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Team CHPC takes second prize at the 2020 International Student Cluster Competition

 

The team of six undergraduate students has done the country proud and scooped second overall prize; results were announced during an online event on 24 June 2020.

The Centre for High Performance Computing’s (CHPC) national team was part of 82 university students from 11 countries that spent a month working feverishly on a cluster located at the National Supercomputing Centre of Singapore to try to win the overall prize of the International Supercomputing Competition (ISC) 2020 Student Cluster Competition.

South Africa was participating for the seventh time in the competition and has made it to the podium each time, winning three times, coming second three times and third once.

The ISC Student Cluster Competition went virtual this year and ran from 1 June to 24 June 2020. As part of this year’s competition, the ISC organising committee joined the global fight against COVID-19, and the competition included applications that address education and applied learning towards accelerating bioscience research and discovery. The student teams were tasked with testing several applications that are used by scientists and researchers to find cures against the virus.

Team South Africa is made up of six undergraduate students from Wits University, the University of the Western Cape and the University of KwaZulu-Natal namely Guy Axelrod, Victoria Bench, Michael Beukman, Sivenathi Madlokazi, Mikhail Vink and Kalreen Govender as well as Stephanie Agenbag who was the reserve from the University of the Western Cape. The team proceeded to the international round after winning the national one held in December 2019 at the CHPC’s National Conference in Johannesburg. Team South Africa is one of the only teams made up of undergraduate students and is also one of the few that does not have the same participants twice. “For the students to spend almost a month on this competition shows a lot of dedication in itself. The novelty of the applications was geared towards drug discovery using HPC. Well done to the entire team, the mentors from the CHPC and the organisers who ensured that this year’s competition take place irrespective of the challenges the world faced.

The participation of the team for the whole month mimicked the actual challenge that NICIS is facing now which is to ensure that we provide HPC resources for COVID-19 combat efforts in the country, whilst simultaneously looking at addressing issues of connectivity to enhance on-line learning.”, said the Centre Manager of the National Integrated Cyberinfrastucture System.

The ISC Student Cluster Competition encourages international teams of university students to showcase their expertise in a friendly, yet spirited competition, that fosters critical skills, professional relationships, competitive spirit and lifelong comradery. Since 2011, ISC has focused on introducing science, technology, engineering, and mathematics students to the world of possibilities that is High Performance Computing (HPC) – its leaders, opportunities and community, and helping develop critical skills that students will use long after completing their current studies. Each team comprised six students and up to two advisers, competes in the competition and takes part in the world’s oldest, and Europe’s premier, conference and networking event for the international HPC community.

 

Over the intense competition days, the teams demonstrate incredible capabilities to obtain the greatest performance across a series of benchmarks and applications. In parallel to their day-to-day learnings, the students’ novel approaches and unique perspectives gained during the competition are integral to our own education – teaching us how HPC influences our world.

 

Last Updated on Wednesday, 24 June 2020 13:35

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South Africa wins International Student Cluster Competition for the fourth time

A team of six South African undergraduate students has taken first prize against 13 teams at the International Supercomputing Conference (ISC) in Frankfurt, Germany. The spectacular success follows four days of working on a selection of tests and applications to optimise and run their computer cluster to demonstrate the performance of their chosen design. The competition took place from 16 to 19 June 2019.

The team of four University of Cape Town students and two University of the Witwatersrand students entered the very rigorous and fiercely contested competition following their success at the national round, where they beat nine other South African teams. The team was one of the few to be made up of 50% men and 50% women. Stefan Schröder, Dillon Heald, Jehan Singh, Clara Stassen, Anita de Mello Koch and Kaamilah Desai, under the supervision of team advisors  and computer engineers David Macleod and Matthew Cawood of the Centre for High Performance Computing (CHPC), took on 102 members of teams from the United Kingdom, United States of America, China, Taiwan, Spain, Switzerland, Estonia and Singapore.  The team took first place with the highest overall score for all the benchmarks they were given.

