsp;was 93.25 points from 100;</li> <li class="show">the current h-index computed by Publish and Perish is 24.</li> </ul> <p>SCPE is included in the <a title="SCPE in extended list of Thompson Reuters" href=";ISSN=1895-1767" target="_blank" rel="noopener">Clarivate Analytics (former Thompson Reuters) Emerging Sources Citation Index</a>, and appears from 2015 in the Web of Science collection.</p> <p><span style="text-decoration: underline;"><em>Publicity</em></span>. SCPE flyer is available <a href="">here</a>.</p> <p class="signature">Editor-in-chief, Prof. Dana Petcu</p> en-US (Dana Petcu) (Silviu Panica) Thu, 10 May 2018 11:53:02 +0300 OJS 60 Introduction to the Special Issue on E-Infrastructures for Excellent Science: Advances in Life Sciences, Digital Cultural Heritage and Climatology <p style="-qt-block-indent: 0; text-indent: 0px; margin: 0px;">It is our pleasure to present this special issue of scientific journal Scalable Computing: Practice and Experience. In this issue (Volume 19, No 2 – June 2018), we selected 14 papers which have gone through review and revision, and represent novel results in Life Sciences, Digital Cultural Heritage, Climatology using state-of-the-art e-infrastructures. E-Infrastructures are currently addressing the challenging needs of researchers for digital services in terms of networking, computing and data management. Virtual research environments (VRE) integrate resources across all layers of the e-infrastructure (networking, computing, data, software, user interfaces) to foster cross-disciplinary data interoperability. VRE are supporting innovation in research via an integrated access to potentially unlimited digital research resources, tools and services across disciplines and user communities.</p> <p style="-qt-block-indent: 0; text-indent: 0px; margin: 0px;">In the content of this special issue the papers are ordered in 4 groups: Climatology (5 papers), Life Sciences (3 papers), Digital Cultural Heritage (2 papers) and Tools and Services (4 papers). Inside the groups, the papers are ordered by alphabetical order (the family name of the first author).</p> <p style="-qt-block-indent: 0; text-indent: 0px; margin: 0px;">Climatology. The first paper presents an online interactive platform that aims to provide weather information about Armenia by integrating observations, model and satellite data. The topic is interesting from the practical point of view and might be very useful, especially for meteorologists. The second paper studies the effect of the dust on climate in the Caucasus region, with a specific focus on Georgia, using the Regional Climate Model RegCM interactively coupled to a dust model. The simulations cover the period 1985-2014 encompassing most of the Sahara, the Middle East, the Great Caucasus with adjacent regions. The third paper provides insight in the performances of wind simulations for high resolution models of the terrain. The presented results rationalize the possibility to run in reasonable time high resolution models, while showing that the impact of turbulence does not have significantly increases the computing requirement. The fourth paper presents adaptation and tuning of the RegCM model for the Balkan Peninsula and Bulgaria and development of a methodology able to predict possible changes of the regional climate for different global climate change scenarios and their impact on spatial/temporal distribution of precipitation, hence the global water budgets, to changes of the characteristics and spatial/temporal distribution of extreme, unfavorable and catastrophic events. The fifth paper presents comparison of two approaches (static and dynamical) used to compute the vibrational spectra of two conformers of the free formic acid molecule. The topic is interesting within the context of the atmospheric chemistry research field and it is of sufficient importance regarding the vibrational spectroscopic data and induced temperature effects of intramolecular motions.</p> <p style="-qt-block-indent: 0; text-indent: 0px; margin: 0px;">Life Sciences. The manuscript from Astsatryan et al. describes a platform, which consists of data repository and workflow management services for Molecular Dynamics simulations. The platform focuses on an interactive data visualization workflow service as a key to perform more in-depth analyzing of research data outputs.</p> <p style="-qt-block-indent: 0; text-indent: 0px; margin: 0px;">The manuscript from Bigovic et al. describes the organic synthesis of three enol carbonate derivatives and the analysis of their interactions with T4 lysozyme L99A/M102Q using molecular dynamics (MD) simulations. The results obtained by different software packages are discussed. The manuscript from Koteska et al. describes a semi-empirical Molecular Dynamics study of irinotecan, a colon cancer drug, using the atom-centered density matrix propagation approach. The described methodology was used to study the structure, dynamics, and rovibrational spectrum of irinotecan.