A+ A A-

Winner: CHPC User Satisfaction Survey

Miss Olayide Adebimpe Arodola, a UKZN masters graduate in Pharmaceutical Chemistry, was selected in a lucky draw, the winner of the CHPC User Satisfaction Survey. She has won a tribal chess set and a travelling laptop bag. 

Olayide has a Masters Degree in Pharmaceutical Chemistry, specialising in molecular modelling and drug design research. She was involved in two of her own projects, which were successfully completed in 2013. In her masters, Olayide excelled exceptionally, she has one publication in a highly ranked peer-reviewed journal and a second one awaiting reviewer’s comment.

Her publication and MSc dissertation are as follows:

  1. Arodola, O.A., Radha Charan, D., and Mahmoud, E.S.S. (2014) QSAR study on diketo acid and carboxamide derivatives as potent HIV-1 integrase inhibitor, Letter of Drug Design and Discovery, 11, 618-627.
  2. Arodola O.A., Molecular Modeling Studies on HIV-1 Inhibitors and their potential use as Anticancer agents, M.Sc dissertation, University of KwaZulu-Natal, 2014.

Her dissertation is not yet published. 

Congratulations Olayide!

Last Updated on Wednesday, 05 November 2014 11:25

Hits: 1936

South Africa retains supercomputing championship

South Africa has successfully defended its championship of the International Student Cluster Competition, winning the overall prize in Leipzig, Germany.

The announcement made on 25 June 2014, shocked many attendees of the International Supercomputing Conference since it is the first time a team wins the competition two years in a row. The South African Team of six was also the youngest as it was made up of undergraduate students only. 

The High Performance Computing (HPC) Advisory Council Student Cluster Challenge is an opportunity to showcase the world's brightest computer science students' expertise in a friendly, yet spirited competition. Team preparations prior to the competition includes working with supervisors and vendor partners to design and build a winning cluster from commercially available components without exceeding the set power limitations, and to learn the predetermined HPC applications. The Dell computing company was the vendor partner behind the South African Team, proving all equipment. Dell also sponsored a trip to its headquarters in Austin, Texas and to the Texas Advanced Computing Center where the team received a tour of the facilities and mentoring from technicians that manage the centres. NVIDIA sponsored Graphics Processing Unit (GPU) accelerators for the team and Mellanox sponsored the interconnect.

South African team members:

·       Eugene de Beste - University of the Western Cape

·       Nicole Thomas - University of the Western Cape

·       Saeed Natha - University of the Western Cape

·       Warren Jacobus - University of the Western Cape

·       Pieter Malan - University of Stellenbosch

·       Ellen Nxala - University of Fort Hare

Team Supervisors:

David Macleod – CHPC

Vernon Nichols – DELL

Nicholas Thorne – CHPC

Technical Specification:

Head Node (Dell R320):

·       Intel E5 v2 Processor

·       8GB RAM

·       400GB RAID1 Array

·       2.4TB RAID0 Array

·       Infiniband FDR

8x Compute Nodes (Dell R720):

·       2x Intel E5-2660v2 Processors

·       64GB RAM

·       NVIDIA 40m GPU

·       Infiniband FDR

Tasks Performed:

Day 1:


High Performance Computing Challenge


Day 2:


Quantum Espresso

High Performance Conjugate Gradient (a surprise application)


Day 3:


Lowest power consumption to complete a task (Surprise Task)


The challenge also featured High Performance LINPACK (HPL) as a side competition. The HPL score does not count towards the overall competition. To win HPL teams have to build a cluster specifically for it by using more GPUs per node and fewer nodes. This however, has a negative impact for the main competition because the team would have fewer CPU cores.

The team that won HPL had two GPUs per node and only 4 nodes. This means they had enough power to use all their GPUs and some of their CPU cores to run LINPACK. Team SA also had 8 GPUs but double the nodes. This means the team only had enough power to run LINPACK on the GPUs. All the CPU cores sat idle.

The South African cluster was deemed better balanced than those of other teams.


Teams entered into the competition included:

·       Ulsan National Institute of Science and Technology (UNIST), South Korea

·       A combined team of students from Massachusetts Institute of Technology (MIT), Bentley University, Northeastern University (NEU), United States

·       The University of Edinburgh (EPCC), United Kingdom

·       Chemnitz University of Technology, Germany

·       University of Hamburg, Germany

·       University of São Paulo, Brazil

·       University of Colorado at Boulder, United States

·       University of Science and Technology of China (USTC), China

·       Two additional university teams from China 

CHPC begins its Winter School next week where the selection for the 2015 team will begin. 

