BEGIN:VCALENDAR VERSION:2.0 PRODID:-//CERN//INDICO//EN BEGIN:VEVENT SUMMARY:Overview of HPC course and textbook DTSTART;VALUE=DATE-TIME:20171206T090000Z DTEND;VALUE=DATE-TIME:20171206T103000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-18@events.chpc.ac.za DESCRIPTION:Prof. Thomas Sterling (Indiana U.) will provide an overview of his HPC course and new textbook. This course\, which provides a modern and accessible introduction to HPC\, has been developed and thoroughly fie ld-tested at Indiana University and is now being adopted at universities a cross the US. Significant resources\, including 80 hours of lecture vide os\, course slides\, student exercises and project material\, will be made available free of charge. Prof. Sterling has a long relationship with C HPC and has been extremely enthusiastic in his support for HPC education i n Africa.\n\nhttps://events.chpc.ac.za/event/6/contributions/18/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/18/ END:VEVENT BEGIN:VEVENT SUMMARY:HPC Topics in African University Courses DTSTART;VALUE=DATE-TIME:20171206T113000Z DTEND;VALUE=DATE-TIME:20171206T130000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-19@events.chpc.ac.za DESCRIPTION:This session will look at current efforts and success in inclu de HPC topics in courses at African universities\, including teaching stra tegies and methodologies. The challenges regarding implementation of HPC education in an African context will be discussed as well solutions and t he next steps forward. A key goal is building and strengthening a commu nity around HPC education in Africa.\n\nhttps://events.chpc.ac.za/event/6/ contributions/19/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/19/ END:VEVENT BEGIN:VEVENT SUMMARY:Detailed projections of future climate change over Africa: the Va riable Resolution Earth System Model and supercomputing on the CHPC Lengau cluster DTSTART;VALUE=DATE-TIME:20171205T120000Z DTEND;VALUE=DATE-TIME:20171205T122000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-21@events.chpc.ac.za DESCRIPTION:Speakers: Francois Engelbrecht (CSIR)\nGlobal Climate Models ( GCMs) have become the main tools to project future climate change. GCMs th at are capable of also simulating the global carbon cycle are referred to as Earth System Models (ESMs). Currently\, about 30 GCMs exist globally\, but only one of these (developed by the CSIRO in Australia) had its origin in the southern hemisphere. Moreover\, Africa is the only continent for w hich GCM projections have not improved moving from Assessment Report Four to Assessment Report Five (AR5) of the Intergovernmental Panel on Climate Change (IPCC)\, indicating a lack of focus on African climate issues in GC M development. Against this background\, a new coupled climate model\, the Variable-resolution Earth System Model (VrESM) is currently under develop ment through collaborative research between the Council for Industrial Res earch (CSIR) in South Africa and the Commonwealth Scientific and Industria l Research Organisation (CSIRO) In Australia. The model employs ocean\, at mosphere and land-surface models all cast on a cube-based grid and can be applied at quasi-uniform horizontal resolution to function as a global cli mate model\, or in stretched-grid mode to function as a high-resolution re gional climate model. The atmospheric model component is the Variable-cubi c Atmospheric Model (VCAM) of CSIRO\, which has evolved from the widely us ed Conformal-cubic Atmospheric Model (CCAM). The CSIRO Atmosphere Biospher e Land Exchange model (CABLE) provides VrESM with a dynamic land-surface\, whilst the ocean is simulated by the newly developed Variable-cubic Ocean Model (VCOM) of the CSIR. VRESM development is taking place with the imme diate objective of generating African-based projections of future global c limate change as a contribution to CMIP6\, whilst the stretched-grid versi on of the model and its component models (e.g. CCAM) is to be used to gene rate simulations of the coupled southern African climate system as part of the second phase of the Coordinated Regional Downscaling Experiment (CORD EX).\n\nHere we present an overview of the numerical architecture and the main component models of VrESM. We proceed to showcase the most detailed p rojections of future climate change ever obtained for the southern African region. These simulations were performed at a resolution of about 8 km in the horizontal for the period 1961-2100 under both low and high mitigatio n scenarios. For each scenario\, six GCMs that contributed to AR5 of the I PCC were first downscaled to 50 km resolution globally using CCAM - as a c ontribution to CORDEX\, and subsequently to 8 km resolution over Cape Town . The projections are analysed with a focus on the current drought in the Cape Town region - insights are provided on whether this drought can be at tributed to climate change and on whether more such droughts can be expect ed under climate change. All VrESM development\, and the application of Vr ESM and its component models\, are taking place on the Lengau cluster of t he CHPC. The talk thus also provides insights into the computational requi rements of performing the high-resolution simulations described above\, in cluding the characteristics of the code in terms of scaling on Lengau.\n\n https://events.chpc.ac.za/event/6/contributions/21/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/21/ END:VEVENT BEGIN:VEVENT SUMMARY:Programmable Storage Systems DTSTART;VALUE=DATE-TIME:20171204T092500Z DTEND;VALUE=DATE-TIME:20171204T095000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-22@events.chpc.ac.za DESCRIPTION:Speakers: Carlos Maltzahn (University of California\, Santa Cr uz)\nStorage systems need to support high-performance for special-purpose data processing applications that run on an evolving storage device techno logy landscape. This puts tremendous pressure on storage systems to suppor t rapid change both in terms of their interfaces and their performance. Bu t adapting storage systems can be difficult because unprincipled changes m ight jeopardize years of code-hardening and performance optimization effor ts that were necessary for users to entrust their data to the storage syst em. We introduce the programmable storage approach\, which exposes interna l services and abstractions of the storage stack as building blocks for hi gher-level services. We also build a prototype to explore how existing abs tractions of common storage system services can be leveraged to adapt to t he needs of new data processing systems and the increasing variety of stor age devices. We illustrate the advantages and challenges of this approach by composing existing internal abstractions into two new higher-level serv ices: a file system metadata load balancer and a high-performance distribu ted shared-log. The evaluation demonstrates that our services inherit desi rable qualities of the back-end storage system\, including the ability to balance load\, efficiently propagate service metadata\, recover from failu re\, and navigate trade-offs between latency and throughput using leases.\ n\nhttps://events.chpc.ac.za/event/6/contributions/22/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/22/ END:VEVENT BEGIN:VEVENT SUMMARY:EMPRESS--Extensible Metadata PRovider for Extreme-scale Scientific Simulations DTSTART;VALUE=DATE-TIME:20171204T095000Z DTEND;VALUE=DATE-TIME:20171204T101500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-23@events.chpc.ac.za DESCRIPTION:Speakers: Jay Lofstead (Sandia National Laboratories)\nSignifi cant challenges exist in the efficient retrieval of data from extreme-scal e simulations. An important and evolving method of addressing these challe nges is application-level metadata management. Historically\, HDF5 and Net CDF have eased data retrieval by offering rudimentary attribute capabiliti es that provide basic metadata. ADIOS simplified data retrieval by utilizi ng metadata for each process' data. EMPRESS provides a simple example of t he next step in this evolution by integrating per-process metadata with th e storage system itself\, making it more broadly useful than single file o r application formats. Additionally\, it allows for more robust and custom izable metadata.\n\nhttps://events.chpc.ac.za/event/6/contributions/23/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/23/ END:VEVENT BEGIN:VEVENT SUMMARY:Scientific Modeling of Storage System Reliability DTSTART;VALUE=DATE-TIME:20171204T090000Z DTEND;VALUE=DATE-TIME:20171204T092500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-25@events.chpc.ac.za DESCRIPTION:Speakers: Matthew Curry (Sandia National Laboratories)\nWhen d esigning large scale storage systems\, failure is always a serious concern that demands constant attention. However\, the ability for system designe rs to objectively evaluate their risk of data loss for a given storage sys tem is minimal. Instead\, they must enumerate possible failure modes\, est imate their relative probability\, identify possible mitigations\, and dec ide whether the expense is worthwhile. This process relies on folk wisdom\ , rules of thumb\, and anecdotal experience. For systems that grow larger and more complex year-by-year\, this methodology is too imprecise to guara ntee safety while ensuring efficiency.\n\nThis talk will detail some of th e progress in the SIMS^2 project\, a collaboration between Sandia National Laboratories\, University of Wisconsin-Madison\, and Los Alamos National Laboratory charged with increasing the science and rigor behind evaluating system designs. It will cover some of the pitfalls of current methods of evaluating systems\, methods for determining complex behavior of aggregate d components\, evaluation of different types of failure modes\, and some i nteresting inflection points for different system designs.\n\nhttps://even ts.chpc.ac.za/event/6/contributions/25/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/25/ END:VEVENT BEGIN:VEVENT SUMMARY:Innovation in the Network and Security Space DTSTART;VALUE=DATE-TIME:20171205T123000Z DTEND;VALUE=DATE-TIME:20171205T130000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-65@events.chpc.ac.za DESCRIPTION:Speakers: Andrew Wilson (LucidView)\nOn Tuesday 5 December\, t he South African NREN has invited Mr A Wilson of LucidView to discuss the innovative work that we has been doing in the network space.\nMr Wilson wi ll be providing an oral presentation on our recent innovations in this are na.\n\nhttps://events.chpc.ac.za/event/6/contributions/65/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/65/ END:VEVENT BEGIN:VEVENT SUMMARY:TVET Connectivity Project DTSTART;VALUE=DATE-TIME:20171205T093000Z DTEND;VALUE=DATE-TIME:20171205T100000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-26@events.chpc.ac.za DESCRIPTION:Speakers: Arno Hart (SABEN)\nSABEN is a non-profit focused on ending bandwidth poverty among Sooth Africa’s schools and colleges. It c ollaborates with the South African National Research and Education Network (SANReN) and procures services from the Tertiary Education and Research N etwork of South Africa (TENET) to provide high capacity bandwidth for scho ols networks and colleges. SABEN also offers other over-the-network servic es such as hosting\, VOIP and video conferencing services.\n\nhttps://even ts.chpc.ac.za/event/6/contributions/26/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/26/ END:VEVENT BEGIN:VEVENT SUMMARY:MODELLING ADVANCED MATERIALS WITH HIGH PERFORMANCE COMPUTING DTSTART;VALUE=DATE-TIME:20171204T090000Z DTEND;VALUE=DATE-TIME:20171204T093000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-27@events.chpc.ac.za DESCRIPTION:Speakers: Richard Catlow (Department of Chemistry\, University College London)\nModelling and simulation are now essential and increasin gly important techniques in materials science. We aim to show the scope an d challenges of the current field by reviewing recent work of the UK High End Computing Materials Chemistry Consortium. We will describe recent appl ications using both force-field and electronic structure techniques to key functional materials\, including catalytic systems\, materials for renewa ble energy technologies\, electronic materials\, ceramics and molecular ma terials. We will consider some of the future prospects and developments in the field.\n\nhttps://events.chpc.ac.za/event/6/contributions/27/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/27/ END:VEVENT BEGIN:VEVENT SUMMARY:Welcome DTSTART;VALUE=DATE-TIME:20171204T070000Z DTEND;VALUE=DATE-TIME:20171204T070500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-28@events.chpc.ac.za DESCRIPTION:https://events.chpc.ac.za/event/6/contributions/28/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/28/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational and experimental study on heats of adsorption of MBT \, MBO and MBI onto pyrite mineral surfaces DTSTART;VALUE=DATE-TIME:20171206T101000Z DTEND;VALUE=DATE-TIME:20171206T103000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-29@events.chpc.ac.za DESCRIPTION:Speakers: Peace Mkhonto (University of Limpopo (MMC))\nThe ads orption of heterocyclic collectors such MBT\, MBO and MBI on pyrite minera l surface are paramount in order to establish understanding on the floatat ion reactivity that may be applicable in a wide range of sulphide minerals . This study explores the heats of adsorption of heterocyclic collectors o nto pyrite mineral surfaces. The computed heat of adsorption energies of c ollectors indicated that the order of adsorption decrease as: MBO > MBI > MBT on both (100) and (111) surfaces. In the case of the pyrite (100) surf ace\, the MBT adsorbed through the exocyclic sulphur atom\, while MBO and MBI adsorbed through the exocyclic sulphur and N atoms onto the 5-coordina ted Fe atom. The pyrite (111) surface was found to be more reactive and di fferent adsorption mechanisms were predicted\, where the MBT exocyclic sul phur atom bridged on the 5-coordinated Fe and surface 2-coordinated sulphu r atoms\, while the N atom adsorbed on the 5-coordinated Fe atom. In the c ase of MBO and MBI\, dissociation of the exocyclic sulphur atom from the c ollector occurred with subsequent interaction with the surface 5-cordinate d Fe and 2-coordinated S atoms. This resulted in the collector carbon atom adsorbing on the surface 2-coordinated S atom\, while the N atom adsorbed on the 5-coordinated Fe atom. The microcalorimetry experimental heats of adsorption of MBT\, MBO and MBI indicated that MBI had the strongest adsor ption and the order of adsorption decrease as: MBI > MBT > MBO.\n\nhttps:/ /events.chpc.ac.za/event/6/contributions/29/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/29/ END:VEVENT BEGIN:VEVENT SUMMARY:Can we reach the heaven of chemical accuracy by climbing Jacob’s Ladder? A DFT validation study for Non-heme Iron complexes DTSTART;VALUE=DATE-TIME:20171205T120000Z DTEND;VALUE=DATE-TIME:20171205T122000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-32@events.chpc.ac.za DESCRIPTION:Speakers: Adedapo Adeyinka (Chemical Resource Beneficiation Fo cus Area\, Northwest University Potchefstroom Campus)\nhttps://events.chpc .ac.za/event/6/contributions/32/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/32/ END:VEVENT BEGIN:VEVENT SUMMARY:Testing and Training Cybersecurity using a virtual platform DTSTART;VALUE=DATE-TIME:20171205T113000Z DTEND;VALUE=DATE-TIME:20171205T120000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-34@events.chpc.ac.za DESCRIPTION:Speakers: Aubrey Labuschagne (CSIR)\, Joey Jansen van Vuuren ( CSIR)\nCybercrime and cyber vulnerabilities are increasing both in number and complexity and pressure is on business and industry to employ cybersec urity professionals that are able to defend systems and infrastructure aga inst cyber-attacks. As a country’s critical infrastructure can be expose d through integration of IoT and Smart Cities\, the need has been identifi ed to develop a platform to conduct various tests focusing on securing the implementations before deployment. The platform provides a virtualised s pace for the simulation or emulation of enterprise networks to conduct var ious forms of testing as well as the training of cybersecurity specialists . This hyper-realistic simulation virtual training environment normally re sembles the enterprise network or operational environments where the cyber workforce can do using red and blue team exercises that can develop their skills to defend their company networks. Doing training on these platform offer the opportunity for a cyber team to work together\, as one team\, a cross multiple security domains to defend their networks\, reinforcing the skills and opportunity for shared security responsibility for the company \, agency or service. In addition it improve their ability to identify adv anced attacks.\nThe Network Emulation and Simulation Laboratory (NESL) at the CSIR\, is developed to support higher education and industry to perfor m network bandwidth and performance modelling\, cybersecurity training\, d evice research and advanced analytics to study cyber risks and to deliver effective and practical security solutions\, all within the safety of an i solated environment. This platform can also be used to do quantitative\, qualitative and realistic assessment of potentially ground-breaking cyber technologies for research and development. It also includes hardware in th e loop and malware capability for the emulation of real attacks.\n\nhttps: //events.chpc.ac.za/event/6/contributions/34/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/34/ END:VEVENT BEGIN:VEVENT SUMMARY:DENSITY FUNCTIONAL STUDY OF ELECTRONIC\, OPTICAL AND ADSORPTION PR OPERTIES DYE ON ANATASE AND BROOKITE TIO2 SURFACES FOR APPLICATION IN DYE SENSITIZED SOLAR CELLS DTSTART;VALUE=DATE-TIME:20171204T113000Z DTEND;VALUE=DATE-TIME:20171204T120000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-35@events.chpc.ac.za DESCRIPTION:Speakers: Eric Maluta (University of Venda)\nTheoretical and c omputational studies of doped TiO2 polymorphous can contribute to a deeper understanding of dye sensitized solar cells. These solar cells represent a promising approach to a direct conversion of sunlight into electrical en ergy at low cost and with high efficiency. The light adsorption occurs in dye molecules adsorbed on a highly porous structure of TiO2 film [1-2]. Th e problem encountered with the TiO2 is its wide band gap which is about 3. 4 eV and show photocatalytic activity under UV light irradiation that acco unts for only a small portion of solar energy\, in contrast to visible lig ht which has a major part of solar energy. Harnessing and effectively util izing sunlight is the most challenging subject for the extensive applicati on of TiO2 as photon absorption [3]. Transition metal doping is one of the most effective approaches to extend the absorption edge of TiO2 to visibl e light region\, which either inserts a new band into the original band ga p\, or modification of the conduction band (CB) or valence band (VB) impro ving the photocatalytic activity of TiO2 to some degree [3-5].\n \nIn the current study\, electronic density of states and optical properties of dop ed and undoped\, Anatase and Brookite surfaces were performed using the fi rst-principles calculations based on Density Functional Theory (DFT) using a plane-wave pseudopotential method. The generalized gradient approximati on (GGA) was employed in the scheme of Perdew-Burke-Ernzerhof (PBE) to des cribe the exchange-correlation functional. All calculations were carried o ut with CASTEP (Cambridge Sequential Total Energy Package) code in Materia ls Studio of Accelrys Inc [6]. The results confirm that the mixing of the dopants induced states with the original Ti 3d and O 2p valence band and conduction band attributes to the band gap\, hence the shifting of the abs orption edge of TiO2 from UV to visible spectrum. The light harvesting eff iciency of the dye molecules were calculated and compared to the experimen tal values. \n\nKeywords: Dye sensitized solar cells\, Density Functional theory\, Bandgap\, Optical and Electronic Properties.\n\nReferences\n\n1. Chou T.P.\, Zhang Q.\, Cao G.\, (2007)\, Effects of dye loading conditi ons on the energy conversion efficiency of ZnO and TiO2 dye-sensitized sol ar cells. Journal of Physical Chemistry C\, 111\, 18804-18811.\n2. Yuas a T.\, Kawakami R.\, Sato Y.\, Mori Y.\, Adachi\, M.\, Yoshikado\, S.\, (2 012)\, Dye adsorption for dye-sensitized solar cell\, Solar Energy Materia ls and Solar Cells\, 102\, 2-7. \n3. Zallen R\, and Moret M.P. The opti cal absorption edge of brookite TiO2. Solid State Commun\, 2006\, 137 154- 157.\n4. Yang K\, Dai Y\, Huang B\, Han S: Theoretical study of N-doped TiO2 rutile crystals. J Phys Chem B 2006\, 110:24011–24014.\n5. Grä tzel M\, and O’Regan B. “A Low-Cost\, High-Efficiency Solar Cell Based on dye sensitized Colloidal TiO2 Films” Nature\, 353\, 737-740\, 199 1.\n6. Clark S.J\, Segall M.D\, Pickard C.J\, Hasnip P.J\, Probert M.I. J\, Refson K and Payne M.C 2005 Z Kristallogr 220 567–570.\n\nhttps://ev ents.chpc.ac.za/event/6/contributions/35/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/35/ END:VEVENT BEGIN:VEVENT SUMMARY:Computations on the CHPC: Evaluation of the COSMO model DTSTART;VALUE=DATE-TIME:20171204T123000Z DTEND;VALUE=DATE-TIME:20171204T124500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-36@events.chpc.ac.za DESCRIPTION:Speakers: patience tlangelani mulovhedzi (scientist)\nThe Sout h African Weather Service (SAWS) is the mandated national meteorological s ervice tasked with providing timely and accurate scientific data in the fi eld of meteorology to the broader South African community\, through a comb ination of both public and commercial services. It is\, therefore\, of gre at importance that the SAWS issues weather forecasts of high quality and v alue. SAWS accomplishes this task\, partially\, through the use of weather forecast models\, with Unified model (UM) from the UK Metoffice serving a s the main operational model.\nWeather forecast models perform differently across different parts of the globe. In order to ensure continuous delive ry of high quality weather forecasts to SAWS stakeholders\, model inter-co mparisons are necessary. The main purpose of model inter-comparison is to examine\, compare and analyse the outcome of different models in order to identify the most suitable model for SAWS. Previous studies have also show n that forecasts from multi-model systems are more skilful than those from one model. In addition to running the UM for operations\, the SAWS is int erested in studying the performance of other models over the country. Two models used in a number of countries have been chosen for this purpose and they are the Weather Research and Forecasting (WRF) and Consortium for Sm all-scale Modelling (COSMO) models.