</p> <p style="-qt-block-indent: 0; text-indent: 0px; margin: 0px;">DCH. The paper of Charalambous and Artopoulos presents the deployment of the Clowder CMS system and the development of extraction services to handle, manage and automatically process Digital Cultural Heritage data in order to enable virtual collaboration for research in the South East and Eastern Mediterranean region. Technical descriptions of the system are given and some results are provided. In the paper of Elfarargy and Rizq a software system called Virtual Museum Framework (VirMuF), which is a set of tools that can be used by non-developers to easily create and publish 3D virtual museums in a very short time is presented. VirMuF is an open-source and teams including software developers can further extend VirMuF to fit their needs.</p> <p style="-qt-block-indent: 0; text-indent: 0px; margin: 0px;">Software Tools and Services. Dimitrov and Stoyanov present the Data Discovery Service supporting the VI-SEEM project Virtual Research Environment - VRE. The solution is based on an open source platform with special customization regarding the data harvesting methods from diverse data sources and updating the available content so that the users will seamlessly access all the data from a single point. The paper of Golubev et al. addresses the problems of optimization of medical image storing and secure access, using the DICOM system. Based on the Moldova DICOM Network architecture, the system enables distributed search, and transportation of DICOM images. Additionally, several optimization problems are addressed by the authors, along with the integration challenges within the VI-SEEM VRE. In the paper of Mishev et al. the design, requirements and implementation of a federated virtual research environment, based on the service orientation paradigm, offering anything as a service solutions, have been considered. The challenges of the service management implementation focusing on interoperability by design and service management standards have been discussed. The manuscript of Vudragovic et al. gives an extensive insight of the development and implementation of the DREAM dust model (DREAMCLIMATE service). Additionally, a use-case study of the premature mortality due to the desert dust in the North Africa - Europe - Middle East region for the 2005 obtained by the application of this model is presented, justifying the model and the applicability of the service itself.</p> <p style="-qt-block-indent: 0; text-indent: 0px; margin: 0px;">We would like to thank all those who kindly contributed to this Special Issue: the authors who submitted their papers, reviewers for their kind help and cooperation, especially to Dr. Zoe Curnia, Dr. Theodoros Christoudias and Dr. George Artopoulos for their valuable remarks and suggestions. Our special gratitude is for the Editor-in-Chief, Professor Dana Petcu, for her constant support.</p> <p style="-qt-block-indent: 0; text-indent: 0px; margin: 0px;">&nbsp;</p> <p style="-qt-paragraph-type: empty; -qt-block-indent: 0; text-indent: 0px; margin: 0px;">&nbsp;</p> Aneta Karaivanova, Anastas Mishev ##submission.copyrightStatement## Thu, 10 May 2018 11:21:20 +0300 Weather Data Visualization and Analytical Platform <p>This article aims to present a web-based interactive visualization and analytical platform for weather data in Armenia by integrating the three existing infrastructures for observational data, numerical weather prediction, and satellite image processing. The weather data used in the platform consists of near-surface atmospheric elements including air temperature, pressure, relative humidity, wind and precipitation. The visualization and analytical platform has been implemented for 2-m surface temperature. The platform gives Armenian State Hydrometeorological and Monitoring Service analytical capabilities to analyze the in-situ observations, model and satellite image data per station and region for a given period.</p> Hrachya Astsatryan, Hayk Grogoryan, Eliza Gyulgyulyan, Anush Hakobyan, Aram Kocharyan, Wahi Narsisian, Vladimir Sahakyan, Yuri Shoukourian, Rita Abrahamyan, Zarmandukht Petrosyan, Julien Aligon ##submission.copyrightStatement## Thu, 10 May 2018 11:27:14 +0300 Effect of Dust Aerosols in Forming the Regional Climate of Georgia <p>The effect of the dust on the climate in the Caucasus region, with a specific focus on Georgia, was investigated with a Regional Climate Model RegCM interactively coupled with a dust model. For this purpose we have executed sets of 30 years simulations (1985–2014) with and without dust effects by RegCM4.7 model with 16.7 km resolution over the Caucasus domain and with 50 km resolution encompassing most of the Sahara, the Middle East, and the Great Caucasus with adjacent regions. Results of calculations have shown that the dust aerosol is an active player in the climate system of Georgia. Mineral dust aerosol influences on temperature and aerosol optical depth spatial and temporally inhomogeneous distribution on the territory of Georgia and generally has been agreed with MODIS satellite data. Results of numerical calculations have shown that dust radiative forcing inclusion has improved simulated summer temperature. The mean annual temperature increased across the whole territory of Georgia in simulations when dust direct effect was considered.