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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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DST interns pay a visit to the centre

A group of 10 interns from the Department of Science and Technology's (DST) International Cooperation and Resources Directorate are currently on a tour of all the department's entities with an element of international relations. The group visited the CHPC recently.

During the visit to the centre, CHPC Research Manager, Dr Werner van Rensburg provided a talk on the work of the centre and the integral role of the other three legs of South Africa's Cyberinfrasture - the South African National Research Network and the Data Intensive Research Initiative of South Africa. 

The interns showed much interest in the technical make-up of Lengau - the centre's computing cluster, how the machine is cooled and the power supply infrastructure for the machine. They also visited the centre's Advanced Engineering lab whose main focus is the evaluation and development of products and technologies for HPC.  

The interns were accompanied by Siphokuhle Zwane from the DST and he is explained the importance of these site visits, "It is important to us that the interns get a full understanding of what the bilateral and multilateral discussions entail technically and that they get a feel of the social impact of the work the department does, something they would not feel sitting in the office, that is why we take them through the sites that have an international relations component", he said. 

The visit ended with a walk-about of the centre and was followed by visits to other sites such as the Cape Town harbour to see the Algoa Research Vessel, Parliament, Hydrogen South Africa at the University of the Western Cape, EndoAfrica at Stellenbosch University and Shark Spotters in Fish Hoek.


Last Updated on Thursday, 21 February 2019 13:56

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CHPC recognised for HPC development in Mozambique

During the MoRENet (Mozambique Research Network) Conference held in Maputo, Mozambique, 10-11 December 2018, the CHPC was recognised for its contribution towards development of HPC in Mozambique. The honourable Minister of Science, Education and Technology, Prof. Jorge Nhambiu, issued the CHPC with a Certificate of Recognition received by Dr Werner Janse van Rensburg, CHPC Research Manager, at the closing ceremony of the MoRENet Conference. This recognition is a positive confirmation of the tireless efforts by CHPC Director, Dr Happy Sithole, to advance engagement with Mozambique as part of the CHPC Square Kilometre Array (SKA) Readiness program. The recognition in particular recognises a number of MoRENet engagement and collaboration events that took place in Mozambique in 2018 as part of the CHPC HPC Ecosystems Project, under leadership of Mr. Bryan Johnston. This include HPC site investigation visits, engagements with potential HPC users in Mozambique, deployment of two sets of HPC hardware (C6100 and Stampede equipment) and systems administrators training. In addition, continued collaboration with Mozambique as part of Southern African Development Commuity HPC initiatives, SKA ministerial engagements, recent initiatives for Mozambique towards European Organisation for Nuclear Research support as part of their HPC offering and the participation of Dr Janse van Rensburg as invited speaker at the MoRENet Conference, demonstrate the active engagement between the CHPC and MoRENet. The highly successful collaboration established in 2018 provides a sound basis for further growth in collaboration opportunities in 2019 between the CHPC and MoRENet.


Last Updated on Wednesday, 19 December 2018 10:44

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CHPC National Conference hits 500 mark

Over 500 delegates participated in the 2018 CHPC National Conference which took place in Cape Town early December. The conference consisted of local and international delegates as well as representatives from the South African Development Community (SADC).  

The comprehensive programme included national and international contributions as well as contributions from cyberinfrastructure system partners: the South African National Research Network and the Data Intensive Research Initiative of South Africa. Captains of the HPC Industry across the globe provided key talks and workshops during the conference week and they included: Patricia Damkrogel, Vice President and General Manager of Intel, Thomas Sterling from Indiana University, USA; Michael Foley who has recently retired from the World Bank, Bhekisipho Twala from the University of South Africa, Khutso  Ngoasheng from the South African  Radio Astronomy Observatory, Elmarie Biermann from the Cyber Security Institute and many others. 

The SADC HPC Collaboration Forum participated in discussions around the HPC framework and implementations plans for a regional HPC facility that would be used to find scientific solutions for common problems and other research in which member states could collaborate. 

Parallel to the intricate workshops, keynote talks and discussions was a platform for South African students to showcase their skills in building supercomputers and their innovative ideas on how to prevent cybercrimesthrough the Student Cluster Competition, and the Student Cyber-Security Challenge.

