BEGIN:VCALENDAR VERSION:2.0 PRODID:-//CERN//INDICO//EN BEGIN:VEVENT SUMMARY:Infiniband In-Network Computing DTSTART;VALUE=DATE-TIME:20181205T113000Z DTEND;VALUE=DATE-TIME:20181205T120000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-807@events.chpc.ac.za DESCRIPTION:Speakers: Yossi Avni (Mellanox Technologies)\nhttps://events.c hpc.ac.za/event/33/contributions/807/ LOCATION: Meeting Room 7 URL:https://events.chpc.ac.za/event/33/contributions/807/ END:VEVENT BEGIN:VEVENT SUMMARY:Understanding Risk in Shared CyberInfrastructure Systems Seminar DTSTART;VALUE=DATE-TIME:20181202T113000Z DTEND;VALUE=DATE-TIME:20181202T130000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-868@events.chpc.ac.za DESCRIPTION:Speakers: Meshack Ndala (CHPC)\nCHPC Cyber Security Symposium (CCSS) – 1 full day\nTopic: Understanding Risk in Shared CyberEcosystems workshop\nAs Technology continues to evolve so are the opportunities and challenges it provides. As a Society that relies largely on technology to bring us benefits\, it also exposes its users to threats by the very natur e of the opportunities it presents\, thus becoming a focal point for Cyber crime\, industrial espionage\, and Cyberattacks. Protecting against these threats is of paramount priority.\nCyber Security domain is inherently dyn amic\, not only does system configuration changes frequently with new rele ases and patches\, but also new attacks and vulnerabilities are regularly discovered. The core threat in Cyber Security is human\, hence intelligent in nature. The attacker adapts to the situation\, target environment\, an d countermeasures.\nAttacks actions are driven by attacker’s exploratory nature\, thought process\, motivation\, strategy\, and preferences.\nThe goal of this workshop is to address some of the challenges faced by Networ k and Security Administrators in their institutions.\nThe workshop will ad dress challenges such as:\n• Iot Threats\n• Blockchain Revolution\n• Ransomware Evolution\n• Future of Cybersecurity\n• New hacking Method ologies\n• Phishing\n• Distributed Denial of Service (DDoS)\n• Malwa re\n• Internal Privilege Misuse\n• Threats actors\n• How to protect your environment\n\nThe following are our invited speakers:\n• Prof Elma rie Bierman: Directory of SA Cyber Security Institute\n• Dr Noelle Cow ling : Stellenbosch University\n• Dr Jabu Mtswene : CSIR\n• Dr Noluxol o Gcaza: CSIR\n• Mr Justine Westcott\n• Mr Sikhumbuzo Mthombeni: Demen sion Data\n• Mr Keti Cedric : Demension Data\n• Mr Richard Hlalele: Un iversity of Johannesburg\, Senior Manager ICT Strategy and Governance\nThe following are workshop Coordinators:\nMr Bigani Sehurutshi: University of Botswana\nMrs Lee-Anne Benjamin: Manager \,Corporate IT Compliance NRF\n\ nhttps://events.chpc.ac.za/event/33/contributions/868/ LOCATION: Meeting Room 9 URL:https://events.chpc.ac.za/event/33/contributions/868/ END:VEVENT BEGIN:VEVENT SUMMARY:Q&A DTSTART;VALUE=DATE-TIME:20181205T102000Z DTEND;VALUE=DATE-TIME:20181205T103000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-884@events.chpc.ac.za DESCRIPTION:https://events.chpc.ac.za/event/33/contributions/884/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/884/ END:VEVENT BEGIN:VEVENT SUMMARY:Chair/Facilitator DTSTART;VALUE=DATE-TIME:20181205T090000Z DTEND;VALUE=DATE-TIME:20181205T090500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-882@events.chpc.ac.za DESCRIPTION:Speakers: Sthembiso Mkhwanazi (CSIR)\nhttps://events.chpc.ac.z a/event/33/contributions/882/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/882/ END:VEVENT BEGIN:VEVENT SUMMARY:Chair/Facilitator DTSTART;VALUE=DATE-TIME:20181205T113000Z DTEND;VALUE=DATE-TIME:20181205T113500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-885@events.chpc.ac.za DESCRIPTION:Speakers: Isak Van der Walt (UP Library)\nhttps://events.chpc. ac.za/event/33/contributions/885/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/885/ END:VEVENT BEGIN:VEVENT SUMMARY:Welcoming Address DTSTART;VALUE=DATE-TIME:20181203T070000Z DTEND;VALUE=DATE-TIME:20181203T071000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-881@events.chpc.ac.za DESCRIPTION:Speakers: HINA PATEL (CSIR)\nhttps://events.chpc.ac.za/event/3 3/contributions/881/ LOCATION: Hall B+C URL:https://events.chpc.ac.za/event/33/contributions/881/ END:VEVENT BEGIN:VEVENT SUMMARY:Integrating HPC and AI in the Exascale Era : Applications and Plat forms DTSTART;VALUE=DATE-TIME:20181204T100000Z DTEND;VALUE=DATE-TIME:20181204T103000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-907@events.chpc.ac.za DESCRIPTION:Speakers: Oliver Blondel (HPE)\nhttps://events.chpc.ac.za/even t/33/contributions/907/ LOCATION: Meeting Room 8+9 URL:https://events.chpc.ac.za/event/33/contributions/907/ END:VEVENT BEGIN:VEVENT SUMMARY:Q&A DTSTART;VALUE=DATE-TIME:20181205T122000Z DTEND;VALUE=DATE-TIME:20181205T123000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-889@events.chpc.ac.za DESCRIPTION:https://events.chpc.ac.za/event/33/contributions/889/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/889/ END:VEVENT BEGIN:VEVENT SUMMARY:HPC insights into chemistry mysteries DTSTART;VALUE=DATE-TIME:20181204T123000Z DTEND;VALUE=DATE-TIME:20181204T125000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-910@events.chpc.ac.za DESCRIPTION:Speakers: Jeanet Conradie (University of the Free State)\nThis contribution is aimed to illustrate how chemical computational results\, obtained by density functional theory calculations on high performance com puters\, provides insight into many observed chemical phenomena\, mysterie s or questions\, such as the following:\nThe structure of water clusters i n bulk water is considered one of the unsolved problems in chemistry. Ho w does the structure of water clusters look like at nanoscopic scale? Ho w do the connecting hydrogen bonds render water ideally suited to life pro cesses\, being easily formed but not too difficult to break? A photochrom ic mercury compound has an orange colour in solution\, but turns blue when sunlight shines on it. Why? How do these orange and blue forms differ in structure? Why is conductivity much higher for a certain iridium comp lex\, than for the related rhodium complex with the same ligand? Why is the transient reaction intermediate within a multi-step red blood cell rea ction not experimentally observable? \nThese and many other puzzling chemi cal problems\, can be addressed very efficiently without experimental erro r\, by computational chemistry conducted on high performance computers\, t hereby bypassing tedious or expensive laboratory techniques.\n\nReferences :\n[1] https://en.wikipedia.org/wiki/Water_cluster\n[2] A. Malloum\, J.J . Fifen\, J. Conradie\, The Journal of Physical Chemistry\, submitted\, MS no jp-2018-08976q.R1\n[3] H. Schwoerer\, K.G. von Eschwege\, G. Bosman\, P. Krok\, J. Conradie\, European Journal of Chemical Physics and Physical Chemistry\, 2011\, 14\, 2653-2658.\n[4] K.G. von Eschwege\, J. Conradie\ , J.C. Swarts\, Journal of Physical Chemistry A\, 2008\, 112\, 2211-2218.\ n[5] J. Conradie\, Journal of Organometallic Chemistry\, 2017\, 833\, 88- 94.\n[6] S. Basu\, R. Grubina\, J. Huang\, J. Conradie\, Z. Huang\, A. Je ffers\, A. Jiang\, X. He\, I. Azarov\, R. Seibert\, A. Mehta\, R. Patel\, S.B. King\, A. Ghosh\, M.T. Gladwin\, D.B. Kim-Shapiro\, Nature Chemical B iology\, 2007\, 3\, 785-794.\n\nhttps://events.chpc.ac.za/event/33/contrib utions/910/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/910/ END:VEVENT BEGIN:VEVENT SUMMARY:Chair/Facilitator DTSTART;VALUE=DATE-TIME:20181205T133000Z DTEND;VALUE=DATE-TIME:20181205T133500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-890@events.chpc.ac.za DESCRIPTION:Speakers: Nobubele Shozi (CSIR)\nhttps://events.chpc.ac.za/eve nt/33/contributions/890/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/890/ END:VEVENT BEGIN:VEVENT SUMMARY:Building HPC infrastructure on public clouds with PBS Works DTSTART;VALUE=DATE-TIME:20181205T120000Z DTEND;VALUE=DATE-TIME:20181205T123000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-893@events.chpc.ac.za DESCRIPTION:Speakers: Alexander Franke ()\nDelivering HPC solutions via cl oud-based resources is still a technical challenge. Beside either running HPC workload on on-premise resources or entirely on cloud resources hybrid approaches can be used for providing a flexible and cost-effective way of running HPC workloads. Based on two examples\, a turn-key SaaS solution ( HyperworkUnlimited Virtual Appliance) and a Cloud Bursting scenario with P BS Control we will discuss what is involved in such setups and how to make it work smoothly.\n\nhttps://events.chpc.ac.za/event/33/contributions/893 / LOCATION: Meeting Room 7 URL:https://events.chpc.ac.za/event/33/contributions/893/ END:VEVENT BEGIN:VEVENT SUMMARY:DIRISA Technology Stack DTSTART;VALUE=DATE-TIME:20181205T113500Z DTEND;VALUE=DATE-TIME:20181205T115000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-886@events.chpc.ac.za DESCRIPTION:Speakers: Claude Fortune (CSIR)\nA brief overview of the Techn ology stack used by DIRISA to provide storage infrastructure and services will be provided.\n\nhttps://events.chpc.ac.za/event/33/contributions/886/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/886/ END:VEVENT BEGIN:VEVENT SUMMARY:The South African Data Management Planning Tool (SA DMP Tool) DTSTART;VALUE=DATE-TIME:20181205T120500Z DTEND;VALUE=DATE-TIME:20181205T122000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-888@events.chpc.ac.za DESCRIPTION:Speakers: Nobubele Shozi (CSIR)\nResearch funders around the w orld are realizing the importance of data management planning. Increasingl y research public funders globally\, now require data management plans to be submitted with research proposals as a condition of funding support. Th is is also true in South Africa where research funders such as the Nationa l Research Foundation (NRF) already require researchers to provide a data management plan as part of their application for research funding. A data management plan can be described as a formal document that outlines how da ta will be dealt with by the researcher before\, during and after the rese arch has been conducted. \nThe DIRISA Data Management Planning (DMP) Tool has been developed to assist South African Researchers to create data mana gement plans that align with the requirements of funders such as the Natio nal Research Foundation (NRF). This presentation will give a brief demo of the tool.\n\nhttps://events.chpc.ac.za/event/33/contributions/888/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/888/ END:VEVENT BEGIN:VEVENT SUMMARY:KEYNOTE 7: Coreless Continuum Computer Architecture DTSTART;VALUE=DATE-TIME:20181205T160000Z DTEND;VALUE=DATE-TIME:20181205T164500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-670@events.chpc.ac.za DESCRIPTION:Speakers: Thomas Sterling (Indiana University)\n**Coreless Con tinuum Computer Architecture**\n\n> *Thomas Sterling* (Department of Intel ligent Systems Engineering\, School of Informatics\, Computing\, and Engin eering\, Indiana University)\n\n\n\n\nAs introduced at CHPC-17\, a new era is dawning: the Neo-Digital Age as semiconductor fabrication enters its f inal phase with nano-scale feature size. For the first time in three decad es\, fundamental technology limitations of device density\, power consumpt ion\, clock rate\, and instruction level parallelism are demanding revolut ionary practices to further expand HPC capabilities into the trans-exascal e performance regime and perhaps beyond. Among the domains of possible cha nge are those uncovered in the prevailing assumptions embodied by the many generations exploiting Moore’s Law\, which no longer apply. These inclu de 1) the use of static methods for parallel application programming and s tatic resource management\, and 2) the implicit underlying principles buri ed in the von Neumann architecture of which essentially all HPC systems ar e since derivatives. An alternative strategy\, bordering on a paradigm shi ft\, reverses conventional methodologies a) to employ dynamic adaptive met hods of resource management and task scheduling\, and b) to eliminate von Neumann bottlenecks\, eliminating even the basic core that has endured as the foundation of HPC architecture design since the late 1940s. Central to the forward looking revolution is the elimination of the FPU/ALU as the p recious resource with the implied objective function of highest possible u tilization. The Continuum Computer Architecture (CCA) has been proposed as a family of alternative architectures that address the current challenge and exploit the future opportunities by fully integration of logic\, memor y\, control\, and communication within a single highly replicated computin g cell. First suggested an abstract in last year’s last Keynote\, this p resentation will expose key details in structure and semantics that will l ayout the conceptual scaffolding for future development and application su ch as machine learning and intelligence\, planning\, scheduling\, hypothes is testing\, facial recognition and many other graph-based application. Qu estions will be encouraged by participants throughout the presentation as well as the Q&A session at the end.\n\nhttps://events.chpc.ac.za/event/33/ contributions/670/ LOCATION: Hall B+C URL:https://events.chpc.ac.za/event/33/contributions/670/ END:VEVENT BEGIN:VEVENT SUMMARY:Bytes are Bytes\, Right? DTSTART;VALUE=DATE-TIME:20181203T123000Z DTEND;VALUE=DATE-TIME:20181203T130000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-672@events.chpc.ac.za DESCRIPTION:Speakers: Matthew Curry (Sandia National Laboratories)\nThroug h the first several decades of computing\, two data storage abstractions/p aradigms dominated common practice: Files and relational databases. While there is significant potential overlap between their use\, it is often eas y to decide which is more efficient for a particular application or worklo ad. However\, over the last twenty years\, teh rise of new patterns for pa rallel and distributed computing (i.e.\, those now loosely grouped under t he "cloud" umbrella) have brought to the fore other kinds of storage techn ologies and techniques. Among this new group of options are NoSQL stores\, object stores\, and key-value stores.\n\nThe lines between these storage technologies are blurred\, both because of overlapping application benefit s and different design choices for various types of packages. What kinds o f workloads benefit most from each paradigm? Who might an HPC user leverag e these technologies? This talk will address these questions and more.\n\n https://events.chpc.ac.za/event/33/contributions/672/ LOCATION: Hall B URL:https://events.chpc.ac.za/event/33/contributions/672/ END:VEVENT BEGIN:VEVENT SUMMARY:Role of High Performance Computing in the Applications of Bio-econ omically Important Proteins DTSTART;VALUE=DATE-TIME:20181204T113000Z DTEND;VALUE=DATE-TIME:20181204T115000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-828@events.chpc.ac.za DESCRIPTION:Speakers: Ozlem Tastan Bishop (Rhodes University)\nThe main re search interest of the Research Unit in Bioinformatics (RUBi) at Rhodes Un iversity is in structural bioinformatics and its applications to bio-econo mically important research questions\, i.e. to drug discovery projects for diseases related to Africa\, and to biodiversity and bioprocessing. Centr e for High Performance Computing (CHPC)\, South Africa\, is regularly used for accelerating computer intensive methods including drug virtual screen ing\, molecular modelling\, quantum mechanics\, molecular mechanics\, mole cular dynamics (MD) and combinations of these techniques. RUBi’s researc h is computationally highly expensive\; i.e. within 3 months (February – April 2018) a total of 7.2 million cpu hours was used. Hence\, CHPC has a great impact on RUBi’s research\, international collaborations and huma n capacity development. This talk focuses on the application of HPC to RUB i’s research projects with some specific examples including analysis of drug resistance of HIV\, identification of new drug targeting sites for ca ncer\, and investigation of proteins related to the production of biofuels . Further\, computational details\, e.g. benchmarking\, compute time\, det ails of software used and/or developed will also be given to demonstrate t he need for HPC resources.\n\nhttps://events.chpc.ac.za/event/33/contribut ions/828/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/828/ END:VEVENT BEGIN:VEVENT SUMMARY:The World of Research Data: When Should Data be Closed\, Shared or Open? DTSTART;VALUE=DATE-TIME:20181205T090500Z DTEND;VALUE=DATE-TIME:20181205T092000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-812@events.chpc.ac.za DESCRIPTION:Speakers: Heila Pienaar (University of Pretoria Library)\nThat research data should be shared with the rest of the world has become almo st evangelical in nature. This paper will try to answer the following ques tions:\n• What are the (real) reasons for ‘forcing’ scientists to op en their data\, even if they are not ready to do so?\n• What right have non-scientists (and scientists) to push indiscriminately for the sharing o f data without taking the nuances of research into consideration?\n\nThis paper will look at the physical characteristics of research data before it can be shared\, a case study of the public humiliation of a excellent res earcher who did not wish to share his data\, as well as the advantages and disadvantages of sharing research data.\n\nhttps://events.chpc.ac.za/even t/33/contributions/812/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/812/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to HPC DTSTART;VALUE=DATE-TIME:20181202T090000Z DTEND;VALUE=DATE-TIME:20181202T103000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-854@events.chpc.ac.za DESCRIPTION:Speakers: Thomas Sterling (Indiana University)\, Maciej Brodow icz (Indiana Univeristy)\nWhere to begin? HPC as a field\, a technology\, and a tool for a diversity of disciplines that are enabled by it is an int erplay of foundational concepts\, rapidly evolving knowledge\, and skill s ets including programming. This one-day tutorial is presented as a beginne rs’ guide to supercomputing to expose the novice to the breadth of issue s needed to begin to understand and use such systems for real-world proble ms. Included are basic concepts\, HPC architecture\, benchmarking\, parall el programming using OpenMP and MPI\, basics of GPU accelerators\, and lib raries. Participants will be shown live demonstrations of all of these tec hniques and given opportunities for hands-on experience using the CHPC Pet aflops scale supercomputer in South Africa. Questions will be welcome from the attendees throughout the presentations.\n\nhttps://events.chpc.ac.za/ event/33/contributions/854/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/854/ END:VEVENT BEGIN:VEVENT SUMMARY:Optimized Artificial Intelligence Solutions by Intel DTSTART;VALUE=DATE-TIME:20181206T090000Z DTEND;VALUE=DATE-TIME:20181206T103000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-871@events.chpc.ac.za DESCRIPTION:Speakers: Michael Steyer ()\, Edmund Preiss (Intel)\nDescripti on:\nJoin us for one day of hands-on sessions on Artificial Intelligence\, and Machine & Deep Learning. Experience a unique opportunity to test out the latest performance optimized frameworks and tools\, advanced coding kn owledge and best practices to get started implementing AI guided by expert s from Intel®.\n\nTarget Audience:\nData Scientist\, application develope rs and HPC benchmarkers targeting the deep learning and machine learning d omain.\n\nPrerequisites:\nBeginning to intermediate level of domain AI kno wledge.\nBasic skills of programming \, ideally some Python knowldege\n\n Type of tutorial: Mix of lectures and hands-on tutorials\n\nSpecial Requir ements:\nAttendees should bring their laptop with an SSH- & VNC client\nAt tendees will get for hands on-labs also access to the CHPC cluster \n\nOut line of full syllabus:\n08:00 Registration\n09:00 Introduction\n• Introd uction round & Agenda \n• Introduction Intel Software Developer Tools \n• Introduction to Machine Learnin g / Deep Learning \n10:30 Morning Refr eshment Break\n11:00 \nClassic Machine Learning Tools\n• Intel performan ce Libraries - MKL & DAAL \n • Intel Distribution for Python (IDP) Introduction \n• IDP Hands on labs \no NumPy & MKL \no K-Means Clustering & DAAL \no SVM & DAAL \n12:30 Lunch\n13:30 \nDeep Learn ing (DL) Tools \n• Intel performance Libraries for DL – MKL-DNN & MLS L \n• Intel optimized Frameworks / Tenso rFlow \no TensorFlow Image Clas sification Hands-on Lab \no In troduction simple CNN \no Monitored Training Session \n15:00 Afternoon Ref reshment Break\n15:30 \nDeep Learning Tools (cont’d) \n• Intel optimi zed Frameworks / TensorFlow (cnt’d) \no Horovod – distributed classification \no Importing external Im ages \no Custom batches \n• Benchmarking distributed TensorFlow (BKMs) \n• Deep Learning Scaling – large s cale results (BigDL/Spark) \n• Wrap-Up & Q&A \n17:00 End of Day\n\nhttps:/ /events.chpc.ac.za/event/33/contributions/871/ LOCATION: Meeting Room 8 URL:https://events.chpc.ac.za/event/33/contributions/871/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to HPC DTSTART;VALUE=DATE-TIME:20181202T113000Z DTEND;VALUE=DATE-TIME:20181202T130000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-855@events.chpc.ac.za DESCRIPTION:Speakers: Thomas Sterling (Indiana University)\, Maciej Brodow icz (Indiana Univeristy)\nWhere to begin? HPC as a field\, a technology\, and a tool for a diversity of disciplines that are enabled by it is an int erplay of foundational concepts\, rapidly evolving knowledge\, and skill s ets including programming. This one-day tutorial is presented as a beginne rs’ guide to supercomputing to expose the novice to the breadth of issue s needed to begin to understand and use such systems for real-world proble ms. Included are basic concepts\, HPC architecture\, benchmarking\, parall el programming using OpenMP and MPI\, basics of GPU accelerators\, and lib raries. Participants will be shown live demonstrations of all of these tec hniques and given opportunities for hands-on experience using the CHPC Pet aflops scale supercomputer in South Africa. Questions will be welcome from the attendees throughout the presentations.