CHPC Conference 2017

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Material Science Codes

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DL_POLY Performance Benchmarking and Scaling

Last Updated on Thursday, 18 August 2016 10:12

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Computational Fluid Dynamics Codes

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Evaluating parallel scaling with typical real-world scaling

Last Updated on Thursday, 18 August 2016 09:26

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CHPC in the News

SA crunches into the collider data grid

South Africa has joined the computing grid for the largest particle accelerator in the world, the Large Hadron Collider (LHC).
The collider, which straddles the border between France and Switzerland and is about 100m underground, is a massive particle accelerator, owned by the European Organisation for Nuclear Research (Cern).

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Cultivating HPC in South Africa

When you think of high-performance computing on a global level, heavy hitters from the US, Europe and Asia may spring to mind. But the democratization of HPC has brought an array of new entrants eager to climb this latter. In South Africa, for example, an emphasis on research and development is helping the nation to not only improve the lives of its citizens, but also make a name for its academic and scientific community along the way.

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CHPC Propels Supercomputing in South Africa

Over at, CHPC Communications Manager Noxolo Moyake describes how the South African Center for High Performance Computing is fostering the use of supercomputing in the region.

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Establishing the Footprint of an African HPC Centre – Creating and Sustaining HPC in South Africa

Increasing investment in research in many western countries is still a matter that sparks debate and maybe even controversy. But increasing research investment in Africa by an African government is a whole new ballgame. The continent continues to battle bread-and-butter challenges, but in 2006, South Africa saw research investment as a tool to drive social and economic development.

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Last Updated on Tuesday, 09 June 2015 11:30

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Lengau Cluster

Lengau Cluster 

CHPC has of 7 June 2016, unveiled a brand new machine and she is called Lengau, seTswana for Cheetah. The peta-scale system consists of Dell servers, powered by Intel processors, using FDR InfiniBand by Mellanox and is managed by the Bright Cluster Manager. 





Intel Xeon (R) E5-2690 V3

Intel Xeon (R) E7-4850

CPU Clock

2.6 GHz

2.2 GHz

CPU Cores



Number of Nodes




126 TB

5 TB

Rpeak 1006 TFlops  
Rmax 782.9 TFlops  


FDR  Infiniband Network

FDR  Infiniband Network

Shared Storage

4 PB Lustre Storage

4 PB Lustre Storage

Launch Date

7 June 2016

7 June 2016


Last Updated on Monday, 13 June 2016 11:35

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Bioinformatics Service Platform

BSP logo


The Department of Science and Technology has contracted with the Council for Scientific and Industrial Research for CHPC to establish and host the Bioinformatics Support Platform (BSP). This contract of the BSP was based on a proposal submitted and approved by DST to expand from the pilot project (which was funded in 2013/14 financial year) into a national platform, with the possibility of extending it into a national institute of applied bioinformatics/computational biology. The BSP is overseen by a steering committee as well as two subcommittees for Services and Training respectively.

Key objectives

The following are the main objectives for the BSP in the 2014/15 financial year:

  • establish and implement a governance framework
  • define business model, service level agreements, and operational procedures
  • assemble a BSP team
  • provide bioinformatics services to academic and industrial researchers
  • provide support to bioinformaticians in lab-based research groups (embedded bioinformaticians);
  • install and maintain relevant software tools and data resources
  • improve the usability and accessibility of CHPC facilities
  • interact with the wider biological science communities and foster formalised collaboration
  • provide a coordinated platform of relevant bioinformatics services
  • facilitate specialised short-term courses and postgraduate training
  • foster collaboration with the private sector
  • engage in international activities to improve capabilities and attract projects and funding


Technical and Research Support

The application scientist (Dane Kennedy) interacts with the commercial/academic researchers, providing programming, application and experiment analysis support, conducts training to improve the affectivity of HPC users, and assists in the setup, running and development of HPC software and job scripts, while the systems engineer (Inus Scheepers) sets up and ensures the availability of computing, storage and network resources for computational biology work, and explores hardware and software options to support and amplify the research efforts. These job functions overlap to some extent. BSP makes use of a dedicated cluster node and virtual machines to stage and manage cluster jobs, deploy various software systems, and host training-related material.


The BSP web site has been set up and populated, linking to the various resources available. The reference databases are regularly and automatically mirrored, and a mailing list, CHPC-Bio, was created on the CHPC list server for community announcements and discussions.


Human Capital Development

The BSP’s training activities will be coordinated by an Education Committee in conjunction with relevant stakeholders, including the South African Bioinformatics Society. They will determine the training needs and develop criteria for hosting or participating in a course and they will also develop appropriate evaluation procedures to ensure a high quality, integrated training programme. 

Last Updated on Tuesday, 17 February 2015 09:04

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CHPC in the News

Documentation for users:

Lengau Cluster Available

CHPC SAGrid Cluster Available

Dirisa Storage Unit Available

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