Last Updated on Monday, 30 June 2014 10:14

Hits: 3134

Tiahne-2 retains No.1 supercomputer status

Tianhe-2, a supercomputer developed by China's National University of Defense Technology has retained its position as the world's No.1 system for the third consecutive time.  Tianhe-2 has performance of 33.86 petaflop/s (quadrillions of calculations per second) on the Linpack benchmark, according to the 43rd edition of the twice-yearly TOP500 list of the world’s most powerful supercomputers.

Please click here for more information.



Last Updated on Monday, 23 June 2014 14:28

Hits: 1733

The year for imprints on international projects

CHPC has made significant progress in ensuring world-class computing services to its user-base, affiliated with international science and technology projects and put human capital development in the fore-front of its planning in the 2013-14 financial year.


CHPC joins SKA

CHPC has joined the Square Kilometre Array (SKA) project and forms part of the Science Data Processing (SDP) Consortium of SKA together with Cambridge University, SKA-SA and Daresbury Laboratories.

Organsations wishing to affiliate with the global project sent proposals to the SKA Office for participation. This was followed by SKA presentations of Work Package Consortia that showcased an overview of the composition, people, work concepts and approach to each particular work package. In the SDP Consortium, centre is set to contribute towards three full-time equivalent work packages: exascale prototypes, tiered data delivery and science support. In the financial year ended, CHPC participated in a number these SKA meetings. At the January 2014 meeting, held at the Juelich Supercomputing Center, final prototypes were discussed. The current heterogeneous architecture test-bed provided by CHPC, with a mixture of accelerators, will form part of the prototypes. The drive to enhance HPC astronomy competence in the centre has resulted in significant progress in the building the relationships with the MeerKAT and SKA teams.


Centre’s Student Cluster Competition wins international competition

Team South Africa scooped overall top honours on 19 June 2013 at the international Student Cluster Challenge in Leipzig, Germany, achieving the highest aggregate points total for all the benchmarks included in the competition (Linpack and the chosen applications) and acing the interview with the judges. South Africa’s resounding success was unsuspected since the country was a first time entrant. The team won over seasoned competitors from USA, China, Germany, UK and Costa Rica.

The Student Cluster Challenge is hosted by the International Supercomputing Conference (ISC) and is an opportunity to showcase student expertise in a friendly yet spirited competition. The Centre for High Performance Computing was the organizer of South African competition. In the challenge, students have a unique opportunity to learn, experience and demonstrate how high-performance computing influences our world and day-to-day learning. Held in collaboration with the High Performance Computing Advisory Council and ISC, the Student Cluster Challenge is designed to introduce the next generation of students to the high performance computing world and community.

One of the students who participated in the national competition, Mathew Cawood, completed his honours degree utilising CHPC resources. He has now been awarded a Master’s studentship and placed in the centre’s the Advance Computer Engineering Lab. The experience in the competition will assist South Africa grow a generation of high performance computing expertise for national economic development and for large projects such as SKA. South Africa will enter as defending champions in June 2014 and hopes to continue flying the flag.


HPC enabled research output

The centre’s computational resources enabled about 60 peer-reviewed publications by users and 55 completions of postgraduate theses in the year. The centre is acknowledged in the published work.

After the successful completion of the pilot Bio-Informatics Service Platform (BSP), an extension of this project was granted by the Department of Science and Technology to increase the level of support for this community.


Tracking the centre’s utilisation in the year that was

The centre received 171 new users registration in the year, 1197 helpdesk calls, a system utilization of over 91% was realised, were 22.6 million total CPU hours was provided to 537 active users with 172713 running jobs.  The centre achieved a system uptime of approximately 83.8% where 5.2% was scheduled downtime for maintenance.

After the implementation of the new workload manager in the third quarter, there was significant improvement of the resource allocation to the research community. The cluster utilisation now averages about 75% with significant improvement of applications’ efficiency, where all CPU reserved for jobs are utilised.


Last Updated on Friday, 06 June 2014 13:46

Hits: 1700

CHPC in the News

CHPC SAGrid Cluster Available

Documentation for users:

Dirisa Storage Unit Available

Lengau Cluster Available

Social Share

FacebookTwitterGoogle BookmarksLinkedin

Website developed by Multidimensions