\n\nhttps://events.chpc.ac.za/ event/33/contributions/855/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/855/ END:VEVENT BEGIN:VEVENT SUMMARY:Exploring Real-Time Semantics in Supercomputing DTSTART;VALUE=DATE-TIME:20181204T120000Z DTEND;VALUE=DATE-TIME:20181204T123000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-842@events.chpc.ac.za DESCRIPTION:Speakers: Maciej Brodowicz (Indiana Univeristy)\nOne of the pr ominent trends in computing is the convergence of supercomputers and embed ded control computers\, which have come to share many of the same requirem ents and limitations. These common attributes include multicore\, power\, reliability\, programmability\, and portability. The increasing use of lig htweight processors like embedded cores in HPC systems prompts the need to unify multiple cores for time dependent embedded control. The challenges arising due to asynchrony of parallel execution\, especially important in the context of non-homogenous many-task programs\, make workload schedulin g for optimal performance and predictability of overall execution time par ticularly difficult. This talk presents results of an NSF sponsored resear ch project attempting to span the gap between the two classes of computer system through the conceptual bridge of a new execution model and its surr ogate runtime system software and programming interface. It extended the P aralleX execution model to the domain of embedded computers by incorporati ng real-time semantics as an intrinsic property of the model so that multi core embedded computer architectures may be treated as a single system exp loiting dynamic adaptive techniques to achieve real-time capability even w hen concurrent processing is required to reduce response time to necessary bounds. Performance figures derived using initial implementation of real- time extensions to the HPX-5 runtime system will also be presented and dis cussed. Questions from the audience are welcome throughout the talk.\n\nht tps://events.chpc.ac.za/event/33/contributions/842/ LOCATION: Meeting Room 8+9 URL:https://events.chpc.ac.za/event/33/contributions/842/ END:VEVENT BEGIN:VEVENT SUMMARY:Untapped Potential of Computational Material Science In Kenya DTSTART;VALUE=DATE-TIME:20181205T094000Z DTEND;VALUE=DATE-TIME:20181205T100000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-713@events.chpc.ac.za DESCRIPTION:Speakers: George Manyali (Masinde Muliro University of Science and Technology)\nComputational material science is taking root in Kenya. Development of big data infrastructure\, high-performance computing facili ties and use of open-source-software will accelerate the growth of this fi eld\, develop competent manpower and improve the economy of the country. T he role played by major public universities in Kenya such as Masinde Mulir o University of Science and Technology\, University of Eldoret\, Kenyatta University and the University of Nairobi in tackling health\, water\, and energy-related issues using computational tools requires long-term funding support. The glaring gap in technology transfer from universities to indu stries in Kenya needs to be addressed in order to harness the full potenti al of computational material science.\n\nhttps://events.chpc.ac.za/event/3 3/contributions/713/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/713/ END:VEVENT BEGIN:VEVENT SUMMARY:Molecular Dynamics and Analysis using BRIDGE DTSTART;VALUE=DATE-TIME:20181206T070000Z DTEND;VALUE=DATE-TIME:20181206T083000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-722@events.chpc.ac.za DESCRIPTION:Speakers: Chris Barnett (University of Cape Town)\, Kevin J. N aidoo (University of Cape Town)\nMolecular Dynamics and analysis can be co mplicated for novitiates and researchers from neighbouring disciplines. Bu ilding upon the Galaxy Project platform\, BRIDGE (Biomolecular Reaction & Interaction Dynamics Global Environment) is a web application that provide s the ability to get started running molecular dynamics and analyses using curated workflows.\n\n**Target Audience:** Computational chemists\, biolo gists\, protein scientists\, crystallographers and anyone interested in ru nning and analysing molecular dynamics simulations who is not familiar wit h the command line.\n\n**Prerequisites:** Basic understanding of chemistry . A basic understanding of or keen interest in molecular dynamics.\n\n**Sp ecial requirements:** Bring a laptop. Have access to the CHPC cluster. Reg ister with BRIDGE. Install molecular viewer e.g. VMD.\n\n\n**Day:** Thursd ay (6 Dec)\n**Duration:** 1 day\n**Size:** 15 seats\n\nhttps://events.chpc .ac.za/event/33/contributions/722/ LOCATION: Meeting Room 9 URL:https://events.chpc.ac.za/event/33/contributions/722/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to HPC DTSTART;VALUE=DATE-TIME:20181202T133000Z DTEND;VALUE=DATE-TIME:20181202T150000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-856@events.chpc.ac.za DESCRIPTION:Speakers: Thomas Sterling (Indiana University)\, Maciej Brodow icz (Indiana Univeristy)\nWhere to begin? HPC as a field\, a technology\, and a tool for a diversity of disciplines that are enabled by it is an int erplay of foundational concepts\, rapidly evolving knowledge\, and skill s ets including programming. This one-day tutorial is presented as a beginne rs’ guide to supercomputing to expose the novice to the breadth of issue s needed to begin to understand and use such systems for real-world proble ms. Included are basic concepts\, HPC architecture\, benchmarking\, parall el programming using OpenMP and MPI\, basics of GPU accelerators\, and lib raries. Participants will be shown live demonstrations of all of these tec hniques and given opportunities for hands-on experience using the CHPC Pet aflops scale supercomputer in South Africa. Questions will be welcome from the attendees throughout the presentations.\n\nhttps://events.chpc.ac.za/ event/33/contributions/856/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/856/ END:VEVENT BEGIN:VEVENT SUMMARY:Simulations of the COSMO model on the CHPC DTSTART;VALUE=DATE-TIME:20181205T100000Z DTEND;VALUE=DATE-TIME:20181205T102000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-784@events.chpc.ac.za DESCRIPTION:Speakers: Patience Mulovhedzi (SAWS)\, Mary-Jane Bopape (SAWS) \nThe South African Weather Service (SAWS)\, as a national meteorological service provider for South Africa (SA) and Southern African Development Co mmunity (SADC) communities\, aims to provide useful and innovative weather \, climate\, and related products and services. Part of SAWS services and products are derived from Numerical Weather Prediction (NWP) models\, of w hich Unified model (UM) from the UK Metoffice is the lead model. Weather f orecast models perform differently across different parts of the globe and for different weather phenomena. In order to ensure continuous delivery o f high quality weather forecasts to SAWS stakeholders\, other NWP models a re examined. The Consortium for Small-scale Modelling (COSMO) model is eva luated and analysed in order to investigate whether it is more/less suitab le for predicting high impact weather events over SA.\nThe COSMO model is a European limited area model driven from Icosahedral Non-hydrostatic (ICO N) global model. The ICON model has a grid spacing of 13km globally\, whic h allows the COSMO to be simulated at a fine horizontal resolution of less than 5km. In this study\, the COSMO model is being run with a grid spacin g of 4.4km and 40 vertical levels\, which allows for accurate numerical pr ediction of near-surface weather conditions (e.g. clouds\, fog\, frontal p recipitation) and simulation of severe weather events triggered by deep mo ist convection (supercell thunderstorms\, intense mesoscale convective com plexes\, prefrontal squallline storms and heavy snowfall from wintertime m esocyclones.\nSimulations of five high impact weather events over SA were done on the CHPC system. The COSMO model is run with a grid spacing of 4.4 km (0.036°) over SADC with a domain ranging from 5 – 56 °E and 40 – 5 °S (1276 x 1026 grid points)\, using a timestep of 30 seconds and a 30 hour lead-time. The model is run on a large queue using 1728 cores with u sing default science settings. Both the pre-processing and model run compl eted in +/- 2.5 hours and the model output was in hourly intervals for 86 variables (80 in sigma coordinates and 6 in pressure coordinates).\nThe se lected variables (parameters) from model output are then evaluated against ground observations from SAWS network\, radar data\, satellite observatio ns\, Global Precipitation Measurement (GPM) and National Centers for Envir onmental Prediction (NCEP) Reanalysis data. Selected parameters for evalua tion include wind speed\, surface temperature\, total precipitation\, clou d cover\, mean sea-level pressure\, surface pressure and geopotential heig ht. The outcome of the model evaluation will be discussed in detail at the conference.\n\nhttps://events.chpc.ac.za/event/33/contributions/784/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/784/ END:VEVENT BEGIN:VEVENT SUMMARY:An Overview of Modelling at Johnson Matthey DTSTART;VALUE=DATE-TIME:20181205T113000Z DTEND;VALUE=DATE-TIME:20181205T115000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-830@events.chpc.ac.za DESCRIPTION:Speakers: Chris Perry (Johnston Matthey)\nOver the past fiftee n years or so\, the number of modellers at Johnson Matthey has grown from one\, to close to twenty\; a firm indication of the importance that JM pla ces in both atomistic\, as well as meso/macroscale modelling. DFT modellin g in particular\, forms an integral part of JM’s research and developmen t efforts in a wide range of areas\, including catalysis\, diagnostic serv ices\, pharmaceutical applications\, and new battery and fuel cell technol ogies. The presentation will provide a brief overview of modelling at JM\, highlighting the types of calculations that we do (with some real world e xamples)\, how modelling fits in with our experimental research programmes \, the HPC resources that we utilize\, and our interactions with the CHPC. \n\nhttps://events.chpc.ac.za/event/33/contributions/830/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/830/ END:VEVENT BEGIN:VEVENT SUMMARY:High-throughput\, atomistic multi-scale modeling with MedeA®-Univ ersal Cluster Expansion (UNCLE) to study alloy structures\, phase-stabilit y and ordering DTSTART;VALUE=DATE-TIME:20181202T090000Z DTEND;VALUE=DATE-TIME:20181202T103000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-857@events.chpc.ac.za DESCRIPTION:Speakers: David Reith (Materials Design Sarl)\, Clifton Masedi (University of Limpopo)\, Malatji Kemerdige (University of Limpopo)\, Ale xander Mavromaras (Materials Design Sarl)\nDescription:\nMedeA-UNiversal C Luster Expansion (UNCLE) expands access to materials and properties at the meso and micro scales. Performing VASP ab-initio calculations on automati cally chosen sets of small models\, MedeA-UNCLE captures the configuration al complexity of real materials at different temperatures by means of Mont e Carlo random sampling. Tight integration with job control in MedeA guara ntees stability and fault tolerance. Graphical tools monitor progress of f ully automated simulations and allow a ready-for-use visualization of resu lts.\nKey Benefits of MedeA-UNCLE:\n• Models systems containing millions of atoms with DFT accuracy\n• User-friendly setup within MedeA Environm ent\n• Workflow-based automation of cluster expansion refinement\n• Ef ficient handling of hundreds of input structures\n• Intuitive graphical analysis and visualization\n• Split and restart complex calculations\n • Extend and expand existing Cluster Expansions\nComputational Character istics:\n• Use Genetic Algorithm or Compressive Sensing \n• Full integ ration with MedeA-VASP and other modules\n• High throughput using the Jo bServer\nProperties from MedeA-UNCLE:\n• Structures of stable phases\n • Vacancy concentrations\n• Miscibility\n• Random mixing energy\n• Phase stability as a function of temperature and concentration\n• Solub ility\n• Order-disorder transition temperature\n• Micro structure\n\nT arget Audience: This one day workshop is intended for undergraduate projec t students\, postgraduate students\, postdoctoral researchers and researc hers who are familiar with the field and want to employ state-of-the art methodology based on the density functional theory to understand bulk materials properties\, phase diagrams\, order- disorder transition temperature\, vancacy concentrations\, miscibility and micro structure.\n\ nType of tutorial: Mix of tutorials and hands-on (mostly practical) \n\nS pecial requirements:\n• Attendees need access to a laptop or workstation \, active CHPC user account cluster. \n• Open source spreadsheet such as Microsoft Excel with graphing capabilities is required for post-processi ng of output data. \n\nOutline of full syllabus:\n1. Introduction to the MedeA® Software environment\na. Structure retrieval\, building\nb. Flowch art interface\nc. High Throughput support \n2. Introduction to Cluster Exp ansion techniques\na. Theoretical background\nb. MedeA® Uncle overview \n 3. MedeA® UNCLE hands-on (bulk) \na. Selected tutorials\n4. MedeA® UNCLE hands-on (surfaces)\na. Selected tutorials\n5. Q&A\, wrap-up\n\nhttps://e vents.chpc.ac.za/event/33/contributions/857/ LOCATION: Meeting Room 8 URL:https://events.chpc.ac.za/event/33/contributions/857/ END:VEVENT BEGIN:VEVENT SUMMARY:High-throughput\, atomistic multi-scale modeling with MedeA®-Univ ersal Cluster Expansion (UNCLE) to study alloy structures\, phase-stabilit y and ordering DTSTART;VALUE=DATE-TIME:20181202T070000Z DTEND;VALUE=DATE-TIME:20181202T083000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-787@events.chpc.ac.za DESCRIPTION:Speakers: David Reith (Materials Design Sarl)\, Clifton Masedi (University of Limpopo)\, Malatji Kemerdige (University of Limpopo)\, Ale xander Mavromaras (Materials Design Sarl)\nDescription:\nMedeA-UNiversal C Luster Expansion (UNCLE) expands access to materials and properties at the meso and micro scales. Performing VASP ab-initio calculations on automati cally chosen sets of small models\, MedeA-UNCLE captures the configuration al complexity of real materials at different temperatures by means of Mont e Carlo random sampling. Tight integration with job control in MedeA guara ntees stability and fault tolerance. Graphical tools monitor progress of f ully automated simulations and allow a ready-for-use visualization of resu lts.\nKey Benefits of MedeA-UNCLE:\n• Models systems containing millions of atoms with DFT accuracy\n• User-friendly setup within MedeA Environm ent\n• Workflow-based automation of cluster expansion refinement\n• Ef ficient handling of hundreds of input structures\n• Intuitive graphical analysis and visualization\n• Split and restart complex calculations\n • Extend and expand existing Cluster Expansions\nComputational Character istics:\n• Use Genetic Algorithm or Compressive Sensing \n• Full integ ration with MedeA-VASP and other modules\n• High throughput using the Jo bServer\nProperties from MedeA-UNCLE:\n• Structures of stable phases\n • Vacancy concentrations\n• Miscibility\n• Random mixing energy\n• Phase stability as a function of temperature and concentration\n• Solub ility\n• Order-disorder transition temperature\n• Micro structure\n\nT arget Audience: This one day workshop is intended for undergraduate projec t students\, postgraduate students\, postdoctoral researchers and researc hers who are familiar with the field and want to employ state-of-the art methodology based on the density functional theory to understand bulk materials properties\, phase diagrams\, order- disorder transition temperature\, vancacy concentrations\, miscibility and micro structure.\n\ nType of tutorial: Mix of tutorials and hands-on (mostly practical) \n\nS pecial requirements:\n• Attendees need access to a laptop or workstation \, active CHPC user account cluster. \n• Open source spreadsheet such as Microsoft Excel with graphing capabilities is required for post-processi ng of output data. \n\nOutline of full syllabus:\n1. Introduction to the MedeA® Software environment\na. Structure retrieval\, building\nb. Flowch art interface\nc. High Throughput support \n2. Introduction to Cluster Exp ansion techniques\na. Theoretical background\nb. MedeA® Uncle overview \n 3. MedeA® UNCLE hands-on (bulk) \na. Selected tutorials\n4. MedeA® UNCLE hands-on (surfaces)\na. Selected tutorials\n5. Q&A\, wrap-up\n\nhttps://e vents.chpc.ac.za/event/33/contributions/787/ LOCATION: Meeting Room 8 URL:https://events.chpc.ac.za/event/33/contributions/787/ END:VEVENT BEGIN:VEVENT SUMMARY:High-throughput\, atomistic multi-scale modeling with MedeA®-Univ ersal Cluster Expansion (UNCLE) to study alloy structures\, phase-stabilit y and ordering DTSTART;VALUE=DATE-TIME:20181202T113000Z DTEND;VALUE=DATE-TIME:20181202T130000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-858@events.chpc.ac.za DESCRIPTION:Speakers: David Reith (Materials Design Sarl)\, Clifton Masedi (University of Limpopo)\, Malatji Kemerdige (University of Limpopo)\, Ale xander Mavromaras (Materials Design Sarl)\nDescription:\nMedeA-UNiversal C Luster Expansion (UNCLE) expands access to materials and properties at the meso and micro scales. Performing VASP ab-initio calculations on automati cally chosen sets of small models\, MedeA-UNCLE captures the configuration al complexity of real materials at different temperatures by means of Mont e Carlo random sampling. Tight integration with job control in MedeA guara ntees stability and fault tolerance. Graphical tools monitor progress of f ully automated simulations and allow a ready-for-use visualization of resu lts.\nKey Benefits of MedeA-UNCLE:\n• Models systems containing millions of atoms with DFT accuracy\n• User-friendly setup within MedeA Environm ent\n• Workflow-based automation of cluster expansion refinement\n• Ef ficient handling of hundreds of input structures\n• Intuitive graphical analysis and visualization\n• Split and restart complex calculations\n • Extend and expand existing Cluster Expansions\nComputational Character istics:\n• Use Genetic Algorithm or Compressive Sensing \n• Full integ ration with MedeA-VASP and other modules\n• High throughput using the Jo bServer\nProperties from MedeA-UNCLE:\n• Structures of stable phases\n • Vacancy concentrations\n• Miscibility\n• Random mixing energy\n• Phase stability as a function of temperature and concentration\n• Solub ility\n• Order-disorder transition temperature\n• Micro structure\n\nT arget Audience: This one day workshop is intended for undergraduate projec t students\, postgraduate students\, postdoctoral researchers and researc hers who are familiar with the field and want to employ state-of-the art methodology based on the density functional theory to understand bulk materials properties\, phase diagrams\, order- disorder transition temperature\, vancacy concentrations\, miscibility and micro structure.\n\ nType of tutorial: Mix of tutorials and hands-on (mostly practical) \n\nS pecial requirements:\n• Attendees need access to a laptop or workstation \, active CHPC user account cluster. \n• Open source spreadsheet such as Microsoft Excel with graphing capabilities is required for post-processi ng of output data. \n\nOutline of full syllabus:\n1. Introduction to the MedeA® Software environment\na. Structure retrieval\, building\nb. Flowch art interface\nc. High Throughput support \n2. Introduction to Cluster Exp ansion techniques\na. Theoretical background\nb. MedeA® Uncle overview \n 3. MedeA® UNCLE hands-on (bulk) \na. Selected tutorials\n4. MedeA® UNCLE hands-on (surfaces)\na. Selected tutorials\n5. Q&A\, wrap-up\n\nhttps://e vents.chpc.ac.za/event/33/contributions/858/ LOCATION: Meeting Room 8 URL:https://events.chpc.ac.za/event/33/contributions/858/ END:VEVENT BEGIN:VEVENT SUMMARY:High-throughput\, atomistic multi-scale modeling with MedeA®-Univ ersal Cluster Expansion (UNCLE) to study alloy structures\, phase-stabilit y and ordering DTSTART;VALUE=DATE-TIME:20181202T133000Z DTEND;VALUE=DATE-TIME:20181202T150000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-859@events.chpc.ac.za DESCRIPTION:Speakers: David Reith (Materials Design Sarl)\, Clifton Masedi (University of Limpopo)\, Malatji Kemerdige (University of Limpopo)\, Ale xander Mavromaras (Materials Design Sarl)\nDescription:\nMedeA-UNiversal C Luster Expansion (UNCLE) expands access to materials and properties at the meso and micro scales. Performing VASP ab-initio calculations on automati cally chosen sets of small models\, MedeA-UNCLE captures the configuration al complexity of real materials at different temperatures by means of Mont e Carlo random sampling. Tight integration with job control in MedeA guara ntees stability and fault tolerance. Graphical tools monitor progress of f ully automated simulations and allow a ready-for-use visualization of resu lts.\nKey Benefits of MedeA-UNCLE:\n• Models systems containing millions of atoms with DFT accuracy\n• User-friendly setup within MedeA Environm ent\n• Workflow-based automation of cluster expansion refinement\n• Ef ficient handling of hundreds of input structures\n• Intuitive graphical analysis and visualization\n• Split and restart complex calculations\n • Extend and expand existing Cluster Expansions\nComputational Character istics:\n• Use Genetic Algorithm or Compressive Sensing \n• Full integ ration with MedeA-VASP and other modules\n• High throughput using the Jo bServer\nProperties from MedeA-UNCLE:\n• Structures of stable phases\n • Vacancy concentrations\n• Miscibility\n• Random mixing energy\n• Phase stability as a function of temperature and concentration\n• Solub ility\n• Order-disorder transition temperature\n• Micro structure\n\nT arget Audience: This one day workshop is intended for undergraduate projec t students\, postgraduate students\, postdoctoral researchers and researc hers who are familiar with the field and want to employ state-of-the art methodology based on the density functional theory to understand bulk materials properties\, phase diagrams\, order- disorder transition temperature\, vancacy concentrations\, miscibility and micro structure.\n\ nType of tutorial: Mix of tutorials and hands-on (mostly practical) \n\nS pecial requirements:\n• Attendees need access to a laptop or workstation \, active CHPC user account cluster. \n• Open source spreadsheet such as Microsoft Excel with graphing capabilities is required for post-processi ng of output data. \n\nOutline of full syllabus:\n1. Introduction to the MedeA® Software environment\na. Structure retrieval\, building\nb. Flowch art interface\nc. High Throughput support \n2. Introduction to Cluster Exp ansion techniques\na. Theoretical background\nb. MedeA® Uncle overview \n 3. MedeA® UNCLE hands-on (bulk) \na. Selected tutorials\n4. MedeA® UNCLE hands-on (surfaces)\na. Selected tutorials\n5. Q&A\, wrap-up\n\nhttps://e vents.chpc.ac.za/event/33/contributions/859/ LOCATION: Meeting Room 8 URL:https://events.chpc.ac.za/event/33/contributions/859/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to Schrödinger’s Drug Discovery Tools DTSTART;VALUE=DATE-TIME:20181202T070000Z DTEND;VALUE=DATE-TIME:20181202T083000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-788@events.chpc.ac.za DESCRIPTION:Speakers: Stephan Ehrlich (Schrödinger GmbH)\nSchrödinger is a leading provider of scientific software in the drug design industry. Th e workshop will give an overview of the drug discovery tools available fro m Schrödinger.