</p> Teimuraz Davitashvili, Nato Kutaladze, Ramaz Kvatadze, Ramaz Alexander Kvatadze, George Mikuchadze ##submission.copyrightStatement## Thu, 10 May 2018 11:30:27 +0300 An Analysis for Parallel Wind Simulation Speedup using OpenFOAM <p>An analysis of speedup for parallel execution of OpenFOAM software for wind simulation over rugged terrain is presented in the paper. Runtime speedup is analyzed using small and medium resolution DEM models for icoFoam and pisoFoam solvers, the latter due to consideration of turbulence, running in the parallel system Avitohol of Institute of Information and Communication Technologies of the Bulgarian Academy of Sciences. The results gave a clearer view about the possibility to run in reasonable time medium and high resolution models in regional scale, while indicating the weight of turbulence calculations for computing runtime requirements.</p> Neki Frasheri, Emanouil Atanassov ##submission.copyrightStatement## Thu, 10 May 2018 11:31:42 +0300 Climate Applications in a Virtual Research Environment Platform <p>Previous atmospheric composition studies were based on extensive computer simulations carried out with good resolution using up-to-date modelling tools and detailed and reliable input data.</p> <p>The oncoming climate changes will exert influence on the ecosystems, on the all branches of the international economy, and on the quality of life. Regional climate models (RCMs) are important instruments used for downscaling climate simulations from Global circulation models (GCMs).</p> <p>The air quality (AQ) impact on human health and quality of life is an issue of great social significance. Evaluating this impact will give scientifically robust basis for elaborating efficient short term measures and long term strategies for mitigation of the harmful effects of air pollution. The AQ impact is evaluated in the terms of Air Quality Indices (AQI). Some extensive numerical simulations of the atmospheric composition fields in Bulgaria and Sofia have been recently performed. A quite extensive data base was created from simulations which were used for different studies of the atmospheric composition, including the AQ climate.</p> <p>Main aims of the numerical experiment presented in this paper are: (1) Adaptation and tuning of the RegCM model for the Balkan Peninsula and Bulgaria and thus development of a methodology able to predict possible changes of the regional climate for different global climate change scenarios and their impact on spatial/temporal distribution of precipitation, hence the global water budgets, to changes of the characteristics and spatial/temporal distribution of extreme, unfavorable and catastrophic events (drought, storms, hail, floods, fires, sea waves, soil erosion, etc.); (2) Development of a methodology and performing reliable, comprehensive and detailed studies of the impact of lower atmosphere parameters and characteristics on the quality of life (QL) and health risks (HR) for the population.</p> Georgi Gadzhev, Ivelina Georgieva, Kostadin Ganev, Vladimir Ivanov, Nikolay Miloshev, Hristo Chervenkov, Dimiter Syrakov ##submission.copyrightStatement## Thu, 10 May 2018 11:33:14 +0300 Dynamic versus Static Approach to Theoretical Anharmonic Vibrational Spectroscopy of Molecular Species Elevant to Atmospheric Chemistry: A Case Study of Formic Acid <p>Vibrational spectra of the two conformers of the free formic acid molecule are computed by two approaches, with a special emphasis on the region of O-H stretching modes. The first approach (referred to as a static one) is based on sequential computation of anharmonic O-H stretching vibrational potential and numerical solution of the vibrational Schr\"{o}dinger equation by the Numerov method. The second approach (referred to as a dynamic one) is based on molecular dynamics (MD) simulations performed within the atom-centered density matrix propagation scheme (ADMP) followed by spectral analysis of the velocity-velocity and dipole moment autocorrelation functions computed from the ADMP MD trajectories. All calculations are carried out within the density functional tight binding (DFTB) formalism. The computed properties are compared to the available experimental data and the advantages of the dynamic versus the static approach are outlined and analyzed in the context of detection of individual and non-covalently bonded molecular species relevant to climate science and atmospheric chemistry.</p> Bojana Koteska, Verce Manevska, Anastas Mishev, Ljupco Pejov ##submission.copyrightStatement## Thu, 10 May 2018 11:36:15 +0300 An Integrated Web-based Interactive Data Platform for Molecular Dynamics Simulations <p>The article aims to introduce an integrated web-based interactive data platform for molecular dynamic simulations using the datasets generated by different life science communities from Armenia. The suggested platform, consisting of data repository and workflow management services, is vital for current and future scientific discoveries in the life science domain. We focus on interactive data visualization workflow service as a key to perform more in-depth analyzes of research data outputs, helping to understand the problems efficiently and to consolidate the data into one collective illustration platform. The functionalities of the integrated data platform is presented as an advanced integrated environment to capture, analyze, process and visualize the scientific data.