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Building High Performance Computing Capability in the African Continent/Happy Sithole

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High-level Meeting & Workshop on Environmental and Scientific Open Data for Sustainable Development Goals in Developing Countries. Madagascar, 4-6 December 2017

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Building High Performance Computing Capability in the African Continent/Happy Sithole

  1. 1. Building High Performance Computing Capability in the African Continent. International Workshop on Environmental and Scientific Open Data for Sustainable Development Goals in Developing Countries 5th September 2017
  2. 2. Background: The CHPC in SA CHPC
  3. 3. User Community: South Africa CHPC Existing Users Future Users
  4. 4. Slide #4 Background  CHPC is national HPC facility funded by the DST and managed by CSIR  It is part of the National Integrated Cyber- Infrastructure System (NICIS)  Started operations in June 2007  Staff complement of 40  CHPC has Research, Technical and Operational divisions  Provide HPC resources and services to universities, science councils and industry  Provide support to large scale science projects such as H3Africa, CERN, SKA and IPCC  Human Capital Development is core to CHPC success
  5. 5. Investment in HPC Systems 2007: IBM e1350; AMD Opteron; 2.4 GHz; 640 cores 2.5TFlops (Linpack) 2008: IBM Blue Gene/P; 0.8 GHz; 4096 c 11.5 Tflops (Linpack) 2009 : Sun Constellation Cluster 2.9/3.0 GHz; 2684 cores 27 Tflops (Linpack) 2010: GPU Cluster; 2.4 GHz 96 cpu cores; 22 GPU’s 16 TFlops (Linpack); 14 TB 2011: Tsessebe Cluster Upgraded 2.9GHz (4032 cores) 61.6 Tflops total (Linpack) 4 PB DIRISA Storage Unit 90 TB GP File System Slide #5
  6. 6. Slide #6 System Configuration Phase 1 Phase 2 Dell PowerEdge C6320 Servers: Standard Compute nodes 128GB (64GB) / node 1 008 1 368 2 x Intel Xeon E5-2690 v3 (Haswell) processors (12 Cores Each  24 cores / node) 24 192 32 832 Dell PowerEdge R930 servers: Large Memory Compute Nodes 1024GB / node (FAT nodes) 5 5 4 x Intel Xeon E7-4850 v3 processors (14 Cores Each  56 cores / node) 280 280 Infiniband FDR 2:1 Blocking (56 Gbps) Parallel Storage (Useable) PB 4 4 Total Number of Racks (including Compute, Login, Management and Storage Nodes) 19 24 Centos 7.1 with Bright Cluster Manager and Altair PBS Pro Total Linpack Performance (Tflop/s) 783 1029 The Road to PetaFLOP 3 May 2016 7 March 2017
  7. 7. Launch of the HPC system • 127 on TOP500 • Awarded the fastest supercomputer in Continent
  8. 8. Slide #8 Materials Science 26% Chemistry 23%Earth Sciences 15% Bioinformatics 12% Health Sciences 11% Astronomy 5% Other 8% Resources at the CHPC CPU Hours: Science Domain Distribution
  9. 9. Slide #9 Who is using the CHPC? # Research Programs: Research Domain Distribution (210 Programs) Materials Science 14% Chemistry 22% Earth Sciences 9%Bioinformatics 17% Health Sciences 5% Astronomy 7% Physics 2% Engineering 13% Applied Mathematics 5% Computer Science 2% Other 4%
  10. 10. Slide #10 Who is using the CHPC? Non-Academic Public  CSIR  SAWS  ARC  NZG  SAAO  SANBI  Sugar Institute  NICD  NECSA SA Academic 75% SA Public 14% SA Industry 7% African Academic 4% Research Programmes Distribution
  11. 11. Slide #11 Student Cluster Competition (SCC): Training undergraduate students in HPC Three stage program: (1) Winter school: 22 teams (2) CHPC National Meeting: 10 Teams (3) ISC: 1 Team representing SA ISC’15 Runner-Up Frankfurt ISC’14 Champions Leipzig ISC’13 Champions Leipzig ISC’16 Champions Frankfurt Human Capital Development