\nParticipants will be introduced to our graphical interfac e\, Maestro 11\, and get some hands-on experience with common tasks like d ocking and pharmacophore based virtual screening. We will also cover the n ewly redesigned enumeration and virtual library design tools available.\nT he workshop will finish with a lecture on more advanced modeling tools\, a nd an open Q&A session.\n\nhttps://events.chpc.ac.za/event/33/contribution s/788/ LOCATION: Meeting Room 7 URL:https://events.chpc.ac.za/event/33/contributions/788/ END:VEVENT BEGIN:VEVENT SUMMARY:Using High Performance Computing to run large-scale WRFChem Acid D eposition Modelling over the Highveld Region of South Africa DTSTART;VALUE=DATE-TIME:20181205T115000Z DTEND;VALUE=DATE-TIME:20181205T121000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-831@events.chpc.ac.za DESCRIPTION:Speakers: Suzanne Cawood (EScience Associates (Pty) Ltd)\nAcid deposition has been studied extensively over the Highveld region of South Africa due to its high density of acid emissions arising mostly from powe r generation and petrochemical production. Although deposition of acid spe cies has been modelled using dispersion models\, the modelling of atmosphe ric chemistry and acid deposition has not been undertaken to any meaningfu l extent in South Africa. Furthermore\, the potential of WRFChem\, the Wea ther\, Research and Forecasting (WRF) model coupled with Chemistry\, has y et to be realized within an African context mainly due to the high computi ng power required to compute even the smallest of domain sizes. With a dom ain size of over 300 000 km2\, which equates to over 75 000 grid cells\, over a two-year modelling period\, computational power was a limiting fac tor to the success of the research. Access to high performance computing a nd more specifically the ability to split the processing across multiple p rocessors is instrumental in running this computationally intensive model. And has been the limiting factor for further research in South Africa on this topic. This presentation provides a review of the benefits of using H igh Performance Computing for running WRFChem when compared with local mic ro-servers.\n\nhttps://events.chpc.ac.za/event/33/contributions/831/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/831/ END:VEVENT BEGIN:VEVENT SUMMARY:Optimized Artificial Intelligence Solutions by Intel DTSTART;VALUE=DATE-TIME:20181206T070000Z DTEND;VALUE=DATE-TIME:20181206T083000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-870@events.chpc.ac.za DESCRIPTION:Speakers: Michael Steyer ()\, Edmund Preiss (Intel)\nDescripti on:\nJoin us for one day of hands-on sessions on Artificial Intelligence\, and Machine & Deep Learning. Experience a unique opportunity to test out the latest performance optimized frameworks and tools\, advanced coding kn owledge and best practices to get started implementing AI guided by expert s from Intel®.\n\nTarget Audience:\nData Scientist\, application develope rs and HPC benchmarkers targeting the deep learning and machine learning d omain.\n\nPrerequisites:\nBeginning to intermediate level of domain AI kno wledge.\nBasic skills of programming \, ideally some Python knowldege\n\n Type of tutorial: Mix of lectures and hands-on tutorials\n\nSpecial Requir ements:\nAttendees should bring their laptop with an SSH- & VNC client\nAt tendees will get for hands on-labs also access to the CHPC cluster \n\nOut line of full syllabus:\n08:00 Registration\n09:00 Introduction\n• Introd uction round & Agenda \n• Introduction Intel Software Developer Tools \n• Introduction to Machine Learnin g / Deep Learning \n10:30 Morning Refr eshment Break\n11:00 \nClassic Machine Learning Tools\n• Intel performan ce Libraries - MKL & DAAL \n • Intel Distribution for Python (IDP) Introduction \n• IDP Hands on labs \no NumPy & MKL \no K-Means Clustering & DAAL \no SVM & DAAL \n12:30 Lunch\n13:30 \nDeep Learn ing (DL) Tools \n• Intel performance Libraries for DL – MKL-DNN & MLS L \n• Intel optimized Frameworks / Tenso rFlow \no TensorFlow Image Clas sification Hands-on Lab \no In troduction simple CNN \no Monitored Training Session \n15:00 Afternoon Ref reshment Break\n15:30 \nDeep Learning Tools (cont’d) \n• Intel optimi zed Frameworks / TensorFlow (cnt’d) \no Horovod – distributed classification \no Importing external Im ages \no Custom batches \n• Benchmarking distributed TensorFlow (BKMs) \n• Deep Learning Scaling – large s cale results (BigDL/Spark) \n• Wrap-Up & Q&A \n17:00 End of Day\n\nhttps:/ /events.chpc.ac.za/event/33/contributions/870/ LOCATION: Meeting Room 8 URL:https://events.chpc.ac.za/event/33/contributions/870/ END:VEVENT BEGIN:VEVENT SUMMARY:The role of the interface in binary polymer blends DTSTART;VALUE=DATE-TIME:20181203T094000Z DTEND;VALUE=DATE-TIME:20181203T100000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-712@events.chpc.ac.za DESCRIPTION:Speakers: Giuseppe Pellicane (University of Kwazulu-Natal)\nPh ysical techniques for surface modification of plastics use surface-active agents\, which are allowed to self-assemble at the surface. Many technique s\, which are important in modern technologies\, use polymer blends\, and there is considerable interest to understand the extent the composition of the surface layer differs from that in the bulk for molten polymer mixtur es. Dynamical and structural properties of polymers in the melt state are strongly influenced by molecular architecture [1-4] and blending polymers with different molecular topologies could be potentially exploited to cont rol interfacial segregation of the polymer film\, and to achieve optimal m echanical properties of the plastic material [5\,6]. However\, a deep unde rstanding of the role of chain architecture and molecular mass in determin ing which species preferentially adsorb at a given interface is lacking. E xperiments to resolve the matter are typically conducted by mixing polymer s possessing the same repeat chemistry\, but different molecular architect ure [10–14]. Here we show the results obtained in large-scale molecular dynamics simulations of linear-cyclic polymer films\, and we find clear ev idence of enhancement of linear polymers at the interface [7]\, in agreeme nt with recent experimental results [8]. The behavior predicted by the sel f-consistent field theory (SCF)\, i.e.\, enhancement of cyclic polymers at the interface [9]\, emerges for relatively long chains. In our presentati on\, we provide a picture of the microscopic mechanisms through which the chain length arbitrates the competition between the different packing cons traints imposed by the loop and linear geometry of the two polymers. We al so discuss the role of enthalpic and entropic factors of the interfacial f ree energy of the system in determining which species in the blend prefere ntially adsorbs at the interface. \n\n[1] Kapnistos\, M\; Lang. M\; Rubin stein\, M\; Roovers\, J.\; Chang\, T\; Vlassopoulos\, D.\, Soc. Rheol. Ann u. Meeting 2006.\n[2] Robertson\, R. M.\; Smith\, D. E.\, Proc. Natl. Acad . Sci. U.S.A. 2007\, 104\, 4824-4827.\n[3] Iyer\, B. V. S.\; Lele\, A. K.\ ; Shanbhag\, S.\, Macromolecules 2007\, 40\, 5995.\n[4] Subramanian\, G.\; Shanbhag S.\, Macromolecules 2008\, 41\, 7239-7242.\n[5] Wu\, S. L.\; Pol ymer Interface and Adhesion\, Marcel Dekker: New York\, 1982.\n[6] Garbass i\, F\; Morra\, M\; Occhiello\, E.\, Polymer Surfaces: From Physics to Tec hnology\; John Wiley and Sons: New York\,1994.\n[7] G. Pellicane\, M. Megn idio-Tchoukouegno\, G. T. Mola\, and M. Tsige\, Physical Review E Rapid Co mmunications\, 93\, 050501 (2016)\; M. Megnidio-Tchoukouegno\, F. M. Gaith o\, G. T. Mola\, M. Tsige\, and G. Pellicane\, Fluid Phase Equilibria\, 44 1\, 33–42 (2017).\n[8] Wang\, S-F\; Li\, X.\; Agapov\, R. L.\; Wesdemiot is\, C.\; Foster\, M. D.\, ACS Macro Letters\, 2012\, 1\, 1024-1027. (2016 ).\n[9] Wu \, D. T.\; Fredrickson\, G. H.\, Macromolecules 1996\, 29\, 791 9-7930.\n\nhttps://events.chpc.ac.za/event/33/contributions/712/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/712/ END:VEVENT BEGIN:VEVENT SUMMARY:An Evaluation of Galaxy and Ruffus Workflows System for DNA-seq An alysis DTSTART;VALUE=DATE-TIME:20181205T123000Z DTEND;VALUE=DATE-TIME:20181205T125000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-719@events.chpc.ac.za DESCRIPTION:Speakers: Olabode Ajayi (South Africa National Bioinformatics Institute)\nFunctional genomics determines the biological functions of gen es on a global scale by using large volumes of data obtained through techn iques including next-generation sequencing (NGS). The application of NGS i n biomedical research is gaining in momentum\, and with its adoption becom ing more widespread\, there is an increasing need for access to customizab le computational workflows that can simplify\, and offer access to\, compu ter-intensive analyses of genomic data. In this study\, the Galaxy and Ruf fus frameworks were designed and implemented with a view to addressing the challenges faced in biomedical research. Galaxy\, a graphical web-based f ramework\, allows researchers to build a graphical NGS data analysis pipel ine for accessible\, reproducible\, and collaborative data-sharing. Ruffus \, a UNIX command-line framework used by bioinformaticians as Python libra ry to write scripts in an object-oriented style\, allows for building a wo rkflow in terms of task dependencies and execution logic. In this study\, a dual data analysis technique was explored which focuses on a comparative evaluation of Galaxy and Ruffus frameworks that are used in composing ana lysis pipelines. To this end\, we developed an analysis pipeline in Galaxy \, and Ruffus\, for the analysis of Mycobacterium tuberculosis sequence da ta. Furthermore\, this study aimed to compare the Galaxy framework to Ruff us with preliminary analysis revealing that the analysis pipeline in Galax y displayed a higher percentage of load and store instructions. In compari son\, pipelines in Ruffus tended to be CPU bound and memory intensive. The CPU usage\, memory utilization\, and runtime execution are graphically re presented in this study. Our evaluation suggests that workflow frameworks have distinctly different features from an ease of use\, flexibility\, and portability\, to architectural designs. Therefore\, in this CHPC Conferen ce\, I will discuss how we composed the NGS bioinformatics data analysis p ipeline in the Galaxy and Ruffus workflow framework and the use of each fr amework in the analysis of Mycobacterium tuberculosis sequence data.\n\nht tps://events.chpc.ac.za/event/33/contributions/719/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/719/ END:VEVENT BEGIN:VEVENT SUMMARY:CHPC PI's and Users BoF DTSTART;VALUE=DATE-TIME:20181205T133000Z DTEND;VALUE=DATE-TIME:20181205T143000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-789@events.chpc.ac.za DESCRIPTION:Speakers: Werner Janse Van Rensburg (CHPC)\nAll CHPC Principal Investigators (PI's) and Users (and prospective new PI's and users) are e ncouraged to attend this Birds-of-a-Feather (BoF) session. \n\nWerner Jans e van Rensburg will give an overview of usage patterns\, research programm e distributions and overall usage statistics of the CHPC Lengau cluster ov er the past 12 months.\n\nIn addition\, discussions will focus on aspects such as:\nRegistration procedures\, user accounts and policies\nStorage (L ustre and Home)\nJob Queues\nAllocation Evaluation and CPU Hour Allocation s\nNew GPU Cluster\nQueries and Helpdesk\nEtc.\n\nThis will be a good oppo rtunity for attendees to ask questions and meet with CHPC staff members in an informal setting.\n\nhttps://events.chpc.ac.za/event/33/contributions/ 789/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/789/ END:VEVENT BEGIN:VEVENT SUMMARY:HPC in the De Beers Marine R&D Context DTSTART;VALUE=DATE-TIME:20181204T115000Z DTEND;VALUE=DATE-TIME:20181204T121000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-792@events.chpc.ac.za DESCRIPTION:Speakers: Imraan Parker (De Beers Marine)\nThe unique nature o f the underwater mining environment has resulted in R&D playing an import role within De Beers Marine. Physical and numerical simulation methods fo rm an integral part of the R&D concept development pipeline. Computationa l Fluid Dynamics has been increasingly used for concept exploration\, risk mitigation as well as to enhance understanding of physical simulations. HPC has been an enabler for using Computational Fluid Dynamics to solve mu lti-phase problems that were previously deemed to be too large and/or comp lex. Most recently\, this capability has been used in the feasibility sta ge of a new marine mining vessel.\n\nhttps://events.chpc.ac.za/event/33/co ntributions/792/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/792/ END:VEVENT BEGIN:VEVENT SUMMARY:Understanding Risk in Shared CyberInfrastructure Systems Seminar DTSTART;VALUE=DATE-TIME:20181202T070000Z DTEND;VALUE=DATE-TIME:20181202T083000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-862@events.chpc.ac.za DESCRIPTION:Speakers: Meshack Ndala (CHPC)\nCHPC Cyber Security Symposium (CCSS) – 1 full day\nTopic: Understanding Risk in Shared CyberEcosystems workshop\nAs Technology continues to evolve so are the opportunities and challenges it provides. As a Society that relies largely on technology to bring us benefits\, it also exposes its users to threats by the very natur e of the opportunities it presents\, thus becoming a focal point for Cyber crime\, industrial espionage\, and Cyberattacks. Protecting against these threats is of paramount priority.\nCyber Security domain is inherently dyn amic\, not only does system configuration changes frequently with new rele ases and patches\, but also new attacks and vulnerabilities are regularly discovered. The core threat in Cyber Security is human\, hence intelligent in nature. The attacker adapts to the situation\, target environment\, an d countermeasures.\nAttacks actions are driven by attacker’s exploratory nature\, thought process\, motivation\, strategy\, and preferences.\nThe goal of this workshop is to address some of the challenges faced by Networ k and Security Administrators in their institutions.\nThe workshop will ad dress challenges such as:\n• Iot Threats\n• Blockchain Revolution\n• Ransomware Evolution\n• Future of Cybersecurity\n• New hacking Method ologies\n• Phishing\n• Distributed Denial of Service (DDoS)\n• Malwa re\n• Internal Privilege Misuse\n• Threats actors\n• How to protect your environment\n\nThe following are our invited speakers:\n• Prof Elma rie Bierman: Directory of SA Cyber Security Institute\n• Dr Noelle Cow ling : Stellenbosch University\n• Dr Jabu Mtswene : CSIR\n• Dr Noluxol o Gcaza: CSIR\n• Mr Justine Westcott\n• Mr Sikhumbuzo Mthombeni: Demen sion Data\n• Mr Keti Cedric : Demension Data\n• Mr Richard Hlalele: Un iversity of Johannesburg\, Senior Manager ICT Strategy and Governance\nThe following are workshop Coordinators:\nMr Bigani Sehurutshi: University of Botswana\nMrs Lee-Anne Benjamin: Manager \,Corporate IT Compliance NRF\n\ nhttps://events.chpc.ac.za/event/33/contributions/862/ LOCATION: Meeting Room 9 URL:https://events.chpc.ac.za/event/33/contributions/862/ END:VEVENT BEGIN:VEVENT SUMMARY:On the co-operation between SAWS and CHPC for forecast continuity and Unified Model research in South Africa DTSTART;VALUE=DATE-TIME:20181204T121000Z DTEND;VALUE=DATE-TIME:20181204T123000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-715@events.chpc.ac.za DESCRIPTION:Speakers: Stephanie Landman (South African Weather Service)\nW eather forecasting using Numerical Weather Prediction (NWP) models is a we ll-established science and based on the fundamental equations of fluid dyn amics. NWP is therefore an important tool for predicting weather and makin g climate projections. The grid spacing used in models is largely dependen t on the available computational resources and processing speed required f or model output availability for timeous decision making. The direct numer ical simulations that are able to capture all processes explicitly are sti ll too far from our reach for practical purposes such as NWP\, seasonal fo recasting and climate change studies.\nThe available computational resourc es have been improving over time\, which have made possible a decrease in the grid spacing used in models. A number of meteorological organisation a re now using grid spacing of 4 km or less for NWP purposes\, especially ov er limited areas. Models used with such high resolution are called Cloud R esolving Models (CRMs) or convective scale models\, and in these models cl ouds are thought to be resolved explicitly. Similar to other meteorologica l organisations SAWS runs their NWP models with a grid spacing of 4.4 km o ver southern Africa and 1.5 km over South Africa. Both these configuration s are made four times a day\, but with different lead times. These simulat ions are made on a CRAY XC30 machine which was procured in 2014. \nThe SAW S CRAY XC30 has 168 nodes with Ivybridge processors. Each model simulation (4 km and 1.5 km) utilizes 1728 cores to complete. The CRAY is also used for operational seasonal forecasting with a coupled atmosphere-ocean mode l and there are plans for more models on air quality\, ocean wave forecast ing and applications research that will be undertaken on the CRAY. With al l the operational applications on the CRAY\, there is limited processing t ime for research activities such as sub-kilometre grid spacing simulations or ensemble forecasting. Big global operational centres such as the Europ ean Centre for Medium Range Weather Forecasts (ECMWF) maintain two HPC res ources\, with the second one available as a backup to their operational sy stem. Due to budget constraints and the high costs of HPC resources\, SAWS does not have such a failover system in-house\, resulting in no or limite d support for operational NWP at SAWS to operational forecasters if the op erational system fails. \nIn order to deal with HPC shortcomings at SAWS a cooperative partnership agreement was entered into with the Centre for Hi gh Performance Computing (CHPC) to facilitate mutual HPC activities\, and training programs to meet the missions of both SAWS and the CHPC. The CHPC is one of the three national cyber-infrastructure pillars that are suppor ted by the South African Department of Science and Technology (DST). The C HPC currently hosts a Dell cluster\, with a total of 1358 nodes with Intel v3 Haswell processes\, and a 4PB Lustre storage. The main objective of th e CHPC is to enable South Africa to become globally competitive and to acc elerate Africa’s socio-economic upliftment through the effective applica tion of high-end Cyberinfrastructure. The CHPC seeks to become an accompli shed and preferred partner for High Performance Computing solutions.\nThe agreed areas of cooperation between SAWS and the CHPC include 1) the use o f the CHPC cluster as a fail-over system for SAWS operations\, 2) the use of the CHPC HPC system for benchmarking purposes to determine future opera tional needs of SAWS\, 3) Use of the CHPC HPC system for research purposes \, and 4) Training on the use of the CHPC cluster. SAWS has been using UK Met Office Unified Model (UM) as its main Numerical Weather Prediction mo del since 2006. As a result of the agreement between SAWS and the CHPC\, t he UM has now been installed on the CHPC cluster. The CHPC cluster was use d successfully for business continuity purposes when SAWS moved offices\, as well as\, as a failover system when there were power issues at the SAWS premises. Before now the UM had only been available at SAWS and to SAWS e mployees due to license restrictions\, resulting in scientists only gettin g exposure to the UM once employed by SAWS. The installation of the UM on the CHPC infrastructure will allow SAWS and other academic and research in stitutions across South Africa access to the UM for research purposes.\n\n https://events.chpc.ac.za/event/33/contributions/715/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/715/ END:VEVENT BEGIN:VEVENT SUMMARY:KEYNOTE 1: New Era in HPC DTSTART;VALUE=DATE-TIME:20181203T074500Z DTEND;VALUE=DATE-TIME:20181203T083000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-836@events.chpc.ac.za DESCRIPTION:Speakers: Trish Damkroger (intel)\nIn this keynote presentatio n\, Trish will discuss the changing landscape of high performance computin g\, key trends\, and the convergence of HPC-AI-HPDA that is transforming o ur industry and will fuel HPC to fulfill its potential as a scientific too l for insight and innovation. Trish will highlight not only key forces dr iving this shift but discuss how this transformation requires a fundamenta l paradigm shift and is opening up unprecedented opportunities for HPC.\n\ nhttps://events.chpc.ac.za/event/33/contributions/836/ LOCATION: Hall B+C URL:https://events.chpc.ac.za/event/33/contributions/836/ END:VEVENT BEGIN:VEVENT SUMMARY:Advancing Computational Science in South African Academia through Social and Cyber Networks DTSTART;VALUE=DATE-TIME:20181204T090000Z DTEND;VALUE=DATE-TIME:20181204T092000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-837@events.chpc.ac.za DESCRIPTION:Speakers: Kevin J. Naidoo (University of Cape Town)\nIn his 20 02 State of the Nation Address\, President Thabo Mbeki identified Informat ion and Communication Technology (ICT) as “a critical and pervasive elem ent in economic development” and recommended the establishment of an “ ICT University”. The establishment of the CHPC in 2005 signalled the fir st pillar in the national research cyberinfrastructure1 and remains a majo r investment that anchors the development and growth of the computational and data sciences stretching across disciplines from science\, through to social science. The recent feverish announcements from pundits through to politicians hailing the onset of the 4th industrial revolution posits a re search landscape where computational science is a central kernel of South Africa’s future economic plan.\n\nLarge parts of the chemical\, biologic al and physical science have had an uptick in production and activity in m odelling\, simulation and data analytics as measured by number of papers p roduced. However\, the challenge of innovative home grown methods to addre ss the national needs of medical science\, the bio-economy and the green r evolution remain unmet. \nI will present a view of the future of computing and data analytics in the biological\, chemical and life sciences. More i mportantly I will discuss a hopeful future scenario where academics across all South African institutions cooperate via the CHPC to advance our inte rnational research profile.