</p> Hrachya Astsatryan, Wahi Narsisian, Eliza Gyulgyulyan, Vardan Baghdasaryan, Armen Poghosyan, Yevgeni Mamasakhlisov, Peter Wittenburg ##submission.copyrightStatement## Thu, 10 May 2018 11:37:33 +0300 Modeling and Molecular Dyanamics Simulations Study of Enol-carbonates and their Derivatives <p>In view of the fact that the mechanisms of the interaction of organic molecules with the properties of the drug occur in most cases by their binding to the receptors (proteins), we wanted to examine the interactions of small organic molecules that we synthesized and certain proteins. In this paper the comparison between molecules, modeled by different software packages, and experimental results is performed. The series of new molecules are synthesized using Barbier reaction of allylation of carbonyl compounds with 4-(bromomethyl)-1,3-dioxol-2-one as a highly fictionalized allylic synthon. Their structure was determined by spectroscopic methods (NMR-, IR- and UV/VIS-spectroscopy and MS-spectrometry), while for three individual molecules analysis of x-ray diffraction (X-ray analysis) was also performed, which gave the final confirmation of the exact arrangement of all atoms in the space. The molecules are represented in standard chemical format, visualized and prepared for simulations. In order to obtain datasets that further can be used to examine and analyze interactions with well-known proteins, molecular dynamic simulations are performed. The purpose of this research was to present that using powerful computer infrastructure and appropriate software tools, an accurate molecule models can be created.</p> Miljan Bigovic, Luka Filipovic, Zarko Zecevic, Bozo Krstajic ##submission.copyrightStatement## Thu, 10 May 2018 11:39:01 +0300 Semiempirical Atom-centered Density Matrix Propagation Approach to Temperature-dependent Vibrational Spectroscopy of Irinotecan <p>In the present study, a molecular dynamics study of irinotecan molecule with the atom-centered density matrix propagation scheme was carried out at AM1 semiempirical level of theory, at series of different temperatures, ranging from 5 K to 300 K. Molecular dynamics simulations were performed within the NVE ensemble, initially injecting (and redistributing among the nuclei) various amounts of nuclear kinetic energies to achieve the desired target temperatures. Subsequently to initial equilibration phase of 2 ps, productive simulations were carried out for 8 ps. The accuracy of simulations and the closeness of the generated trajectory to those at the Born-Oppenheimer surface were carefully followed and analyzed. To compute the temperature-dependent rovibrational density of states spectra, the velocity-velocity autocorrelation functions were computed and Fourier-transformed. Fourier-transformed dipole moment autocorrelation functions were, on the other hand, used to calculate the temperature-dependent infrared absorption cross section spectra. The finite-temperature spectra were compared to those computed by a static approach, i.e. by diagonalization of mass-weighted Hessian matrices at the minima located on the potential energy surfaces. Thermally-induced spectral changes were analyzed and discussed. The advantages of finite-temperature statistical physics simulations based on semiempirical Hamiltonian over the static semiempirical ones in the case of complex, physiologically active molecular systems relevant to intermolecular interactions between drugs and drug carriers were pointed out and discussed.</p> Bojana Koteska, Maja Simonoska Crcarevska, Marija Glavas Dodov, Jasmina Tonic Ribarska, Ljupco Pejov ##submission.copyrightStatement## Thu, 10 May 2018 11:40:14 +0300 Enabling virtual collaboration in Digital Cultural Heritage in the SEEM region <p>It has been observed that many researchers in the humanities do not use digital tools to their full extent for their research. Some of the most pressing needs of researchers in Digital Cultural Heritage (DCH) are data storage and handling and large scale computing. Linking these researchers to experienced groups will significantly improve productivity and research innovation in DCH. This work presents our efforts in enabling virtual collaboration for research in the South East and Eastern Mediterranean region and more specifically the deployment of the Clowder CMS system and the development of extraction services to handle, manage and automatically process DCH data. We give technical descriptions of the system and provide some results and discussions of our efforts to enable virtual collaboration between regional level DCH researchers in the context of the Horizon 2020 funded VI-SEEM project.</p> Panayiotis Charalambous, George Artopoulos ##submission.copyrightStatement## Thu, 10 May 2018 11:41:36 +0300 VirMuF: The Virtual Museum Framework <p>With the immergence of 3D object digitization technologies, many museums are digitizing their collections using 3D scanning, photogrammetry and other techniques. These large 3D collections are not only great for documentation and preservation, but they are also a great means for introducing these collections to a wider audience worldwide through virtual museums. However, developing Virtual Museums can be a costly process considering that it needs a team of talented software developers, 3D designers and other software/hardware tools. In this paper we present VirMuF (Virtual Museum Framework), which is a set of tools that can be used by non-developers to easily create and publish 3D virtual museums in a very short time. This way, Museum staff doing collection digitization can also publish 3D virtual museums to exhibit these collections. VirMuF is open-source; hence, teams including software developers can further extend VirMuF to fit their needs.