\nThis study will focus on the COSMO mo del\, which is a limited area model driven from Icosahedral Non-hydrostati c (ICON) global model. The ICON model runs with a grid spacing of 13km glo bally\, and therefore COSMO cab be set up to run with a grid spacing that is smaller than 5km and therefore provide higher resolution simulations. T he COSMO model is being run with a grid spacing of 2.8km and 50 vertical l evels in Germany\, which allows for accurate numerical prediction of near- surface weather conditions (e.g. clouds\, fog\, frontal precipitation) and simulation of severe weather events triggered by deep moist convection ( supercell thunderstorms\, intense mesoscale convective complexes\, prefron tal squallline storms and heavy snowfall from wintertime mesocyclones). In this study\, the COSMO model will be used to simulate selected case studi es\, and verified against the SAWS observations.\n\nhttps://events.chpc.ac .za/event/6/contributions/36/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/36/ END:VEVENT BEGIN:VEVENT SUMMARY:The degradation of phosphate derived ligands in hydrometallurgical solvent extraction DTSTART;VALUE=DATE-TIME:20171206T121000Z DTEND;VALUE=DATE-TIME:20171206T123000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-37@events.chpc.ac.za DESCRIPTION:Speakers: Daniel Jansen van Vuuren (North-West University)\nht tps://events.chpc.ac.za/event/6/contributions/37/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/37/ END:VEVENT BEGIN:VEVENT SUMMARY:Applications of machine learning: Developing natural language proc essing technology for South Africa's official languages DTSTART;VALUE=DATE-TIME:20171205T120000Z DTEND;VALUE=DATE-TIME:20171205T122000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-38@events.chpc.ac.za DESCRIPTION:Speakers: Febe de Wet (Stellenbosch University)\nRecent develo pments in the field of machine learning (ML) have been influenced by advan ces in computational technology as well as the availability of large volum es of data. One field in which progress has been accelerated substantially is Natural Language Processing (NLP). NLP is a broad research field inclu ding topics such as natural language understanding and natural language ge neration. The aim of research in this field is to enable natural language interaction between humans and machines.\n\nThis talk will present some of the ML techniques involved in NLP and will provide a brief overview of ho w things have changed as a result of Big Data and Huge Machines. The devel opment of automatic speech recognition (ASR) technology will be presented as a case in point with specific emphasis on efforts to develop ASR techno logy for the 11 official languages of South Africa during the last 20 year s.\n\nhttps://events.chpc.ac.za/event/6/contributions/38/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/38/ END:VEVENT BEGIN:VEVENT SUMMARY:Intel HPC and AI Technologies DTSTART;VALUE=DATE-TIME:20171204T120000Z DTEND;VALUE=DATE-TIME:20171204T123000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-40@events.chpc.ac.za DESCRIPTION:Speakers: Aljeshi Ahmed (Intel Corporation)\nIn this presentat ion\, attendees will hear about the latest Intel Technologies in AI and HP C. This will include Processors\, Fabric\, Accelerators\, and some s/w as well. Also\, I will touch base on some of Intel recent strategic acquisi tions (e.g. Nervana\, MobileEye\, and Movidius). I will also include some benchmarks on different CPU's/applications that we tested.\n\nhttps://eve nts.chpc.ac.za/event/6/contributions/40/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/40/ END:VEVENT BEGIN:VEVENT SUMMARY:A DFT study of the ring opening mechanism of tetraethyl-2-aryl-1\, 2-epoxygembisphosphonates DTSTART;VALUE=DATE-TIME:20171205T124000Z DTEND;VALUE=DATE-TIME:20171205T130000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-41@events.chpc.ac.za DESCRIPTION:Speakers: Thishana Singh (DUT)\nA DFT investigation of the rin g opening mechanism of tetraethyl 2-aryl-1\,2-epoxygembisphosphonates on t he C-O bonds of the oxirane ring using ammonia as the nucleophile were car ried out. Thermodynamic data obtained in both the gas phase and solvent si mulations showed that the ring opening is favoured at the less hindered ca rbon (C2) of the oxirane ring. Varia-tion of the substituent on C2 to lowe r the activation energy revealed electron-donating methoxybenzene to be th e best sub-stituent in this study.\n\nhttps://events.chpc.ac.za/event/6/co ntributions/41/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/41/ END:VEVENT BEGIN:VEVENT SUMMARY:CHPC Industry Engagement Meeting DTSTART;VALUE=DATE-TIME:20171207T070000Z DTEND;VALUE=DATE-TIME:20171207T072000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-42@events.chpc.ac.za DESCRIPTION:Speakers: Werner Janse Van Rensburg (CHPC)\nThe CHPC's non-aca demic users are invited to the annual industry engagement meeting\,to be h eld on the morning of 7 December\, with informal discussions to be continu ed during lunch. The purpose of the meeting is to touch base with existin g non-academic users\, discuss common points of interest and to inform pro spective new commercial users. The meeting will consist of a presentation by CHPC staff\, followed by brief presentations by users and a group disc ussion. The intention is for the CHPC to learn from the users' experience \, and to inform the users of future plans.\n\nhttps://events.chpc.ac.za/e vent/6/contributions/42/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/42/ END:VEVENT BEGIN:VEVENT SUMMARY:Charge transport\, interfacial interactions and synergistic mechan ism in BiNbO4/MWO4 (M = Zn and Cd) heterostructures for hydrogen productio n: insights from a DFT+U study DTSTART;VALUE=DATE-TIME:20171204T120000Z DTEND;VALUE=DATE-TIME:20171204T122000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-43@events.chpc.ac.za DESCRIPTION:Speakers: Francis Opoku (Department of Applied Chemistry\, Uni versity of Johannesburg)\nhttps://events.chpc.ac.za/event/6/contributions/ 43/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/43/ END:VEVENT BEGIN:VEVENT SUMMARY:What infrastructure is necessary for successful research data mana gement (RDM) at universities? DTSTART;VALUE=DATE-TIME:20171206T115500Z DTEND;VALUE=DATE-TIME:20171206T122000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-44@events.chpc.ac.za DESCRIPTION:Speakers: Heila Pienaar (University of Pretoria)\nThe presenta tion will cover the following elements for RDM success:\n• RDM life c ycle\n• Research data elements in the research life cycle with intern ational examples\n• What can be seen as RDM infrastructure\n• IT infrastructure\n• Library infrastructure\n• Research office inf rastructure\n• Recommendations and conclusion\n\nhttps://events.chpc. ac.za/event/6/contributions/44/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/44/ END:VEVENT BEGIN:VEVENT SUMMARY:Lead optimization: calculating relative binding free energies with FEP+ DTSTART;VALUE=DATE-TIME:20171204T101000Z DTEND;VALUE=DATE-TIME:20171204T103000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-46@events.chpc.ac.za DESCRIPTION:Speakers: Stephan Ehrlich (Schrodinger GmbH)\nThe prediction o f relative free energies of binding within a congeneric ligand series can be a potential key contribution to the process of ligand optimization. Whe n accurate enough (approx. 1 log unit in the binding constant)\, free ener gy predictions can help to reduce the effort spent in compound synthesis a nd also the total time spent by reducing the number of iterations in the d esign process.\n\nTraditionally\, fast empirical approaches like rigid-rec eptor docking dominated the field for decades due to their low computation al cost\, but have proven to be very limited in their predictive power in lead optimization and often required a large amount of experience to inter pret since the success of the results can be highly target specific.\n\nNo wadays we are witnessing the beginning of a new era for relative binding f ree energy predictions due to the emergence of free energy perturbation (F EP) calculations. The general concept is quite old\, and the first calcula tions on small systems were carried out more than twenty years ago. Thanks to a number of scientific and technological advances\, we are now finally able to use FEP on a broader scope in real world applications.\n\nThe tal k will briefly outline the main features of Schrodinger’s FEP+ solution\ , which combines a number of recent advances in the field. FEP+ features h igh performance MD code that makes use of GPU computing\, augmented by enh anced sampling schemes (‘replica-exchange solute tempering’)\, to achi eve sufficient sampling to provide converged free energy estimates with mo dest hardware investment. Error analysis based on cycle-closure correction provides a measure of reliability for the calculations. On the force fiel d side\, the accurate all-atom force field OPLS3 is used\, including a pro tocol to conveniently parameterize missing torsional parameters. Together with an automated setup procedure\, this enables free energy calculations within real-world industrial projects. \n\nBeyond the technical overview\, the presentation will outline a few interesting cases from literature and internal efforts where FEP+ has been used retrospectively and prospective ly in order to give an idea about Schrödinger’s efforts in extending th e domain of applicability of the technique.\n\nhttps://events.chpc.ac.za/e vent/6/contributions/46/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/46/ END:VEVENT BEGIN:VEVENT SUMMARY:A high performance computing approach to cosmic-ray modulation. DTSTART;VALUE=DATE-TIME:20171205T124000Z DTEND;VALUE=DATE-TIME:20171205T130000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-57@events.chpc.ac.za DESCRIPTION:Speakers: Katlego Moloto (NWU)\nThe transport of cosmic-rays h ighly energetic charged particles originating from astrophysical sources\, in the heliosphere\, the region dominated by plasma of solar origin\, can be modelled using the Parker transport equation (TPE). We solve this equa tion using a 3D time-dependent stochastic numerical solver\, taking into a ccount the various processes that modulate the intensities of these cosmic rays on their way to the inner heliosphere and thus to Earth. Where they can pose significant radiation hazard to\, e.g. astronauts. This numerical technique lends itself to large-scale parallel computing. Preliminary res ults of cosmic-rays intensities computed using the CHPC cluster will be pr esented.\n\nhttps://events.chpc.ac.za/event/6/contributions/57/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/57/ END:VEVENT BEGIN:VEVENT SUMMARY:Modelling the variability of convection over East Rand South Afric a DTSTART;VALUE=DATE-TIME:20171204T121500Z DTEND;VALUE=DATE-TIME:20171204T123000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-118@events.chpc.ac.za DESCRIPTION:Speakers: Sifiso Mbatha (South African Weather Service)\nhttps ://events.chpc.ac.za/event/6/contributions/118/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/118/ END:VEVENT BEGIN:VEVENT SUMMARY:Spin-transfer torque field switching of magnetization in verticall y-stacked multilayers DTSTART;VALUE=DATE-TIME:20171205T092000Z DTEND;VALUE=DATE-TIME:20171205T094000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-50@events.chpc.ac.za DESCRIPTION:Speakers: Aniekan Ukpong (UKZN)\nTheoretical and computational analysis of the magnetotransport properties and spin-transfer torque fiel d-induced switching of magnetization density in vertically-stacked multila yers is presented. Atom-resolved magnetic moments and spin-transfer torque s are computed at finite bias within linear response approximation to the spin-density reformulation of the van der Waals density functional theory. Dynamical spin excitations are computed as a function of a spin-transfer torque induced magnetic field along the magnetic easy axis\, and the corre sponding spin polarization perpendicular to the easy axis is obtained. A g iant anisotropic magnetoresistance of 3200% is obtained in the nonmagnetic -metal-capped Fe/hBN/graphene/hBN/Pt multilayer architecture. The magnitud e of the spin-transfer torque is found to increase as the tunneling spin c urrent increases\, and this activates the magnetization switching process due to increased charge accumulation. This mechanism causes substantial sp in backflow\, which manifests as rapid undulations in the bias-dependent t unneling spin currents. The implication of these findings on the design of nanoscale spintronic devices with spin-transfer torque tunable magnetizat ion density is discussed. Insights from this study are expected to enhance the prospects for developing and integrating artificially assembled van d er Waals multilayer heterostructures as the preferred material platform fo r efficient engineering of spin switches for spintronic applications.\n\nh ttps://events.chpc.ac.za/event/6/contributions/50/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/50/ END:VEVENT BEGIN:VEVENT SUMMARY:ELSI: A unified software interface for Kohn-Sham electronic struct ure solvers DTSTART;VALUE=DATE-TIME:20171206T095000Z DTEND;VALUE=DATE-TIME:20171206T101000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-51@events.chpc.ac.za DESCRIPTION:Speakers: Victor Yu (Duke University)\nSolving the electronic structure from a generalized or standard eigenproblem is often the bottlen eck in large-scale molecular and materials simulations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially a ll current electronic structure codes\, based on similar matrix expression s\, and by high-performance computation. We present a unified software int erface\, ELSI (elsi-interchange.org)\, that simplifies the implementation and optimal use of multiple Kohn-Sham electronic structure solvers. ELSI o ffers reasonable default parameters for the solvers\; dynamic switch betwe en solvers within a single calculation\; and automatic conversion between input and internal working matrix formats. Comparative benchmarks performe d with multiple solvers on distributed memory supercomputing architectures are shown for system sizes up to tens of thousands of atoms.\n\nhttps://e vents.chpc.ac.za/event/6/contributions/51/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/51/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational Aeroacoustic Modelling Using Hybrid RANS/LES Methods With Modified Acoustic Analogies DTSTART;VALUE=DATE-TIME:20171206T095000Z DTEND;VALUE=DATE-TIME:20171206T101000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-54@events.chpc.ac.za DESCRIPTION:Speakers: Zamashobane Zama (University of Cape Town)\nThis stu dy considers a numerical approach to identifying noise mechanisms in tande m\ncylinders to understand aircraft landing gear as a primary contributor to airframe noise\nduring approach and landing. Fluctuations in the flow p roperties induced by turbulence\nare computed as well as the corresponding propagations. A hybrid IDDES turbulence\nmodel is employed\, to compute t he boundary layer and fluctuations in the flow properties. Larsson et al. modified Curle’s analogy leading to the derivation of a version of\nCurl e’s analogy that makes use of strictly time derivatives which has been p roven to be\nless sensitive to numerical errors. Brentner and Farassat der ived a formulation of the\nFfowcs-Williams and Hawkings analogy for a perm eable surface enclosing the acoustic\nsources which accounts for the quadr upole acoustic sources in the flow without the costly\ncalculation of a vo lume integral. This study will consider the impact of neglecting the\nvolu me sources through a comparison of the two modified versions of Curle’s and FWH\nanalogies with the results of other CFD practitioners as well as experimental data.\n\nhttps://events.chpc.ac.za/event/6/contributions/54/ LOCATION:Velmoré Hotel Estate Voltaire URL:https://events.chpc.ac.za/event/6/contributions/54/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational study of anatase TiO2 as an anode material energy st orage devices DTSTART;VALUE=DATE-TIME:20171204T095000Z DTEND;VALUE=DATE-TIME:20171204T101000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-59@events.chpc.ac.za DESCRIPTION:Speakers: Mulatedzi Gandamipfa (University of Limpopo)\nThe in creasing demand for powering systems of portable electronic devices and ze ro-emission vehicles stimulates research towards high energy and high volt age systems is a challenge. Given these exciting properties\, it becomes n ecessary not only to synthesize such solid-state and molecular systems but also to model their properties at an appropriate size and time scale. In this work we have predicted the structural parameters for TiO2 polymorphs and these parameters were found to be in agreement with an experimental da ta. We also calculated the band gap energies\, predicted band structures a nd density of states for these polymorphs in an effort to validate the DFT B+ potentials. The geometry optimizations were performed using DFTB+ poten tials that we derived. Moreover\, these properties will determine which Ti O2 polymorph can be used as an anode material in future storage devices.\n \nhttps://events.chpc.ac.za/event/6/contributions/59/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/59/ END:VEVENT BEGIN:VEVENT SUMMARY:Tuning the electronic\, magnetic and optical properties of 2D mate rials: Ab initio insights DTSTART;VALUE=DATE-TIME:20171204T093000Z DTEND;VALUE=DATE-TIME:20171204T095000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-62@events.chpc.ac.za DESCRIPTION:Speakers: Cecil Ouma (North West University)\nThe past decade has witnessed unprecedented advances in ab initio modelling of material pr operties. These advances have largely been attributed in part to algorithm refinements within codes implementing standard ab initio approaches such as density functional theory (DFT) and also to the advances made in high p erformance computing. It is thus now possible to model systems that were t raditionally computationally expensive such as defects\, extended surfaces and even nanoparticles. In this study the application of DFT to investiga te the electronic\, magnetic and optical properties of pristine and doped transition metal dichalcogenides (TMDCs)\, holey doped nitrogenated graph ene g-C2N and graphene like GaN (g-GaN) is presented. Transition metal (TM ) and lanthanide ion doping on the electronic\, magnetic\, optical propert ies of materials have also been taken into account. A more recent study on van der Waals hetero-structures/nanocomposites of graphene and graphene l ike AlN (g-AlN) for Li-ion battery (LIB) anode applications will also be p resented in summary.\n\nhttps://events.chpc.ac.za/event/6/contributions/62 / LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/62/ END:VEVENT BEGIN:VEVENT SUMMARY:Mechanisms of the Sea-Air CO2 Flux Seasonal Cycle biases in CMIP5 Earth Systems Models in the Southern Ocean DTSTART;VALUE=DATE-TIME:20171205T095000Z DTEND;VALUE=DATE-TIME:20171205T100500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-66@events.chpc.ac.za DESCRIPTION:Speakers: Precious Mongwe (CSIR NRE)\nThe Southern Ocean forms a key component of the global carbon cycle. Recent studies\, however\, sh ow that CMIP5 Earth System Models (ESM) disagree on the representation of the seasonal cycle of the CO2 flux (FCO2) and compare poorly to observatio ns in the Southern Ocean. This model-observations bias has important impli cations on the ability of ESMs to predict century scale CO2 sink and relat ed climate feedbacks. In this study\, we used a specialized diagnostic ana lysis on 10 CMIP5 models in the Southern Ocean to discriminate the role of the major drivers\, namely the temperature control and the concentration of dissolved inorganic carbon (DIC). Our analysis shows that the FCO2 bias es in CMIP5 models cluster in two major groups . Group A models (MPI-ESM-M R\, NorESM2 and HadGEM-ES) are characterized by exaggerated primary produc tion such that biologically driven DIC changes mainly regulate the seasona l cycle of FCO2. Group-B (CMCC-CESM\, GFDL-ESM2M\, IPSL-CM5A-MR\, MRI-ESM\ , CanESM2\, CNRS-CERFACS) overestimates the role of temperature and thus t he change in CO2 solubility becomes a dominant driver of FCO2 variability. While CMIP5 models mostly show a singular dominant influence of these two extremes\, observations show a modest influence of both\, with a dominanc e of DIC regulation. We found that CMIP5 models overestimate cooling and w arming rates during autumn and spring with respect to observations. Becaus e of this\, the role of solubility is overestimated\, particularly during these seasons (autumn and spring) in group B models\, to the extent of con tradicting the biological CO2 uptake during spring. Group A does not show this solubility driven bias due to the overestimation of DIC draw down. Th is finding strongly implies that the inability of the CMIP5 ESMs to resolv e CO2 biological uptake during spring might be crucially related to the se nsitivity of the pCO2 to temperature in addition to underestimated biologi cal CO2 uptake.\n\nhttps://events.chpc.ac.za/event/6/contributions/66/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/66/ END:VEVENT BEGIN:VEVENT SUMMARY:System administrator’s tools and techniques for user-facing soft ware DTSTART;VALUE=DATE-TIME:20171203T070000Z DTEND;VALUE=DATE-TIME:20171203T072000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-67@events.chpc.ac.za DESCRIPTION:Speakers: Milfeld Kent (TACC)\, Nicholas Thorne (Texas Advance d Computing Center)\nHPC services continue to provide ever increasing reso urces and many academic disciplines that formerly did not rely on computat ional resources are becoming interested in utilizing computational resourc es to analyze their problems. This gives us a strong incentive to provide more assistance to users over a wider range of disciplines which in turn t axes resources at HPC facilities. This leads us to investigate and/or deve lop the necessary tools to support easy-use and performant environments wh en running computations on HPC systems. TACC has developed a large number of tools that we can categorize as “user-facing software” that our use rs run (sometimes without their knowledge) to ensure that their jobs perfo rm well\, and give assistance to debugging efforts when jobs fail. We have selected four important tools\, and plan to conduct a hands-on set up for administrators and/or provide details on configuration and management of them. They are primarily focused on environment control and performance an alysis: Lmod\, containerization (Singularity)\, Tau and REMORA.\n\nOne of TACC’s most successful open-source software packages is Lmod – the Lua based version of the “Environment Modules”. It is the first thing all TACC users encounter and learn to use when they login to a TACC system. W e discuss and deploy this tool\, and demonstrate what system administrator s and package maintainers need to know to build/install/maintain an enviro nment module tool. We also explain how users benefit from Lmod\, and the s imple and advanced use cases.\n\nWe often see communities in specific doma in sciences build out similar environments that they want imported into HP C systems. They invest many hours in building these environments (same as we do at TACC for the environment that we present to users) and these envi ronments usually end up in containers. Containerization substantially impa cts system administrators because they are environments within the main en vironment\, and many of them have substantial security implications. We de monstrate how to make containers available and investigate the typical usa ge.