\n\nhttps://events.chpc.ac.za/event/33/contribu tions/837/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/837/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to CUDA and Parallel Programming DTSTART;VALUE=DATE-TIME:20181202T070000Z DTEND;VALUE=DATE-TIME:20181202T083000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-861@events.chpc.ac.za DESCRIPTION:Speakers: Rob Farber (TechEnablement)\nDescription:\nThe goal of this workshop is to introduce students to CUDA and provide them with an understanding of parallel programming. CUDA is more than a few new keywor ds. One must understand SIMD and the pitfalls of serialization. \n\nStuden ts will leave with basic CUDA skills and some OpenACC knowledge plus usefu l machine learning and big data tools as well. My “from Hello World to e xascale machine learning in one slide” will also be covered as data para llel training fits on GPUs nicely.\n\nTarget Audience:\nAnyone with C/C++ programming skills in the Unix environment who wishes to learn about paral lel programming and CUDA. The material will be 60% beginner\, 30% interme diate\, and 10% advanced. \n\nPrerequisites:\nC/C++ along with an ability to edit and compile programs in a Unix environment\n\nSpecial requirements :\nUsers will have access to a CHPC system with GPUs. \n\nAttendees should bring their own laptops. The ability to view pdf or PowerPoint files is r equired.\n\nOutline of full syllabus:\n08:00 Registration\n09:00 Introduct ion and morning talk (30 minutes)\n Login details and extracting th e workshop material (15 minutes)\n Section 01: Parallel intro and a first CUDA program)\n Section 02: Profiling on a GPU\n\n\n10:30 Mo rning Refreshment Break\n11:00 Section 03: More CUDA and the Thrust Interf ace\n Section 04: “From Hello World to TF/s machine learning”\n 12:30 Lunch\n13:30 Afternoon talk \n Section 05: Controlling parall el resources\n Section 06: C++ objects and transparent host/GPU dat a movement \n15:00 Afternoon Refreshment Break\n15:30 Section 07: Task lev el parallelism on a GPU\n Section 08: Managing big data\, CUDA as a scripting language via dynamic load/link\n17:00 End of Day\n\n\nAdditiona l Comments:\nStudents can work at their own pace. \nIntroductory students will learn the basics of CUDA and the profiler as well as how to think in parallel and understand the impact of parallel hardware on performance.\nI ntermediate/advanced students will hone their thinking about parallel prog ramming and the limitations and advantages of GPU hardware. Extra credit e xercises will challenge them.\nAll students will learn how to use machine learning and the ability to explore this hot field and leave with a tool t hat allows them to train and predict using their own data sets and neural network architectures. Further\, they learn how to work with and collabora te using big data.\n\nhttps://events.chpc.ac.za/event/33/contributions/861 / LOCATION: Meeting Room 10 URL:https://events.chpc.ac.za/event/33/contributions/861/ END:VEVENT BEGIN:VEVENT SUMMARY:High Performance Computing for Nature Inspired Metaheuristics DTSTART;VALUE=DATE-TIME:20181205T090000Z DTEND;VALUE=DATE-TIME:20181205T092000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-829@events.chpc.ac.za DESCRIPTION:Speakers: Nelishia Pillay (University of Pretoria)\nGenetic al gorithms and genetic progamming are metaheuristics taking inspi-\nration f rom Darwin’s theory of evolution to solve optimization problems. Ge-\nne tic algorithms explore a solution space to find solutions to problems whil e\ngenetic programming works in a program space to identify a program whic h\nwhen executed will find an optimal solution to the problem. Both these\ napproaches have high runtimes when applied to complex problems and are\nu sually implemented using distributed computing in these instances. More\nr ecently\, genetic algorithms and genetic programming have been employed\nb y hyper-heuristics and have been used for the automated design of machine\ nlearning and search techniques. Hyper-heuristics explore the heuristic sp ace\nrather than the solution space and hence search in the heuristic spac e is\nmapped to the solution space. Automated design of machine learning a nd\nsearch techniques is an emerging field aimed at removing the load of d e-\nsign\, which is a time consuming task\, from the researcher. This will also\nenable non-experts to use machine learning toolkits that automate t he de-\nsign and hence allow the researcher to focus on the problem being solved.\nThe use of genetic algorithms and genetic programming in hyper-he uristics\nand for automated design require additional processing time. The talk will\nfirstly look at the high performance computing architectures i mplemented\nby our research group to reduce the runtimes of genetic progra mming and\ngenetic algorithms\, particularly for hyper-heuristics and auto mated design.\nAn overview of some of the real-world problems that this ha s enabled us\nto solve will then be presented. These include inducing huma n competitive\nheuristics for solving timetabling problems\, network intru sion detection in\nthe area of computer security\, the automated design of techniques for finan-\ncial forecasting\, computer security\, packing and logistics problems and the\nintroduction of multi-space search algorithms that perform search over more\nthan once space with applications in packi ng and forecasting.\n\nhttps://events.chpc.ac.za/event/33/contributions/82 9/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/829/ END:VEVENT BEGIN:VEVENT SUMMARY:High performance computing in pyrometallurgy DTSTART;VALUE=DATE-TIME:20181204T094000Z DTEND;VALUE=DATE-TIME:20181204T100000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-838@events.chpc.ac.za DESCRIPTION:Speakers: Driaan Bezuidenhout (Mintek)\nPyrometallurgy refers to high temperature (>1600°C) extraction of valuable metals from mineral ore deposits. Most pyrometallurgical processes occur in furnaces of variou s types in which many complex phenomena are occurring simultaneously. Almo st none of these phenomena can be observed directly due to the extreme con ditions inside furnace vessels. Computational modelling is invaluable in u nderstanding the processes in and around furnaces and is often used for de sign and optimization. Problems vary from simple CFD analyses to coupled m ultiphysics applications such as magnetohydrodynamic models of plasma arcs . \n\nHigh performance computing is a valuable tool for developing increas ed understanding and better engineering for these challenging problems. A few case studies are given: DC furnace arc modelling\, multiphase flow thr ough furnace tap-holes\, combustion in a rotary converter and settling of metal and slag.\n\nhttps://events.chpc.ac.za/event/33/contributions/838/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/838/ END:VEVENT BEGIN:VEVENT SUMMARY:High Throughput Computing in bioinformatics: workflows\, container s and emerging paradigms DTSTART;VALUE=DATE-TIME:20181204T090000Z DTEND;VALUE=DATE-TIME:20181204T093000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-896@events.chpc.ac.za DESCRIPTION:Speakers: Peter van Heusden (South Africa National Bioinforma tics Institute)\nNext Generation Sequencing has brought genomic analysis w ithin the range of a great number of laboratories\, while increasing the d emand for bioinformatic analysis. These typically comprise workflows compo sed out of chains of analyses with data flowing between workflow steps. Su ch analysis is amenable to High Throughput Computing\, a form of high perf ormance computing characterised by a focus on overall analysis throughput rather than optimisation of a single application. In recent years workflow languages and container technologies have become a key part in composing efficient\, reproducible and re-usable bionformatic workflows. These techn ologies\, however\, pose a challenge for High Performance Computing provid ers as they require different characteristics from an execution environmen t to that provided by traditional HPC clusters. These challenges will be d iscussed and some approaches to solving them will be discussed.\n\nhttps:/ /events.chpc.ac.za/event/33/contributions/896/ LOCATION: Meeting Room 8+9 URL:https://events.chpc.ac.za/event/33/contributions/896/ END:VEVENT BEGIN:VEVENT SUMMARY:A quantum future of computation DTSTART;VALUE=DATE-TIME:20181203T094000Z DTEND;VALUE=DATE-TIME:20181203T100000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-875@events.chpc.ac.za DESCRIPTION:Speakers: Matthias Troyer (Microsoft)\nStill in early developm ent\, quantum computing is already overturning our contemporary notions of computational methods and devices. Using new concepts of computing based in quantum physics\, quantum computers will be able to solve certain probl ems that are completely intractable on any imaginable classical computer\, such as accurate simulations of molecules and materials\, or breaking pub lic key encryption. I will describe the hardware and software architecture of quantum computers and Microsoft’s full stack approach\, from novel t opological quantum bits to real-world quantum applications. I will attempt to dispel myths and hype surrounding the field and present a realistic as sessment of the potential of these devices\, and the specific application areas on which they are expected to have a large impact.\n\nhttps://events .chpc.ac.za/event/33/contributions/875/ LOCATION: Hall B URL:https://events.chpc.ac.za/event/33/contributions/875/ END:VEVENT BEGIN:VEVENT SUMMARY:Quantum Sensing a New View of the Universe as Revolutionary as the First Telescope DTSTART;VALUE=DATE-TIME:20181203T090000Z DTEND;VALUE=DATE-TIME:20181203T092000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-895@events.chpc.ac.za DESCRIPTION:Speakers: Ian Shipsey (University of Oxford)\nThe use of quant um sensors to investigate gravity\, dark matter\, and the early universe i s in the vanguard of a 2nd Quantum revolution\; as significant as the firs t deployment of telescopes it will transform the way we understand the wor ld. The technological innovation that is the engine of society’s develop ment has been initiated and fuelled by fundamental scientific research\; from Faraday’s work on electricity to the development of the world wide web. In the 20th century the application of our best understanding of the sub atomic world – quantum mechanics- generated new knowledge about th e world and new technologies that improve the human condition. Examples in clude semiconductor microelectronics\, photonics\, the global positioning system (GPS)\, and magnetic resonance imaging (MRI). These technologies un derpin significant parts of the economies of developed nations\, we refer to this as the “1st Quantum Revolution”. Future scientific and technol ogical discoveries from the application of quantum mechanics may be even m ore impactful – a 2nd Quantum Revolution. The areas that will be potent ially transformed include biology\, the defence sector and fundamental sci ence. It is the latter that is the focus of this talk.\n\nhttps://events.c hpc.ac.za/event/33/contributions/895/ LOCATION: Hall B URL:https://events.chpc.ac.za/event/33/contributions/895/ END:VEVENT BEGIN:VEVENT SUMMARY:Optimized Artificial Intelligence Solutions by Intel DTSTART;VALUE=DATE-TIME:20181206T133000Z DTEND;VALUE=DATE-TIME:20181206T150000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-873@events.chpc.ac.za DESCRIPTION:Speakers: Michael Steyer ()\, Edmund Preiss (Intel)\nDescripti on:\nJoin us for one day of hands-on sessions on Artificial Intelligence\, and Machine & Deep Learning. Experience a unique opportunity to test out the latest performance optimized frameworks and tools\, advanced coding kn owledge and best practices to get started implementing AI guided by expert s from Intel®.\n\nTarget Audience:\nData Scientist\, application develope rs and HPC benchmarkers targeting the deep learning and machine learning d omain.\n\nPrerequisites:\nBeginning to intermediate level of domain AI kno wledge.\nBasic skills of programming \, ideally some Python knowldege\n\n Type of tutorial: Mix of lectures and hands-on tutorials\n\nSpecial Requir ements:\nAttendees should bring their laptop with an SSH- & VNC client\nAt tendees will get for hands on-labs also access to the CHPC cluster \n\nOut line of full syllabus:\n08:00 Registration\n09:00 Introduction\n• Introd uction round & Agenda \n• Introduction Intel Software Developer Tools \n• Introduction to Machine Learnin g / Deep Learning \n10:30 Morning Refr eshment Break\n11:00 \nClassic Machine Learning Tools\n• Intel performan ce Libraries - MKL & DAAL \n • Intel Distribution for Python (IDP) Introduction \n• IDP Hands on labs \no NumPy & MKL \no K-Means Clustering & DAAL \no SVM & DAAL \n12:30 Lunch\n13:30 \nDeep Learn ing (DL) Tools \n• Intel performance Libraries for DL – MKL-DNN & MLS L \n• Intel optimized Frameworks / Tenso rFlow \no TensorFlow Image Clas sification Hands-on Lab \no In troduction simple CNN \no Monitored Training Session \n15:00 Afternoon Ref reshment Break\n15:30 \nDeep Learning Tools (cont’d) \n• Intel optimi zed Frameworks / TensorFlow (cnt’d) \no Horovod – distributed classification \no Importing external Im ages \no Custom batches \n• Benchmarking distributed TensorFlow (BKMs) \n• Deep Learning Scaling – large s cale results (BigDL/Spark) \n• Wrap-Up & Q&A \n17:00 End of Day\n\nhttps:/ /events.chpc.ac.za/event/33/contributions/873/ LOCATION: Meeting Room 8 URL:https://events.chpc.ac.za/event/33/contributions/873/ END:VEVENT BEGIN:VEVENT SUMMARY:BOF: HPC Ecosystems DTSTART;VALUE=DATE-TIME:20181205T133000Z DTEND;VALUE=DATE-TIME:20181205T143000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-874@events.chpc.ac.za DESCRIPTION:Speakers: Bryan Johnston (CHPC)\nThe HPC Ecosystems Project is continuing to support HPC deployment initiatives throughout Africa\, with two new partner sites receiving their first HPC systems in 2018. Addition ally\, the Ecosystems Project continues to deliver educational content and training to address workforce preparation for both new users and seasoned professionals.\n\nAlthough the CHPC is responsible for the leadership and oversight of the Project\, the success of the Project greatly depends on the broader HPC Ecosystems community’s engagements and collaboration.\n\ nThis CHPC-coordinated BoF will engage all stakeholders in helping to dete rmine the roadmap for 2019 (and beyond). Particular focus will be given to discussing the following points:\n\n\n* feedback from partner sites\n* ch allenges faced by partner sites\n* HPC Ecosystems software stack \n* deter mining the training needs of the HPC Ecosystems community\, \n* possible f uture opportunities for collaboration\, research and hardware acquisition\ n\nhttps://events.chpc.ac.za/event/33/contributions/874/ LOCATION: Meeting Room 7 URL:https://events.chpc.ac.za/event/33/contributions/874/ END:VEVENT BEGIN:VEVENT SUMMARY:AI is impacting HPC everywhere DTSTART;VALUE=DATE-TIME:20181203T113000Z DTEND;VALUE=DATE-TIME:20181203T115000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-822@events.chpc.ac.za DESCRIPTION:Speakers: Rob Farber ()\nThe convergence of AI and HPC has cre ated a fertile venue that is ripe for imaginative researchers - versed in AI technology - to make a big impact in a variety of scientific fields. Fr om new hardware to new computational approaches\, the true impact of deep- and machine learning on HPC is\, in a word\, “everywhere”. \nJust as technology changes in the personal computer market brought about a revolut ion in the design and implementation of the systems and algorithms used in high performance computing (HPC)\, so are recent technology changes in ma chine learning bringing about an AI revolution in the HPC community. Expec t new HPC analytic techniques including the use of GANs (Generative Advers arial Networks) in physics based modeling and simulation as well as reduce d precision math libraries such as NLAFET and HiCMA to revolutionize many fields of research. Other benefits of the convergence of AI and HPC includ e the physical instantiation of data flow architectures in FPGAs and ASICs plus the development of powerful data analytic services.\n\nhttps://event s.chpc.ac.za/event/33/contributions/822/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/822/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational modelling and capabilities in metal and alloys DTSTART;VALUE=DATE-TIME:20181203T115000Z DTEND;VALUE=DATE-TIME:20181203T121000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-793@events.chpc.ac.za DESCRIPTION:Speakers: Hasani Chauke (Univesity of Limpopo)\nThe research i s based on the development and design of metal alloys with special applica tions in various industries\, from automotive and medical to aeronautical. These alloys have unique properties and behaviour under pressure and temp erature conditions. Focus will be on the precious metal\, iron-aluminium\, titanium and titanium-based systems for shape memory alloys\, as well as zirconium-niobium systems. A density functional theory based semi-empirica l approach is employed to explore material properties at zero temperature\ ; while molecular dynamics techniques are also carried out to predict the stability\, strength\, behaviour and the extent of transformation temperat ure. The overview on computational codes and usage of HPC will be discusse d. Furthermore\, the advances on machine learning approaches towards titan ium cluster development and growth will also be indicated.\n\nhttps://even ts.chpc.ac.za/event/33/contributions/793/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/793/ END:VEVENT BEGIN:VEVENT SUMMARY:Integrating Containers with Storage DTSTART;VALUE=DATE-TIME:20181203T113000Z DTEND;VALUE=DATE-TIME:20181203T120000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-794@events.chpc.ac.za DESCRIPTION:Speakers: Jay Lofstead (Sandia National Laboratories)\nContain er technology offers a convenient way to package an application and suppor ting libraries such that moving them from platform to platform can be done without having to rebuild. Additional features\, such as stateless execut ion enable restarting a containerized application with minimal penalty els ewhere. Combining better support for storage into the container ecosystem breaks this stateless model\, but offers advantages. This talk will examin e the advantages and penalties of this approach and offer solutions to eas e adopting the idea.\n\nhttps://events.chpc.ac.za/event/33/contributions/7 94/ LOCATION: Hall B URL:https://events.chpc.ac.za/event/33/contributions/794/ END:VEVENT BEGIN:VEVENT SUMMARY:The CHPC’s role in key projects at Aerotherm DTSTART;VALUE=DATE-TIME:20181205T092000Z DTEND;VALUE=DATE-TIME:20181205T094000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-795@events.chpc.ac.za DESCRIPTION:Speakers: Wian Van Der Merwe (Aerotherm)\nComputational Fluid Dynamics (CFD) is a mathematical tool used for commercial and research pro blems\, to predict flow- and thermal characteristics in a wide variety of applications. Aerotherm has been using CFD to improve and design flow-rela ted systems in the South African industry since 1995. The ever increasing demand for higher performance drives the need for more comprehensive CFD m odels. Such high fidelity models\, however\, require sufficient resources to be completed in reasonable timeframes. This talk will discuss how the C HPC plays a crucial role in the success of key CFD projects at Aerotherm.\ n\nhttps://events.chpc.ac.za/event/33/contributions/795/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/795/ END:VEVENT BEGIN:VEVENT SUMMARY:Optimized Artificial Intelligence Solutions by Intel DTSTART;VALUE=DATE-TIME:20181206T113000Z DTEND;VALUE=DATE-TIME:20181206T130000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-872@events.chpc.ac.za DESCRIPTION:Speakers: Michael Steyer ()\, Edmund Preiss (Intel)\nDescripti on:\nJoin us for one day of hands-on sessions on Artificial Intelligence\, and Machine & Deep Learning. Experience a unique opportunity to test out the latest performance optimized frameworks and tools\, advanced coding kn owledge and best practices to get started implementing AI guided by expert s from Intel®.\n\nTarget Audience:\nData Scientist\, application develope rs and HPC benchmarkers targeting the deep learning and machine learning d omain.\n\nPrerequisites:\nBeginning to intermediate level of domain AI kno wledge.\nBasic skills of programming \, ideally some Python knowldege\n\n Type of tutorial: Mix of lectures and hands-on tutorials\n\nSpecial Requir ements:\nAttendees should bring their laptop with an SSH- & VNC client\nAt tendees will get for hands on-labs also access to the CHPC cluster \n\nOut line of full syllabus:\n08:00 Registration\n09:00 Introduction\n• Introd uction round & Agenda \n• Introduction Intel Software Developer Tools \n• Introduction to Machine Learnin g / Deep Learning \n10:30 Morning Refr eshment Break\n11:00 \nClassic Machine Learning Tools\n• Intel performan ce Libraries - MKL & DAAL \n • Intel Distribution for Python (IDP) Introduction \n• IDP Hands on labs \no NumPy & MKL \no K-Means Clustering & DAAL \no SVM & DAAL \n12:30 Lunch\n13:30 \nDeep Learn ing (DL) Tools \n• Intel performance Libraries for DL – MKL-DNN & MLS L \n• Intel optimized Frameworks / Tenso rFlow \no TensorFlow Image Clas sification Hands-on Lab \no In troduction simple CNN \no Monitored Training Session \n15:00 Afternoon Ref reshment Break\n15:30 \nDeep Learning Tools (cont’d) \n• Intel optimi zed Frameworks / TensorFlow (cnt’d) \no Horovod – distributed classification \no Importing external Im ages \no Custom batches \n• Benchmarking distributed TensorFlow (BKMs) \n• Deep Learning Scaling – large s cale results (BigDL/Spark) \n• Wrap-Up & Q&A \n17:00 End of Day\n\nhttps:/ /events.chpc.ac.za/event/33/contributions/872/ LOCATION: Meeting Room 8 URL:https://events.chpc.ac.za/event/33/contributions/872/ END:VEVENT BEGIN:VEVENT SUMMARY:HPC platform efficiency and challenges for a system builder DTSTART;VALUE=DATE-TIME:20181205T123000Z DTEND;VALUE=DATE-TIME:20181205T130000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-791@events.chpc.ac.za DESCRIPTION:Speakers: Martin Hilgeman (Technical Director HPC)\nWith all t he advances in massively parallel and multi-core computing with CPUs and a ccelerators\, it is often overlooked whether the computational work is bei ng done in an efficient manner. This efficiency is largely being determine d at the application level and therefore puts the responsibility of sustai ning a certain performance trajectory into the hands of the user. It is ob served that the adoption rate of new hardware capabilities is decreasing a nd lead to a feeling of diminishing returns. At the same time\, the well-k nown laws of parallel performance are limiting the perspective of a system builder. The presentation tries gives an overview of these challenges and what can be done to overcome them. The overview will be amended by a few case studies and optimization strategies on real applications.