This year, following the theme of the conference on how HPC transforms for the future, increasing the participation of women in HPC was prominent. This was supported by the introduction of a sponsorship for an outstanding woman in the Student Cluster Challenge.

The award in this newly introduced category, sponsored by Intel, was taken by Ms Mapule Madzena, a student from the University of the Free State. She was hailed as the best female student and walked away with R64 500.

Student Cluster and Cyber Security Competitions

Six students from the University of Cape Town (UCT) and the University of the Witwatersrand (WITS), who came out tops at a national student cluster competition to build a supercomputer, will fly the South African flag high at the International Student Cluster competition in Germany, in June next year.

During the competition, 10 teams of students from various universities in the country battled it out to build small high performance computing clusters on the exhibition floor – using hardware provided by CHPC and its industrial partners – and raced to demonstrate the best performance across a series of benchmarks and applications.

Sefan Schroder, Dilon Heald, Jehan Singh and Clara Staasen from UCT; Anita de Mello Koch and Kaamilah Desai from WITS, will test their skills against their international counterparts’ when they compete with students from 11 countries that including China, Germany, Poland, Singapore and Thailand, among others.

In the cybersecurity challenge, the University of Pretoria came first, followed by Stellenbosch University. This competition provides a platform for students to compete in real-time and come up with ideas that could protect South Africa from cybercrimes. The winning team will compete at an appropriate international competition, such as the European Cyber Security Challenge.

Speaking at the conference, DST Chief Director: Emerging Research Areas and Infrastructure, Dr Daniel Adams, said that the event was critical to develop the skills needed in the country.

“The DST remains committed to supporting skills development and new interventions. The CHPC is a great platform to stimulate the pipeline and boost human capital development. Initiatives such as these have led to slow, but steady, improvement in the enrolment of doctoral degrees,” he said.

CHPC Director, Dr Happy Sithole was impressed with the calibre of student who participated in the competitions. “I am very proud of the kind of innovation displayed by the students. I believe that they will represent us well at international stages.These competitions are critical to equip the future generation with cyberinfrastructure, supercomputing experience and expose science, technology, engineering, mathematics and innovation students to an array of opportunities”.

Over the years, South Africa has performed well at the International Student Cluster competition, wining it in 2013, 2014 and 2016, while coming second in 2015 and 2017. In June this year, the team came third, after two teams from China at the cluster challenge in Frankfurt, Germany.

Dr Sithole was also pleased with the progress made in building a strong high performance computing community in the country.

“This year, our focus was on the transformation of both the use and development of cyberinfrastructure, which will help the industries, academics and the nations from across the continent. Looking back at the first meeting where we engaged in the discussions of building a strong high performance computing community in South Africa, and advocating for financial support from government, significant growth has been achieved. Notably, it is now a continental focus, not only on computing, but overall cyberinfrastructure growth and demonstration of impact", he said.

Student Poster Competition

The conference also had 60 students showcasing their research posters for work conducted through the use of high performance computin. The poster students were judged mostly by external adjudicators under the following criteria: quality of the poster, the high performance computing content and quality of research, their ability to communicate the science content and the general impression of the presentation. The winner of the Masters-level poster was Beauty Shibiri from the University of Limpopo for the abstract title: Investigating the Structural and Volume Changes of Composite Layered-Spinel Nanoporous Li-Mn-O Electrode Materials. In the Doctoral-level, the award went to Elkana Rugut from WITS for the abstract title: Thermoelectric Properties of CdAl204 spinel.

Exhibition area

The expo zone of the conference consisted of industries who provided valuable support to the funding of the conference, companies like Intel (diamond sponsor), Altair and DellEMC (platinum sponsors) and Mellanox and Hewlett Packard (gold sponsors) ensured that the CHPC is able to bring leading speakers to add to the stature of the conference. 

Other sponsors included Student Cluster Competition sponsors: DELLEMC, Eclise Holdings, Altair, Bright Computing, Mellanox, Microsoft and Intel; as well as Student Cyber Security Challenge sponsors: Microsoft and MWR.

A glipmse at CHPC 2018

Please visit the gallery to see photos from the conference.

Student Cluster Competition video can be viewed here.

Student Cyber Security challenge video can be viewed here.

Last Updated on Thursday, 13 December 2018 11:01

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