\n\nHigh Performance in HPC systems is something administrators\, devel opers and users should view as paramount in the design of applications\, a nd setting up the optimal environment for production runs. The TAU profil er and analysis utility provides data for evaluating performance\, similar to the GNU profiler\, but has an advanced GUI interface to make analysis easier (and for viewing events). Another package\, REMORA\, is a resource monitoring tool\, also developed at TACC\, which allows users to easily c ollect execution data (memory\, numa\, i/o\, networking and cpu load). Th e management\, best usage practices and synergy between the TAU and REMORA tools will be presented.\n\nhttps://events.chpc.ac.za/event/6/contributio ns/67/ LOCATION:Velmoré Hotel Estate Voltaire URL:https://events.chpc.ac.za/event/6/contributions/67/ END:VEVENT BEGIN:VEVENT SUMMARY:Women in High Performance Computing in South Africa DTSTART;VALUE=DATE-TIME:20171206T133000Z DTEND;VALUE=DATE-TIME:20171206T135000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-69@events.chpc.ac.za DESCRIPTION:Speakers: Regina Maphanga (CSIR)\nThe first session on Women i n High Performance Computing in South Africa was proposed and held during 2016 annual conference. The major aim of the initiative was to establish a network of Women in HPC in SA\, by bringing them together during the meet ing. The session was supported and attended by both men and women\, and mo st importantly was supported by CHPC management team. An interim steering committee comprising of women from various institutions and disciplines wa s established and will take the initiative going forward. Consequently\, w e propose to have a session during 2017 annual conference. \nIt is envisag ed that at the end of the session and beyond\, the following goals would b e achieved:\n\n• Create a long-term platform for interaction and ment oring among the women.\n\n• Encourage more female learners and studen ts to consider careers in HPC.\n\n• Contribute in increasing the numb er of women and girls participation in HPC through training and networking .\n\n• Share information and resources that foster growth for women i n HPC.\n\nhttps://events.chpc.ac.za/event/6/contributions/69/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/69/ END:VEVENT BEGIN:VEVENT SUMMARY:South African Record Rainfalls DTSTART;VALUE=DATE-TIME:20171204T120000Z DTEND;VALUE=DATE-TIME:20171204T121500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-72@events.chpc.ac.za DESCRIPTION:Speakers: Jan Vermeulen (South African Weather Service)\nSouth African and world rainfall records are compared and new 5-minute\, 10-min ute\, 15-minute and a possible yearly records for SA is reported. \n\n42.4 mm\, 70.8 and 76.0 mm were recorded by an Automatic Weather Station (AWS) at Levubu in Limpopo for 5\, 10 and 15 minutes respectively from a thunde rstorm 26 February 2016. A rainfall of 4299 mm was recorded for the year 2 000 at Matiwa in Limpopo (Makhado district) from Tropical Cyclone Eline an d other tropical systems that affected the area.\n\nMapumulo Prison Automa tic Rainfall Station (ARS) in eastern KwaZulu-Natal recorded 138.2 mm/hour 16:15 and 16:25 twice 27 January. Mapumulo's daily rainfall was 186.6 mm and the ARS lies halfway between Stanger and Kranskop. It is the SA record rainfall intensity for one hour pending the validation of the 218 mm in 4 0 minutes at Swartkoppies 22 km to south of Johannesburg 13 January 1951 r ecorded by an 8 inch standard rain gauge. The clock hourly rainfall record according to the Climate database is 125 mm 19:00 5 March 1997 at Bisho. Followed by 123 mm 16:00 at Mapumulo.\n\nA cloudburst occurs if rainfall r ate is equal to or greater than 100 mm per hour.\n\nhttps://events.chpc.ac .za/event/6/contributions/72/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/72/ END:VEVENT BEGIN:VEVENT SUMMARY:DMol3/COSMO-RS Prediction of Aqueous Solubility and Reactivity of Selected Azo Dyes: Effect of Global Orbital Cut-off and COSMO Segment Vari ation DTSTART;VALUE=DATE-TIME:20171205T100000Z DTEND;VALUE=DATE-TIME:20171205T102000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-75@events.chpc.ac.za DESCRIPTION:Speakers: Olaide Wahab (Department of Applied Chemistry\, Univ ersity of Johannesburg\, P. O. Box 17011\, Doornfontein Campus\, 2028\, Jo hannesburg\, South Africa)\nhttps://events.chpc.ac.za/event/6/contribution s/75/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/75/ END:VEVENT BEGIN:VEVENT SUMMARY:Intel AI Workshop DTSTART;VALUE=DATE-TIME:20171203T070000Z DTEND;VALUE=DATE-TIME:20171203T072000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-76@events.chpc.ac.za DESCRIPTION:Speakers: Stephen Blair-Chappell (Bayncore)\nJoin us for a ful l day of technical sessions dedicated to Artificial Intelligence / Deep Le arning showing how these technologies can be implemented on existing and u pcoming CPUs and how performance can be scaled to any workload!\n\nhttps:/ /events.chpc.ac.za/event/6/contributions/76/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/76/ END:VEVENT BEGIN:VEVENT SUMMARY:Enabling The Era of Data-Centric HPC DTSTART;VALUE=DATE-TIME:20171205T113000Z DTEND;VALUE=DATE-TIME:20171205T120000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-78@events.chpc.ac.za DESCRIPTION:Speakers: Yossi Avni (Mellanox Technologies)\nThe latest revol ution in High Performance Computing and Artificial Intelligence is the mov e to a Data-Centric architecture\, a collaborative effort among industry\, academia\, and manufacturers to reach Exascale performance by taking a ho listic system-level approach to fundamental performance improvements. Data -Centric architecture exploits system efficiency and optimizes performance by creating synergies between the hardware and the software and between d ifferent hardware components. The boundaries between compute\, interconnec t and storage have change\, in order to enable data analysis everywhere. T he s\n\nhttps://events.chpc.ac.za/event/6/contributions/78/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/78/ END:VEVENT BEGIN:VEVENT SUMMARY:The Dawning of the Neo-Digital Age in the Era of Nano-Scale Techno logy DTSTART;VALUE=DATE-TIME:20171206T160000Z DTEND;VALUE=DATE-TIME:20171206T164500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-79@events.chpc.ac.za DESCRIPTION:Speakers: Thomas Sterling (Indiana University)\nThis is the Da wning of the Neo-Digital Age\; a unique period brought on by the end of Mo ore’s Law as semiconductor fabrication enters its final phase with nano- scale feature size. The Neo-Digital Age also corresponds to a time when en ergy constraints at the chip level and the system level bound power consum ption and indirectly the clock rate of device logic. It will prove to be a n epoch of innovation\, in part out of desperation to achieve yet further significance performance gains even with the emerging barriers\, but also through an explosion of creativity in computer architecture not seen since the 1980s. Ideas are already percolating and being considered by academia \, industry\, and even industry who has held fast to approaches based on i ncremental changes to otherwise conventional methodologies. Such currently pursued strategies include neuromorphic\, quantum computing\, cellular au tomata and others. Some of these have their roots in research of prior dec ades. This plenary presentation will discuss in some detail one possible n eo-digital class of computing\, the Continuum Computer Architecture\, and at greater depth one specific example being explored\, the Simultac Fonton . Analysis suggests that the Simultac non-von Neumann architecture using t oday’s semiconductor technology could deliver a peak exaflops performanc e at 10% the expected cost of a conventional derivative machine at exascal e\, 10% power consumption\, and 1% size. The Simultac use of dynamic adapt ive introspection and the HPX+ runtime system software support based on th e ParalleX execution model (previously discussed) will significantly enhan ce efficiency\, scalability\, and user productivity. Questions will be enc ouraged by participants throughout the presentation as well as the Q&A ses sion at the end.\n\nhttps://events.chpc.ac.za/event/6/contributions/79/ LOCATION:Velmoré Hotel Estate Tres Sage Plenary Hall URL:https://events.chpc.ac.za/event/6/contributions/79/ END:VEVENT BEGIN:VEVENT SUMMARY:Investigation of the interaction between selected divalent cations and the novel Schistosoma mansoni Universal stress protein G4LZI3. DTSTART;VALUE=DATE-TIME:20171206T100000Z DTEND;VALUE=DATE-TIME:20171206T102000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-80@events.chpc.ac.za DESCRIPTION:Speakers: Priscilla Masamba (University of Zululand)\nSchistos omiasis\, despite several eradication and elimination attempts\, still rep resents one of the most debilitating parasitic diseases of poverty amongst all the Neglected Tropical Diseases. Economically challenged countries be ar the full brunt of the disease\, coupled with those of other diseases of public health importance such as malaria\, HIV/AIDS and tuberculosis. Pra ziquantel (PZQ)\, a first-line treatment drug has been in use for the last three decades\, but has recently showed traces of drug resistance\, hence alternative treatment regimen becomes a priority. Universal stress protei ns have been postulated to be upregulated in the Schistosoma worm in respo nse to hazardous environmental conditions. More so\, three divalent cation s have been postulated to play a role in the mechanism of action of PZQ in bringing about therapeutic response against schistosomiasis. Therefore\, this study was aimed at investigating the interaction between these divale nt cations and a novel Usp G4LZI3 protein that has been hypothesized as a possible vaccine candidate. Bioinformatics was used to predict the seconda ry structure of the protein\, and to generate a 3D model of the protein be fore the cations were docked against the G4LZI3 protein. These in silico r esults were then validated using Isothermal Titration Calorimetry\, by tit rating the divalent cations against purified and concentrated fractions of the protein. Preliminary results confirmed Ca2+\, Mg2+ and Zn2+ as putati ve ligands and additionally identified ATP and AMP as possible interacting molecules. However\, biophysical studies only showed interaction between Mg2+ and the novel G4LZI3 protein. These results provide prospects for fut ure studies towards anti-schistosomal drug development.\n\nhttps://events. chpc.ac.za/event/6/contributions/80/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/80/ END:VEVENT BEGIN:VEVENT SUMMARY:Computation and the future of biological research DTSTART;VALUE=DATE-TIME:20171206T113000Z DTEND;VALUE=DATE-TIME:20171206T120000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-81@events.chpc.ac.za DESCRIPTION:Speakers: Fourie Joubert (University of Pretoria)\nClassic bio logical research where individual molecules or organisms are studied in is olation\, is rapidly being complemented by high-throughput highly-parallel research approaches. The implications are profound for established resear chers\, but even more so for new post-graduate students entering nearly al l fields of biology.\n\nThis is particularly true for the high impact that massive scale genomic studies are having on work in organisms ranging for m viruses and bacteria\, up to mammals and humans. Highlights of bioinform atics-related work performed at the CHPC will be shown\, including the For est Molecular Biology programme\, the Tree Pathology Co-operative programm e\, the Maize Fungal Pathogen programme\, the HIV Computational Immunology programme\, the Malaria Transcriptomics programme and the Cancer Genomics programme.\n\nThis will be combined with some speculation around the futu re needs of all biological researcher to be able to operate in a computati onal and particularly a high-performance computational environment.\n\nhtt ps://events.chpc.ac.za/event/6/contributions/81/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/81/ END:VEVENT BEGIN:VEVENT SUMMARY:Deep Learning: Research Directions and Upcoming Challenges DTSTART;VALUE=DATE-TIME:20171205T113000Z DTEND;VALUE=DATE-TIME:20171205T120000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-82@events.chpc.ac.za DESCRIPTION:Speakers: Davide Bacciu (University of Pisa)\nThe focus of thi s talk is an analysis of the upcoming trends in Deep Learning research\, i n particular as regards the most promising application fields which are li kely to benefit from the AI revolution. We will take a deep dive into Deep Learning applications to Life Science and the Internet of Things\, highli ghting the challenges and advantages related to working on data with a str uctured representation. We will show examples ranging from sensor time ser ies to labelled trees representing subclonal cancer populations\, all the way to more complex graph structures capturing the articulated interaction s between brain areas during cognitive processes. Particular focus will be given to the challenges and opportunities for the HPC and application dev elopers communities.\n\nhttps://events.chpc.ac.za/event/6/contributions/82 / LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/82/ END:VEVENT BEGIN:VEVENT SUMMARY:2017 HPC Landscape and Technology Trends DTSTART;VALUE=DATE-TIME:20171204T133000Z DTEND;VALUE=DATE-TIME:20171204T135000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-84@events.chpc.ac.za DESCRIPTION:Speakers: Michael Feldman (TOP500.org)\nAs the exascale era ap proaches\, the landscape of high performance computing is changing rapidly . The advent of AI and machine learning has emerged as a major influence i n HPC system and component design\, and has encouraged users to rethink th eir traditional workflows. TOP500 News Editor Michael Feldman will recap s ome of the most important developments in this area that took place over t he last year and discuss the broader ramifications for the HPC community.\ n\nhttps://events.chpc.ac.za/event/6/contributions/84/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/84/ END:VEVENT BEGIN:VEVENT SUMMARY:Limits of Langmuir DTSTART;VALUE=DATE-TIME:20171206T090000Z DTEND;VALUE=DATE-TIME:20171206T093000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-85@events.chpc.ac.za DESCRIPTION:Speakers: Eric van Steen (Catalysis Insititute\, Department of Chemical Engineering\, University of Cape Town)\nLangmuir was awarded the Nobel prize in 1932 for his contribution to surface chemistry\, a field o f utmost importance technically seeing that over 70% of all chemicals are produced in a surface-catalysed reaction. He proposed a bold theory on the adsorption of molecules at surfaces\, on which basis the rate of heteroge neously catalysed reactions are typically described. The fundamental assum ptions underlying the Langmuir theory include inter alia neglecting adsorb ate-adsorbate interactions and single type of surface (site). These condit ions are not necessarily fulfilled when dealing with catalysis by metals\, especially when dealing with reactions at industrial conditions (high pre ssure) catalysed by nano-sized metal crystallites. \n\nTheoretical chemist ry can give detailed insight in surface chemistry. In particular\, the con ditions at which adsorbate-adsorbate interactions become important and the ir consequences can nowadays be easily explored using DFT. In this talk\, the adsorbate-adsorbate interactions of species adsorbed on Fe(100) invol ved in the methanation\, and O/OH co-adsorption on Pt(111) and Pt(100)-sur faces will be discussed.\n\nhttps://events.chpc.ac.za/event/6/contribution s/85/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/85/ END:VEVENT BEGIN:VEVENT SUMMARY:10 Minutes Q&A DTSTART;VALUE=DATE-TIME:20171206T102000Z DTEND;VALUE=DATE-TIME:20171206T103000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-86@events.chpc.ac.za DESCRIPTION:https://events.chpc.ac.za/event/6/contributions/86/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/86/ END:VEVENT BEGIN:VEVENT SUMMARY:High Performance Computing at the South African Weather Service DTSTART;VALUE=DATE-TIME:20171204T113000Z DTEND;VALUE=DATE-TIME:20171204T120000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-87@events.chpc.ac.za DESCRIPTION:Speakers: Mary-Jane Bopape (South African Weather Service)\nTh e South African Weather Service (SAWS) is the national weather forecast an d climate prediction agency and only atmospheric alerting authority in Sou th Africa. The SAWS runs numerical models to simulate weather and climate over a variety of time scales\, ranging from very short-range (0-12 hours) to multi-decadal timescales in what is termed a “seamless forecasting s ystem” for the successful execution of its mandate. In 2013\, the SAWS m andate was amended to also include air quality monitoring and modelling. T he SAWS also runs marine and ocean models\, as well as application models to help in decision making in sectors such as agriculture\, water resource management\, health\, aviation\, as well as energy. A critical enabling t echnology utilised by SAWS to perform the simulations described is a High Performance Computing (HPC) system and SAWS currently has a CRAY XC30 syst em. The current SAWS system is not enough for SAWS to conduct both its ope rational activities and research activities. Furthermore\, the SAWS does n ot have a failover system to ensure business continuity in the event that the CRAY system fails to run. In order to address these issues\, the SAWS and the Centre for High Performance have signed Memorundum of Agreement wh ich will allow the SAWS to use the CHPC cluster as a fail-over system as w ell as for research purposes. Six research programmes that will address di fferent research areas and timescales that the SAWS is working on have bee n agreed on\, namely\, 1) Very Short-Range Forecasting\, 2) Short and Med ium Range Forecasting\, 3) Long-Range Forecasting\, 4) Climate Change and Variability\, 5) Air Quality Studies as well as 6) Applications Research. The talk will provide an overview on planned work\, work in progress and w ork already done on the CHPC cluster in the different research programmes of the SAWS.\n\nhttps://events.chpc.ac.za/event/6/contributions/87/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/87/ END:VEVENT BEGIN:VEVENT SUMMARY:CODE-RADE offloading software building from sites. DTSTART;VALUE=DATE-TIME:20171205T101500Z DTEND;VALUE=DATE-TIME:20171205T103000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-88@events.chpc.ac.za DESCRIPTION:Speakers: Sean Murray (CHPC\, CSIR)\nCODE-RADE is a platform f or user-driven\, continuous integration and delivery of research applicati ons in a distributed environment. Starting with 6 hypotheses describing th e problem at hand\, we put forward technical and social solutions to these . Combining widely-used and thoroughly-tested tools\, we show how it is po ssible to manage the dependencies and configurations of a wide range of sc ientific applications\, in an almost fully-automated way\, via constant in tegration tools and delivery into cvmfs.\nDue to the complexity and number both of scientific packages as well as computing platforms\, delivering t hese applications to end users has always been a significant challenge thr ough the grid era\, and remains so in the cloud era.\n\nThe CODE-RADE plat form is a means for developing trust between public computing and data inf rastructures on the one hand and various developer and scientific communit ies on the other hand. Predefined integration tests are specified for any new application\, allowing the system to be user-driven. This greatly acce lerates time-to-production for scientific applications\, while reducing th e workload for administrators of HPC\, grid and cloud installations togeth er with the people maintaining the software. Specific examples will be giv en for the HPC facility in Cape Town and the distributed grid resources wi thin South Africa. We will give some insight into how this platform could be extended to address issues of reproducibility and collaboration in scie ntific research in Africa. Finally\, the mechanism of giving credit for wo rk done which is citable will be explained.\n\nhttps://events.chpc.ac.za/e vent/6/contributions/88/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/88/ END:VEVENT BEGIN:VEVENT SUMMARY:Will AI transform your research and software? DTSTART;VALUE=DATE-TIME:20171204T100000Z DTEND;VALUE=DATE-TIME:20171204T103000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-90@events.chpc.ac.za DESCRIPTION:Speakers: Kiernan Mike (Microsoft)\nhttps://events.chpc.ac.za/ event/6/contributions/90/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/90/ END:VEVENT BEGIN:VEVENT SUMMARY:Machine learning tools for visualising big data. DTSTART;VALUE=DATE-TIME:20171204T090000Z DTEND;VALUE=DATE-TIME:20171204T093000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-91@events.chpc.ac.za DESCRIPTION:Speakers: Amit Mishra (University of Cape Town)\nUnsupervised machine learning can be used to infer the hidden relationships inside of b ig data where there exists unknown structure and frameworks. Component ba sed analysis seeks to reveal the correlation and variation within a datase t\, processing and understanding these results can be challenging. 3D and 2D visualisation is used as a tool for expressing these n-th dimensional results in a simple and easily understood fashion. Unorganised streaming d ata separated into its principle components reveals anomalies and outliers which can be quickly detected to prevent data corruption.\n\nhttps://even ts.chpc.ac.za/event/6/contributions/91/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/91/ END:VEVENT BEGIN:VEVENT SUMMARY:The enzymatic mechanism of Human Immunodeficiency Virus type 1 (HI V-1) protease: are we there yet? DTSTART;VALUE=DATE-TIME:20171205T101000Z DTEND;VALUE=DATE-TIME:20171205T103000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-92@events.chpc.ac.za DESCRIPTION:Speakers: Monsurat Motunrayo Lawal (UKZN)\n**Introduction**\nT he catalytic mechanism of the Human Immunodeficiency Virus type 1 (HIV-1) protease (PR) is one of the most studied aspartate protease representative . Both experimental and theoretical techniques have been harnessed to pro vide profound understanding on a number of possible reaction pathways for the catalysis of HIV-1 PR on its natural substrate/ligand. Most of these studies have investigated the stepwise general acid/base mechanism with li ttle attention on a synchronous model in which the proteolytic reaction co uld occur as a one-step concerted process. Jaskólski et al. first put th is proposal forward in 1991 in which the hydrolytic reaction is viewed as a one-step process\; the nucleophile (water molecule) and electrophile (an acidic proton) attack the scissile bond in a concerted manner. \n**Aim a nd objective**\nHerein\, the one-step concerted catalytic mechanism of HIV -1 PR on its natural substrate and a fluoride derivative was studied using density functional theoretical (DFT) method. \n**Method**\nThe reaction was modeled to proceed through the formation of a six-membered ring transi tion state structure\, which was facilitated by a pre-reaction enzyme-subs trate complex at B3LYP/6-31+G(d) level of theory using Gaussian 09 program suite. The applied in silico model allows the elucidation activation par ameters\, kinetics\, solvent contributions and quantum chemical properties for this system.