\n\nhttps:// events.chpc.ac.za/event/33/contributions/791/ LOCATION: Meeting Room 7 URL:https://events.chpc.ac.za/event/33/contributions/791/ END:VEVENT BEGIN:VEVENT SUMMARY:INDUSTRY CROSSFIRE: Market Update: HPC\, Hyperscale\, and AI DTSTART;VALUE=DATE-TIME:20181203T133000Z DTEND;VALUE=DATE-TIME:20181203T143000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-797@events.chpc.ac.za DESCRIPTION:Speakers: Addison Snell (Intersect360 Research)\nFresh from th e SC18 conference\, Addison Snell of Intersect360 Research will give a mar ket overview presentation of developments and predictions for HPC\, Hypers cale\, and AI. Views will include the latest market forecasts\, and a rund own of the big news from SC18 — what was hot\, and what was not. \n\n Following the presentation\, Addison will transition directly into the fa st-paced CHPC Vendor Showdown panel\, an audience favorite\, in which repr esentatives of participating vendor companies will answer pointed question s\, head-to-head\, and be awarded points based on who answered the questio n the best for the audience.\n\nhttps://events.chpc.ac.za/event/33/contrib utions/797/ LOCATION: Hall B+C URL:https://events.chpc.ac.za/event/33/contributions/797/ END:VEVENT BEGIN:VEVENT SUMMARY:TensorFlow as HPC Infrastructure? DTSTART;VALUE=DATE-TIME:20181204T113000Z DTEND;VALUE=DATE-TIME:20181204T120000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-798@events.chpc.ac.za DESCRIPTION:Speakers: Peter Braam ()\nTensorFlow is the system driving Goo gle's ML efforts. Many components make up this system\, including a sophi sticated user-friendly development environment\, highly optimized language features and compilers\, ultra-high performance custom chips called Tenso r Processing Units (TPU)\, and scalable deployment on the world's devices. TPU pods may well eclipse traditional performance boundaries of the top HPC systems at a much lower cost. We will review TensorFlow's SW and HW environment\, which begs the question of how usable it might be for HPC.\ n\nhttps://events.chpc.ac.za/event/33/contributions/798/ LOCATION: Meeting Room 8+9 URL:https://events.chpc.ac.za/event/33/contributions/798/ END:VEVENT BEGIN:VEVENT SUMMARY:Developing Africa's first Earth System Model on the CHPC Lengau cl uster DTSTART;VALUE=DATE-TIME:20181203T092000Z DTEND;VALUE=DATE-TIME:20181203T094000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-843@events.chpc.ac.za DESCRIPTION:Speakers: Nicolette Chang (CSIR)\nClimate change is the most s erious collective environmental challenge ever faced by modern humankind. It is a problem with global reach\, but the research effort to address it is disproportionately concentrated in the northern hemisphere and in devel oped countries. Southern hemispheric and African climate issues differ fro m those that drive the research and modelling effort in the north. In part icular\, oceans dominate the southern hemisphere and the land is largely o ccupied by arid systems and tropical forests. African terrestrial ecosyste ms and processes\, Southern Ocean physics\, biochemistry and circulation dynamics as well as Southern Hemisphere atmospheric processes are under-st udied and poorly represented in global models - despite being globally imp ortant contributors to earth system processes. In particular\, of the abou t thirty currently existing coupled ocean-atmosphere global circulation mo dels (CGCMs) and Earth System Models (ESMs) suitable for the projection of future climate change\, only one model had its genesis in the Southern He misphere. Towards addressing this disproportionality\, and in alignment wi th the South African Department of Science & Technology's Global Change Gr and Challenge\, the CSIR and partners are invested in building a Variable- resolution Earth System Model (VrESM)\, with the aim of contributing proje ctions of future climate change to the Coupled Model Intercomparison Proje ct Phase 6 (CMIP6) and Assessment Report 6 (AR6) of the IPCC. VrESM is the first African-based Earth System Model (ESM) and has as component models the variable-cubic atmospheric model (VCAM) of the CSIRO\, a dynamic land- surface model (CABLE)\, the variable cubic ocean model (VCOM) and an ocean biogeochemistry model (PISCES). \nVrESM is formulated on the non-orthogon al\, quasi-uniform cubic grid of Purser and Rancic (1998). Its atmospheric component VCAM has been developed by the Commonwealth Scientific and Indu strial Research Organisation (CSIRO). VCAM is a σ-coordinate model that u ses a semi-implicit semi-Lagrangian approach to solve the hydrostatic prim itive equations. VCAM has inherited the comprehensive physical parameteris ations of the Conformal-Cubic Atmospheric Model (CCAM) (McGregor\, 2005b). The dynamic land-surface model used is the CSIRO Atmosphere Biosphere Lan d Exchange model (CABLE). CABLE includes a dynamic river routing scheme ad apted from the CSIRO Mk3.5 CGCM. The VrESM ocean component VCOM has been d eveloped by the CSIR. This model solves the Boussinesq hydrostatic equatio ns in a z-coordinate in momentum-conservation form\, using a split-explici t solution procedure. VCOM is coupled to the PISCES ocean biochemistry mod el. Coupling of the ocean\, atmospheric and land-surface components takes place every time-step. It is envisaged that VrESM will be applied on a 10 0 km horizontal resolution grid within CMIP6\, with a longer-term plan of performing global eddy-resolving (10 km resolution) simulations depending on the availability of supercomputing resources at the Centre for High Per formance Computing (CHPC) of the CSIR. Our path over the next 5 years (to wards and beyond AR6) is firstly technical\, in further developing and opt imising the VrESM on the computer cluster at the CHPC and secondly scienti fic\, in understanding the underlying mechanisms that are often parameteri zed rather than resolved in global climate models – followed by subseque nt improvements and optimizing the model with this new knowledge. In parti cular\, South Africa has invested significantly in resources to investigat e and undertake long term observations that resolve critical dynamics in t he oceans to our south. From this investment has emerged a competitive edg e in building the first ESM that realistically represent Southern Ocean bi ochemistry and the role of the Southern Ocean in the African and global cl imate systems. In this presentation\, we will present the unique aspects o f the VrESM numerical solution procedure as applied on the cube-based grid . A variety of model applications (including simulations of present-day an d future climate) will also be shown\, with a focus on Southern Hemisphere and African climate processes.\n\nhttps://events.chpc.ac.za/event/33/cont ributions/843/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/843/ END:VEVENT BEGIN:VEVENT SUMMARY:KEYNOTE 5: The MeerKAT Science Data Processing Journey DTSTART;VALUE=DATE-TIME:20181205T070000Z DTEND;VALUE=DATE-TIME:20181205T074500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-834@events.chpc.ac.za DESCRIPTION:Speakers: Khutso Ngoasheng (South African Radio Astronomy Obse rvatory)\nOn the 13th July 2018 the Deputy President of the Republic of So uth Africa\, David Mabuza\, unveiled the MeerKAT telescope array. \nThe M eerKAT telescope is a mid-frequency 64-antenna array radio telescope. The MeerKAT telescope generates a large amount of data. The Science Data Proce ssing subsystem is responsible for ingesting the telescope data\, cleaning the data\, packaging that data for scientific analysis\, delivering that data to science groups\, and storing that data for future use. \nIn order to achieve these objectives\, the Science Data Processing team has had to innovate in how to build the appropriate high performance computer systems to meet MeerKAT telescope performance and capacity requirements. Project constraints included budget\, human resources\, technology availability\, and problem novelty. \nKhutso Ngoasheng will narrate the audience through the journey to delivering the MeerKAT telescope's Science Data Processor. He will talk briefly about current activities and challenges within the S cience Data Processing subsystem. He will also introduce potential future paths for the Science Data Processor\, especially in the Square Kilometre context.\n\nhttps://events.chpc.ac.za/event/33/contributions/834/ LOCATION: Hall B+C URL:https://events.chpc.ac.za/event/33/contributions/834/ END:VEVENT BEGIN:VEVENT SUMMARY:Digital Earth South Africa: from satellites to insights DTSTART;VALUE=DATE-TIME:20181204T123000Z DTEND;VALUE=DATE-TIME:20181204T130000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-802@events.chpc.ac.za DESCRIPTION:Speakers: Imraan Saloojee (SANSA)\nhttps://events.chpc.ac.za/e vent/33/contributions/802/ LOCATION: Meeting Room 8+9 URL:https://events.chpc.ac.za/event/33/contributions/802/ END:VEVENT BEGIN:VEVENT SUMMARY:Machine Learning with Quantum Computers DTSTART;VALUE=DATE-TIME:20181203T092000Z DTEND;VALUE=DATE-TIME:20181203T094000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-846@events.chpc.ac.za DESCRIPTION:Speakers: Francesco Petruccione (UKZN)\nQuantum machine learni ng investigates how quantum computers can be used for data-driven predicti on and decision making. The talk introduces to this relatively young disci pline and shows the potential of "Big Data" applications on near-term quan tum computers\, as they can be found in the cloud at present. Data encodin g into quantum states\, quantum algorithms and routines for inference and optimisation\, as well as the construction and analysis of genuine ``quant um learning models'' will be introduced.\n\nhttps://events.chpc.ac.za/even t/33/contributions/846/ LOCATION: Hall B URL:https://events.chpc.ac.za/event/33/contributions/846/ END:VEVENT BEGIN:VEVENT SUMMARY:Quantum Computing - Panel Discussion DTSTART;VALUE=DATE-TIME:20181203T100000Z DTEND;VALUE=DATE-TIME:20181203T103000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-845@events.chpc.ac.za DESCRIPTION:Speakers: Peter Braam (-)\nTo be confirmed\n\nhttps://events.c hpc.ac.za/event/33/contributions/845/ LOCATION: Hall B URL:https://events.chpc.ac.za/event/33/contributions/845/ END:VEVENT BEGIN:VEVENT SUMMARY:Women in High Performance Computing Africa (WHPC-Africa) DTSTART;VALUE=DATE-TIME:20181204T133000Z DTEND;VALUE=DATE-TIME:20181204T150000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-721@events.chpc.ac.za DESCRIPTION:Speakers: Khomotso Maenetja (UL)\nDescription:\nThe last sessi on on Women in High Performance Computing in South Africa was proposed and held during 2017 annual conference. The major aim of the initiative was t o establish a network of Women in HPC in SA\, by bringing them together du ring the meeting. The session was supported and attended by both men and w omen\, and most importantly was supported by CHPC management team. An inte rim steering committee comprising of women from various institutions and d isciplines was established\, and will take the initiative going forward. C onsequently\, we propose to have a session during 2018 annual conference. \nIt is aimed that at the end of the session and beyond\, the following go als would be achieved:\n\n• Being part of the solution: instructions for advocates and allies.\n• Best practices from organizations on improving workplace diversity.\n• Managing the two body problem and achieving eff ective work-life balance\n• Encourage more female learners and students to consider careers in HPC\n• Contribute in increasing the number of wom en and girls participation in HPC through training and networking.\n• Sh are information and resources that foster growth for women in HPC.\n\nBoth men and Women are welcome to attend.\n\nhttps://events.chpc.ac.za/event/3 3/contributions/721/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/721/ END:VEVENT BEGIN:VEVENT SUMMARY:Understanding and Mitigating Interference between MPI and I/O Traf fic on Fat-tree Networks DTSTART;VALUE=DATE-TIME:20181203T120000Z DTEND;VALUE=DATE-TIME:20181203T123000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-674@events.chpc.ac.za DESCRIPTION:Speakers: Kevin A. Brown (Tokyo Institute of Technology)\nMany important HPC applications are communication-bound and/or I/O-bound. Thes e applications depend on efficient inter-process communication and I/O ope rations\, hence\, network interference can cause significant performance d egradation. Unfortunately\, most modern HPC systems use the same network i nfrastructure for both MPI and I/O traffic\, with multiple jobs sharing th e system concurrently. The scarcity of studies that investigate the interf erence between MPI and I/O jobs leaves us with only a vague understanding of how these types of traffic interact with each other\; the interference characteristics are not well explored and neither are the strategies for a voiding this interference in order to improve performance.\n\nIn this talk \, we discuss the important characteristics of the interference between I/ O and MPI traffic on fat-tree networks\, exposing the impact of factors su ch as message size\, job size\, and communication frequency on the resulti ng interference. We show the extent to which MPI traffic is more sensitive to interference than I/O traffic on a fully provisioned fat-tree network\ , and we categorize configurations that can cause even an I/O job to be sl owed by 1.9X due to interference from MPI traffic. This work has pinpointe d the most significant aspect of the performance trends: the I/O-congestio n threshold. This threshold refers to the frequency of sending I/O request s when MPI jobs start experiencing detrimental performance degradation due to I/O interference while\, simultaneously\, I/O traffic becomes relative ly insensitive to MPI interference.\n\nThe insights gained from the interf erence characterization can be used with knowledge of the network topology to mitigate the effects of this inter-job interference on application per formance. Our work shows how careful placement of jobs and I/O servers can \, independently\, mitigate interference. Additionally\, I/O throttling ca n be guided by the I/O-congestion threshold to improve MPI performance by up to 200% while incurring only a 18% slowdown in the I/O performance.\n\n https://events.chpc.ac.za/event/33/contributions/674/ LOCATION: Hall B URL:https://events.chpc.ac.za/event/33/contributions/674/ END:VEVENT BEGIN:VEVENT SUMMARY:Introducing the Square Kilometer Array (SKA) Mid Data Centre Facil ity DTSTART;VALUE=DATE-TIME:20181204T093000Z DTEND;VALUE=DATE-TIME:20181204T100000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-799@events.chpc.ac.za DESCRIPTION:Speakers: Jeremy Main (SARAO / SKA South Africa)\nAs part of h osting the Square Kilometer Array (SKA) mid frequency radio telescope in t he Northern Cape Karoo region\, the South Africa Radio Astronomy Observato ry (SARAO) will be providing suitable facilities to house the computing\, networking and data storage for both the Science Data Processor (SDP) and an SKA Regional Science Centre (SRC). These two facilities are expected to host petascale computing\, exascale storage capacity and network connecti vity in order of 8 Tbps by 2024. The facilities are expected to be located in Cape Town\, over 700 kms from the Central Signal Processor (CSP) at th e Telescope core site near the town of Carnarvon.\n\nThe purpose of this p resentation is to share the latest information that will be used to define requirements for the construction of the two co-located facilities\, each with their own governance models\, operation models and potentially uniqu e approaches to fulfilling the computing infrastructure requirements.\n\nC urrently SARAO is working together with the SKA Organisation (SKAO)\, the Department of Science and Technology (DST) South Africa and the Western Ca pe Government (WCG) on initial plans and aims to start to journey of engag ing with other stakeholders\, gathering information and improving accuracy of detailed information with the aim to assist with the planning that wil l ultimately lead to construction of the required facilities.\n\nhttps://e vents.chpc.ac.za/event/33/contributions/799/ LOCATION: Meeting Room 8+9 URL:https://events.chpc.ac.za/event/33/contributions/799/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to CUDA and Parallel Programming DTSTART;VALUE=DATE-TIME:20181202T133000Z DTEND;VALUE=DATE-TIME:20181202T150000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-865@events.chpc.ac.za DESCRIPTION:Speakers: Rob Farber (TechEnablement)\nDescription:\nThe goal of this workshop is to introduce students to CUDA and provide them with an understanding of parallel programming. CUDA is more than a few new keywor ds. One must understand SIMD and the pitfalls of serialization. \n\nStuden ts will leave with basic CUDA skills and some OpenACC knowledge plus usefu l machine learning and big data tools as well. My “from Hello World to e xascale machine learning in one slide” will also be covered as data para llel training fits on GPUs nicely.\n\nTarget Audience:\nAnyone with C/C++ programming skills in the Unix environment who wishes to learn about paral lel programming and CUDA. The material will be 60% beginner\, 30% interme diate\, and 10% advanced. \n\nPrerequisites:\nC/C++ along with an ability to edit and compile programs in a Unix environment\n\nSpecial requirements :\nUsers will have access to a CHPC system with GPUs. \n\nAttendees should bring their own laptops. The ability to view pdf or PowerPoint files is r equired.\n\nOutline of full syllabus:\n08:00 Registration\n09:00 Introduct ion and morning talk (30 minutes)\n Login details and extracting th e workshop material (15 minutes)\n Section 01: Parallel intro and a first CUDA program)\n Section 02: Profiling on a GPU\n\n\n10:30 Mo rning Refreshment Break\n11:00 Section 03: More CUDA and the Thrust Interf ace\n Section 04: “From Hello World to TF/s machine learning”\n 12:30 Lunch\n13:30 Afternoon talk \n Section 05: Controlling parall el resources\n Section 06: C++ objects and transparent host/GPU dat a movement \n15:00 Afternoon Refreshment Break\n15:30 Section 07: Task lev el parallelism on a GPU\n Section 08: Managing big data\, CUDA as a scripting language via dynamic load/link\n17:00 End of Day\n\n\nAdditiona l Comments:\nStudents can work at their own pace. \nIntroductory students will learn the basics of CUDA and the profiler as well as how to think in parallel and understand the impact of parallel hardware on performance.\nI ntermediate/advanced students will hone their thinking about parallel prog ramming and the limitations and advantages of GPU hardware. Extra credit e xercises will challenge them.\nAll students will learn how to use machine learning and the ability to explore this hot field and leave with a tool t hat allows them to train and predict using their own data sets and neural network architectures. Further\, they learn how to work with and collabora te using big data.\n\nhttps://events.chpc.ac.za/event/33/contributions/865 / LOCATION: Meeting Room 10 URL:https://events.chpc.ac.za/event/33/contributions/865/ END:VEVENT BEGIN:VEVENT SUMMARY:Infrastructure Services Towards Data Sharing DTSTART;VALUE=DATE-TIME:20181205T135000Z DTEND;VALUE=DATE-TIME:20181205T140500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-818@events.chpc.ac.za DESCRIPTION:Speakers: Ina Smith (Academy of Science of South Africa)\nOne of the principal benefits of and drivers for Open Science is the open use of shared infrastructures for science. The digital age offers huge opport unities for the accelerated creation of and networked access to data for r esearch. The exploitation of this through the Internet\, the Web\, Grids\ , e-Science\, Research Infrastructures\, Open Science Clouds and Platforms has been a major driver of many areas of scientific progress and a key fe ature of science policy and investment (in particular disciplines or in cr oss-disciplinary programmes).\n\nGlobal north investment in research infra structures\, data commons and Open Science Clouds is a direct result of th e scientific benefits achieved in the last 15-20 years through networked a ccess to data resources and computing power. It is essential that African countries and Africa as a continent keep pace with these developments.\n\ nThere is growing awareness globally that it is not enough to create netwo rk or compute infrastructure in a way that is abstracted from research dis ciplines and concrete use cases. Moreover\, and of crucial importance is the recognition that data require the investment of stewardship to ensure that they can be fully exploited. Again this has been variously expressed : data should be a first class object\, data as infrastructure\, intellige nt openness or FAIR data. With ever more useful refinements\, these argum ents point towards the same end: a necessary feature of research infrastru ctures is a rich environment of data resources that are Findable\, Accessi ble\, Interoperable and Reusable (FAIR)\; as Open as Possible and stewarde d for the long term as part of the record and resource of science.\n\nThe most obvious challenges\, relate investment and the funds needed for such infrastructures. But they also relate to coordination. A great deal can be achieved through coordination of resources and investment in shared inf rastructures. The development of high-speed educational research networks and improved access to HPC clusters is proceeding and there are some inst ances of experimentation with cloud computing for science. The challenge is to achieve the vision\, strategy and coordination that will ensure thes e investments will enable to African researchers to engage with the Open\, data-intensive science of the 21st century. This means building on the i nfrastructure a shared layer providing access to compute and research tool s of various sorts and to data that is Open and FAIR. A lot can be learnt from activities globally\, particularly in Europe and Australia. A major challenge is to determine how such levels of coordination can be achieved between African research systems and institutions. Without such coordina tion and the attendant economies of scale and cost sharing\, the developme nt of research infrastructures will be far slower\, more expensive\, ad ho c and susceptible to quicker technical redundancy or obsolescence.