Competition sponsors

The team received a number of sponsorships for this competition including hardware, software and training. The total value of the South African team’s cluster was about R6 million and comprised of sponsorships from Dell EMC, Intel, Nvidia and Mellanox.

The CHPC holds the national round annually and sends different teams of undergraduate computer science and computer engineering students to participate in the international competition. Team South Africa has won the competition four times, in 2013, 2014, 2016 and 2019, and has taken second place twice, in 2015 and 2017. The teamcame third in 2018.

It all began in 2012, when a team of CHPC staff attended ISC in Germany and realised the potential of the Student Cluster Competition as an opportunity to create awareness for high-performance computing as a career and to develop the high-performance computing pipeline in the country. The team started planning a national competition that would culminate in a team of six who would represent South Africa on the international stage.

Getting started: Selecting teams for participation in the South African round

The team selection phase coincides with the CHPC’s Winter School. It is designed to impart critical knowledge for building a cluster, which includes using Linux systems, the basic software stack of a cluster, and considerations which should be taken into account when choosing hardware. Universities around the country are invited to send teams of four and the CSIR ensures that teams are entered from as many universities as possible, so that students from all backgrounds are given a chance to learn and compete. Team selection concludes with an assignment that requires each team to build a prototype cluster in the cloud. The teams selected from this round proceed to the national round of the Student Cluster Competition.

Getting to Team South Africa: Competing nationally

In the national CHPC Student Cluster Competition, participants build small high-performance clusters out of hardware provided by the CHPC and its industrial partners. The contest takes place at the annual CHPC National Conference. The participants are given a selection of applications to optimise and run on their cluster to demonstrate the performance of their design. 

Each team is assigned a budget and a parts list from one of the CHPC's industry partners. With this budget and parts list, the team must design a cluster, taking into consideration the set of applications that will be used to benchmark the cluster. Once the cluster's design is finalised, the hardware specification is submitted to the CHPC's partners for manufacturing.

The hardware, as specified in the cluster design, is delivered to the CHPC National Conference. There, the teams unpack their equipment, construct their cluster, install the software stack and perform benchmarks. The teams are judged on a combination of the performance of the applications and the design of the cluster.

South African team representatives go through extensive training after winning the national round, including travelling to the Texas Advanced Computing Centre in the United States of America, where they receive training from experienced administrators of supercomputing clusters on the design and administration of supercomputers.

Winning formula

According to the team advisor and manager of the CHPC’s Advanced Computer Engineering Lab, David Macleod, the South African team’s winning formula is to have dedicated students and sponsors. “Our sponsors are excellent and allowed the team to choose equipment without restriction or compromise. In turn the students put in a lot of time and effort before the competition and arrived at the competition well prepared,” he says.

“It really is excellent national progress. We have demonstrated consistently that talent and skills abound in our country. These teams come from different universities and provinces – showing that this is now national DNA,” says Dr Happy Sithole, Acting Director of the CHPC and Centre Manager of the National Cyberinfrastructure System (NICIS).

Last Updated on Thursday, 27 June 2019 06:35

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CHPC's Lengau hangs-on in the Top500 List

The CHPC's Lengau supercomputer has placed 496th on the computing comnunity's Top500 List. The list was announced at the International Supercomputing Conference in Frankfurt, Germany in June 2019. 

For the first time, all 500 systems deliver a petaflop or more on the High Performance Linpack (HPL) benchmark, with the entry level to the list now at 1.022 petaflops. Lengau has appeared on the Top500 List since her launch in June 2016 and is currently at 1.029 petaflops. In her first appearance in June 2016, she was at number 121. 

The Top 500 List lists computers ranked by their performance on the LINPACK benchmark (The LINPACK Benchmarks measure a system's floating point computing power. Introduced by Jack Dongarra, they measure how fast a computer solves a dense n by n system of linear equations, which is a common task in science and engineering). The list is announced in June and in November each year. With over 32000 cores, Lengau remains one of the fastest computers on the African continent, with a utilisation that averagares at 90%.