\n**Result**\nTheoretically determined activation free en ergy of 19 kcal mol-1 obtained was very close to approximately 18 kcal mol -1 reported from experiment. The fluorinated peptide substrate has an act ivation free energy of 12 kcal mol-1 which is 7 kcal mol-1 lower than natu ral substrate.\n**Implications of result** \nThis investigation could pote ntially serve as a basis towards understanding the enzymatic mechanism of homodimeric enzymes and could also guide future design of better HIV-1 PR inhibitors through fluorinating the scissile nitrogen of the natural subst rates\; an ongoing perspective from our research group.\n\nhttps://events. chpc.ac.za/event/6/contributions/92/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/92/ END:VEVENT BEGIN:VEVENT SUMMARY:Beyond Li-ion: Computational Modelling Studies on Stability of Li- S-Se System DTSTART;VALUE=DATE-TIME:20171204T124000Z DTEND;VALUE=DATE-TIME:20171204T130000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-94@events.chpc.ac.za DESCRIPTION:Speakers: Cliffton Masedi (CSIR/UL)\nRecent rechargeable batte ries are mainly based on conventional lithium intercalation chemistry\, us ing lithium transition metal oxides as cathode material with typical capac ities of 120-160 mA.h/g. The low energy density and/ or high cost of these cathode materials have limited their large scale production and applicati on in Li ion batteries. Exploration of new cathode materials is consequent ly necessary to realise more efficient energy storage systems. Lithium sul phur cells have a promise of providing 2-5 times the energy density of Li- ion cells\, however\, they suffer poor cycling performance. Improvements t hat are effected by using Li/SeSx system in different electrolytes have be en reported. \nIn the current study we employ computational modelling meth ods to explore stability\, structural and electronic properties of dischar ge products formed in the Li/SeSx battery\, which has potential to offer h igher theoretical specific energy and remedies the challenges that Li-S ba ttery encounters. First principle methods were used to calculate thermodyn amic properties of Li2S and Li2Se\, which agreed with available experiment al results. A cluster expansion technique generated new stable phases of Li/SSex system and Monte Carlo simulations determined concentration and te mperature ranges in which the systems mix. Interatomic Born Meyer potentia l models for Li2S and Li2Se were derived and validated and used to explore high temperature structural and transport properties of mixed systems.\n\ nhttps://events.chpc.ac.za/event/6/contributions/94/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/94/ END:VEVENT BEGIN:VEVENT SUMMARY:Prospects for improving coastal modelling in the Benguela region DTSTART;VALUE=DATE-TIME:20171205T093000Z DTEND;VALUE=DATE-TIME:20171205T095000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-96@events.chpc.ac.za DESCRIPTION:Speakers: Thulwaneng Mashifane (South African Environmental Ob servation Network)\nhttps://events.chpc.ac.za/event/6/contributions/96/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/96/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to HPC DTSTART;VALUE=DATE-TIME:20171203T070000Z DTEND;VALUE=DATE-TIME:20171203T150000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-97@events.chpc.ac.za DESCRIPTION:Speakers: Matthew Anderson (Indiana University)\, Thomas Sterl ing (Indiana University)\nThis tutorial will provide an entry-level presen tation of the basic concepts\, knowledge\, and skills associated with a st rong foundation in modern supercomputing. This introductory treatment is b ased on a first-year graduate course taught jointly at several universitie s and currently at Indiana University. Variations of this tutorial have be en given at SC11\, SC12\, ISC13\, ISC14\, ISC15\, ISC16\, CHPC16\, and ISC 17. The tutorial will describe supercomputer architecture including multi- core organization and GPUs\, parallel programming models like OpenMP and M PI\, simple parallel algorithms\, system software and tools for scheduling \, debugging\, performance monitoring and tuning\, and underlying technolo gy trends and future directions of this rapidly changing field. Emphasis w ill be given to practical information including current generation systems \, sources of available software\, and links for further reading. This tut orial provides the broadest outreach to people new to the field\, students \, managers\, policy makers\, and those needing a refresh in this rapidly advancing domain. Live demonstrations will be presented throughout the tut orial on the Big Red II+ Petaflops computer at Indiana University. This fu ll-day tutorial will include hands-on use for those attendees wishing to e ngage the learning experience at this depth. Questions will be welcomed th roughout the presentation.\n\nhttps://events.chpc.ac.za/event/6/contributi ons/97/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/97/ END:VEVENT BEGIN:VEVENT SUMMARY:Accelerating the 3-D FFT using a heterogeneous FPGA architecture DTSTART;VALUE=DATE-TIME:20171205T090000Z DTEND;VALUE=DATE-TIME:20171205T092500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-98@events.chpc.ac.za DESCRIPTION:Speakers: Matthew Anderson (Indiana University)\nFuture Exasca le architectures will likely make extensive use of computing accelerators such as Field Programmable Gate Arrays (FPGAs) given that these accelerato rs are very power efficient. Oftentimes\, these FPGAs are located at the n etwork interface card (NIC) and switch level in order to accelerate networ k operations\, incorporate contention avoiding routing schemes\, and perfo rm computations directly on the NIC and bypass the arithmetic logic unit ( ALU) of the CPU. This talk explores just such a heterogeneous FPGA archite cture in the context of two kernels that are driving applications in leade rship machines: the 3- D Fast Fourier Transform (3-D FFT) and Asynchronous Multi-Tasking (AMT). The machine explored here is a DataVortex system whi ch consists of conventional processors but with programmable logic incorpo rated in the memory architecture. The programmable logic controls the netw ork and is incorporated both in the network interface cards and the networ k switches and implements a contention avoiding network routing. Both the 3-D FFT and AMT kernels show compelling performance for deployment to FFT driven applications in both molecular dynamics and density functional theo ry.\n\nhttps://events.chpc.ac.za/event/6/contributions/98/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/98/ END:VEVENT BEGIN:VEVENT SUMMARY:Modelling of Multiphase Flow in Process Equipment: The Trade-off b etween Accuracy and Computational Efficiency DTSTART;VALUE=DATE-TIME:20171206T113000Z DTEND;VALUE=DATE-TIME:20171206T120000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-102@events.chpc.ac.za DESCRIPTION:Speakers: Muaaz Bhamjee (University of Johannesburg)\nProcess equipment behaviour is characterised by multiscale multiphase interactions namely: liquid-gas\, fluid-particle\, particle-particle and particle-wall interactions. The understanding of these interactions\, ideally\, requir es a general solution to the full turbulent Navier-Stokes equations combin ed with a unifying theory for granular flow. However\, in the absence of s uch breakthroughs advances in Computational Fluid Dynamics (CFD) and Compu tational Granular Dynamics (CGD) are essential. \n\nIt is evident from the literature that significant advances in the theory of fluid and granular dynamics has had a positive bearing on the advancement of the industrial v alue of chemical\, metal and mineral processing industries [1\,2\,3]. Acco rding to Joshi and Ranade [1] CFD is a technology that can be used to achi eve these advances from the fluid dynamics perspective. In the same light\ , Pöschel and Schwager [3] assert that computational granular dynamics (C GD) is also necessary to achieve these advances. Based on the advances in both fields it is clear that a combination of both is required to make the necessary leaps in technology required to achieve the above. However\, th e combined modelling of the complex physics is often computationally inten sive\, leaving the practitioner with the trade-off between the accuracy of the model predictions and the computational efficiency of the model.\n\nT he aim of this research is to improve the understanding of the physics of such flows and to provide accurate and computationally efficient models to be used in design optimisation of mineral processing processes and equipm ent. Currently hydrocyclones have been used as the examplar. However\, bro ader applications are being introduced. Multiple vartiations of Navier-Sto kes and Lattice Boltzmann Method (LBM) based models\, coupled with the Dis crete Element Method (DEM)\, are employed in the research. The models are benchmarked against experiment to determine accuracy and also benchmarked against each other for computational efficiency.\n\nThe major contribution of this research is the demonstration that the LBM can provide prediction s of the multiphase flow and interactions in a hydrocyclone that are at le ast comparable to\, and in some cases superior to\, the Navier-Stokes base d approach whilst remaining more computationally efficient (or comparable) to the Navier-Stokes based approach. Future work will focus on the develo pment of a stable two-fluid LBM model and coupled a LBM-DEM model.\n\n[1] J. B. Joshi and V. V. Ranade\, “Computational fluid dynamics for designi ng process equipment:\nexpectations\, current status\, and path forward\, ” Industrial & Engineering Chemistry Research\,\nvol. 42\, pp. 1115–11 28\, 2003.\n\n[2] H. E. Van den Akker\, “Toward a truly multiscale compu tational strategy for simulating turbulent two-phase flow processes\,” I ndustrial and Engineering Chemistry Research\, vol. 49\, pp. 10780–10797 \, 2010.\n\n[3] T. Pöschel and T. Schwager\, Computational Granular Dynam ics: Models and Algorithms\, 1st ed. Heidelberg\, New York: Springer-Berli n\, 2005.\n\nhttps://events.chpc.ac.za/event/6/contributions/102/ LOCATION:Velmoré Hotel Estate Voltaire URL:https://events.chpc.ac.za/event/6/contributions/102/ END:VEVENT BEGIN:VEVENT SUMMARY:The identification of highly potent peptide scaffolds for the trea tment of hormone resistant prostate cancer DTSTART;VALUE=DATE-TIME:20171205T095000Z DTEND;VALUE=DATE-TIME:20171205T101000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-105@events.chpc.ac.za DESCRIPTION:Speakers: Lester Sigauke (Rhodes University)\nThe risk of pros tate cancer in men has grown significantly over the last 5 years while the chemotherapeutic market for prostate cancer treatment is a $5 billion dol lar global industry. The growth of hormone sensitive cases of cancer treat ment failure has motivated the rise of alternative approaches to its chemo therapeutic treatment. One such approach involves targeting the microtubul e-associated protein/microtubule affinity-regulating kinase 4 (MARK4) prot ein. MARK4 is a kinase involved in signal transduction and is a possible c hemotherapeutic target for prostate cancer treatment. Peptides possess a l arge chemical space that can rapidly identify potent scaffolds for drug de sign strategies. We populated a virtual library of over 50\,000 unique\, l ead-like synthesisable peptides suited to drugging the MARK4 catalytic ATP recognition site using DerivatizeME an in-house development virtual libra ry builder. High-throughput virtual screening of the virtual library ident ified 100 hits based on binding probabilities expressed as molecular docki ng binding energies. Rapid simulation based screening of these hits identi fied 10 highly potent peptide scaffolds for chemical synthesis in order to identify peptide inspired drug precursors. Further interrogation of these hits for the treatment of hormone resistant prostate cancer through pertu rbing signal transduction via targeting the MARK4 protein will enable us t o be better positioned to win the war against prostate cancer.\n\nhttps:// events.chpc.ac.za/event/6/contributions/105/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/105/ END:VEVENT BEGIN:VEVENT SUMMARY:HPC Storage – the two distinct challenges DTSTART;VALUE=DATE-TIME:20171204T101500Z DTEND;VALUE=DATE-TIME:20171204T104000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-107@events.chpc.ac.za DESCRIPTION:Speakers: Wolfgang Mertz (CTO HPC Dell EMC Isilon)\nTraditiona lly when architecting the storage for an HPC environment the focus is on p erformance of the file system. There is another challenge though\, as one has to manage all the files that are used for input or created as output\ , typically over a long period of time. There is even value in this data that can be mined via modern analytics methods (aka Hadoop) or used for AI /ML. This session will outline why it is essential to use different solut ions to address “the performance challenge” and “the persistent data challenge”.\n \nBiography: Wolfgang holds a PhD on computer aided engin eering. In his more than 25 years in the IT industry he held various tech nical and strategic positions. He focuses on understanding the verticals ’ specific processes\, needs and applications\, which he then links to t he IT product’s features and capabilities in order to achieve the best r esults for the customers. In his current role as CTO for EMEA in Dell EMC ’s Unstructured Storage Team he specializes mainly HPC and related verti cals. Wolfgang also follows the immense transformations IT is currently u ndergoing\; this especially includes the new capabilities data lakes\, big data analytics and AI/ML offer.\n\nhttps://events.chpc.ac.za/event/6/cont ributions/107/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/107/ END:VEVENT BEGIN:VEVENT SUMMARY:Numerical modeling of transients in the solar modulation of astrop articles DTSTART;VALUE=DATE-TIME:20171205T113000Z DTEND;VALUE=DATE-TIME:20171205T120000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-110@events.chpc.ac.za DESCRIPTION:Speakers: Marius Potgieter (North-West University)\nA three-di mensional (3D)\, time-dependent numerical model for the solar modulation o f astroparticles (cosmic rays) is constructed based on solving the relevan t transport equation applicable to the heliosphere which is the electrodyn amic influence sphere of the Sun. The model is using the Stochastic Differ ential Equation (SDE) approach which provides numerical advantages. The mo del is designed to simulate transient events which originate from the Sun and propagate outwards with the solar wind to produce sharp and relative s hort term decrease\, called Forbush Deceases (FDs)\, in the intensity of a stroparticles. These charged particles with energies above 1 MeV arrive at the Earth from Galactic space (cosmos). In order to study the main featur es of these FDs\, a complicated diffusion barrier must be constructed taki ng into account all relevant physics\, such as convection\, diffusion\, ad iabatic energy loses and particle drifts. The model and results will be di scussed.\n\nhttps://events.chpc.ac.za/event/6/contributions/110/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/110/ END:VEVENT BEGIN:VEVENT SUMMARY:Exploring chemical space using in silico studies to identify novel inhibitors of Acetylcholinesterase\, a target for Alzheimer’s disease DTSTART;VALUE=DATE-TIME:20171204T093000Z DTEND;VALUE=DATE-TIME:20171204T095000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-112@events.chpc.ac.za DESCRIPTION:Speakers: Carl Johan van der Westhuizen (University of Pretori a)\nAlzheimer’s disease (AD) is the leading cause of dementia.[1] The nu mber of AD cases is increasing at an alarming rate\, which is mostly the r esult of increases in both the population and the average life expectancy due to advances in modern medicine. AD has been shown to be twice as preva lent in African-Americans\, calling it the “Silent Epidemic of Alzheimer ’s Disease”.[2] This suggests that the disease is particularly relevan t to South Africa and Africa due to its demographics. As such\, there is a dire need for the development of effective treatments of AD. \n\nAcetylch olinesterase (AChE) is a protein that has been identified for the treatmen t of AD\, with four AChE inhibitors having been approved for treatment by the FDA. These inhibitors have significant side-effects and/or short-term bio-availability. It is suggested that AChE inhibitors can act as dual inh ibitors by both inhibiting AChE and prevent Amyloid Beta (Aβ) aggregation also associated with AD. \n\nThe binding pocket of AChE is ~20 Å deep go rge which is highly solvated. It has been shown that the majority of the s ide-chain residues are highly flexible and this flexibility should be cons idered when screening is performed. In addition\, the entrance of the bind ing pocket known as the Peripheral Anionic Site (PAS) contributes to Aβ a ggregation. Using High Through-put Virtual Screening (HTVS)\, potential in hibitors of AChE from the BioFocus library of 20’000 housed at the CSIR were identify by using ensemble docking. Ensemble docking involves using m ultiple conformations of the same protein to take the flexibility of the a ctive site into account. In doing so\, an improved enrichment in the resul ts is obtained where fewer false negatives occur and alternative interacti ons are also considered. Furthermore\, ensemble docking scales linearly wi th increasing number of receptor conformations\, whereas if screening of c ompounds was performed with the active site being considered flexible the computational resources would increase exponentially with increasing numbe r of flexible residues.\n\nSignificant validation testing was initially do ne on the HTVS model to check that an acceptable enrichment was obtained b y testing the model against known active compounds and decoys. The majorit y of the receptor structures were obtained from the Protein Database (PDB) . To improve the model further\, more receptor structures were generated b y performing Inducted Fit Docking (IFD) with compounds that were false neg atives during the initial HTVS model. \n\nPromising hits identified from t he BioFocus library will be submitted for bioassay to confirm the inhibiti on against AChE and Aβ aggregation.\n\nReferences\n\n(1) Anand\, R.\; Gill\, K. D.\; Mahdi\, A. A. Neuropharmacology 2014\, 76 (PART A)\, 27.\n \n(2) Alzheimer’s Association. Alzheimer’s Dement. 2014\, 10 (2)\, 1.\n\nhttps://events.chpc.ac.za/event/6/contributions/112/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/112/ END:VEVENT BEGIN:VEVENT SUMMARY:Understanding rainfall distribution over the Drakensberg Mountain Range under weak synoptic conditions. DTSTART;VALUE=DATE-TIME:20171205T102000Z DTEND;VALUE=DATE-TIME:20171205T103500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-113@events.chpc.ac.za DESCRIPTION:Speakers: Ridick Roland TAKONG (University of Cape Town)\nUnde rstanding rainfall variability under weak synoptic forcing is crucial for improving weather forecast and climate projections with Numerical Weather and climate models. Rainfall variability under strong synoptic-scale forc ing is dictated by large scale features whereas under weak synoptic-scale forcing\, it is dictated by local-scale features. However\, most of these local scale features are not well resolved by low resolution numerical we ather and climate models which are used for operational weather forecast and climate projections. Consequently\, the models may underestimate or ov erestimate the intensity of climate extremes. The analysis of the characte ristics of wet weak synoptic days from observation and reanalysis data ove r the Drakensberg Mountain Range (DMR) revealed that although the reanalys is data captures the observed characteristics of wet weak synoptics days\, it underestimates the frequency and intensity because of its coarse horiz ontal resolution. Therefore\, using Self-organizing maps (SOM) and high r esolution simulations with the Weather Research and Forecasting (WRF) mode l\, we investigated the characteristics of rainfall under weak synoptic sc ale forcing over the DMR. The results of the SOM classification of Wet Wea k Synoptic Days rainfall revealed four main rainfall patterns under weak s ynoptic conditions over the DMR. The simulation of these rainfall patterns with the WRF model revealed that the WRF model greatly improves reanalysi s data and brings it closer to observation and that a WRF model horizontal resolution of at least 18km is required to capture most of the local scal e processes influencing rainfall formation under weak synoptic conditions. Hence\, higher resolutions (less than 18km) simulations may not be necess ary which implies a lower computational cost for simulations.\n\nhttps://e vents.chpc.ac.za/event/6/contributions/113/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/113/ END:VEVENT BEGIN:VEVENT SUMMARY:Adjusting empirical relationships in a turbulence model DTSTART;VALUE=DATE-TIME:20171206T123000Z DTEND;VALUE=DATE-TIME:20171206T125000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-119@events.chpc.ac.za DESCRIPTION:Speakers: Gareth Erfort (Stellenbosch University)\nThis talk f ocuses on the methodology taken in adjusting turbulence model coefficients based on historical data. The problem background as to why the turbulence model needed to be adjusted and how the HPC was able to generate data for surrogate model optimization.\nThe SST transition model as 1st described by Menter in 2001\, makes use of empirical relationships to capture the ef fect of transitional flow in CFD. These relationships were made public in 2006\, for a variety of geometries. The determination of these relationshi ps were based on experimental data and aimed to ensure the correct flow ef fects\, but do not capture the physics of the flow. While the model has b een in use for some time and proven accurate in both academic and industry applications\, the specific relationships remain proprietary in commercia l codes (such as ANSYS). The open source software openFOAM was selected to perform CFD simulations in an effort to identify relationships specific t o airfoil geometries. Without performing experimental tests on an airfoil\ , historic experimental data was used as the test case. In particular the NACA0012 foil was selected for its extensive collection of published exper imental data.