</p> Mohammed Elfarargy, Amr Rizq ##submission.copyrightStatement## Thu, 10 May 2018 11:42:59 +0300 Solutions for Data Discovery Service in a Virtual Research Environment <p>Scientific computing requires many and large volumes of complex structured data and metadata that are scattered across data centers. Researchers find it difficult to discover the specific data they need for their research. Traditional search engines, such as Google, are not effective in most of these cases. Moreover, some of the scientific data are confidential and are not publicly indexed. Therefore, it is necessary to develop a custom solution that satisfies the researchers' need for flexible search. This article introduces the Data Discovery Service designed to serve the Virtual Research Environment (VRE) during the VI-SEEM project. The solution is based on a specially configured and upgraded version of the CKAN platform. The main installation procedure is described, as well as the authors' contributions for the purpose of regularly harvesting data from different sources and updating the available content on which user queries are to be executed.</p> Vladimir Dimitrov, Stiliyan Stoyanov ##submission.copyrightStatement## Thu, 10 May 2018 11:46:50 +0300 DICOM data processing optimization in medical information systems <p>The problem of storage and visualization of medical images collected by various medical equipment is actual for latest 10 years for every medical institution. On the other hand, access to the medical investigation datasets and solving the problem of personal patient data security is important for scientific community and institutions that require this data. "DICOM Network" project was developed for solving these problems for different actors in the system based on the various customized roles. This article describes the problems and possible solutions for optimization of medical images storing, providing stable and secure access, based on the distributed warehouse for huge volumes of data with different levels of access.</p> <p>.</p> Alexandr Golubev, Peter Bogatencov, Grigore Secrieru ##submission.copyrightStatement## Thu, 10 May 2018 11:45:33 +0300 Improving Service Management for Federated Resources to Support Virtual Research Environments <div class="page" title="Page 1"> <div class="layoutArea"> <div class="column"> <p>Virtual research environments provide an easy access to e-Infrastructures for researchers by creating an abstracted service-oriented layer on top of the available resources. Using the portal, researchers can focus on the research workflow and data analysis while being provided with a consolidated unified view of all tools necessary for their activities. The sustainable lifecycle of a virtual research environment can only be achieved if it is going to be used with high quality of experience by a large body of users. Aiming for this goal, in this paper we analyse the requirements and implementation of a cross-community virtual research environment that brings together researchers from three different domains. Promoting interdisciplinary research and cooperation, the federated virtual research environment is based on the service orientation paradigm, offering anything as a service solutions. Thus, the main pillar for a successful implementation of this solution is the careful design and management of the underlying elementary services and service compositions. The rest of the paper discusses the challenges of the service management implementation focusing on interoperability by design and service management standards.</p> </div> </div> </div> Anastas Mishev, Sonja Filiposka, Ognjen Prnjat, Ioannis Liabotis ##submission.copyrightStatement## Thu, 10 May 2018 11:48:22 +0300 VI-SEEM DREAMCLIMATE Service <p>Premature human mortality due to cardiopulmonary disease and lung cancer is found in epidemiological studies to be correlated to increased levels of atmospheric particulate matter. Such negative dust effects on the human mortality in the North Africa - Europe - Middle East region can be successfully studied by the DREAM dust model. However, to assess health effects of dust and its other impacts on the environment, a detailed modelling of the climate for a period of one year in a high-resolution mode is required. We describe here a parallel implementation of the DREAM dust model, the DREAMCLIMATE service, which is optimised for use on the high-performance regional infrastructure provided by the VI-SEEM project. In addition to development and integration of this service, we also present a use-case study of premature mortality due to desert dust in the North Africa - Europe - Middle East region for the year 2005, to demonstrate how the newly deployed service can be used.</p> Dusan Vudragovic, Luka Ilic, Petar Jovanovic, Slobodan Nickovic, Aleksandar Bogojevic, Antun Balaz ##submission.copyrightStatement## Thu, 10 May 2018 11:49:52 +0300