Lengau continues to put the country in the company of leading supercomputing nations. She has over 1500 registered users, 500 of which are actively engaged in over 200 research programmes. 

 

Last Updated on Thursday, 20 June 2019 19:22

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CHPC starts the year with Linux and Python training

The Centre for High performance Computing (CHPC) had a busy start to the year, with human capital development collaborations involving two of its stakeholders, North West University (NWU) and the National Institute for Theoretical Physics (NITheP).

NWU- CHPC Programming with Linux and Python collaboration:

As one of the universities that make use of the CHPC supercomputer, NWU sent a special request to the CHPC to send high performance computing specialists to conduct a five-day programming workshop aimed at providing basic to intermediate programming skills to the university’s teaching staff and postgraduate students.

The training took place from 14 to18 January at the university’s Potchefstroom campus.

The training consisted of two-days of Introduction to Linux (Ubuntu) and three days of Introduction to Python programming. The university received 75 applications for this workshop, of which 34 were accepted. The hands-on training was aimed at staff and postgraduate students in the fields of chemistry, physics, mathematics, applied mathematics, biology, bioinformatics, computer science and engineering, who had no prior knowledge of the programming languages.

Professor Du Toit Strauss of the NWU’s Centre for Space Research (CSR) says, “Our students need to be prepared to tackle the contemporary challenges posed by the fourth industrial revolution. Therefore, computational skills are essential. These hands-on training courses provide the participants with the necessary skills, and we are grateful to the CHPC for giving us and our students the opportunity be a part of this”.

“Based on the number of applications we received, it is clear that there is a need for similar training workshops and to branch out and become more inclusive across all disciplines in academia,” says Katlego Moloto, also associated with the CSR.

2019 CHPC-NITheP Summer School

In late January 2019, the CHPC and NITheP combined the 9th CHPC Introductory Programming School and the30th Chris Engelbrecht Summer School in a joint venture aimed at bridging the gap between theoretical studies and high performance computing. The workshop took place from 26 January 2019 until 6 February 2019, at the Premier Resort. The school that was attended by 70 students and speakers targeted Master’s and Doctoral students engaged in science and engineering degrees in South African Universities. The syllabus covered an introduction toLinux, which covered a basic introduction to the Linux command line, bash scripting and Introduction to PBS Pro and job submission at CHPC. It was conducted by Dr Krishna Govender, CHPC Research Scientist, with the support of Dr Daniel Moeketsi, CHPC Research Scientist and HPC Technician, Zama Mtshali.

Dr Andrew Gill, CHPC Research Scientist, then led the session on Python Programming and was supported by HPC Technicians William Phukungwane and Sakhile Masoka. Their session covered the basics of python and syntax, advanced function, using matplotlib with python and the use of advanced mathematical packages, such as numpy and scipy.

The school was complimented by other institutions that conducted tutorials and talks around related topics, such as Foundations of Theoretical and Computational Physics, Foundations of Theoretical and Computational Biology, Foundations of Theoretical and Computational Chemistry, Foundations of Quantum Information Processing and Computation and Machine Learning as a Tool for Theoretical and Computational Science.

Why is training in Linux and Python so important in the world of big data?

CHPC’s scientists Drs Daniel Moeketsi, Krishna Govender and Andrew Gill are some of the CHPC staff who run training courses in Python and Linux regularly, both in South Africa and in the Square Kilometre Array’s African Very Long Baseline Interferometry Network partner countries.

Dr Moeketsi explains that almost all of the top 500 supercomputers in the world are using Linux, including the CHPC’s Lengau machine. “In this intervention, the centre is assisting in training students and researchers to be proficient in Linux and Python, so that they can maximise their use of Lengau. This training is crucial for high performance computing and big data science,” he says.

Last Updated on Thursday, 21 February 2019 13:51

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