\n\nhttps://events.chpc.ac.za/event/6/contributions/119/ LOCATION:Velmoré Hotel Estate Voltaire URL:https://events.chpc.ac.za/event/6/contributions/119/ END:VEVENT BEGIN:VEVENT SUMMARY:Big Data Meets HPC: Exploiting HPC Technologies for Accelerating B ig Data Processing and Management DTSTART;VALUE=DATE-TIME:20171203T070000Z DTEND;VALUE=DATE-TIME:20171203T072000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-120@events.chpc.ac.za DESCRIPTION:Speakers: Xiaoyi Lu (The Ohio State University)\nThe convergen ce of HPC\, Big Data\, and Deep Learning is the next game-changing busines s opportunity. Apache Hadoop\, Spark\, gRPC/TensorFlow\, and Memcached are becoming standard building blocks in handling Big Data oriented processin g and mining. Recent studies have shown that default designs of these comp onents can not efficiently leverage the features of modern HPC clusters\, like Remote Direct Memory Access (RDMA) enabled high-performance interconn ects\, high-throughput parallel storage systems (e.g. Lustre)\, Non-Volati le Memory (NVM). In this tutorial\, we will provide an in-depth overview o f the architecture of Hadoop\, Spark\, gRPC/TensorFlow\, and Memcached. \n \nWe will examine the challenges in re-designing networking and I/O compon ents of these middleware with modern interconnects\, protocols (such as In finiBand\, RoCE) and storage architectures. Using the publicly available s oftware packages in the High-Performance Big Data project (HiBD\, http://h ibd.cse.ohio-state.edu)\, we will provide case studies of the new designs for several Hadoop/Spark/gRPC/TensorFlow/Memcached components and their as sociated benefits. Through these\, we will also examine the interplay betw een high-performance interconnects\, storage (HDD\, NVM\, and SSD)\, and m ulti-core platforms to achieve the best solutions for these components and applications on modern HPC clusters. \n\nWe also present in-depth case-st udies with modern Deep Learning tools (e.g.\, Caffe\, TensorFlow\, BigDL) with RDMA-enabled Hadoop\, Spark\, and gRPC.\n\nhttps://events.chpc.ac.za/ event/6/contributions/120/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/120/ END:VEVENT BEGIN:VEVENT SUMMARY:Progress on The SADC Cyberinfrastructure Framework: Supporting Ope n Data and Open Science in the region DTSTART;VALUE=DATE-TIME:20171206T070000Z DTEND;VALUE=DATE-TIME:20171206T074500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-121@events.chpc.ac.za DESCRIPTION:Speakers: Tshiamo Motshegwa (University Of Botswana)\nThere i s a convergence of data and compute intensive paradigms and a p roliferation of research and projects in these areas and applications. There also is a global trend in developing distributed federated high perf ormance data cyberinfrastructures and e-infrastructures to support to rese arch\, encourage collaborations and to facilitate data sharing for open sc ience.\n\nThese cyberinfrastructures can also be used to share exp ensive instruments and resources including high performance computing ( HPC)\,radio telescopes\, genomics databases\, electron scanning microscope s etc. through connected research networks. These efforts are typically aimed at accelerating research and discovery across domains and countries often reinforcing National\, Regional or Continental objectives or geopoli tical objectives such as integration.\n\nRegionally\, the Southern African Development Community (SADC) countries have engaged and developed a regio nal collaborative Cyberinfrastructure Framework. The vision is of:\n\n*An education\, research and innovation environment that provides for human c apital development and shared access to unique or distributed facilities t o impact socioeconomic development in the SADC region and promote knowledg e based economy.*\n\nhttps://events.chpc.ac.za/event/6/contributions/121/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/121/ END:VEVENT BEGIN:VEVENT SUMMARY:A next generation institutional repository for ALL South African r esearch DTSTART;VALUE=DATE-TIME:20171206T113000Z DTEND;VALUE=DATE-TIME:20171206T115500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-124@events.chpc.ac.za DESCRIPTION:Speakers: Mark Hahnel (figshare)\nThe institutional repository (IR) has played an integral role in the scholarly infrastructure over the last 25 years. As the dissemination of digital information at the institu tional level is accelerating and research outputs are diversifying\, we fi nd ourselves at a crossroads of the future direction of the IR. To compoun d the complexity\, not only do researchers want to share research in a var iety of formats\, they want to share it in ways the traditional scholarly publishing model does not cater to. \n\nWith the rise of new cultures in r esearch\, there is an increasing desire to publish results early and often \, iterate on research\, and conduct peer review in a more transparent way after the point of publication. With this new style of scholarly communic ation on the horizon\, some have signaled the death knell of the IR\, howe ver with some technical improvements\, we at Figshare see the IR as the na tural home for ALL scholarly outputs\, including research data. In this ta lk we will discuss national pilots of figshare infrastructure to allow all South African academics to get credit for their research.\n\nhttps://even ts.chpc.ac.za/event/6/contributions/124/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/124/ END:VEVENT BEGIN:VEVENT SUMMARY:Molecular modelling of ligands\, receptors and enzymes for in sili co drug discovery DTSTART;VALUE=DATE-TIME:20171205T090000Z DTEND;VALUE=DATE-TIME:20171205T093000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-125@events.chpc.ac.za DESCRIPTION:Speakers: Tahir Pillay (University of Pretoria)\nOver the past two decades\, computational or in silico methods have been increasingly a pplied to the process of drug development and testing. These methods inc lude the use of quantitative structure-activity relationships\, database searching\, pharmacophores\, homology models and other molecular modeling approaches. With the advent of cheminformatics techniques in drug design\, molecules with promising efficacy can be developed in a comparatively sho rt time span. Public chemical databases can be screened and the compounds predicted for behaviour as inhibitors or activators. The highly sophistic ated pharmacoinformatics tools available can assist in the generation of e ven subatomic descriptors that provide high predictivity for activity.\n\n https://events.chpc.ac.za/event/6/contributions/125/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/125/ END:VEVENT BEGIN:VEVENT SUMMARY:Performance Analysis of an HPC Implementation for Large-Scale Prop agation Prediction DTSTART;VALUE=DATE-TIME:20171206T093000Z DTEND;VALUE=DATE-TIME:20171206T095000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-126@events.chpc.ac.za DESCRIPTION:Speakers: Johan Havenga (North-West University)\nThe concept o f Dynamic Spectrum Access (DSA)\, allows under-utilised radio frequency (R F) spectrum to be made available for Secondary Users (SUs) when not utilis ed by the Primary User (PU). A geolocation database is currently the prefe rred approach by regulators to deploy DSA in the TV-bands\, i.e. TV white space networks. Central to the geolocation database is the computation nod e\, responsible for performing RF propagation predictions over a large are a. RF field strengths are computed for all PU transmitters to determine th e geographic location of spectrum available to SUs. RF propagation predict ion is computationally intensive and time-consuming\, effectively becoming the limiting factor in extending the geolocation based approach for DSA t o other parts of the spectrum. We present a High-Performance Cluster Compu ter (HPCC) implementation for the computation node. Four propagation model s are implemented and adapted for parallelisation. Our performance analysi s indicates computational speed-up for all propagation models on the HPCC and factors affecting linear scalability are identified. The HPCC implemen tation is used to study the impact that the choice of propagation model h as on spectrum availability to SU’s.\n\nhttps://events.chpc.ac.za/event/ 6/contributions/126/ LOCATION:Velmoré Hotel Estate Voltaire URL:https://events.chpc.ac.za/event/6/contributions/126/ END:VEVENT BEGIN:VEVENT SUMMARY:STRUCTURE PROPERTY RELATIONSHIPS IN ORGANIC SOLAR CELLS MATERIALS DTSTART;VALUE=DATE-TIME:20171204T122000Z DTEND;VALUE=DATE-TIME:20171204T124000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-129@events.chpc.ac.za DESCRIPTION:Speakers: Sandile Mamba (UKZN)\nhttps://events.chpc.ac.za/even t/6/contributions/129/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/129/ END:VEVENT BEGIN:VEVENT SUMMARY:Heatwaves in the future warmer climate of South Africa DTSTART;VALUE=DATE-TIME:20171204T124500Z DTEND;VALUE=DATE-TIME:20171204T130000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-131@events.chpc.ac.za DESCRIPTION:Speakers: Innocent Mbokodo (South African Weather Service)\nHe atwaves in the future warmer climate of South Africa\n\nhttps://events.chp c.ac.za/event/6/contributions/131/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/131/ END:VEVENT BEGIN:VEVENT SUMMARY:Modelling the low frequency variability of the Indian Ocean. DTSTART;VALUE=DATE-TIME:20171205T100500Z DTEND;VALUE=DATE-TIME:20171205T102000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-132@events.chpc.ac.za DESCRIPTION:Speakers: Mthetho Sovara (CHPC/UCT/CSIR)\nThis study investiga tes the low-frequency variability of the Indian Ocean based on Coupled Mod el Intercomparison Project (CMIP5) model outputs\, observed and reanalysis datasets\, and CSIR ocean models. While the existence of semi-annual and annual signals is well known the presence of decadal to multi-decadal sign als is less understood. In the South African context\, the variability of the Indian Ocean associated with large-scale\, low-frequency modes of vari ability\, has implications for the predictability of the regional climate driven by ocean dynamics. Thus far\, low pass filtered Ocean Temperature\, Sea Surface height\, and zonal and meridional components of the ocean cur rents are subjected to spectral analysis for identification of statistical ly significant periodicities at the low-frequency timescale. This study al so aims to report the relationship between low-frequency variability in th e Indonesian Throughflow (ITF) outflow region and the southern Indian Ocea n (SIO) in the decadal to multi-decadal timescale.\n\nhttps://events.chpc. ac.za/event/6/contributions/132/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/132/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational Fluid Dynamics in Renewable Energy and High-Speed Tr ansport DTSTART;VALUE=DATE-TIME:20171206T090000Z DTEND;VALUE=DATE-TIME:20171206T093000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-133@events.chpc.ac.za DESCRIPTION:Speakers: Ken Craig (Professor)\nhttps://events.chpc.ac.za/eve nt/6/contributions/133/ LOCATION:Velmoré Hotel Estate Voltaire URL:https://events.chpc.ac.za/event/6/contributions/133/ END:VEVENT BEGIN:VEVENT SUMMARY:H3ABioNet –enabling bioinformatics and big data research in Afri ca DTSTART;VALUE=DATE-TIME:20171206T090000Z DTEND;VALUE=DATE-TIME:20171206T093000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-134@events.chpc.ac.za DESCRIPTION:Speakers: Nicola Mulder (University of Cape Town)\nBioinformat ics\, or computational biology\, is the application of computing to the an alysis and interpretation of biological data. With the emergence and reduc ing cost of new laboratory technologies for high throughput data generatio n\, African scientists are increasingly generating bigger and more complex datasets. This has led to significant challenges in all aspects of data m anagement\, including transfer\, storage\, analysis and interpretation. On e of the initiatives which aims to address these challenges is H3ABioNet\, a Pan-African bioinformatics network established to build the capacity fo r large scale genomics research on the continent. A major project within H 3ABioNet has been the design of a new genotyping array for African populat ions\, which identifies genetic differences between individuals that may b e causative of specific diseases. The design of the array required signifi cant computing hardware at several different stages due to the size and co mplexity of the data and algorithms. The project incorporated over 4000 hu man genome sequences\, with collectively over 100 million genetics changes (Single nucleotide variants)\, that needed to be analysed by multiple dif ferent software tools\, with millions of statistical tests. Through necess ity\, the H3Africa array design project utilized the CHPC resources for da ta transfer\, storage and processing. This talk will outline the need for high performance computing in bioinformatics\, using the array design proj ect as an example\, and will also discuss the challenges in big data in th e biomedical sciences in Africa and some of the solutions implemented thro ugh H3ABioNet.\n\nhttps://events.chpc.ac.za/event/6/contributions/134/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/134/ END:VEVENT BEGIN:VEVENT SUMMARY:FAMSEC-based insight on the chemical nature of the XH...HY (X\,Y = C\,N) intramolecular interactions DTSTART;VALUE=DATE-TIME:20171206T115000Z DTEND;VALUE=DATE-TIME:20171206T121000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-136@events.chpc.ac.za DESCRIPTION:Speakers: Ignacy Cukrowski (University of Pretoria)\nhttps://e vents.chpc.ac.za/event/6/contributions/136/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/136/ END:VEVENT BEGIN:VEVENT SUMMARY:An Assessment of the Maturity of the SA NREN DTSTART;VALUE=DATE-TIME:20171205T100000Z DTEND;VALUE=DATE-TIME:20171205T103000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-138@events.chpc.ac.za DESCRIPTION:Speakers: Leon Staphorst (Director: SANReN)\nThe South African National Research and Education Network (SA NEN) is a collaborative effor t by the Tertiary Education and Research Network of Of South Africa (TENET ) and the South African National Research Network (SANReN) than has panned more than a decade. While the SA NREN initially ha the primary goal to pr ovide the South African higher education and research communities with unc onstrained bandwidth at a fraction of the costs of the commercial market\, it has now evolved to also provide a wide variety of advanced services an d participates in various international initiatives. As such\, it has evol ved from a mere connectivity provider to a an extremely advanced NREN that is now regarded as one of the world's leading Research and Education (R&E ) networks\, as is evident from it's membership in the Global R&E Chief Ex ecutive Office (CEO) Forum. This presentation will consider the progress t hat the SA NREN has made in recent times in providing connectivity and oth er advanced services to its beneficiairies\, and measure this against the NREN maturity model developed by TENET to gauge the successful development of NRENs throughout Africa.\n\nhttps://events.chpc.ac.za/event/6/contribu tions/138/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/138/ END:VEVENT BEGIN:VEVENT SUMMARY:A DFT study of the ODH of n-hexane over isolated H3VO4 and H4V2O7 DTSTART;VALUE=DATE-TIME:20171206T123000Z DTEND;VALUE=DATE-TIME:20171206T125000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-139@events.chpc.ac.za DESCRIPTION:Speakers: Nkululeko Damoyi (Mangosuthu University of Technolog y)\nCatalytic (H3VO4 and H4V2O7) oxidative dehydrogenation (ODH) mechanist ic studies of the reaction of n-hexane to 1- and 2-hexene have been conduc ted by means of Density Functional Theory (DFT).\n\nThe aim of this study was to gain insight about the catalytic mechanistic pathways for the conve rsion of n-hexane to 1- and 2-hexene. The 3-hexene pathway was omitted bec ause the isomer is not observed in our experiments\, nor reported in liter ature. The chosen models for the study were the isolated H3VO4 and H4V2O7 clusters\, with the H3VO4 unit comprising one vanadyl bond\, V(V)=O\, and the H4V2O7 cluster comprising two vanadyl bonds and the bridging O atom in the V(V)-O-V(V) unit. The calculated rate-determining step is β-hydrogen abstraction from the C6H14 chain by vanadyl O to produce the complex inte rmediates with reduced V(IV) centres in accumulated V(IV)-OH bonds and act ivation barriers of ΔE# = +27.4 (H3VO4) and +32.7 (H4V2O7) kcal/mol. Both these values are lower than the value calculated for the H-abstraction by the bridging O in H4V2O7 (ΔE# = +43.9 kcal/mol). The energetically favou rable propagation steps that may lead to olefins involve α-H abstraction (1-hexene) and γ-hydrogen abstraction (2-hexene) on the radical intermedi ate fragment (⋅C6H13) by vanadyl O from a different site or by gas-phase molecular O2. The gas-phase pathway may dominate at lower n-hexane to oxy gen molar ratios combined with low V(V)=O surface areas and be subdued at higher molar ratios in combination with high V(V)=O surface areas. However \, chemisorption of the radical intermediate (∙C6H13) on the surface O s ites may lead to undesired products including oxygenates. This may explain the low yields of 1- and 2-hexene (\n\nhttps://events.chpc.ac.za/event/6/ contributions/139/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/139/ END:VEVENT BEGIN:VEVENT SUMMARY:CHPC Induction Mini-course DTSTART;VALUE=DATE-TIME:20171207T113000Z DTEND;VALUE=DATE-TIME:20171207T115000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-141@events.chpc.ac.za DESCRIPTION:Speakers: Kevin Colville (CHPC)\nhttps://events.chpc.ac.za/eve nt/6/contributions/141/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/141/ END:VEVENT BEGIN:VEVENT SUMMARY:Opening of the 11th CHPC Conference DTSTART;VALUE=DATE-TIME:20171204T073000Z DTEND;VALUE=DATE-TIME:20171204T074500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-164@events.chpc.ac.za DESCRIPTION:Speakers: Happy Sithole (CHPC)\nhttps://events.chpc.ac.za/even t/6/contributions/164/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/164/ END:VEVENT BEGIN:VEVENT SUMMARY:Towards A National Research Data Management Strategy for South Afr ican Universities DTSTART;VALUE=DATE-TIME:20171206T095500Z DTEND;VALUE=DATE-TIME:20171206T102000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-143@events.chpc.ac.za DESCRIPTION:Speakers: Dale Peters (UCT)\, Mark Hahnel (figshare)\nAmidst a growing number of Open Science mandates for data sharing and reuse\, Sout h African universities are scrambling to provide services to the research community to facilitate compliance with the various requirements of numero us international funding agencies. The impending burden posed on instituti ons to fund this requirement was brought sharply into focus with the intro duction of a similar mandate by the national research funding agency\, the very lifeblood on which the academic enterprise is reliant.\nThis paper w ill outline a journey of collaborative effort towards the concept of a sha red data service in an exceptional paradigm shift enabled by a proposal fo r a Tier 2 data node in the national cyberinfrastructure. Insights will be shared of a process of converging interest in a national strategy for res earch data management\, led by DIRISA\, the Data Intensive Research Initia tive of South Africa\, a component of the National Integrated Cyberinfrast ructure System (NICIS).\n\nhttps://events.chpc.ac.za/event/6/contributions /143/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/143/ END:VEVENT BEGIN:VEVENT SUMMARY:Striving to the End-User HPC Sweet Spot: Altair Perspective DTSTART;VALUE=DATE-TIME:20171205T120000Z DTEND;VALUE=DATE-TIME:20171205T123000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-144@events.chpc.ac.za DESCRIPTION:Speakers: Ernst Burger (Altair Engineering S.A. (Pty) Ltd)\nHP C technology is advancing more rapidly than at any time in the history of computing. Exa-scale compute frameworks will start to emerge in the comin g years and will offer enormous raw compute power. Coupled with this\, var ious commercial vendors are developing user-centric HPC business models in the cloud to drive access to these capabilities. The potential of this t echnology to help solve real-world problems and advance our understanding of the physical world that we live in is clear. As HPC technologists we s hould ask ourselves the question: How can we make HPC technology ubiquito us in the general computing frameworks of end-users of the technology?\n\n https://events.chpc.ac.za/event/6/contributions/144/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/144/ END:VEVENT BEGIN:VEVENT SUMMARY:DFT for isomers in solution\, redox potentials\, transition states and favored reaction products DTSTART;VALUE=DATE-TIME:20171206T113000Z DTEND;VALUE=DATE-TIME:20171206T115000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-145@events.chpc.ac.za DESCRIPTION:Speakers: Karel von Eschwege (University of the Free State)\nA part from merely computationally running molecular energy optimizations an d determining optimal geometries\, a large variety of other techniques and applications also exist. \nIn this presentation uncomplicated methods ar e shared by which:\n1. isomer geometries in solution may be determined by involving TDDFT\,\n2. redox potentials of series of metal complexes are de termined merely from optimization HOMO & LUMO energies\,\n3. transition st ates of photo-excited species are established from energy minima on comput ed energy surfaces\, and\n4. favored complex reaction products are compute d by means of reaction energy and molecular orbital calculations.\n\nRefer ences:\n1. Dithizone and its Oxidation Products – a DFT\, Spectroscopic and X-Ray Structural Study\, Von Eschwege\, K. G.\; Conradie\, J.\; Kuhn\, A.\, J. Phys. Chem. A\, 115\, 14637-14646\, 2011\, http://pubs.acs.org/do i/pdf/10.1021/jp208212e\n2. Redox Potentials of Ligands and Complexes – a DFT Approach\, Von Eschwege\, K. G.\; Conradie\, J.\, SA Journal of Chem istry\, 64\, 203–209\, 2011\, http://reference.sabinet.co.za/webx/access /electronic_journals/chem/chem_v64_a33.pdf\n3. Ultrafast Photochemistry of Dithizonatophenylmercury(II)\, Schwoerer\, H.\; Von Eschwege\, K. G.\; Bo sman\, G.\; Krok\, P.\; Conradie\, J.\, ChemPhysChem\, 2653-2658\, 2011\, http://onlinelibrary.wiley.com/doi/10.1002/cphc.201100337/abstract\n4. Syn thesis and structure of dithizonato complexes of antimony(III)\, copper(II ) and tin(IV)\, Trevor T. Chiweshe\, Marilé Landman\, Jeanet Conradie & K arel G. von Eschwege\, Journal of Coordination Chemistry\, 2016\, 69(5) 78 8–800\, http://dx.doi.org/10.1080/00958972.2016.1145213\n\nhttps://event s.chpc.ac.za/event/6/contributions/145/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/145/ END:VEVENT BEGIN:VEVENT SUMMARY:Transforming Artificial Intelligence into Business Advantage DTSTART;VALUE=DATE-TIME:20171204T074500Z DTEND;VALUE=DATE-TIME:20171204T083000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-146@events.chpc.ac.za DESCRIPTION:Speakers: Sharad Gandhi (Market.Consult)\nArtificial Intellige nce is the “Next Big Thing.” Artificial Intelligence (AI) is the most\ nprofound innovation by humans\, with a far deeper and wider impact on our lives\, than\nall preceding innovations from steam engine of 1712 to the Internet. AI has the\npotential to transform the very role of humans in ou r society. Its disruptive power is\nevidenced in a growing number of appli cations even today – Apple’s Siri\, Amazon Echo\,\nGoogle Assistant\, IBM Watson and Tesla cars.\n\nWhat is AI? What can it do (and not do)? How does it work? Where can it be applied?