\n\nThis paper will report on an African Open Science Platform ICT Infrastructure Framework and Roadmap\, guiding African countries towards preparing for a coordinated initiative\, addressing Open Science and Open Access needs acr oss disciplines. South Africa continues to be a main player as will be ind icated in this paper\, together with countries such as Kenya. This paper w ill demonstrate that collaboration and coordination are possible and much needed\, towards addressing the objectives of the SA National Development Plan and the UN Science\, Technology and Innovation Strategy for Africa 20 24.\n\nhttps://events.chpc.ac.za/event/33/contributions/818/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/818/ END:VEVENT BEGIN:VEVENT SUMMARY:The simultaneous Optimization of the Nose and Tail Geometry of a H igh Speed Train for Drag and Crosswind Stability DTSTART;VALUE=DATE-TIME:20181205T121000Z DTEND;VALUE=DATE-TIME:20181205T123000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-832@events.chpc.ac.za DESCRIPTION:Speakers: Andrea Beneke (Prospective Industry and current acad emic user)\, Ken Craig (University of Pretoria)\nThe national rail policy as formulated by the South African government requires that by the year 20 50 all current narrow or Cape gauge main rail lines be replaced by standar d gauge tracks. In addition\, they require that a number of key role playe rs\, of which Transnet is but one\, should work toward the implementation of high speed rail on these new tracks by the same year. The document furt her stipulates that the onus of responsibility of planning and developing the necessary skill in order to achieve the aforementioned\, lies with the se role players.\nThe first step that Transnet is taking to bridge this ga p and move South Africa forward is called the MC25 project\; a medium spee d passenger commuter that will connect Gauteng and Polokwane. The aim of t he project is both economic upliftment as well as a means of addressing a skills deficit with Transnet. The work that was completed was meant to add ress the latter\, with specific focus on the external aerodynamics of a hi gh speed train. \nThis project not only included a study of the external flow field surrounding a high speed train\, but also the simultaneous opti mization of the train nose and tail for drag and crosswind stability which were determined by the aerodynamic investigation to be the primary causes of concern for high speed trains. Due to the flow complexities and sheer magnitude of the simulations\, the computing capabilities that the CHPC of fered was critical to arriving at an optimal solution.\n\nhttps://events.c hpc.ac.za/event/33/contributions/832/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/832/ END:VEVENT BEGIN:VEVENT SUMMARY:Examining the Threat Landscape of Social Engineering in an Emergin g Society DTSTART;VALUE=DATE-TIME:20181204T100000Z DTEND;VALUE=DATE-TIME:20181204T102500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-809@events.chpc.ac.za DESCRIPTION:Speakers: Francois Mouton ()\nSocial Engineering has become th e go-to attack methodology in the 21 st Century. Organisations and governm ents have a vested interest in securing sensitive information as well as t he trust of clients or citizens. Technology on its own is no longer a suff icient safeguard against information theft. Employees\, often the weak lin k in an information security system\, could be influenced or manipulated b y the attacker to divulge sensitive information\, thus allowing unauthoris ed individuals to gain access to protected systems. As technology develop ed\, social engineering became commonly used for technology related crimes . This is no longer the case as we see it reverting back to its original u se of mobilising communities to perform or act in ways assumed to be ‘op timal’ or ‘correct’. This is typically either for personal gain of t he attacker or to influence people to subscribe to the attacker’s societ al belief system. \n\nThrough the utilisation of real-life social engineer ing examples\, the formal process of social engineering and techniques uti lised to abuse the inherent trust of individuals is explored. This particu lar discussion focuses on the psyche of an individual and discusses the ba sic human instinct of trust. The concept of trust is something that diffe rs based on environmental conditions and socio-economic upbringing. Trust will however\, always remain a basic human instinct. A ‘functioning’ s ociety relies on the fact that individuals have inherent trust. For exampl e\, most people inherently ‘trust’ institutions to manage financial as pects of life\, similarly\, they “trust” that other people in turn wil l obey those same institutions. Not having this basic form of trust could send society into a state of chaos. As a result\, this discussion examines the extent to which\nscepticism can aid society and in turn allow individ uals to protect themselves. In the end\, everyone has a need of being acce pted and ultimately\, all of us just want to belong…\n\nhttps://events.c hpc.ac.za/event/33/contributions/809/ LOCATION: Meeting Room 10 URL:https://events.chpc.ac.za/event/33/contributions/809/ END:VEVENT BEGIN:VEVENT SUMMARY:Bandwidth and its influence on tertiary education DTSTART;VALUE=DATE-TIME:20181204T093000Z DTEND;VALUE=DATE-TIME:20181204T095500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-810@events.chpc.ac.za DESCRIPTION:Speakers: Sune Von Solms (University of Johannesburg)\nIn Sout h Africa\, increased access to educational resources is altering the colle ctive face of education. Many in the education field see new technologies as powerful tools to help universities meet the needs of ever-more-diverse student populations. Digital devices\, software applications\, interactiv e digital textbooks\, e-books\, online assessments and various learning pl atforms offer unimaginable options for tailoring education to each individ ual student’s academic strengths and weaknesses\, personal preferences a nd financial position. Without a doubt\, one key enabler for these educati onal technologies is fast\, robust and reliable broadband. Reliable broadb and not only assists on-site students and lecturers at university campuses \, but also enables off-site faculty and students to participate in online learning experiences. Our increased dependence on these online learning t echnologies will continue to increase the demand for more and more bandwid th.\n\nThis talk looks at the staggering numbers surrounding the use of fa st\, robust and reliable broadband at tertiary educational institutions. W e consider the growth in Internet traffic at educational institutions\, ba ndwidth costs and the advancement of educational technological tools and m edia\n\nhttps://events.chpc.ac.za/event/33/contributions/810/ LOCATION: Meeting Room 10 URL:https://events.chpc.ac.za/event/33/contributions/810/ END:VEVENT BEGIN:VEVENT SUMMARY:The 2017 High Impact Weather Events over South Africa DTSTART;VALUE=DATE-TIME:20181205T133500Z DTEND;VALUE=DATE-TIME:20181205T135000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-891@events.chpc.ac.za DESCRIPTION:Speakers: Mary-Jane Bopape (South African Weather Service)\nTh e mandate of the South African Weather Service (SAWS) is to provide weathe r\, climate and air quality related information\, products\, services and solutions that contribute to the safety of life and property in the air\, land and sea. To deliver on its mandate\, SAWS operates a comprehensive we ather observation network and also runs models in operational mode. The ob servation network includes 14 operational some S-band and C-band radars wh ich cover most of the country. SAWS also operates a lighting detection net work which has been in operation since 2006. Further SAWS also access sate llite information in near real time and this information is especially hel pful for areas where there is no radar network. The United Kingdom Met Off ice (UKMO) Unified Model (UM) is used for short range forecasting and is o perated with a grid spacing of 4.4km and 1.5 km. For the medium range time scale\, SAWS downloads data from the European Centre for Medium-Range Weat her Forecasts (ECMWF) and National Centers for Environmental Prediction (N CEP) Global Ensemble Forecasting System (GEFS). In this presentation the p erformance of SAWS in issuing warnings of high impact weather events that took place in 2017 will be assessed against the model simulations that are produced both at SAWS as well as the ECMWF simulations. Moreover\, the as sessment of the performance will also be checked against the availability of the radar and satellite data in the nowcasting timescale. The general s tatistics will be presented for floods and heavy rainfall events\, thunder storms including hail storms and tornadoes\, as well as strong winds that were reported in print media. Initial results indicate that SAWS issued wa rnings for 21/26 veld fires\, 28/51 heavy rain or flooding events\, 18/32 thunderstorms and 9/18 strong winds 24 hours in advance. The data that is valuable for warnings that are issued 24 hours or longer before the event occurs is produced by models. Closer to the events\, the critical infrastr ucture is that associated with near real-time observations. In the present ation we will also show the effects of the availability of the observation s to warnings issued by SAWS. The presentation will also highlight challen ges associated with managing both observation and model simulation data.\n \nhttps://events.chpc.ac.za/event/33/contributions/891/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/891/ END:VEVENT BEGIN:VEVENT SUMMARY:CORDEX projections of changing tropical cyclones in the IPCC SR1.5 report as performed on the CHPC's Lengau cluster DTSTART;VALUE=DATE-TIME:20181204T100000Z DTEND;VALUE=DATE-TIME:20181204T102000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-827@events.chpc.ac.za DESCRIPTION:Speakers: F.A. Engelbrecht ()\, Mavhungu Muthige ()\nThe Paris Agreement which was achieved in December 2015\; holds signatory countries responsible for keeping the increase in global average temperatures well below 2°C with respect to the to the pre-industrial period and to strive to limit the temperature increase to 1.5°C \, recognising that this will reduce the impacts of climate change. Given this impetus at global level\, it is of paramount importance to consider the implications of the 1.5 \, 2\, and 3 °C thresholds in the tropical cyclone activities within the Sou th West Indian Ocean Basin.Using the Coordinated Regional Downscaling Expe riment-Africa (CORDEX) regional climate models\, we downscale six global c limate models of the Coupled Model Inter-comparison Project Phase 5 (CMIP5 ) to high resolution with the aid of computing power from the south Africa n (CHPC) Centre for High Performance Computing’s Lengau Cluster.This ser ves towards studying changes in tropical cyclone tracks over the South Wes t Indian Ocean under different extents of global warming(1.5\, 2 and 3° C of warming with respect to pre-industrial conditions). It is projected th at the number of tropical cyclones making landfalls over southern Africa u nder global warming will decrease\, with 2 °C being a critical threshold\ , after which the rate of cyclone frequency with further temperature incre ases no longer has a diminishing effect.\n\nhttps://events.chpc.ac.za/even t/33/contributions/827/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/827/ END:VEVENT BEGIN:VEVENT SUMMARY:Moving more data\, faster - SANReN Data Transfer Pilot Service DTSTART;VALUE=DATE-TIME:20181204T090000Z DTEND;VALUE=DATE-TIME:20181204T092500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-811@events.chpc.ac.za DESCRIPTION:Speakers: Sakhamuzi Hadebe (CSIR - SANReN CA)\, Kasandra Pilla y (SANReN)\nMoving masses of data is a challenge. In most cases networks o ptimized for business operations are neither designed for nor capable of s upporting the data movement requirements of data intensive research. When scientists attempt to run data intensive applications over these so called “general purpose”/enterprise networks\, the result is often poor perf ormance – in many cases poor enough that the science mission is signific antly impacted. At its worst this means either not\ngetting the data\, get ting it too late or resorting to “desperate” measures such as shipping disks around. The South African National Research Network (SANReN) is cur rently piloting a data transfer service with the goal of changing this for our researchers/scientists and optimising the transfer of datasets across the network. The service makes use of data transfer nodes configured in a science\nDMZ architecture using specially designed data transfer tools to efficiently and securely move data.\nThis presentation will present an ov erview of the science DMZ\, data transfer nodes\, tools and services that we have implemented as part of the SANReN Data Transfer Pilot project as w ell as preliminary results we’ve achieved.\n\nhttps://events.chpc.ac.za/ event/33/contributions/811/ LOCATION: Meeting Room 10 URL:https://events.chpc.ac.za/event/33/contributions/811/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to HPC DTSTART;VALUE=DATE-TIME:20181202T070000Z DTEND;VALUE=DATE-TIME:20181202T083000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-848@events.chpc.ac.za DESCRIPTION:Speakers: Thomas Sterling (Indiana University)\, Maciej Brodow icz (Indiana Univeristy)\nWhere to begin? HPC as a field\, a technology\, and a tool for a diversity of disciplines that are enabled by it is an int erplay of foundational concepts\, rapidly evolving knowledge\, and skill s ets including programming. This one-day tutorial is presented as a beginne rs’ guide to supercomputing to expose the novice to the breadth of issue s needed to begin to understand and use such systems for real-world proble ms. Included are basic concepts\, HPC architecture\, benchmarking\, parall el programming using OpenMP and MPI\, basics of GPU accelerators\, and lib raries. Participants will be shown live demonstrations of all of these tec hniques and given opportunities for hands-on experience using the CHPC Pet aflops scale supercomputer in South Africa. Questions will be welcome from the attendees throughout the presentations.\n\nhttps://events.chpc.ac.za/ event/33/contributions/848/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/848/ END:VEVENT BEGIN:VEVENT SUMMARY:Integrating Data Upload Service With Digital Object Identifier Sys tem DTSTART;VALUE=DATE-TIME:20181205T115000Z DTEND;VALUE=DATE-TIME:20181205T120500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-887@events.chpc.ac.za DESCRIPTION:Speakers: Mbuyiselo Ndlovu (CSIR Employee)\nExtended Title: A n Investigation into the integration of Digital Object Identifier (DOI) an d Data Upload Service for use in Data Intensive Research in South Africa ( DIRISA).\n\nAbstract: The use of Digital Object Identifiers has become an increasingly important topic within the research and data space. This is m ainly due to the fact that researchers want their data to be easily findab le\, accessible and searchable. The Data Intensive Research Initiative of South Africa (DIRISA) has realised this need and is creating a system that can allow researchers to mint their own identifiers based on handle.net s ystem. These identifiers can be referred to as Digital Object Identifiers (DOI’s). However\, in order to mint identifiers the researchers need to upload data and provide metadata.\n\nhttps://events.chpc.ac.za/event/33/co ntributions/887/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/887/ END:VEVENT BEGIN:VEVENT SUMMARY:Tuning and optimisation of parallel programs on the CHPC supercomp uter DTSTART;VALUE=DATE-TIME:20181202T113000Z DTEND;VALUE=DATE-TIME:20181202T130000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-876@events.chpc.ac.za DESCRIPTION:Speakers: SAMUEL "STICKS" MABAKANE (CENTRE FOR HIGH PERFORMANC E COMPUTING)\nDescription:\nThis session will cover various aspects of ana lysing and optimising parallel programs to achieve optimum performance on the supercomputer. Tuning and Analysis Utilities (TAU) callgraph visualiza tion system will demonstrate how to analyse different objects (e.g. module s\, routines and functions) and identify performance bottlenecks within pa rallel applications. \n\nTarget Audience:\nParallel program users\, devel opers and administrators\n\nPrerequisites:\nAttendees must at least have k nowledge of compiling and running parallel applications on a cluster. \n\n Type of Tutorial: \nMix of lectures and practicals\n\nSpecial Requirement s:\nNo need for attendees to have laptops. Presenter will demonstrate prac tical exercises on his laptop.\n\nOutline:\n08:00\nRegistration\n09:00\n\n 10:30\nMorning Refreshment Break\n11:00\n\n12:30\nLunch\n13:30\nTuning and optimisation of parallel programs on the CHPC supercomputer\n15:00\nAfter noon Refreshment Break\n15:30\nTuning and optimisation of parallel program s on the CHPC supercomputer\n17:00\nEnd of Day\n\nhttps://events.chpc.ac.z a/event/33/contributions/876/ LOCATION: Meeting Room 4 URL:https://events.chpc.ac.za/event/33/contributions/876/ END:VEVENT BEGIN:VEVENT SUMMARY:Next-generation DNA sequencing: why HPC is becoming a vital compon ent of biological research DTSTART;VALUE=DATE-TIME:20181204T092000Z DTEND;VALUE=DATE-TIME:20181204T094000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-898@events.chpc.ac.za DESCRIPTION:Speakers: Peter Teske (University of Johannesburg)\nDuring the past decade\, massive parallel DNA sequencing technologies have completel y changed the way in which genetic data are generated and analysed. Instea d of sequencing a few hundred nucleotides and focusing on a handful of gen es\, it is now possible to generate data from entire genomes. The human ge nome contains about 3 billion nucleotides\, and even this is tiny compared to some plant genomes. The resulting datasets are so large that it is imp ossible to assemble and analyse them without HPC. In this presentation\, I demonstrate some of the HPC pipelines my lab uses to assemble genomic dat a and reconstruct evolutionary relationships between species. These data s ets are small compared to what we have planned for the near future\, highl ighting the necessity to invest more heavily in HPC resources in South Afr ica and help the country’s biologists become internationally competitive . I also focus on the present reluctance of many traditional geneticists t o adopt the new technology\, and suggest that this bottleneck needs to be closed by finding common ground between biologists\, computer scientists a nd other stakeholders. In the near future\, we need to jointly train bioin formatics students who operate at the interface of the different disciplin es.\n\nhttps://events.chpc.ac.za/event/33/contributions/898/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/898/ END:VEVENT BEGIN:VEVENT SUMMARY:CHPC Industry engagement session DTSTART;VALUE=DATE-TIME:20181206T070000Z DTEND;VALUE=DATE-TIME:20181206T083000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-720@events.chpc.ac.za DESCRIPTION:Speakers: Werner Janse Van Rensburg (CHPC)\nThe CHPC will be e ngaging with its non-academic users on Thursday 6 December. The format of the meeting will be similar to previous years\, and mostly involves recei ving feedback from the active commercial and public sector user base. \n\ nThe purpose of the meeting is to strengthen collaboration with the non-ac ademic users\, exchange experiences and discuss the way forward. Attendee s who are currently active CHPC users will be requested to give a short in troduction to their HPC-related work.\n\nAlthough the focus of the meeting will be to engage with past and current non-academic users\, the meeting will also be open to any individual or organisation wishing to learn more about what the CHPC offers to industry and the public sector.\n\nhttps://e vents.chpc.ac.za/event/33/contributions/720/ LOCATION: Meeting Room 10 URL:https://events.chpc.ac.za/event/33/contributions/720/ END:VEVENT BEGIN:VEVENT SUMMARY:CHPC Industry engagement session DTSTART;VALUE=DATE-TIME:20181206T113000Z DTEND;VALUE=DATE-TIME:20181206T130000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-853@events.chpc.ac.za DESCRIPTION:Speakers: Werner Janse Van Rensburg (CHPC)\nThe CHPC will be e ngaging with its non-academic users on Thursday 6 December. The format of the meeting will be similar to previous years\, and mostly involves recei ving feedback from the active commercial and public sector user base. \n\ nThe purpose of the meeting is to strengthen collaboration with the non-ac ademic users\, exchange experiences and discuss the way forward. Attendee s who are currently active CHPC users will be requested to give a short in troduction to their HPC-related work.\n\nAlthough the focus of the meeting will be to engage with past and current non-academic users\, the meeting will also be open to any individual or organisation wishing to learn more about what the CHPC offers to industry and the public sector.\n\nhttps://e vents.chpc.ac.za/event/33/contributions/853/ LOCATION: Meeting Room 10 URL:https://events.chpc.ac.za/event/33/contributions/853/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to CUDA and Parallel Programming DTSTART;VALUE=DATE-TIME:20181202T090000Z DTEND;VALUE=DATE-TIME:20181202T103000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-863@events.chpc.ac.za DESCRIPTION:Speakers: Rob Farber (TechEnablement)\nDescription:\nThe goal of this workshop is to introduce students to CUDA and provide them with an understanding of parallel programming. CUDA is more than a few new keywor ds. One must understand SIMD and the pitfalls of serialization. \n\nStuden ts will leave with basic CUDA skills and some OpenACC knowledge plus usefu l machine learning and big data tools as well. My “from Hello World to e xascale machine learning in one slide” will also be covered as data para llel training fits on GPUs nicely.\n\nTarget Audience:\nAnyone with C/C++ programming skills in the Unix environment who wishes to learn about paral lel programming and CUDA. The material will be 60% beginner\, 30% interme diate\, and 10% advanced. \n\nPrerequisites:\nC/C++ along with an ability to edit and compile programs in a Unix environment\n\nSpecial requirements :\nUsers will have access to a CHPC system with GPUs. \n\nAttendees should bring their own laptops. The ability to view pdf or PowerPoint files is r equired.\n\nOutline of full syllabus:\n08:00 Registration\n09:00 Introduct ion and morning talk (30 minutes)\n Login details and extracting th e workshop material (15 minutes)\n Section 01: Parallel intro and a first CUDA program)\n Section 02: Profiling on a GPU\n\n\n10:30 Mo rning Refreshment Break\n11:00 Section 03: More CUDA and the Thrust Interf ace\n Section 04: “From Hello World to TF/s machine learning”\n 12:30 Lunch\n13:30 Afternoon talk \n Section 05: Controlling parall el resources\n Section 06: C++ objects and transparent host/GPU dat a movement \n15:00 Afternoon Refreshment Break\n15:30 Section 07: Task lev el parallelism on a GPU\n Section 08: Managing big data\, CUDA as a scripting language via dynamic load/link\n17:00 End of Day\n\n\nAdditiona l Comments:\nStudents can work at their own pace. \nIntroductory students will learn the basics of CUDA and the profiler as well as how to think in parallel and understand the impact of parallel hardware on performance.