  12. 12. Objectives • To assist SKA partner countries in establishing functional cyber- infrastructure components necessary to undertake science activities in radio astronomy. • To catalyse the development of a cadre of scientists and students equipped with relevant skills to undertake scientific activities in radio astronomy. • To build institutional capacities in targeted universities, research institutions and government departments to promote development of cyber-infrastructure in support of radio astronomy activities in SKA partner countries; • To mobilise funding and technical resources for relevant cyber- infrastructure and computational skills development in SKA partner countries; and • To facilitate strategic partnerships and collaborative efforts, both regionally and globally, in support of the development of relevant cyber- infrastructure and skills in SKA partner countries.
  13. 13. Big Data Proposal • Partner countries will provide a host institution to drive the developments of computing resources for the telescopes and for other relevant applications. • The designated host institution will fund the operational and maintenance costs of the computing and data storage infrastructure to agreed standards. • South Africa and international collaborators to provide training program in HPC and astronomy. • Introduce HPC modules in the curriculum at universities.
  14. 14. Model of access to HPC. • Strategy to repurpose HPC systems out of national production for local processing capabilities or training facilities. • Develop partnership with universities in partner countries to develop training programs. • Texas Advanced Computing Center, Cambridge and CHPC provided equipment. • South Africa, through DST provided some funding for additional network and storage equipment.
  15. 15. Slide #15
  16. 16. Computing Developments: Madagascar Contacts: IOGA (Institute & Observatory of Geophysics) U.Tana, U.Antsiranana, U.Toliara, U.Fianar Training: Sysadmin Data Science (linux+python+HPC intro) Intro to Astronomy (with NRAO in USA) Projects: Astro, Hydrology, Earth sciences, mathematics (3 CHPC users) Curriculum development for Astrophysics: MSc student (proposed post-doc placed in SA)
  17. 17. Slide #17 HPC on Common Ground Workshop Participants from Partner Countries attending the HPC “On-Common Ground” Workshop in Salt Lake City, USA.
  18. 18. Slide #18 Preparation of HPC systems
  19. 19. Slide #19 Badise Mosesane at CERN The CERN Summer Student Program accepts a limited number of students from over 60 countries to spend eight weeks at CERN. Students work side-by-side with student-peers and scientists on some of the world’s biggest experiments. http://www.stem-trek.org/2017/07/28/badisa-wk4/
  20. 20. Progress on SKA Readiness Item Comments Next stages HPC roll-out for Phase 1 (Botswana, Zambia, Namibia, Madagascar, Mauritius) All countries received the computing equipment and storage and network equipment. • Continue to drive utilisation of the systems and ensure sustainability. • HW Refresher through Stampede Training Workshops Astronomy, HPC , Materials Science, Bioinformatics and Climate Modelling. Emphasize the outputs such as students training, Flagship projects and publications. HPC roll-out for Phase 2 (Ghana, Kenya and Mozambique) Ghana received the equipment. Only two sites (Kenya and Mozambique) remaining. Engagements with Kenya and Mozambique on-going. Deployment of Software. Active research in Material Science and partnership with Newton Fund projects. CHPC, Development in Africa with Radio Astronomy (DARA) and Cardiff University. Research Cloud Research Project within SKA- SDP continuing. On-going preparation for deployment of OpenStack at all sites..
  21. 21. Slide #21 Progress in HPC Delivery Completed Progressing Not Started Infrastructure Staff Development Status of Hardware Power & cooling Datacentre ID'ed Equipment shipped SysAdmin / Linux Dedicated time SysAdmin Course Projects Working Group Operation al Used Needs Support Equipment To Operate Mauritius: University of Mauritius (UoM) 3 3 3 2 3 3 2 3 3 3 3 Namibia: Namibia University of Science & Technology (NUST) 3 3 3 3 3 3 2 3 3 2 3 Namibia: University of Namibia (UNAM) 3 3 3 3 3 3 2 3 3 2 3 Botswana: University of Botswana (UB) 3 3 * 3 3 3 3 3 3 3 3 Zambia: ZAMREN 3 3 2 3 3 3 3 3 3 3 3 Madagascar: University of Antananarivo (IOGA) 3 3 2 2 2 2 2 2 1 1 1 Ghana:: 3 3 3 2 3 2 2 3 2 1 3

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