\nThis presentation is designed to demystify AI and help your company to harness its\nunique power to smarten and uplift your business. Using successful business cases the\npresentati on highlights how and where AI is being used. It provides a roadmap for\nc ompanies starting AI projects with approaches for discovering innovation o pportunities\nthat add business and customer value with AI. Finally\, it o ffers a structured approach\nwith “AI&U Canvas” for developing a succe ssful business model with innovative AI ideas.\n\nThe presentation will to uch upon radical transformations using AI\, with its newly\nacquired magic of Machine Learning\, for industries as varied as Automotive\, Finance\,\ nManufacturing\, Retail\, Healthcare\, Tax and Legal Consultation\, Securi ty and Agriculture.\nSimilarly\, almost all horizontal business functions like Customer Service\, Human\nResources\, Procurement\, Production\, Sale s and Marketing benefit enormously from AI.\nJeff Bezos\, CEO and Founder of Amazon says\, “Machine Learning will improve every\nbusiness\, every government organization\, every philanthropy … basically\, there is not an\ninstitution in the world that cannot be improved with Machine Learning .”\n\nThe use of AI for future competitiveness is a must. As a result\, it is extremely important\nfor everyone\, especially for business decision makers\, to understand the power\,\nsignificance\, and relevance that AI will have not only on our lives but also on business\nand society as a who le.\n\nAI is inevitable. The time to capitalize on AI is now.\n\nhttps://e vents.chpc.ac.za/event/6/contributions/146/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/146/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational modeling as a complementary and predictive tool in m aterials science research DTSTART;VALUE=DATE-TIME:20171205T090000Z DTEND;VALUE=DATE-TIME:20171205T092000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-147@events.chpc.ac.za DESCRIPTION:Speakers: George Amolo (Technical University of Kenya)\nWith t he recent scenario of affordable computers with large RAM and storage capa bilities as well as the availability of high performance computing facilit ies\, research in materials science using ab initio techniques has rapidly grown. The research focus has now gradually shifted from fundamental scie nce investigations to properties of materials that have applications in en vironmental preservation\, search for as well as adoption of alternative f uels and green energy at large\, health\, among others\, which have an exp ected impact on the quality of life. In the last few years our group has w orked on hard materials for cutting and shaping in industry as well as mat erials for energy conversion and materials for electronic applications. In particular\, we have investigated hardness in Transition Metals Carbides and Nitrides (TMCNs) and extended to other indicators such as shear modulu s\, rigidity and brittleness\; metal electrode contacts on diamond surface s for diamond electronics\; metal hydride materials for applications in hy drogen fuel storage and the electronic structure of the interface of dye/T iO2 in dye sensitized solar cells (DSSC)\, among others. Highlights of the finding of these cases and recent advances are provided. These examples\, among others\, are provided to show how computational modeling richly sup ports experimental work and yet can also be used to provide useful informa tion that may not directly be accessible to experiments.\n\nhttps://events .chpc.ac.za/event/6/contributions/147/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/147/ END:VEVENT BEGIN:VEVENT SUMMARY:Ocean-biogeochemical model sensitivity in the Southern Ocean towar ds the development of the earth system model\, CSIR-VR-ESM DTSTART;VALUE=DATE-TIME:20171205T090000Z DTEND;VALUE=DATE-TIME:20171205T093000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-148@events.chpc.ac.za DESCRIPTION:Speakers: Nicolette Chang (CSIR)\nModelling the earth system i s a balance between available computing power and model complexity\, parti cularly as an earth system model comprises of multiple individual\, intera cting numerical models each representing different system components such as the atmosphere\, land and ocean. In addition\, these models are run for very long periods to simulate hundreds of years of earth/climate evolutio n. For the development of the CSIR Variable Resolution Earth System Model (VR-ESM)\, we discuss the compromises of computation versus complexity mad e in configuring the ocean-biogeochemistry component. \n\nThe Southern Oce an is a key region for global carbon exchange: both physical and biologica l mechanisms drive carbon from the atmosphere to the surface ocean and the n to the deep ocean and conversely. Our research shows that the spatial sc ales of the surface ocean dynamics are important in driving these exchange s\, these range from the mesoscale O(10-100km) to the submesoscale O(1km). However\, the ocean components of earth system models (and thus the assoc iated biogeochemical model) were generally run at coarse resolutions of 10 0km or more\, and have recently incorporated the mesoscale through model r esolution. Submesoscale-resolving tends to be reserved for the local to re gional ocean domain. Leveraging the representation of the necessary mesosc ale and submesoscale ocean features over a global ocean with the computati onal power of the CHPC is a key decision in the configuring of VR-ESM. For the ocean model\, this can be done by the choice of model resolution and/ or the use of subgrid-scale parameterizations.\n\nWe have used the ocean-i ce-biogeochemistry modeling platform NEMO to perform sensitivity tests usi ng varying model resolution and subgrid-scale parameterizations in order t o best represent the necessary ocean-biogeochemical dynamics in the Southe rn Ocean. This leads to optimizing the ocean model configuration in VR-ESM with consideration to cpus and wall time.\n\nhttps://events.chpc.ac.za/ev ent/6/contributions/148/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/148/ END:VEVENT BEGIN:VEVENT SUMMARY:Best Practices… No\, Good Enough Practices\, for Building an eRe search enabled Institution - The NWU eResearch Story DTSTART;VALUE=DATE-TIME:20171206T090000Z DTEND;VALUE=DATE-TIME:20171206T093000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-204@events.chpc.ac.za DESCRIPTION:Speakers: Anelda Van der Walt (NWU/Talarify)\nWhat is eResearc h? Depending on the point of view\, eResearch may be defined as heavily re liant on cyber infrastructure and data science skills or as research data management\, repositories\, and open science policies\, or actually anythi ng in between. Institutions embarking on the eResearch journey should not underestimate the value (both in terms of time and money) that can be gai ned by first defining what the term means in their own context\, before di ving in to establish an institutional eResearch programme.\n\n“eResearch ”\, “eScience”\, and “cyber infrastructure” are terms that have become popular in recent years mostly due to the change in research that i s caused by technology advancement: faster internet penetrating more commu nities\; cheaper data storage\, memory and processing power\; higher resol ution microscopes and cameras\; high-throughput research equipment\, and m ore. Various national initiatives attempt to address eResearch needs\, inc luding the Centre for High Performance Computing (CHPC)\, the Data Intensi ve Research Initiative of South Africa (DIRISA)\, and the South African Re search Infrastructure Roadmap (SARIR) with its various interdisciplinary p rojects to name a few. These national projects complements resources and p rogrammes available at institutional level. For a researcher as well as re search support staff to be successful\, it is critical to be aware of chan ging research practices and funder requirements as well as resources and o pportunities available at the various levels - institutional\, regional\, national\, and international. eResearch initiatives have started to take o ff at a number of academic institutions across South Africa in the past fe w years.\n\nAt North-West University (NWU) the eResearch Initiative offici ally commenced in July 2015 and was driven from the IT director’s office with support from the DVC Research\, Technology and Innovation. Stakehold ers like the Research Support Office\, the Libraries\, all faculties and r esearch entities were invited to collaborate from the outset and have play ed a critical role in the success of the initiative thus far. The NWU eRes earch Initiative is characterised by (i) broad participation across both s upport and academic environments\, (ii) involvement from all career stages - from undergraduates to National Research Foundation (NRF)-rated researc hers\, (iii) integration with and leveraging of regional\, national\, and international communities and initiatives\, and (iv) a collaborative cultu re.\n\nA visual aid (included in the abstract and published under an open license) was developed to help communicate the focus and aims of the NWU e Research Initiative to various stakeholders. The focus areas are:\n\n - re search data management\; \n - computational and digital research\;\n - ope n science\;\n - reproducible research\;\n - and funding (alternative sourc es).\n\nFive key activities are associated with each of these focus areas. They include creating awareness\, running training events\, community dev elopment\, integration with related initiatives\, and coming up with ways to make the various activities sustainable.\n\n![The NWU eResearch Initiat ive][1]\n\nOne of the most successful initiatives on which eResearch was b uilt at NWU\, is the Carpentries workshops and train-the-trainer events. T hese workshops have provided an opportunity to simultaneously address at l east four out of the five focus areas as well as four of the five key acti vities per event. Not only have we been able to develop computational capa city through running Carpentry workshops\, but more than 25 researchers an d students were also trained as instructors who can propagate the informat ion and training they have received.\n\nIn this presentation we will share lessons learned about building an eResearch enabled institution. The pres entation will include recommendations for institutions that are embarking on eResearch initiatives of their own. These recommendations will take int o consideration the diminishing amounts of funding that are available at r esearch and higher education institutions to tackle new challenges. \n\n\n [1]: https://ndownloader.figshare.com/files/9524437/preview/9524437/prev iew.jpg\n\nhttps://events.chpc.ac.za/event/6/contributions/204/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/204/ END:VEVENT BEGIN:VEVENT SUMMARY:The three big challenges scientists are confronted with in today ’s data driven research – data\, intelligence and interaction. DTSTART;VALUE=DATE-TIME:20171206T074500Z DTEND;VALUE=DATE-TIME:20171206T083000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-149@events.chpc.ac.za DESCRIPTION:Speakers: Kiernan Mike (Microsoft)\nPlease join Rüdiger Dorn\ , Director of Cloud Strategy in the office of the CTO of Microsoft\, wher e he will highlight trends and examples around how compute infrastructures can be scaled\, latency can be reduced and the computational throughput c an be multiplied. How the arrival of AI and ML allows researchers to tap i nto toolkits that can augment their work in the area of cognitive services \, analytics and machine learning. Lastly with ever increasing data volume s and higher complexity of models\, how there is a need to re-think how to visualize\, interpret and collaborate on scientific insights\, and how ne w technical opportunities like holograms and augmented reality can help?\n \nhttps://events.chpc.ac.za/event/6/contributions/149/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/149/ END:VEVENT BEGIN:VEVENT SUMMARY:10 Minutes Q&A DTSTART;VALUE=DATE-TIME:20171206T124500Z DTEND;VALUE=DATE-TIME:20171206T130000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-150@events.chpc.ac.za DESCRIPTION:https://events.chpc.ac.za/event/6/contributions/150/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/150/ END:VEVENT BEGIN:VEVENT SUMMARY:Unconventional use of Intel XeonPHI Knights Landing DTSTART;VALUE=DATE-TIME:20171205T092500Z DTEND;VALUE=DATE-TIME:20171205T095000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-151@events.chpc.ac.za DESCRIPTION:Speakers: Antonio Cisternino (University of Pisa)\nIn this tal k we will look at Knights Landing capabilities and its use for computation s that are not strictly accelerator-oriented. The platform supports hetero geneous computations given the flexibility of their cores\, allowing vecto r code to execute side by side along with more enterprise-oriented codes.\ n\nhttps://events.chpc.ac.za/event/6/contributions/151/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/151/ END:VEVENT BEGIN:VEVENT SUMMARY:Speech by the Director-General\, Department of Science & Technolog y DTSTART;VALUE=DATE-TIME:20171204T071500Z DTEND;VALUE=DATE-TIME:20171204T072500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-152@events.chpc.ac.za DESCRIPTION:Speakers: Phil Mjwara (DST)\nhttps://events.chpc.ac.za/event/6 /contributions/152/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/152/ END:VEVENT BEGIN:VEVENT SUMMARY:Molecular modelling of lanthanide(III) chloride complexes with the nitrogen ligand DPA: AIM/NCI analysis and ligand conformational search DTSTART;VALUE=DATE-TIME:20171205T122000Z DTEND;VALUE=DATE-TIME:20171205T124000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-153@events.chpc.ac.za DESCRIPTION:Speakers: Cameron Matthews (Nelson Mandela University)\n**Intr oduction**\n\nGeometry optimizations were performed on the crystal structu re asymmetric units as determined for the novel lanthanide coordination co mpounds: LaCl$_{\\text{3}}$(DPA)$_{\\text{2}}$\, µ-Cl$_{\\text{2}}$-[PrCl $_{\\text{2}}$(H$_{\\text{2}}$O)(DPA)]$_{\\text{2}}$\, [LnCl$_{\\text{2}}$ (DPA)$_{\\text{2}}$]Cl (Ln = Nd\,Dy & Y). \n\nLanthanide complexes are kno wn to be stereochemically labile\, with variable \ncoordination numbers ra nging from 2-12. This is due to the localization of f-electrons near the core region of the metal nucleus and the associated ligand-to-metal ionic bonding. The conformation of the ligands would therefore be highly depend ent on their respective environment\, i.e. on the strength of both intra- \nand intermolecular interactions. [1] \n\nThis study will focus mainly on identifying and characterizing intramolecular interactions that contribut e to the overall stability of the geometry of the complexes\, in the gas-p hase (*in vacuo*). Hydrogen bonding being one of the most important examp les of stabilizing interactions. \n\n**Theoretical methods**\n\nAll geomet ry optimisations were carried out with the *Gaussian 09* [2] software pack age.\n\nThe geometry optimisation calculations\, of the lanthanide complex es\, were performed using density functional theory (DFT) at the M06-D3/au g-cc-pVTZ/RECP level. For each lanthanide metal center the ‘core’ ele ctrons were represented by a small-core (28 electron) Stuttgart-Dresden (S DD) quasi-relativistic effective core potential (ECP)\, while the remainin g ‘valence’ electrons (incl. f-electrons) were explicitly modelled usi ng the energy-optimized (14s13p10d8f6g)/ [6s6p5d4f3g] atomic natural orbit al (ANO) Gaussian valence basis sets of Cao and Dolg .[3] \nAtoms-in-molec ules (AIM) electron density topological analysis [4]\, shown in Fig. 1\, a nd non-covalent interaction (NCI) analysis [5]\, shown in **Fig. 2**\, wer e performed on the energy minimized structures\, using the software packag e Multiwfn [6].\n\nInitial optimizations on DPA were performed using the M 06-D3/6-311++G(d\,p) level\, followed by the larger aug-cc-pVTZ basis set. \n\n**Ligand conformational search**\n\nThe ligand geometry optimizations were successfully performed on 621 initial geometries\, which were generat ed by identifying all unique permutations of four principle dihedral angle s\, in 60° increments\, found in the N-donor ligand *bis*(pyridin-2-ylmet hyl)amine (*DPA*). The total number of input geometries were reduced by a ccounting for the inherent symmetry present in the *DPA* molecule\, in ord er to prevent the redundant optimisation of equivalent initial geometries. \n\n**AIM/ NCI analysis**\n\nOne of the principle components of the atoms- in-molecules (AIM) approach involves locating stationary points in space w here the curvature of electron density are characterised according to the following four categories [10]\, see **Fig.1**: \n \n - Nuclear critica l points [NCPs\, (3\, -3)]\n - Bond critical points [BCPs\, (3\, -1)]\n - Ring critical points [RCPs\, (3\, +1)]\n - Cage critical points [CCPs\, (3 \, +3)]\n\nNon-covalent interaction (NCI) analysis supplements the aforeme ntioned approach\, particularly where weak interactions may exist in the a bsence of BCPs. [5] This approach identifies regions in space where attra ctive interactions (sign(λ$_{\\text{2}}$)ρ0) dominate\, see **Fig. 2**.\ n\n**Acknowledgements**\n\nThe author would like to thank Dr. Eric C. Host ena for solving the crystal structures of the aforementioned inorganic com plexes\, via single-crystal XRD\, as well as Dr. Abubak’r Abrahams for h is support. The author would like to acknowledge the Centre for High Perf ormance Computing (CHPC) of CSIR\, in South Africa\, for enabling access t o usage of computational resources to conduct this research.\n\nhttps://ev ents.chpc.ac.za/event/6/contributions/153/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/153/ END:VEVENT BEGIN:VEVENT SUMMARY:Your DNS\, My DNS - National risk and DNS infrastructure DTSTART;VALUE=DATE-TIME:20171205T120000Z DTEND;VALUE=DATE-TIME:20171205T123000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-156@events.chpc.ac.za DESCRIPTION:Speakers: Barry Irwin (Rhodes University)\nThe Domain Name Sys tem (DNS) is critical to the operation of the\nmajority of services on t he Internet at large. Many organisations\nhowever pay relatively little at tention to this foundational protocol.\nWhether this be in terms of the op erational aspects of the DNS \ninfrastructure\, or even the choice of regi strars and domain name\nservers. This talk explores the analysis of sever al snapshots of one of\nthe internet TLD zones\, and the subsequent identi fication of 'hotspots'\nwithin the system which serve as potential areas o f weakness. Attacks\nagainst these identified infrastructural points\, w hether by malicious\nactions such as seen in 2016 with the Marai botnet or by national \ninterests in which those systems reside\, could have far re aching impacts\non network infrastructure. A number of recommendations a re put forward\nas to how to improve the state of DNS security. In particu lar a\nchecklist for organisations to consider when considering operationa l\nrisk in operating DNS.\n\nhttps://events.chpc.ac.za/event/6/contributio ns/156/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/156/ END:VEVENT BEGIN:VEVENT SUMMARY:Trends in systems and how to get efficient performance DTSTART;VALUE=DATE-TIME:20171205T123000Z DTEND;VALUE=DATE-TIME:20171205T130000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-157@events.chpc.ac.za DESCRIPTION:Speakers: Martin Hilgeman (Dell EMC)\nWith all the advances in massively parallel and multi-core computing with CPUs and accelerators it is often overlooked whether the computational work is being done in an ef ficient manner. This efficiency is largely being determined at the applica tion level and therefore puts the responsibility of sustaining a certain p erformance trajectory into the hands of the user. It is observed that the adoption rate of new hardware capabilities is decreasing and lead to a fee ling of diminishing returns. This presentation shows the well-known laws o f parallel performance from the perspective of a system builder. It also c overs through the use of real case studies\, examples of how to program fo r energy efficient parallel application performance.\n\nhttps://events.chp c.ac.za/event/6/contributions/157/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/157/ END:VEVENT BEGIN:VEVENT SUMMARY:Student Cluster Competition Awards DTSTART;VALUE=DATE-TIME:20171206T171000Z DTEND;VALUE=DATE-TIME:20171206T173000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-158@events.chpc.ac.za DESCRIPTION:Speakers: Happy Sithole (CHPC)\nhttps://events.chpc.ac.za/even t/6/contributions/158/ LOCATION:Velmoré Hotel Estate Tres Sage Plenary hall URL:https://events.chpc.ac.za/event/6/contributions/158/ END:VEVENT BEGIN:VEVENT SUMMARY:Student Cyber Security Challenge Awards DTSTART;VALUE=DATE-TIME:20171206T165500Z DTEND;VALUE=DATE-TIME:20171206T171000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-159@events.chpc.ac.za DESCRIPTION:Speakers: Renier van Heerden (SANReN\, CSIR)\nhttps://events.c hpc.ac.za/event/6/contributions/159/ LOCATION:Velmoré Hotel Estate Tres Sage Plenary hall URL:https://events.chpc.ac.za/event/6/contributions/159/ END:VEVENT BEGIN:VEVENT SUMMARY:Panel Discussion: Making Data Sharing Work DTSTART;VALUE=DATE-TIME:20171206T133000Z DTEND;VALUE=DATE-TIME:20171206T143000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-161@events.chpc.ac.za DESCRIPTION:Speakers: Tshiamo Motshegwa (University Of Botswana)\nQuestion s:\n1. What are the obstacles to data sharing and how can these be address ed?\n2. How can we raise awareness among researchers on data sharing?\n3. How can data sharing be incentivised?\n4. What resources are needed to mak e data sharing work?\n\nhttps://events.chpc.ac.za/event/6/contributions/16 1/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/161/ END:VEVENT BEGIN:VEVENT SUMMARY:Probing the catalytic mechanism of an antifibrotic copper metallod rug DTSTART;VALUE=DATE-TIME:20171204T095000Z DTEND;VALUE=DATE-TIME:20171204T101000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-165@events.chpc.ac.za DESCRIPTION:Speakers: Lizelle Lubbe (University of Cape Town)\nAngiotensin -1-converting enzyme (ACE) is a zinc metalloprotease consisting of two dom ains with distinct inhibitor binding affinities despite their 90% active s ite identity. While the C-domain controls blood pressure\, the N-domain i s selective for cleaving the antifibrotic N-acetyl-Ser–Asp–Lys–Pro p eptide. Selective N-domain inhibition thus shows potential for the treatm ent of fibrosis. Contrary to conventional competitive ACE inhibitors such as Lisinopril\, catalytic metallodrugs irreversibly inactivate ACE through the oxidation of active site residues. Since the metallodrug is recycled from the irreversibly inactivated target\, it is effective at sub-stoichio metric concentrations and less likely to cause side-effects/toxicity. The aim of this study was to elucidate the molecular mechanism responsible for N-selective ACE inactivation by Cu-Gly-Gly-His-Lisinopril (CuGGHLis).