\nI ntermediate/advanced students will hone their thinking about parallel prog ramming and the limitations and advantages of GPU hardware. Extra credit e xercises will challenge them.\nAll students will learn how to use machine learning and the ability to explore this hot field and leave with a tool t hat allows them to train and predict using their own data sets and neural network architectures. Further\, they learn how to work with and collabora te using big data.\n\nhttps://events.chpc.ac.za/event/33/contributions/863 / LOCATION: Meeting Room 10 URL:https://events.chpc.ac.za/event/33/contributions/863/ END:VEVENT BEGIN:VEVENT SUMMARY:Strategies and Challenges of HPC education and training DTSTART;VALUE=DATE-TIME:20181205T090000Z DTEND;VALUE=DATE-TIME:20181205T103000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-839@events.chpc.ac.za DESCRIPTION:Speakers: Weronika Filinger (EPCC at The University of Edinbur gh\, PRACE)\, Emmanouil-Ioannis Farsarakis ()\nDescription:\nThe HPC field is constantly expanding\, increasing its geographical and scientific reac h. This expansion brings more diversity\, enriching the community\, but al so more training and educational challenges. To address the educational ga ps and ensure a continuous growth of HPC practitioners a number of interna tional initiatives appeared within the HPC educational community. The PRAC E online courses (MOOCs)\, ACM SIGHPC Education Chapter\, HPC Carpentry an d International HPC Certification Program are some of them. For these init iatives to thrive and be useful they need input and support from community members around the world. Come\, join us or give your feedback! It’s ne eded.\n\nTarget Audience:\nAnyone involved or interested in HPC education and training\, including students.\n\nOutline of Programme:\nThis session will focus on presenting work done to help address educational challenges faced by the HPC community. More specifically\, the session will focus on the PRACE online courses (MOOCs)\, ACM SIGHPC Education Chapter\, HPC Carp entry and International HPC Certification Program.\n\nAlthough many of the challenges faced by HPC educators are common and don’t depend on a spec ific location or affiliation\, some such challenges are more specific to g roups of users. Quite often accommodating the extra needs of a smaller gro up\, not only benefits the group in question\, but can also benefit the co mmunity as a whole. If done correctly\, small changes to the education mat erial can improve the learning experience of a significant number of leane rs. \n\nBesides presenting the ideas behind the above-mentioned educati onal efforts\, the session will aim to understand the challenges and educa tional needs faced by the African HPC community to influence the direction in which the global HPC training and education efforts are heading. \n\ nThe session is meant to be useful to all participants so it will include a number of brief presentations\, followed by Q&A sessions and a general d iscussion. The speakers are either directly involved in or have links to a ll of the above mentioned initiatives so are in position to answer questio ns and act on the received feedback. \n\nThe proposed session outline:\n\n Presentations interspaced with Q&As:\n\n• MOOCs\n• HPC Carpentry\n• HPC Certification Program\n• ACM SIGHPC Education chapter\n\nPresentatio ns and Q&A sessions will be followed by a discussion on interests\, challe nges\, suggestions for improvements etc.\, possibly with a survey running in the background to drive the conversation. \n\nThe session will then clo se with a summary of its outcomes\, any actions identified during the sess ion and information for participants on how to continue the conversation a nd engagement.\n\nhttps://events.chpc.ac.za/event/33/contributions/839/ LOCATION: Meeting Room 7 URL:https://events.chpc.ac.za/event/33/contributions/839/ END:VEVENT BEGIN:VEVENT SUMMARY:Challenges and Opportunities for African Genomics Research DTSTART;VALUE=DATE-TIME:20181205T092000Z DTEND;VALUE=DATE-TIME:20181205T093500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-816@events.chpc.ac.za DESCRIPTION:Speakers: Sumir Panji (UCT Computational Biology Division / H3 ABioNet)\nFor the promise of genomics to drive precision medicine to be re alized\, numerous human genome sequence samples and high depth coverage an d from a variety of populations is required. Through initiatives like H3Af rica\, population scale genomics is being applied to help characterize div erse African populations that have currently not been featured in the geno mics revolution. African genomes represent an uncharacterized portion of h uman genomics and may hold opportunities for novel discoveries. \n\nGenomi cs data however is big data\, the collection\, transfer\, storage and anal yses of genomics data poses challenges to the infrastructure needed to man age such data. Key to human genomics data is governance policies that cont rol the access of sensitive genetic data and achieving a balance between n ot being a barrier to access data that drives scientific discoveries\, and at the same time protect the individuals that provide data. Associated wi th human genomics data is the rich diversity of meta-data that provide con textual information of the data. Some of the meta-data can be shared\, oth er meta-data that might possibly make a sample identifiable will need to b e under controlled access. Meta-data standards that are interoperable are required for the sharing of data and also for any meta-analysis to be cond ucted and form the core of good data management when dealing with copious volumes of data. The adoption of FAIR principals (Findable\, Accessible\, Interoperable and Reusable) is becoming prevalent across all scientific di sciplines and in some cases mandated by different funding agencies. The te chnological adoption needed to turn FAIR principals into reality is non-tr ivial\, but achievable and should be incorporated within good data managem ent practices. \n\nFor genomics data to be translated into actionable outc omes with impacts\, intensive computational processing and analyses of the data needs to be undertaken to convert information into knowledge. Tradit ionally in bioinformatics numerous software packages\, versions and depend encies are needed to undertake an analyses which can run into 100s or 1000 s of computational hours making reproducibility of the science a key issue . Development of computational workflows and containerized environments wi th user defined software stacks which can be hosted on various high perfor mance computing systems enables the sharing of software environments\, ver sions\, and computational workflows leading to reproducible science.\n\nht tps://events.chpc.ac.za/event/33/contributions/816/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/816/ END:VEVENT BEGIN:VEVENT SUMMARY:KEYNOTE 4: Security Intelligence: Data to Cyber War DTSTART;VALUE=DATE-TIME:20181204T074500Z DTEND;VALUE=DATE-TIME:20181204T083000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-894@events.chpc.ac.za DESCRIPTION:Speakers: Elmarie Biermann (Cyber Security Institute)\nThe adv ent of the fourth industrial revolution results in devices\, endpoints and sensors continually being added to extract and gather data from networks\ , systems and people. Ensuring security on all these entities is vital\, b ut more so the ability to move from data to information to knowledge and f inally intelligence in this big data environment. In terms of the cyber wa rfare space\, power will be in the hands of those who control information and that can extract\, analyse and apply security intelligence in a dynami c environment.\n\nhttps://events.chpc.ac.za/event/33/contributions/894/ LOCATION: Hall B+C URL:https://events.chpc.ac.za/event/33/contributions/894/ END:VEVENT BEGIN:VEVENT SUMMARY:DST DG Opening Address and NICIS Brand Identity Launch DTSTART;VALUE=DATE-TIME:20181203T071000Z DTEND;VALUE=DATE-TIME:20181203T073000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-878@events.chpc.ac.za DESCRIPTION:Speakers: Phil Mjwara (DST)\nAddress by Department of Science and Technology Director General\, Dr Phil Mjwara\n\nhttps://events.chpc.ac .za/event/33/contributions/878/ LOCATION: Hall B+C URL:https://events.chpc.ac.za/event/33/contributions/878/ END:VEVENT BEGIN:VEVENT SUMMARY:Understanding Risk in Shared CyberInfrastructure Systems Seminar DTSTART;VALUE=DATE-TIME:20181202T090000Z DTEND;VALUE=DATE-TIME:20181202T103000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-867@events.chpc.ac.za DESCRIPTION:Speakers: Meshack Ndala (CHPC)\nCHPC Cyber Security Symposium (CCSS) – 1 full day\nTopic: Understanding Risk in Shared CyberEcosystems workshop\nAs Technology continues to evolve so are the opportunities and challenges it provides. As a Society that relies largely on technology to bring us benefits\, it also exposes its users to threats by the very natur e of the opportunities it presents\, thus becoming a focal point for Cyber crime\, industrial espionage\, and Cyberattacks. Protecting against these threats is of paramount priority.\nCyber Security domain is inherently dyn amic\, not only does system configuration changes frequently with new rele ases and patches\, but also new attacks and vulnerabilities are regularly discovered. The core threat in Cyber Security is human\, hence intelligent in nature. The attacker adapts to the situation\, target environment\, an d countermeasures.\nAttacks actions are driven by attacker’s exploratory nature\, thought process\, motivation\, strategy\, and preferences.\nThe goal of this workshop is to address some of the challenges faced by Networ k and Security Administrators in their institutions.\nThe workshop will ad dress challenges such as:\n• Iot Threats\n• Blockchain Revolution\n• Ransomware Evolution\n• Future of Cybersecurity\n• New hacking Method ologies\n• Phishing\n• Distributed Denial of Service (DDoS)\n• Malwa re\n• Internal Privilege Misuse\n• Threats actors\n• How to protect your environment\n\nThe following are our invited speakers:\n• Prof Elma rie Bierman: Directory of SA Cyber Security Institute\n• Dr Noelle Cow ling : Stellenbosch University\n• Dr Jabu Mtswene : CSIR\n• Dr Noluxol o Gcaza: CSIR\n• Mr Justine Westcott\n• Mr Sikhumbuzo Mthombeni: Demen sion Data\n• Mr Keti Cedric : Demension Data\n• Mr Richard Hlalele: Un iversity of Johannesburg\, Senior Manager ICT Strategy and Governance\nThe following are workshop Coordinators:\nMr Bigani Sehurutshi: University of Botswana\nMrs Lee-Anne Benjamin: Manager \,Corporate IT Compliance NRF\n\ nhttps://events.chpc.ac.za/event/33/contributions/867/ LOCATION: Meeting Room 9 URL:https://events.chpc.ac.za/event/33/contributions/867/ END:VEVENT BEGIN:VEVENT SUMMARY:Understanding Risk in Shared CyberInfrastructure Systems Seminar DTSTART;VALUE=DATE-TIME:20181202T133000Z DTEND;VALUE=DATE-TIME:20181202T150000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-869@events.chpc.ac.za DESCRIPTION:Speakers: Meshack Ndala (CHPC)\nCHPC Cyber Security Symposium (CCSS) – 1 full day\nTopic: Understanding Risk in Shared CyberEcosystems workshop\nAs Technology continues to evolve so are the opportunities and challenges it provides. As a Society that relies largely on technology to bring us benefits\, it also exposes its users to threats by the very natur e of the opportunities it presents\, thus becoming a focal point for Cyber crime\, industrial espionage\, and Cyberattacks. Protecting against these threats is of paramount priority.\nCyber Security domain is inherently dyn amic\, not only does system configuration changes frequently with new rele ases and patches\, but also new attacks and vulnerabilities are regularly discovered. The core threat in Cyber Security is human\, hence intelligent in nature. The attacker adapts to the situation\, target environment\, an d countermeasures.\nAttacks actions are driven by attacker’s exploratory nature\, thought process\, motivation\, strategy\, and preferences.\nThe goal of this workshop is to address some of the challenges faced by Networ k and Security Administrators in their institutions.\nThe workshop will ad dress challenges such as:\n• Iot Threats\n• Blockchain Revolution\n• Ransomware Evolution\n• Future of Cybersecurity\n• New hacking Method ologies\n• Phishing\n• Distributed Denial of Service (DDoS)\n• Malwa re\n• Internal Privilege Misuse\n• Threats actors\n• How to protect your environment\n\nThe following are our invited speakers:\n• Prof Elma rie Bierman: Directory of SA Cyber Security Institute\n• Dr Noelle Cow ling : Stellenbosch University\n• Dr Jabu Mtswene : CSIR\n• Dr Noluxol o Gcaza: CSIR\n• Mr Justine Westcott\n• Mr Sikhumbuzo Mthombeni: Demen sion Data\n• Mr Keti Cedric : Demension Data\n• Mr Richard Hlalele: Un iversity of Johannesburg\, Senior Manager ICT Strategy and Governance\nThe following are workshop Coordinators:\nMr Bigani Sehurutshi: University of Botswana\nMrs Lee-Anne Benjamin: Manager \,Corporate IT Compliance NRF\n\ nhttps://events.chpc.ac.za/event/33/contributions/869/ LOCATION: Meeting Room 9 URL:https://events.chpc.ac.za/event/33/contributions/869/ END:VEVENT BEGIN:VEVENT SUMMARY:Q&A DTSTART;VALUE=DATE-TIME:20181205T142000Z DTEND;VALUE=DATE-TIME:20181205T143000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-892@events.chpc.ac.za DESCRIPTION:https://events.chpc.ac.za/event/33/contributions/892/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/892/ END:VEVENT BEGIN:VEVENT SUMMARY:Molecular Dynamics and Analysis using BRIDGE DTSTART;VALUE=DATE-TIME:20181206T090000Z DTEND;VALUE=DATE-TIME:20181206T103000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-849@events.chpc.ac.za DESCRIPTION:Speakers: Chris Barnett (University of Cape Town)\, Kevin J. N aidoo (University of Cape Town)\nMolecular Dynamics and analysis can be co mplicated for novitiates and researchers from neighbouring disciplines. Bu ilding upon the Galaxy Project platform\, BRIDGE (Biomolecular Reaction & Interaction Dynamics Global Environment) is a web application that provide s the ability to get started running molecular dynamics and analyses using curated workflows.\n\n**Target Audience:** Computational chemists\, biolo gists\, protein scientists\, crystallographers and anyone interested in ru nning and analysing molecular dynamics simulations who is not familiar wit h the command line.\n\n**Prerequisites:** Basic understanding of chemistry . A basic understanding of or keen interest in molecular dynamics.\n\n**Sp ecial requirements:** Bring a laptop. Have access to the CHPC cluster. Reg ister with BRIDGE. Install molecular viewer e.g. VMD.\n\n\n**Day:** Thursd ay (6 Dec)\n**Duration:** 1 day\n**Size:** 15 seats\n\nhttps://events.chpc .ac.za/event/33/contributions/849/ LOCATION: Meeting Room 9 URL:https://events.chpc.ac.za/event/33/contributions/849/ END:VEVENT BEGIN:VEVENT SUMMARY:Molecular Dynamics and Analysis using BRIDGE DTSTART;VALUE=DATE-TIME:20181206T113000Z DTEND;VALUE=DATE-TIME:20181206T130000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-850@events.chpc.ac.za DESCRIPTION:Speakers: Chris Barnett (University of Cape Town)\, Kevin J. N aidoo (University of Cape Town)\nMolecular Dynamics and analysis can be co mplicated for novitiates and researchers from neighbouring disciplines. Bu ilding upon the Galaxy Project platform\, BRIDGE (Biomolecular Reaction & Interaction Dynamics Global Environment) is a web application that provide s the ability to get started running molecular dynamics and analyses using curated workflows.\n\n**Target Audience:** Computational chemists\, biolo gists\, protein scientists\, crystallographers and anyone interested in ru nning and analysing molecular dynamics simulations who is not familiar wit h the command line.\n\n**Prerequisites:** Basic understanding of chemistry . A basic understanding of or keen interest in molecular dynamics.\n\n**Sp ecial requirements:** Bring a laptop. Have access to the CHPC cluster. Reg ister with BRIDGE. Install molecular viewer e.g. VMD.\n\n\n**Day:** Thursd ay (6 Dec)\n**Duration:** 1 day\n**Size:** 15 seats\n\nhttps://events.chpc .ac.za/event/33/contributions/850/ LOCATION: Meeting Room 9 URL:https://events.chpc.ac.za/event/33/contributions/850/ END:VEVENT BEGIN:VEVENT SUMMARY:Molecular Dynamics and Analysis using BRIDGE DTSTART;VALUE=DATE-TIME:20181206T133000Z DTEND;VALUE=DATE-TIME:20181206T150000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-851@events.chpc.ac.za DESCRIPTION:Speakers: Chris Barnett (University of Cape Town)\, Kevin J. N aidoo (University of Cape Town)\nMolecular Dynamics and analysis can be co mplicated for novitiates and researchers from neighbouring disciplines. Bu ilding upon the Galaxy Project platform\, BRIDGE (Biomolecular Reaction & Interaction Dynamics Global Environment) is a web application that provide s the ability to get started running molecular dynamics and analyses using curated workflows.\n\n**Target Audience:** Computational chemists\, biolo gists\, protein scientists\, crystallographers and anyone interested in ru nning and analysing molecular dynamics simulations who is not familiar wit h the command line.\n\n**Prerequisites:** Basic understanding of chemistry . A basic understanding of or keen interest in molecular dynamics.\n\n**Sp ecial requirements:** Bring a laptop. Have access to the CHPC cluster. Reg ister with BRIDGE. Install molecular viewer e.g. VMD.\n\n\n**Day:** Thursd ay (6 Dec)\n**Duration:** 1 day\n**Size:** 15 seats\n\nhttps://events.chpc .ac.za/event/33/contributions/851/ LOCATION: Meeting Room 9 URL:https://events.chpc.ac.za/event/33/contributions/851/ END:VEVENT BEGIN:VEVENT SUMMARY:Introduction to CUDA and Parallel Programming DTSTART;VALUE=DATE-TIME:20181202T113000Z DTEND;VALUE=DATE-TIME:20181202T130000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-864@events.chpc.ac.za DESCRIPTION:Speakers: Rob Farber (TechEnablement)\nDescription:\nThe goal of this workshop is to introduce students to CUDA and provide them with an understanding of parallel programming. CUDA is more than a few new keywor ds. One must understand SIMD and the pitfalls of serialization. \n\nStuden ts will leave with basic CUDA skills and some OpenACC knowledge plus usefu l machine learning and big data tools as well. My “from Hello World to e xascale machine learning in one slide” will also be covered as data para llel training fits on GPUs nicely.\n\nTarget Audience:\nAnyone with C/C++ programming skills in the Unix environment who wishes to learn about paral lel programming and CUDA. The material will be 60% beginner\, 30% interme diate\, and 10% advanced. \n\nPrerequisites:\nC/C++ along with an ability to edit and compile programs in a Unix environment\n\nSpecial requirements :\nUsers will have access to a CHPC system with GPUs. \n\nAttendees should bring their own laptops. The ability to view pdf or PowerPoint files is r equired.\n\nOutline of full syllabus:\n08:00 Registration\n09:00 Introduct ion and morning talk (30 minutes)\n Login details and extracting th e workshop material (15 minutes)\n Section 01: Parallel intro and a first CUDA program)\n Section 02: Profiling on a GPU\n\n\n10:30 Mo rning Refreshment Break\n11:00 Section 03: More CUDA and the Thrust Interf ace\n Section 04: “From Hello World to TF/s machine learning”\n 12:30 Lunch\n13:30 Afternoon talk \n Section 05: Controlling parall el resources\n Section 06: C++ objects and transparent host/GPU dat a movement \n15:00 Afternoon Refreshment Break\n15:30 Section 07: Task lev el parallelism on a GPU\n Section 08: Managing big data\, CUDA as a scripting language via dynamic load/link\n17:00 End of Day\n\n\nAdditiona l Comments:\nStudents can work at their own pace. \nIntroductory students will learn the basics of CUDA and the profiler as well as how to think in parallel and understand the impact of parallel hardware on performance.\nI ntermediate/advanced students will hone their thinking about parallel prog ramming and the limitations and advantages of GPU hardware. Extra credit e xercises will challenge them.\nAll students will learn how to use machine learning and the ability to explore this hot field and leave with a tool t hat allows them to train and predict using their own data sets and neural network architectures. Further\, they learn how to work with and collabora te using big data.\n\nhttps://events.chpc.ac.za/event/33/contributions/864 / LOCATION: Meeting Room 10 URL:https://events.chpc.ac.za/event/33/contributions/864/ END:VEVENT BEGIN:VEVENT SUMMARY:Tuning and optimisation of parallel programs on the CHPC supercomp uter DTSTART;VALUE=DATE-TIME:20181202T133000Z DTEND;VALUE=DATE-TIME:20181202T150000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-877@events.chpc.ac.za DESCRIPTION:Speakers: SAMUEL "STICKS" MABAKANE (CENTRE FOR HIGH PERFORMANC E COMPUTING)\nDescription:\nThis session will cover various aspects of ana lysing and optimising parallel programs to achieve optimum performance on the supercomputer. Tuning and Analysis Utilities (TAU) callgraph visualiza tion system will demonstrate how to analyse different objects (e.g. module s\, routines and functions) and identify performance bottlenecks within pa rallel applications. \n\nTarget Audience:\nParallel program users\, devel opers and administrators\n\nPrerequisites:\nAttendees must at least have k nowledge of compiling and running parallel applications on a cluster. \n\n Type of Tutorial: \nMix of lectures and practicals\n\nSpecial Requirement s:\nNo need for attendees to have laptops. Presenter will demonstrate prac tical exercises on his laptop.