\n\n Kinetic characterization of inhibitor binding with fluorogenic assays show ed that CuGGHLis binding was potent and non-selective (Ndom Ki =44.94±1.8 4nM\; Cdom Ki =15.57±1.30nM). Catalytic inactivation was subsequently stu died by monitoring remaining enzyme activity over time in the presence of redox co-reactants and CuGGHLis at IC20. In the presence of H2O2 and ascor bate\, minimal diffuse radical oxidation of the Ndom was observed. Upon ad dition of CuGGHLis\, however\, the Ndom was rapidly and completely inactiv ated. Interestingly\, the Cdom displayed greater diffuse radical oxidation and none catalysed by CuGGHLis.\n\nInsight into the mechanism was gained by characterizing residual activity through Michaelis Menten kinetics. Thi s revealed that CuGGHLis catalyzed oxidation of Ndom residues involved in binding and hydrolysis of the non-domain selective substrate whereas Cdom residues were unaffected. No oxidative protein cleavage was detected by SD S-PAGE and silver staining\, suggesting inactivation through side chain ox idation. Mass spectrometry will reveal the sites of metal-catalysed oxidat ion while X-ray crystallography will identify the CuGGHLis binding site. \ n\nTime-course kinetic assays described the Cdom's lower thermal stability \, higher dependence on detergent stabilization and greater diffuse radica l oxidation. This is thought to be due to the unique hinging behaviour and higher carbohydrate content of the Ndom. Both domains were fully glycosyl ated with complex glycans\, explicitly solvated and subjected to molecular dynamics simulations. While the Cdom active site is exposed to diffuse ra dicals\, the Ndom is shielded by a glycan interaction network surrounding the molecule.\n\nThis study provides further insight into the mechanism of N-selective irreversible inactivation by CuGGHLis. In future\, these find ings will aid the design of a new class of selective antifibrotic ACE inhi bitors effective at sub-stoichiometric doses.\n\nhttps://events.chpc.ac.za /event/6/contributions/165/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/165/ END:VEVENT BEGIN:VEVENT SUMMARY:Representative of the Mayor's office DTSTART;VALUE=DATE-TIME:20171204T070500Z DTEND;VALUE=DATE-TIME:20171204T071500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-166@events.chpc.ac.za DESCRIPTION:https://events.chpc.ac.za/event/6/contributions/166/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/166/ END:VEVENT BEGIN:VEVENT SUMMARY:OpenPOWER Workshop DTSTART;VALUE=DATE-TIME:20171207T070000Z DTEND;VALUE=DATE-TIME:20171207T072000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-167@events.chpc.ac.za DESCRIPTION:Speakers: Ganesan Narayanasamy (TECHNOLOGY leader)\nThis works hop will explore\nacceleration opportunities in existing and upcoming work flows. We will also explore the creation of a community & ecosystem around POWER9 acceleration technology for academics and industry practitioners.\ n\nhttps://events.chpc.ac.za/event/6/contributions/167/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/167/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational Modeling to support the development of biosensing de vices DTSTART;VALUE=DATE-TIME:20171204T090000Z DTEND;VALUE=DATE-TIME:20171204T093000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-171@events.chpc.ac.za DESCRIPTION:Speakers: Krishna Bisetty (Department of Chemistry\, Durban Un iversity of Technology\, Durban)\nhttps://events.chpc.ac.za/event/6/contri butions/171/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/171/ END:VEVENT BEGIN:VEVENT SUMMARY:Dramatic Changes for HPC Storage and IO DTSTART;VALUE=DATE-TIME:20171205T074500Z DTEND;VALUE=DATE-TIME:20171205T083000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-173@events.chpc.ac.za DESCRIPTION:Speakers: Peter Braam (-)\nhttps://events.chpc.ac.za/event/6/c ontributions/173/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/173/ END:VEVENT BEGIN:VEVENT SUMMARY:Machine Learning Based Bitcoin Price Prediction DTSTART;VALUE=DATE-TIME:20171205T124000Z DTEND;VALUE=DATE-TIME:20171205T130000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-205@events.chpc.ac.za DESCRIPTION:Speakers: Matthew Finlayson (Student)\nBlockchain based crypto currencies are proving themselves to be both popular and unpredictable. In this project we attempt to design a software system to predict the price movement of Bitcoin using Machine Learning techniques. We focus on feature selection\, data processing and the training of various classifier neural networks.\n\nhttps://events.chpc.ac.za/event/6/contributions/205/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/205/ END:VEVENT BEGIN:VEVENT SUMMARY:Effect of pressure on structural\, mechanical\, dynamical and elec tronic properties of ReSe2 :A theoretical investigation DTSTART;VALUE=DATE-TIME:20171204T101000Z DTEND;VALUE=DATE-TIME:20171204T103000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-174@events.chpc.ac.za DESCRIPTION:Speakers: Mahmoud Mahmoud (The University of the Witwatersrand )\nEffect of pressure on structural\, electronic\, mechanical\, and Dynami cal properties of ReSe 2 has been investigated using the first-principles calculations.These calculations are based on density functional theory and were performed using the generalized gradient approximation with the empi rical van der Waals correction. The calculated lattice parameters ReSe2 un der effect of pressure are consistent with the available experimental valu es upto 9.03 GPa\, which motivated us to explore the stated prperties beyo nd the 9.03 Gpa limit. The lattice parameters and volume of ReSe2 decrease with the increasing pressure whereas the total enthalpy increases. The me chanical properties are predicted using the Voigt–Reuss–Hill approxima tion from which there is an inverse relationship between volume and pressu re implying that as we subject ReSe2 to large pressure the material become s somehow more compact due to reduced inter-atomic distance hence increase in magnitude of elastic coefficients as well as bond strength. The Dynami cal instability was investigated by computing the phonon frequency to chec k for imaginary modes. ReSe2 is dynamically stable below 40 GPa. The band gap was estimated using the Perdew-Burke-Ernzerhof (PBE) and modified Beck e–Johnson potential\, which confirmed that as pressure\nincreased\, the band gap decreased in almost a linear manner.\n\nhttps://events.chpc.ac.za /event/6/contributions/174/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/174/ END:VEVENT BEGIN:VEVENT SUMMARY:HPC configuration management using Puppet 5 DTSTART;VALUE=DATE-TIME:20171207T070000Z DTEND;VALUE=DATE-TIME:20171207T072000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-177@events.chpc.ac.za DESCRIPTION:Speakers: Charl Möller (University of Stellenbosch)\nIn this workshop we will install and configure Puppet 5\, a configuration manageme nt system\, to manage our compute cluster.\n\nWe will install and configur e the Puppet server\, PuppetDB database\, a Puppet agent and multiple modu les from the Puppet Forge. Best practises will be implemented\, including using Hiera and saving configurations to Git.\n\nThe workshop will be hand s-on. Please ensure you have a working installation of Hyper-V\, VMware (W orkstation or Player) or VirtualBox. Copies of the VMDK/VHDX files will be provided.\n\nhttps://events.chpc.ac.za/event/6/contributions/177/ LOCATION:Velmoré Hotel Estate Voltaire URL:https://events.chpc.ac.za/event/6/contributions/177/ END:VEVENT BEGIN:VEVENT SUMMARY:Accelerating Big Data Processing and Associated Deep Learning on M odern HPC Clusters and Clouds DTSTART;VALUE=DATE-TIME:20171204T123000Z DTEND;VALUE=DATE-TIME:20171204T130000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-178@events.chpc.ac.za DESCRIPTION:Speakers: Xiaoyi Lu (The Ohio State University)\nThe convergen ce of HPC\, Big Data\, and Deep Learning is becoming the next game-changin g business opportunity. Apache Hadoop\, Spark\, gRPC/TensorFlow\, and Memc ached are becoming standard building blocks in handling Big Data oriented processing and mining. Modern HPC bare-metal systems and Cloud Computing p latforms have been fueled by the advances in multi-/many-core architecture s\, RDMA-enabled networking\, NVRAMs\, and NVMe-SSDs during the last decad e. This talk will provide an in-depth overview of the architecture of Hado op\, Spark\, gRPC/TensorFlow\, Memcached\, and the associated Deep Learnin g frameworks. We will examine the challenges in re-designing networking an d I/O components of these middleware with modern interconnects\, protocols (such as InfiniBand\, RoCE) and storage architectures. This talk will pro vide case studies of the new designs for several Hadoop/Spark/gRPC/TensorF low/Memcached components and their associated benefits. Through these\, we will also examine the interplay between high-performance interconnects\, storage (HDD\, NVM\, and SSD)\, and multi-core platforms (e.g.\, Xeon x86\ , OpenPOWER) to achieve the best solutions for these components and applic ations on modern HPC clusters and clouds. We also present in-depth case-st udies with modern Deep Learning tools (e.g.\, Caffe\, TensorFlow\, BigDL) running over RDMA-enabled Hadoop\, Spark\, and gRPC.\n\nhttps://events.chp c.ac.za/event/6/contributions/178/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/178/ END:VEVENT BEGIN:VEVENT SUMMARY:In silico identification and structural bioinformatics of druggabl e protein targets in Schistosoma Species DTSTART;VALUE=DATE-TIME:20171206T122000Z DTEND;VALUE=DATE-TIME:20171206T124000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-180@events.chpc.ac.za DESCRIPTION:Speakers: Raphael Taiwo Aruleba (University of Zululand)\nSchi stosomiasis is a debilitating disease caused by a parasitic flatworm found in freshwater. After malaria\, this disease is the second most prevalent disease in Africa and is endemic in the tropical and subtropical regions o f the world. Morbidity and mortality attributed to this infection are very high with about 240 million people infected\, 800 million persons at risk of the infection and at least 280\,000 deaths annually. With the exponent ial increase in prevalence\, Praziquantel (PZQ) remains the only effective drug in the antischistosomal arsenal\, which is effective\, but ineffecti ve against the juvenile worm. More so\, resistance to PZQ has been widely reported of late. Therefore\, it is of paramount importance to develop eff ective alternative antischistosomal compounds using bioinformatics based t ools utilizing the broad-spectrum therapeutic capabilities of Antimicrobia l Peptides (AMPs). These AMPs are essential components of the innate immun e system and are responsible for the complete destruction and immunomodula tory effects in the host defence against pathogenic organisms. Twenty puta tive antischistosomal AMPs were identified using an in silico mathematical algorithm\, Hidden Markov Models (HMMER) but of which six were selected b ased on their E-values for further exploration. Physicochemical parameters of these six AMPs were computed and their 3D structures were determined u sing the Iterative Threading ASSEmbly Refinement (I-TASSER) server. Subseq uently\, the STITCH database was queried to retrieve novel Schistosoma pro teins that can potentially serve as targets for the identified AMPs. Glyco syltransferase and Axonemal dynein intermediate chain protein were identif ied as the novel druggable target proteins. Thereafter\, the physicochemic al characterization and prediction of the 3D structural elements of the af orementioned proteins were carried out as well. Finally\, PatchDock was us ed to dock the 3D structures of the putative antischistosomal AMPs against the 3D structures of the druggable proteins. Overall\, TAK3 showed a good binding affinity with glycosyltransferase and TAK6 displayed the highest binding affinity with axonemal dynein intermediate chain.*emphasized text* \n\nhttps://events.chpc.ac.za/event/6/contributions/180/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/180/ END:VEVENT BEGIN:VEVENT SUMMARY:Expanding the borders of Nelson Mandela University – Strategic p artnerships to enable high speed university connectivity in Nelson Mandela Bay DTSTART;VALUE=DATE-TIME:20171205T090000Z DTEND;VALUE=DATE-TIME:20171205T093000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-185@events.chpc.ac.za DESCRIPTION:Speakers: Creswell Du Preez (Nelson Mandela University)\nThe u niversity landscape in South Africa has significantly changed since the la tter part of 2015. Never before has issues of sustainability been more pre valent and universities are\, more than ever\, exploring strategic partner ships in order to sustainably provide connected student spaces in support of its academic agenda. Through creative and opportune partnerships with t he Nelson Mandela Bay Metropole (NMBM) as well as Vodacom and MTN\, the Ne lson Mandela University was not only able to connect its satellite campuse s with high-speed fibre\, but also provide university connectivity from el even public libraries across the metropole and the Nelson Mandela Bay Worl d Cup Stadium. The new Wi-Fi hotspots within the NMBM libraries were set-u p to be extensions of the Nelson Mandela University network and provides s tudents with Wi-Fi services comparable to what they would receive through the campus computer labs. The Nelson Mandela Bay Stadium was connected to the university network within the span of one week and this connectivity\, in conjunction with connectivity in public libraries\, proved critical in salvaging the university’s 2016 academic year when its main campuses we re closed due to student unrest.\n\nhttps://events.chpc.ac.za/event/6/cont ributions/185/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/185/ END:VEVENT BEGIN:VEVENT SUMMARY:Using docking and molecular dynamics to design potent and selectiv e anticancer\, anti-osteoclastogenic and anti-malarial compounds DTSTART;VALUE=DATE-TIME:20171205T093000Z DTEND;VALUE=DATE-TIME:20171205T095000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-217@events.chpc.ac.za DESCRIPTION:Speakers: Andre Stander (University of Pretoria)\nDocking and molecular dynanmics simulations using Autodock Vina and Gromacs were used to identify selective inhibitors of cancer-\, osteoclastogenic- and malari a-associated proteins. Selective benzotriazepine inhibitors of bromodomain 4 were identified and synthesized. The compounds show micromolar growth i nhibition of several cancer cell lines\, as well as potent inhibition of o steoclastogenesis without cytotoxicity against osteoclast progenators. \n\ nPotent inhibitors of malaria cytochrome bc1 proteins were identified and synthesized. The most potent compound inhibited in vitro asexual malaria p arasite growth to 50% of the control at a concentration of 64nM. The compo und showed no activity against human HepG2 cells at 5uM.\n\nThe present st udy will discuss how freely available docking and molecular dynamics tools are able to help researchers narrow down new\, potent and selective pharm aceutically relevant compounds.\n\nhttps://events.chpc.ac.za/event/6/contr ibutions/217/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/217/ END:VEVENT BEGIN:VEVENT SUMMARY:The Demand for High Performance Computing in Kenya: Special Intere st Groups as vehicles for promoting research collaboration DTSTART;VALUE=DATE-TIME:20171205T070000Z DTEND;VALUE=DATE-TIME:20171205T074500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-186@events.chpc.ac.za DESCRIPTION:Speakers: Meoli Kashorda (KENET)\nKenya Education Network (KEN ET) is the National Research and Education of Kenya\nresponsible for build ing and operating the research infrastructures for the academic community\ nin Kenya. \nThe research infrastructures include a high speed national ne twork with low-\ncongestion international links to global research & educa tion networks including TENET /\nSANREN in South Africa. \nThis talk will describe how KENET has created Special Interest\nGroups (SIGs) in order to discover and promote research collaboration in three main priority\nareas \, namely\, engineering\, computational modelling and materials science (C MMS)\, and\neducational technology. The talk shall describe the innovative methods used to discover\nresearch champions in different areas and the j oint activities of one of the Special SIG on CMMS\nin the period 2016-2017 . \nKenya plans to build the capacity of Kenyan researchers in the use of\ nHPC for researchers with the support of CHPC and other grid infrastructur es operators such as\nthe European Grid Infrastructure (EGI). The talk sha ll describe how KENET has setup a low-\ncost Certification Authority (CA) that has been accredited by EUGRIDPMA. The certificates\nissued by the CA would allow Kenyan researchers to access EGI to supplement their computing \nneeds. The talk concludes that any African NREN can facilitate access to HPC and Grid\nComputing facilities in any part of the world and therefore to promote research collaboration and\nproductivity.\n\nhttps://events.ch pc.ac.za/event/6/contributions/186/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/186/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational modelling of furnace tapholes – a case study in li fe at the interface between academic and industrial research DTSTART;VALUE=DATE-TIME:20171206T120000Z DTEND;VALUE=DATE-TIME:20171206T123000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-187@events.chpc.ac.za DESCRIPTION:Speakers: Markus Erwee (Mintek)\, Quinn Reynolds (Mintek)\nPyr ometallurgical smelting furnaces are used in the production of many commod ities of strategic and economic importance in South Africa including ferro chromium\, platinum-group metals\, titanium dioxide\, manganese alloys\, a nd others. Most furnaces make use of tapholes\, channels through the furna ce wall and lining\, in order to facilitate the removal of molten process material from inside the vessel. Correct understanding and operation of th e taphole is essential for optimal performance of such furnaces [1]. Depen ding on the smelting process being used the furnace may use a single tapho le for all material\, or separate tapholes for different phases such as sl ag and metal. Tapholes are typically located in a taphole assembly\, a spe cialised section of the furnace sidewall designed for this purpose.\n\nFlu id flow of molten material through furnace tapholes during tapping is a co mplex problem\, and its qualitative and quantitative behaviour is generall y governed by a combination of taphole geometry and properties of the tapp ed fluid [1\,2]. Understanding the interaction between these parameters an d the operating conditions inside the furnace is important for determinati on of tapping flowrates and wear phenomena.\n\nIn this presentation\, a te chnical overview of recent work at Mintek on computational modelling of fl uid flow through furnace tapholes will be presented. In addition\, the rel ationship between fundamental research and industrial development in the p yrometallurgical sector will be explored in the context of taphole modelli ng. In particular\, factors which can limit innovation in pyrometallurgy – such as strong risk sensitivity\, harsh macro-economic climates\, and long lead times for adoption of new technologies – will be addressed. Th e leveraging of academic research using facilities such as CHPC is seen as a critical and necessary step in the process of engaging with industrial clients and technology partners\, especially in the relatively new and dis ruptive field of computational modelling.\n\n1. Nelson\, L.R. and Hunderma rk\, R.J. (2016). ‘The tap-hole’ – key to furnace performance\, J. S AIMM\, 116(5)\, p 465\n2. Reynolds\, Q.G. and Erwee\, M.W. (2017). Multiph ase fluid flow modelling of furnace tapholes\, Proc. CFD 2017\, p 521\n\nh ttps://events.chpc.ac.za/event/6/contributions/187/ LOCATION:Velmoré Hotel Estate Voltaire URL:https://events.chpc.ac.za/event/6/contributions/187/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to Schrödinger’s drug discovery tools DTSTART;VALUE=DATE-TIME:20171203T070000Z DTEND;VALUE=DATE-TIME:20171203T150000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-188@events.chpc.ac.za DESCRIPTION:Speakers: Stephan Ehrlich (Schrodinger GmbH)\nSchrödinger is a leading provider of scientific software in the drug design industry. The workshop will give an overview of the drug discovery tools available from Schrödinger. Participants will be introduced to our new graphical interf ace\, Maestro 11\, and will work through hands-on examples for tasks like docking\, pharmacophore based virtual screening and building homology mode ls. The workshop will also touch on recent improvements on FEP+\, our fram ework to run MD based free energy calculations. It will conclude with a ge neral Q&A session were participants can discuss their own scientific proje cts.\nA trial version of our software will be available to participants pr ior to the workshop. Please bring your own laptop!\n\nhttps://events.chpc. ac.za/event/6/contributions/188/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/188/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational Intelligence and Algorithmic Mechanism Design: an Ap plication in Revenue Optimisation DTSTART;VALUE=DATE-TIME:20171204T113000Z DTEND;VALUE=DATE-TIME:20171204T120000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-190@events.chpc.ac.za DESCRIPTION:Speakers: Fulufhelo Nelwamondo (CSIR)\nMechanism Design lies i n the area of game theory\, with aims to design games whose equilibria hav e desired objectives such as high efficiency or revenue optimisation. Algo rithmic Mechanism Design focuses on Mechanism Design in algorithmically-co mplex scenarios\, and it employs various analytics tools with consideratio ns on computational constraints that exist in polynomial time. What makes this area more challenging is the trade-off between computational constrai ns and game-theoretic constrains. This talk will present this challenge\, through a simple case study in the application of revenue optimisation in the area of auctions. A number of issues such as the computational hardnes s\; convexity and a Vickrey–Clarke–Groves (VCG) mechanism\, which is a generic truthful mechanism for achieving a socially-optimal solution\, wi ll be presented. The convergence of the challenges and the need for High P erformance Computing environment will also be presented. The talk will end by discussing the current state of the field and how mechanism design is applied in computational settings\, the challenges for further research.\n \nhttps://events.chpc.ac.za/event/6/contributions/190/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/190/ END:VEVENT BEGIN:VEVENT SUMMARY:Phase diagram for the adsorption of oxygen and water on Pt(100) an d Pt(111) DTSTART;VALUE=DATE-TIME:20171205T094000Z DTEND;VALUE=DATE-TIME:20171205T100000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-218@events.chpc.ac.za DESCRIPTION:Speakers: Pierre Cilliers (Catalysis Insititute\, Department o f Chemical Engineering\, University of Cape Town)\nhttps://events.chpc.ac. za/event/6/contributions/218/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/218/ END:VEVENT BEGIN:VEVENT SUMMARY:Bioinformatics gone Wild! DTSTART;VALUE=DATE-TIME:20171206T093000Z DTEND;VALUE=DATE-TIME:20171206T100000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-191@events.chpc.ac.za DESCRIPTION:Speakers: Morne Du Plessis (National Zoological Gardens of Sou th Africa)\nThe National Zoological Gardens of South Africa (NZG) has a st rong research component focused on conservation of Wildlife. This is achie ved via the Research and Scientific Services Department. In keeping with t he times\, and considering ongoing advances in newer research technologies \, the NZG has moved toward greater implementation of aspects such as Next Generation Sequencing and the Bioinformatics analysis thereof in its rese arch. As such our research currently includes (a) small genome and organel le sequencing assembly and annotation (b) microsatellite development from NGS data (c) microbiome analysis\, as well as (d) genotyping by sequencing \, all in a wildlife context. While the organization has acquired access t o some resources for the analysis of these large datasets\, there is certa inly a requirement for access to additional resources capable of handling even larger datasets as well as multiple datasets simultaneously. Via a p artnership with the CHPC the NZG is therefore currently in the process of optimizing and implementing workflows which address their big data analysi s needs. The presentation aims to outline the research activities of the v arious groups within NZG\, in the NGS-Bioinformatics context\, along with the resource requirements that the CHPC would supply\, in order to ensure the successful implementation of this exciting partnership.\n\nhttps://eve nts.chpc.ac.za/event/6/contributions/191/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/191/ END:VEVENT BEGIN:VEVENT SUMMARY:Machine Learning in the Era of Data Intensive Astronomy DTSTART;VALUE=DATE-TIME:20171204T093000Z DTEND;VALUE=DATE-TIME:20171204T100000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-192@events.chpc.ac.za DESCRIPTION:Speakers: Russ Taylor (Inter-University Institute for Data Int ensive Astronomy)\nThe construction of MeerKAT and emergence of the Africa n VLBI network marks the beginning of the radio astronomy big data revolut ion in South Africa\, and the first steps of the scientific and data pathw ay to the Square Kilometre Array (SKA). This journey to the SKA represents one of the most significant data challenges in scientific research of the coming decade. To rise to the scientific opportunity of this new data era requires the research community to develop new infrastructure\, software systems and algorithm to process\, analyse and mine these data for scienti fic knowledge. But the size of the data\, the complexity of the signals c ontained therein\, and the sophistication of the analytics needed\, means we cannot rely on the old approaches for human interaction with the data. Machine learning techniques may be an important part of the solution. I will review the data-to-science landscape of the SKA\, and touch on specif ic challenges where algorithmic approaches are falling short but machine l earning may offer a way forward.\n\nhttps://events.chpc.ac.za/event/6/cont ributions/192/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/192/ END:VEVENT BEGIN:VEVENT SUMMARY:Using the Open Source CFD GUI in FreeCAD DTSTART;VALUE=DATE-TIME:20171207T113000Z DTEND;VALUE=DATE-TIME:20171207T150000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-193@events.chpc.ac.za DESCRIPTION:Speakers: Johan Heyns (CSIR)\nThe computational fluid dynamics (CFD) workbench for FreeCAD was developed to provide South African indust ry and academia with a cost-effective solution for modelling fluid flow. T his workbench aims to help users set up and run CFD analyses. It guides th e user in selecting the relevant physics\, specifying the material propert ies\, generating a mesh\, assigning boundary conditions and setting the so lver settings before running the simulation. Where possible\, best practic es are included to improve the stability of the solvers.\n\nDuring the wor kshop\, we will give an overview of the technology and demonstrate how to: \n* Create the geometry\;\n* Selection of simulation parameters\;\n* Speci fy boundary conditions\;\n* Unstructured mesh generation\;\n* Initiate the run and monitor residuals\; and\n* Visualise the results\n\nThe CFD workb ench is available as an add-on to FreeCAD while more information on the wo rkbench as well as\, additional\, training material are available on the O penSim community website: https://opensimsa.github.io/\n\nhttps://events.c hpc.ac.za/event/6/contributions/193/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/193/ END:VEVENT BEGIN:VEVENT SUMMARY:Parallel visualization on Lengau with Paraview and VisIt DTSTART;VALUE=DATE-TIME:20171203T113000Z DTEND;VALUE=DATE-TIME:20171203T115000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-195@events.chpc.ac.za DESCRIPTION:Speakers: Charles Crosby (CHPC)\nThis workshop will touch on t he following topics:\n\n 1. Overview of the 3D visualization codes Paravie w and VisIt\n 2. Similarities and differences between Paraview & VisIt\n 3 . Limitations of single core processing of large data sets\n 4. OpenGL\, V irtualGL and Mesa\n 5. Different approaches to remote visualization - VNC or X-forwarding\n 6. Different approaches to parallelisation\n 7. Decompos ed datasets\n 8. Tutorial illustrating remote parallel visualization with Paraview\n 9. Tutorial illustrating remote parallel visualization with Vis It\n 10. Introductory remarks on the concept of in-situ visualization\n 11 . Concluding remarks\n\nhttps://events.chpc.ac.za/event/6/contributions/19 5/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/195/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational chemistry methods in understanding the properties of porous material DTSTART;VALUE=DATE-TIME:20171205T113000Z DTEND;VALUE=DATE-TIME:20171205T120000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-196@events.chpc.ac.za DESCRIPTION:Speakers: Catharine Esterhuysen (Department of Chemistry and P oymer Science\, University of Stellenbosch)\nIntermolecular interactions p lay a fundamentally important role in the properties of solid materials. F or instance\, molecules ("guests") are taken up into porous materials ("ho sts") as a result of the interactions between these species\, while the ma nner in which they interact has an influence on the sorption ability of th e porous material. Several examples from our work will be used to show tha t calculations performed using the CHPC's computational facility allow us to explain the role that intermolecular interactions play in the unusual s orption properties of various porous compounds. For instance\, the interac tions between carbon dioxide and a host porous metal-organic framework yie ld anomalous sorption isotherms.[1] Similarly\, intermolecular interaction s are responsible for the change in colour of a crystalline porous compoun d during sorption of certain solvents along an hourglass pattern. Calculat ions show that the origin of this effect is that the channels in the porou s framework are anisotropic\, allowing sorption only from particular faces .[2] Calculations also enabled us to understand the changing intermolecula r interactions involved in two other porous compounds that could allow the frameworks to undergo large structural changes during sorption and desor ption\, while still maintaining the integrity of the crystalline nature of the compound. [3]\n\n\n----------\n\n\n[1] Bezuidenhout\, C. X.\; Smith\, V. J.\; Bhatt\, P. M.\; Esterhuysen\, C.\; Barbour\, L. J. Angew. Chem. I nt. Ed. 2015\, 54\, 2079–2083.\n[2] Bezuidenhout\, C. X.\; Esterhuysen\, C.\; Barbour\, L. J. Chem. Commun.\, 2017\, 53\, 5618–5621.\n[3] Bezuid enhout\, C. X.\; Smith\, V. J.\; Esterhuysen\, C.\; Barbour\, L. J. J. Am. Chem. Soc. 2017\, 139\, 5923–5929.\n\nhttps://events.chpc.ac.za/event/6 /contributions/196/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/196/ END:VEVENT BEGIN:VEVENT SUMMARY:Evaluation of Soil Moisture in the Coupled CCAM-CABLE Model over S outh Africa Using In-Situ and ESA CCI Satellite Observations DTSTART;VALUE=DATE-TIME:20171205T122000Z DTEND;VALUE=DATE-TIME:20171205T124000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-206@events.chpc.ac.za DESCRIPTION:Speakers: Floyd Khosa (CSIR)\nThis study evaluates the perform ance of the coupled CCAM-CABLE model estimates of soil moisture against in -situ measurements from the Skukuza flux tower and ESA CCI satellite obser vations both at a point and regional scale. In situ measurements are used to evaluate the accuracy of the soil moisture products at a point (locatio n of the flux tower) through the use of conventional statistical measures such as correlation coefficient\, normalised mean bias\, root mean square error (RMSE) and coefficient of efficiency. The coupled CCAM-CABLE simulat ions performed best compared with observations for the surface soil moistu re and root zone soil moisture for both the dry (March to October) and wet (November to April) seasons. There is evidence of overestimation of obser ved soil moisture by the various products. Differences in model performanc e at the surface and the root zone were observed. Following the evaluation at the site level\, we further evaluated the performance of CCAM-CABLE\, ESA CCI and GLEAM model projections over a grid covering parts of South Af rica using correlation coefficient and root mean square difference (RMSD). There is disagreement (i.e. strong negative correlation) between CCAM-CAB LE and ESA-CCI mainly during the wet season especially for the ESA-passive product. However\, there is moderate to strong correlation between ESA CC I and CCAM-CABLE during the dry period. Similarly\, there is evidence of a greement between the GLEAM models and CCAM-CABLE especially during the dry period for most of the grid. The models generally agree on the estimates of root zone soil moisture with correlation coefficients ranging between 0 .7 and 1\, and RMSD between 0 and 20% for savanna areas\, and correlation coefficient between 0.2 to 0.5\, and RMSD of 20 to 40% for the grassland. We conclude that the soil moisture estimated using the coupled CCAM-CABLE is comparable with satellite and in situ observations at different soil de pths and scales.\n\nhttps://events.chpc.ac.za/event/6/contributions/206/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/206/ END:VEVENT BEGIN:VEVENT SUMMARY:Setting Up Basic Molecular Dynamics (MD) Calculations at CHPC Usin g DL_POLY Code” DTSTART;VALUE=DATE-TIME:20171207T113000Z DTEND;VALUE=DATE-TIME:20171207T115000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-207@events.chpc.ac.za DESCRIPTION:Speakers: Cliffton Masedi (CSIR/CHPC)\, Raesibe Sylvia Ledwaba (University of Limpopo)\nProposal for a Tutorial at 2017 CHPC National Me eting\n \nTitle: “Setting Up Basic Molecular Dynamics (MD) Calculations at CHPC Using DL_POLY Code”\n\nLecturer(s): 1. Sylvia Ledwaba\, Universi ty of Limpopo\, raesibe.ledwaba@ul.ac.za\n\n2. Cliffton Masedi\, Universit y of Limpopo/CSIR\, cmasedi@csir.co.za \nDescription:\nMolecular dynamics (MD) is a computer simulation method for studying the physical movements o f atoms and molecules. The MD method can assist one in obtaining the stati c quantities and dynamic quantities. This method gives a route to dynamica l properties of the system: transport coefficients\, time-dependent respon ses to perturbations\, rheological properties and spectra. The atoms and m olecules are allowed to interact for a fixed period of time\, giving a vie w of the dynamic evolution of the system. The DL_POLY Code parallel molecu lar dynamics simulation package will be utilised for exploration of such p roperties of molecular systems.\n \nDuration: 1 day (6 hours)\n\nSize: ( max number of available seats)\n\nTarget Audience:\nThis one day workshop is intended for undergraduate project students\, postgraduate students \, postdoctoral researchers and researchers who are familiar with the fie ld and want to employ state-of-the art methodology based on the densi ty functional theory to understand bulk materials properties\, surf ace science and heterogeneous catalysis phenomena.\nPrerequisites: Familia rity with UNIX or Linux environment.\n\nType of tutorial: Mix of tutorial s and hands-on (mostly practical)\n\nSpecial requirements:\n\nAttendees ne ed access to a laptop or workstation\, active CHPC user account cluster wi th access to DL_POLY software.\nOpen source spreadsheet such as Microsoft Excel with graphing capabilities is required for post-processing of outpu t data. \nFree visualization softwares (e.g. VMD\, VESTA\, etc.)\, necess ary for structure visualization. \nOutline of full syllabus:\nIntroducti on to Molecular Dynamics\nProperties of Molecular Dynamics\nSimulation cod e (DL_POLY)\nFitting and validation of interatomic potentials\nSetting up molecular dynamic simulations\nForce Field Models/ Interatomic Potentials\ nGeneral Description\nPotential Models (Buckingham + Three-Body)\nCompatib ility of Interatomic Potentials\nValidation\nHands-on exercises on:\nConst ruction of Structure File\nValidation of Interatomic Potentials\nGenerati on of DL_POLY input files\nSubmission of Calculations at CHPC_Lengau\n\nht tps://events.chpc.ac.za/event/6/contributions/207/ LOCATION:Velmoré Hotel Estate Martells URL:https://events.chpc.ac.za/event/6/contributions/207/ END:VEVENT BEGIN:VEVENT SUMMARY:Intel Plenary TBA DTSTART;VALUE=DATE-TIME:20171204T160000Z DTEND;VALUE=DATE-TIME:20171204T162000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-208@events.chpc.ac.za DESCRIPTION:Speakers: Bill Magro (Intel)\nhttps://events.chpc.ac.za/event/ 6/contributions/208/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/208/ END:VEVENT BEGIN:VEVENT SUMMARY:Learning image interest and saliency from pairwise image compariso ns DTSTART;VALUE=DATE-TIME:20171205T122000Z DTEND;VALUE=DATE-TIME:20171205T124000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-209@events.chpc.ac.za DESCRIPTION:Speakers: Michael Burke (Council for scientific and industrial research/ University of Witwatersrand)\nVideo cameras are increasingly de ployed in exploration\, monitoring and surveillance applications. These ca meras produce vast amounts of information\, which needs to be condensed in to manageable quantities for both storage and human-operator evaluation. W hile data compression can address the former\, this does not aid operators \, who are often faced with the daunting task of analysing lengthy video s equences. As a result\, a system that automatically flags interesting imag es or information and presents this to an operator in a concise manner is highly desirable. \n\nThis talk will show how the 'interest' value of an i mage can be inferred by means of a Bayesian ranking framework operating on pairwise image comparisons obtained from users. These interest values can then be used to automatically flag images likely to be of use to a human operator. Algorithm modifications showing how these interest posteriors ca n be improved by applying Gaussian process smoothing to convolutional neur al network feature representations (general datasets) will be discussed an d storyboarding applications introduced. The talk will also show how image saliency maps highlighting content of interest to a user can be produced as a byproduct of the interest inference process.\n\nhttps://events.chpc.a c.za/event/6/contributions/209/ LOCATION:Velmoré Hotel Estate De Voir URL:https://events.chpc.ac.za/event/6/contributions/209/ END:VEVENT BEGIN:VEVENT SUMMARY:Poster Awards DTSTART;VALUE=DATE-TIME:20171206T164500Z DTEND;VALUE=DATE-TIME:20171206T165500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-210@events.chpc.ac.za DESCRIPTION:Speakers: Happy Sithole (CHPC)\nhttps://events.chpc.ac.za/even t/6/contributions/210/ LOCATION:Velmoré Hotel Estate Tres Sage Plenary hall URL:https://events.chpc.ac.za/event/6/contributions/210/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to Parallel Computing with OpenMP DTSTART;VALUE=DATE-TIME:20171207T070000Z DTEND;VALUE=DATE-TIME:20171207T072000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-214@events.chpc.ac.za DESCRIPTION:Speakers: Milfeld Kent (TACC)\nhttps://events.chpc.ac.za/event /6/contributions/214/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/214/ END:VEVENT BEGIN:VEVENT SUMMARY:Understanding and Controlling Processor Affinity DTSTART;VALUE=DATE-TIME:20171205T095000Z DTEND;VALUE=DATE-TIME:20171205T101500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-216@events.chpc.ac.za DESCRIPTION:Speakers: Milfeld Kent (TACC)\nhttps://events.chpc.ac.za/event /6/contributions/216/ LOCATION:Velmoré Hotel Estate Tres Sage URL:https://events.chpc.ac.za/event/6/contributions/216/ END:VEVENT BEGIN:VEVENT SUMMARY:An Integrative Approach to Generating a Reference Transcriptome fo r Sugarcane DTSTART;VALUE=DATE-TIME:20171206T120000Z DTEND;VALUE=DATE-TIME:20171206T122000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-220@events.chpc.ac.za DESCRIPTION:Speakers: Robyn Jacob (South African Sugarcane Research Instit ute)\nThe sugarcane industry is a substantial agricultural activity in Sou th Africa\, which contributes significantly to the country’s gross domes tic product and positively impacts on the lives of over a million people. Economic loss due to *Eldana saccharina*\, a lepidopteran stem-borer\, is estimated to be R900 million per annum. A better understanding of the mole cular mechanisms involved in resistance against eldana would be an importa nt step towards targeted breeding of resistant sugarcane varieties. In a g enomic context\, sugarcane is classed as an ‘orphan crop’ as no genome assembly is currently available. However\, next generation sequencing (NG S) technologies have enabled large scale sequencing of genomes and transcr iptomes providing the data needed to uncover these mechanisms. Commercial sugarcane cultivars (*Saccharum* spp. hybrids) have large and complex poly ploid genomes. Moreover\, it is not known how gene expression is influence d by the multiple alleles created due to the aneuploid and polyploid natur e of the genome. Our aim is to harness the wealth of in-house and publicly available genomic and transcriptomic data in order to construct a referen ce transcriptome for use in sugarcane RNA-seq studies\, whilst overcoming the limitations of *de novo* transcriptome assembly with low coverage data . Not only will this project endeavour to uncover the molecular mechanisms underpinning resistance to eldana\, but the approach taken should allow t he development of a generic and modular analysis pipeline capable of creat ing reference transcriptomes\, in the absence of a reference genome\, in o ther non-model plant species.\n\nhttps://events.chpc.ac.za/event/6/contrib utions/220/ LOCATION:Velmoré Hotel Estate Satre URL:https://events.chpc.ac.za/event/6/contributions/220/ END:VEVENT BEGIN:VEVENT SUMMARY:Incentives driving data sharing: an African perspective DTSTART;VALUE=DATE-TIME:20171206T122000Z DTEND;VALUE=DATE-TIME:20171206T124500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-221@events.chpc.ac.za DESCRIPTION:Speakers: Ina Smith (Academy of Science of South Africa (ASSAf ))\nThe Open Science movement – focused on making research data\, softwa re code and experimental methods publicly available and transparent - is s teadily gaining momentum. According to Gewin (2016)\, “[A]a spirit of op enness is gaining traction in the science community\, and is the only way\ , say advocates\, to address a 'crisis' in science whereby too few finding s are successfully reproduced. Furthermore\, they say\, it is the best way for researchers to gather the range of observations that are necessary to speed up discoveries or to identify large-scale trends.” \n \nAlthough many researchers are already sharing their raw data and data sets\, there are researchers who still question why they should share their data\, and what benefits are in it for them. In other words\, how will they be incent ivized\, when others use the outputs of their hard work. These issues also apply on national and institutional levels\, across the world. Very few c ountries and institutions have policies in place regarding the management (incl. curation) and sharing of data as an outcome of funded research proj ects.\n\nThrough this talk\, some initial findings on incentives for shari ng data from the African Open Science Platform project will be presented.\ n\nhttps://events.chpc.ac.za/event/6/contributions/221/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/221/ END:VEVENT BEGIN:VEVENT SUMMARY:Libraries enabling Open Data: UCTs new Institutional Data Reposito ry DTSTART;VALUE=DATE-TIME:20171206T093000Z DTEND;VALUE=DATE-TIME:20171206T095500Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-222@events.chpc.ac.za DESCRIPTION:Speakers: Niklas Zimmer (University of Cape Town)\nA presentat ion on UCT Libraries implementing an Institutional Data Repository (IDR) s ervice for UCT. Included are: 1. an overview of drivers for Open Access Da ta Science support (Mandates and Policies\, as well as benefits)\, 2. a de scription of how a suitable mechanism for compliance was identified (in th e context of a federated\, national approach)\; 3. a brief discussion of k ey features of the platform (Figshare for Institutions) in practice (live instance of the UCT IDR)\, including outreach (naming competition\, data d rop-in sessions et al)\; 4. some closing remarks on various considerations (technical\, operational\, and conceptual).\n\nhttps://events.chpc.ac.za/ event/6/contributions/222/ LOCATION:Velmoré Hotel Estate Rendezvous URL:https://events.chpc.ac.za/event/6/contributions/222/ END:VEVENT BEGIN:VEVENT SUMMARY:Validation of the OSCAR-5 Code System against Experimental Data on Fuel Burnup and Material Activation in Research Reactors DTSTART;VALUE=DATE-TIME:20171206T093000Z DTEND;VALUE=DATE-TIME:20171206T095000Z DTSTAMP;VALUE=DATE-TIME:20260511T034709Z UID:indico-contribution-6-223@events.chpc.ac.za DESCRIPTION:Speakers: Francois van Heerden (Necsa)\nThe IAEA (Internationa l Atomic Energy Agency) Cooperative Research Project (CRP) 2026\, entitled "Benchmarks of Computational Tools against Experimental Data on Fuel Burn up and Material Activation for Utilization\, Operation and Safety Analysis of Research Reactors"\, provides a valuable opportunity to validate calcu lations tools against quality experimental data. As part of this multi-nat ional effort\, Necsa (South African Nuclear Energy Corporation) contribute d operational and experimental data of the SAFARI-1 research reactor\, and also performed simulations for four other reactors from around the world\ , using both in-house developed and external codes. The OSCAR-5 systems is the latest iteration of the in-house developed code system which currentl y supports the operation of the SAFARI-1 reactor\, and a number of other r esearch reactors around the world. This version for the first time incorpo rates support for high fidelity modeling\, and therefore has a strong HPC component. \n\nThis talk will give an overview of the calculational syste m\, in particular how and where computational resources are used\, and su mmarize some initial validation results for the five reactors modeled.\n\n https://events.chpc.ac.za/event/6/contributions/223/ LOCATION:Velmoré Hotel Estate URL:https://events.chpc.ac.za/event/6/contributions/223/ END:VEVENT END:VCALENDAR