\n\nOutline:\n08:00\nRegistration\n09:00\n\n 10:30\nMorning Refreshment Break\n11:00\n\n12:30\nLunch\n13:30\nTuning and optimisation of parallel programs on the CHPC supercomputer\n15:00\nAfter noon Refreshment Break\n15:30\nTuning and optimisation of parallel program s on the CHPC supercomputer\n17:00\nEnd of Day\n\nhttps://events.chpc.ac.z a/event/33/contributions/877/ LOCATION: Meeting Room 4 URL:https://events.chpc.ac.za/event/33/contributions/877/ END:VEVENT BEGIN:VEVENT SUMMARY:CHPC Director Address DTSTART;VALUE=DATE-TIME:20181203T073000Z DTEND;VALUE=DATE-TIME:20181203T074500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-880@events.chpc.ac.za DESCRIPTION:Speakers: Happy Sithole (CHPC)\nAddress by Director of the CHP C\, Dr Happy Sithole\n\nhttps://events.chpc.ac.za/event/33/contributions/8 80/ LOCATION: Hall B+C URL:https://events.chpc.ac.za/event/33/contributions/880/ END:VEVENT BEGIN:VEVENT SUMMARY:Modelling Dry Flue Gas Desulfurisation in a Circulating Fluidized Bed. DTSTART;VALUE=DATE-TIME:20181203T121000Z DTEND;VALUE=DATE-TIME:20181203T123000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-714@events.chpc.ac.za DESCRIPTION:Speakers: Louis Le Grange (North-West University)\nThe burning of fossil fuels is identified as the biggest source of Sulfur dioxide (S0 2) emissions in South Africa. SO2 is a colourless gas with a nasty smell. It impacts both human health in the form of diminishing lung function and the environment through the effects of acid rain leading to deforestation. In order to meet minimum emissions standards for S02\, as provided by the Air Quality Act of South Africa\, big emitters such as Eskom and Sasol ar e required to implement Flue Gas Desulfurization (FGD) plants. Current FGD plants in South Africa are wet operated – that is\, a sorbent like Calc ium Hydroxide ( Ca(OH)2 ) is mixed with water and sprayed as slurry into f lue gas. In order to save water\, dry FGD processes are considered. One su ch process is called Dry FGD using a Circulating Fluidized Bed (CFB). Duri ng this process dry Ca(OH)2 is introduced into a flue gas stream while wat er is separately introduced as a fine spray. SO2 is then reduced in a reac tion involving the flue gas\, Ca(OH)2 particles and water droplets.\nThe m ain reactor of a Dry FGD CFB plant is the vertical riser\, which can typic ally be 3m in diameter and 20m high. The riser acts as a container in whic h the SO2 in the flue gas is exposed to the Ca(OH)2 particles and water dr oplets. Of importance are the residence time and the riser hold-up\, which forms part of the overall successful design of a dry SO2 scrubber. Comput ational Fluid Dynamics is used to model the gas-solid two-phase mixture. T he two-phase flow regime extends from dense to dilute turbulent flow\, whi ch renders the solution especially challenging. A Probability Density Func tion (PDF) approach is used to represent the microscale dynamics while fil tering methods are used to yield practical solution on the scale of the pl ant. \nTwo codes are used for modelling the two-phase flows namely Neptune _CFD\, which is the research code partly owned by EDF in France\, and Open FOAM\, which allows the user to make fundamental changes in the source cod e. Both these codes are run at CHPC. The results of the study presented fo cus on transient runs performed on CHPC. Optimization of nodes and cores w ere done to yield the most effective solver parallelization for these code s. Hold-up and resident times of particles are predicted inside the riser. The mathematical models of the riser application of two-phase flows repre sent from the biggest computerized parallel models in this field.\n\nhttps ://events.chpc.ac.za/event/33/contributions/714/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/714/ END:VEVENT BEGIN:VEVENT SUMMARY:Digital Scholarship - Surviving a Digital and Data Intensive World DTSTART;VALUE=DATE-TIME:20181205T093500Z DTEND;VALUE=DATE-TIME:20181205T095000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-814@events.chpc.ac.za DESCRIPTION:Speakers: Isak Van der Walt (University of Pretoria)\nAccordin g to Feeney\, Mary & Ross\, Seamus in Information Technology in Humanities Scholarship\, British Achievements\, Prospects\, and Barriers https://www .jstor.org/stable/20755828\, The growth of digital media means that the ma in areas of scholarship can each benefit from expansions in their own way thanks to the infinite shareability of digital content.\n\nWith the ever-e xpanding affordances that new digital media and research tools provide us\ , the underlying question is what form of control\, training\, validation and systems need to be in-place to ensure efficient data management throug hout the whole research life-cycle? Often organisations focus on the effic ient data management during a specific phase\; however\, we need to ensure that best practices on research data management are applied throughout. D igital Scholarship Centres can play a key role in providing guidance\, tra ining and even systems to bring together an overarching portfolio of servi ces and products that can steer digital and data intensive research.\n\nTh is presentation will provide you with insight into the progress the Univer sity of Pretoria has made in establishing its own Digital Scholarship Cent re\, its successes and failures.\n\nhttps://events.chpc.ac.za/event/33/con tributions/814/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/814/ END:VEVENT BEGIN:VEVENT SUMMARY:UNISA Research Data Management: A Case Study DTSTART;VALUE=DATE-TIME:20181205T095000Z DTEND;VALUE=DATE-TIME:20181205T100500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-815@events.chpc.ac.za DESCRIPTION:Speakers: Makaba Macanda (UNISA)\nThe drivers and principles f or managing research data at the University of South Africa is driven by t he increasing number of policies published by funders of research to ensur e the validation of research results. The funder requirements expects the following from research outputs:\n• To make provision for data reuse\,\n • To enable actionable and socially beneficial science from publicly fun ded research.\n\nThe purpose of the project is to ensure that research dat a is stored\, preserved\, retained\, made accessible for use and reuse\, a nd/or disposed of\, according to legal\, statutory\, ethical and funding b odies’ requirements.\n\nUnisa Library was mandated to investigate the Da ta Curation readiness at Unisa in 2010. Research was conducted and it was concluded that\, that Data Curation cannot take place in isolation in the library. It was then decided to change the concept documents from data cu ration to Research Data Management\, holistically. The project is driven f rom Unisa Library and in particular Information Resources Content Manageme nt (IRCM).\n\nThe paper will provide a case study analysis of the transiti on in the implementation of the Research Data Management and the interdepe ndencies.\n\nhttps://events.chpc.ac.za/event/33/contributions/815/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/815/ END:VEVENT BEGIN:VEVENT SUMMARY:ILIFU RDM Research Project: Progress Report DTSTART;VALUE=DATE-TIME:20181205T140500Z DTEND;VALUE=DATE-TIME:20181205T142000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-817@events.chpc.ac.za DESCRIPTION:Speakers: Alecia Naidu (University of Cape Town)\nILIFU is the isiXhosa word for Cloud\, an apt representation of the first node in the data infrastructure funded by the Department of Science and Technology to support the National Integrated Cyberinfrastructure System of South Africa . This presentation will provide an overview of the ILIFU model of shared infrastructure as a data-intensive research facility for big data managem ent\, storage and analysis. It will focus primarily on the Research Data M anagement (RDM) component of the project from conception to its current le vel of operationalisation. \n\nThe current progress will be shared with th e community to raise awareness of the RDM project\, its methodology and it s structure. The overall project has a strong emphasis on the development of policies and guidelines to assist researchers who will be working on th e data intensive infrastructure. The project is also developing a Work Int egrated Learning programme to enable the placement of postgraduate studen ts and mid-career personnel with the various projects in order to assist w ith the implementation of the RDM policies and guidelines as well as gaini ng work experience in data science. Significantly\, the RDM research proj ect fulfils an important additional function in support of institutional c apacity building across participating institutions\, where project finding s will serve to promote institutional policy and service development. \n\ nThe presentation will offer insights into data governance\, the challenge s and opportunities of the ILIFU RDM project\, and the interaction betwee n scientists and information professionals in building an African data inf rastructure.\n\nhttps://events.chpc.ac.za/event/33/contributions/817/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/817/ END:VEVENT BEGIN:VEVENT SUMMARY:Effects of Island Shape on Magnetostatic Interactions in Bit Patte rned Media for Data Storage DTSTART;VALUE=DATE-TIME:20181203T123000Z DTEND;VALUE=DATE-TIME:20181203T125000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-717@events.chpc.ac.za DESCRIPTION:Speakers: Josephat Kalezhi (Copperbelt University)\nBit patter ned media is one of the promising approaches to extend magnetic recording densities in hard-disk drives beyond recording densities of one Terabit (1 0^{12}) per square inch. In this approach\, the magnetic medium is pattern ed into nanometer-sized magnetic islands where each island can be consider ed to represent a binary digit. The islands are magnetically isolated but experience magnetostatic interactions between them. This study investigate s magnetostatic interactions between islands of various shapes for various island separations using micromagnetic simulations. The shapes range from truncated elliptic cones to cylinders. The computation of magnetostatic i nteractions is a major time-consuming task in a micromagnetic simulation. These interactions scale with O(N^{2}) operations\, where N is the number of interacting mesh elements in discretized islands. To carry out simulati ons\, an open-source finite element micromagnetics package called magpar w as used. The island mesh was generated using netgen\, a tetrahedral mesh g enerator. An open source visualization tool called paraview was used view the outputs of simulations. Open MPI was used in the simulations. Twelve c ores on one node were used in this work. The interactions between islands have been compared against dipole-dipole interactions where each island is assumed to be a dipole. The study has shown that for islands considered\, the effect of island shape is important for island separations less than twice the island width\, centre to centre. The dipole approximation is onl y sufficient for island separations beyond twice the island width. This re sult further suggests an improvement in the computation of time-consuming magnetostatic interactions between large numbers of islands by treating di stant islands as dipoles.\n\nhttps://events.chpc.ac.za/event/33/contributi ons/717/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/717/ END:VEVENT BEGIN:VEVENT SUMMARY:CHPC Industry engagement session DTSTART;VALUE=DATE-TIME:20181206T090000Z DTEND;VALUE=DATE-TIME:20181206T103000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-852@events.chpc.ac.za DESCRIPTION:Speakers: Werner Janse Van Rensburg (CHPC)\nThe CHPC will be e ngaging with its non-academic users on Thursday 6 December. The format of the meeting will be similar to previous years\, and mostly involves recei ving feedback from the active commercial and public sector user base. \n\ nThe purpose of the meeting is to strengthen collaboration with the non-ac ademic users\, exchange experiences and discuss the way forward. Attendee s who are currently active CHPC users will be requested to give a short in troduction to their HPC-related work.\n\nAlthough the focus of the meeting will be to engage with past and current non-academic users\, the meeting will also be open to any individual or organisation wishing to learn more about what the CHPC offers to industry and the public sector.\n\nhttps://e vents.chpc.ac.za/event/33/contributions/852/ LOCATION: Meeting Room 10 URL:https://events.chpc.ac.za/event/33/contributions/852/ END:VEVENT BEGIN:VEVENT SUMMARY:Research Data Management: The Security Imperatives DTSTART;VALUE=DATE-TIME:20181205T100500Z DTEND;VALUE=DATE-TIME:20181205T102000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-883@events.chpc.ac.za DESCRIPTION:Speakers: Uche M. Mbanaso ()\nResearch data management (or RDM ) is a growing phenomenon\, and is largely concerned with the creation\, o rganization\, storage\, safeguarding\, and dissemination of data related t o research works. One of the key components of RDM activity is safeguardin g the data\, which undoubtedly includes security of the data. However\, re search data security is hardly discussed in the literature resulting to hu ge gap in assuring its security properties. Unarguably\, research data com es in various forms and formats\, and of different intrinsic value. It mea ns that the sensitivity of research data may vary from research thematic a rea or environment\, and may contain significant sensitive data that can n ecessitate some degree of security. This requires understanding of securit y requirements to proportionately safeguard research data. In this present ation\, data security is examined in the context of research data especial ly confidentiality\, integrity\, authenticity\, availability\, non-repudia tion and trustworthiness attributes. A framework is proposed on how resear chers and research data management operators can preserve research data se curity proportionally.\n\nhttps://events.chpc.ac.za/event/33/contributions /883/ LOCATION: Meeting Rooms 8+9 URL:https://events.chpc.ac.za/event/33/contributions/883/ END:VEVENT BEGIN:VEVENT SUMMARY:First−Principles Study of Semiconductor-Based Photocatalyst Mate rials for Environmental Remediation DTSTART;VALUE=DATE-TIME:20181203T100000Z DTEND;VALUE=DATE-TIME:20181203T102000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-716@events.chpc.ac.za DESCRIPTION:Speakers: Penny Govender (Department of Applied Chemistry\, Un iversity of Johannesburg)\nDue to increasingly global environmental and en ergy crises\, visible light semiconductor photocatalyst with a tunable ban dgap and optical properties have received attention. For this reason\, dev eloping efficient and cost–effective photocatalysts for environmental re mediation is a growing need\, and semiconductor photocatalysts have now re ceived more interest due to their excellent photocatalytic stability and a ctivity. The charge transfer\, catalytic stability\, electronic and optica l properties of several semiconductor–based photocatalyst materials were systematically studied using first–principles study. All the calculatio ns were performed using the Cambridge Serial Total Energy Package (CASTEP) code [1] implemented in Materials Studio 2016 [2] with the plane–wave u ltrasoft pseudopotentials method [3] and Perdew–Burke–Ernzerhof (PBE) functional for the exchange and correlation contribution [4]. All the simu lations were done using the resources provided by the Centre for High Perf ormance Computing (CHPC)\, Rosebank\, Cape Town [5]. The proposed photocat alyst materials show high photocatalytic activity under visible light irra diation with good stability and reduced bandgap compared to the bulk semic onductor. The heterostructures formed a type−II band alignment to accele rate the interfacial charge transfer process and the photocatalytic activi ty. By comparing the relative ratio of effective mass and band alignment r esults\, we could conclude that heterostructures have not only superior mo bility of charge carriers\, but also higher separation of photoinduced ele ctrons and holes.\n\nReferences\n[1] M. Segall\, P.J. Lindan\, M.a. Prober t\, C. Pickard\, P. Hasnip\, S. Clark and M. Payne. First–principles sim ulation: ideas\, illustrations and the CASTEP code. Journal of Physics: Co ndensed Matter 14 (2002) 2717–2744.\n[2] Materials Studio simulation env ironment. Release 2016\, Accelrys Software Inc\, San Diego\, CA (2016) \n [3] D. Vanderbilt. Soft self–consistent pseudopotentials in a generalize d eigenvalue formalism. Physical Review B 41 (1990) 7892–7895.\n[4] J.P. Perdew\, K. Burke and M. Ernzerhof. Generalized Gradient Approximation Ma de Simple. Physical Review Letters 77 (1996) 3865–3868.\n[5] Center for High Performance Computing. CHPC.\n\nhttps://events.chpc.ac.za/event/33/co ntributions/716/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/716/ END:VEVENT BEGIN:VEVENT SUMMARY:KEYNOTE 3: NRENs: The Pathways to Global Knowledge and Collaborati on DTSTART;VALUE=DATE-TIME:20181204T070000Z DTEND;VALUE=DATE-TIME:20181204T074500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-808@events.chpc.ac.za DESCRIPTION:Speakers: Michael Foley (World Bank)\nThe presentation will fo cus on the key aspects of the report of the World Bank on "The Role and St atus of National Research and Education Networks in Africa" [1]\, which ar e applicable universally. The aim of this report\, which is an open educat ion resource\, was to provide guidance to governments\, institutions\, and development partners on how to approach the provision of advanced informa tion and communication technology (ICT) services to the higher education a nd research community in Africa. The premise of the report that the organi zation of ICT services and connectivity is best provided by a dedicated or ganization called the National Research and Education Network (NREN) is ba sed on international best practice and is applicable worldwide.\n\nBeginni ng with a brief overview of progress to date in all regions in Africa\, in cluding North Africa\, the presentation will dwell more extensively on the important but often invisible role that NRENs play in the creation and th e sharing of knowledge. NRENs not only provide the essential connectivity services to higher education institutions\, but they do it uniquely withi n a global community that has its own rules and agreements for access and identity. In this way they provide customized services to the academic com munity that are not part of the offering of commercial Internet Service Pr oviders (ISPs). The creation of an NREN in a country\, that is also connec ted to its neighbours and globally\, is a vital step to break through the academic isolation that universites and colleges may have experienced in t he past and it can be the catalyst to be invited to join international res earch consortia. Creating new knowledge through research is now a thorough ly collaborative global endeavour\, but partipation is limited to those wi th adequate connectivity. And teaching and learning itself\, the ‘E’ i n NREN\, has moved beyond dependence on textbooks and local lectures to an exercise in independent learning based on researching multiple sources of knowledge\, which are primarily in digital form and accessible through el ectronic networks.\n\nThe presentation will outline the case for the estab lishment of an NREN\, along with the services that it may provide\, with p ossible governance models\, and the various ways it can be made financial y sustainable. Finally\, the trends in the use of ICT in higher education and how they might affect the operation of NRENs are discussed as a prelud e to guidance on how to go about establishing or strengthening an NREN\, w ith recommendations to the government\, the private sector\, institutions\ , and development partners. \n\n\n[1] https://openknowledge.worldbank.org/ handle/10986/26258\n\nhttps://events.chpc.ac.za/event/33/contributions/808 / LOCATION: Hall B+C URL:https://events.chpc.ac.za/event/33/contributions/808/ END:VEVENT BEGIN:VEVENT SUMMARY:KEYNOTE 6: Big Data Analytics: Does Data Quality Really Matter? DTSTART;VALUE=DATE-TIME:20181205T074500Z DTEND;VALUE=DATE-TIME:20181205T082500Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-819@events.chpc.ac.za DESCRIPTION:Speakers: Bhekisipho Twala (University of South Africa)\nBig D ata analytics is the often complex process of examining large and varied d ata sets -- or Big Data -- to uncover information including hidden pattern s\, unknown correlations\, market trends and customer preferences that can help organizations make informed business decisions\, including new reven ue opportunities\, more effective marketing\, better customer service\, im proved operational efficiency and competitive advantages over rivals. Nume rous industrial and research databases have quality issues including outli ers\, noise\, missing values\, and so on. In fact\, it is not uncommon to encounter databases that have up to a half of the entries missing\, making it very difficult to mine them using data analysis methods that can work only with complete data. Currently\, comprehensive analysis and research o f quality standards and quality assessment methods for big data are lackin g. First\, this talk summarizes reviews of data quality research. We then analyze the data characteristics of the Big Data environment\, and present quality challenges faced by Big Data. Finally\, we construct a dynamic as sessment process for data quality.\n\nhttps://events.chpc.ac.za/event/33/c ontributions/819/ LOCATION: Hall B+C URL:https://events.chpc.ac.za/event/33/contributions/819/ END:VEVENT BEGIN:VEVENT SUMMARY:High throughput computing considerations for Public Health Genomic s DTSTART;VALUE=DATE-TIME:20181203T090000Z DTEND;VALUE=DATE-TIME:20181203T092000Z DTSTAMP;VALUE=DATE-TIME:20260413T052828Z UID:indico-contribution-33-905@events.chpc.ac.za DESCRIPTION:Speakers: Alan Christoffels (University of the Western Cape)\n Bioinformatics occupies the space between biology and computing and aims t o answer\nquestions in biology using analytical and computing methodology. At the South African\nNational Bioinformatics Institute (SANBI)\, our res earch focus is on methods to store\, retrieve\nand analyze genetic informa tion that spans both communicable and non-communicable\ndiseases. In the c ontext of Public Health\, that is a need to interrogate genetic informatio n\n(DNA) from both hosts (human) and pathogens (bacterial or viruses) to u nderstand\nsusceptibility to diseases and ultimately to track infection tr ends in real time.\nThe ever-increasing volume of data being generated in the public domain places a strain on\nin-house computing resources. While the computing facility at SANBI-UWC is adequate for\ninitial R&D\, these r esources are inadequate to complete projects timeously. The nature of\nthe bioinformatics workflows that require CHPC resources can be grouped into (1) high\nthroughput computing resources that are needed to describe the 1 000s of genetic messages\nin a genome\, versus (2) high performance comput ing resources that is needed to model a\ndrug-protein interaction environm ent - these simulations require days/weeks of dedicated\ncompute time.\nWe have leveraged the CHPC facility in the context of infectious disease res earch with a\nview to analyze genetic variation in bacterial genomes\, and to identify drug targets in\npathogen genomes. These analyzes requires an environment that is able to support\nreproducible workflows and virtualiz ation of the software environment. Examples of these\nuse cases will be de scribed.\n\nhttps://events.chpc.ac.za/event/33/contributions/905/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/905/ END:VEVENT END:VCALENDAR