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NMMU hosts the 6th CHPC Introduction to Programming with Linux and Python School

CHPC started its week-long Programming with Linux and Python School at the Nelson Mandela Metropolitan University (NMMU), North Campus on Monday 18 January 2016.

About 60 Masters and Doctoral students in fields of science and engineering from universities all over South Africa gathered at the ICT Department of the university for the basic scientific programming course intended to introduce postgraduate students to Linux (Ubuntu) and programming with Python. The students are in the fields of chemistry, physics, mathematics, applied mathematics, biology, bioinformatics, computer science and engineering and are without prior or sound knowledge of Linux and Python scripting. The CHPC, as a national computing facility, is tasked with ensuring that South African researchers are able to run their scientific applications or codes on its multi-million Rand systems and to do this, researchers need to be trained on the best and most efficient ways of utilising this national investment. Training users allows them full control of their work with less help-desk support as CHPC systems run on Linux and therefore Python and Linux scripting skills are essential for HPC. The CHPC help-desk is available to support users further.

The course is practical in nature, with students spending the full six days in a computer lab doing hands-on practical work. Since 2011, the CHPC has trained over 200 students some of which already completed their doctorates studies in field related to High Performance Computing (HPC) and joined industry and academia.

The first two days cover:

Overview of Ubuntu Linux desktop, Running commands and getting help, Browsing the file system, the bash shell, Standard I/O and pipe users, groups and permissions, vi and vim editor basics, Linux file system in-depth, advanced topics in users, groups and permissions, printing, introduction to string processing and string processing with regular expressions, finding and processing files, investigating and managing processes, introduction to PBS Pro and; job submission at the CHPC.

The next four days cover:

Python basics and Python objects, numbers, sequences, dictionaries, conditional and loops, files and input/output; and error and exceptions. The course runs from 18-23 January 2016 and is conducted by the CHPC annually.

Last Updated on Thursday, 21 January 2016 14:05

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CHPC installs new system

CHPC users will notice that systems are currently inaccessible as has been communicated by the centre from the end of last year. At the CHPC National Conference in December 2015, the centre unveiled its new PETAFLOP (PFLOP) machine, a computer with processing speeds capable of a thousand-trillion floating point operations per second.

The installation of the new system means CHPC users can expect downtime as the current systems will be put out of commission and removed from 8 January 2016. It is estimated that the new system will be available to users from 8 February 2016, following the installation and testing phase.  

The increase in computing resources means the centre minimises the waiting time that users were subjected to, enabling CHPC to provide improved services to its growing clientele.

The new system consists of Dell servers, powered by Intel processors, using FDR InfiniBand by Mellanox and is managed by the Bright Cluster Manager. 

 

Last Updated on Friday, 08 January 2016 12:17

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Wits wins 2015 Student Cluster Competition

 

Wits University has for a second-year running, snatched the top position in the annual CHPC Student Cluster Competition, making Wits the main component of the South African national team that will proceed to the international competition. 
The event took place at the CHPC National Conference held at the CSIR international Convention Centre, 30 November - 4 December 2015. Nine teams were given a budget and a parts-list for the cluster they were to build, they then chose a design and made important decisions on what the main features of their machines would be. They were then given some benchmarks and surprise applications to run on their machines and a panel of international judges made assessments of their hard work. 

Prizes

Best Perseverance Award: Supercomputing Smoothy & White Hats
Most Creative Team: Team UKZN
Best Cluster Design: Super C's
Best Team Work: Deep Thought
Best Network Performance: Quad Core 2

Awards

3rd Place: Blink 10110110
2nd Place, highest Linpack and highest efficiency: Quad Core 1
1st Place: Wits 1
The South African competition is made up of teams of four while the international level requires teams of six. So the judges selected two members from the Stellenbosch University's team to make up the team to represent South Africa in Frankfurt, Germany in June 2016. 
In February 2016, the team of six will be visiting the Dell High Performance Computing Research and Development facility and the Texas Advances Computing Center in Austin, Texas. 
Watch here for the competition and the awards

Last Updated on Thursday, 07 January 2016 15:35

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Student Poster Winners at CHPC 2015 Conference

The CHPC National Conference held from 30 November to 4 December 2015 featured 20 student researchers who demonstrated their work through posters. Thy came from various South African institutions of higher learning and across many research domain and showcased their CHPC facilitated research.  

A panel of five independent judges, experts in the fields of engineering, biomedical applications, computational chemistry and material science evaluated the posters, most of which were in one of these fields. Five evaluation criteria were used, namely: presentation, use of high performance computing (HPC), scientific merit, quality of work and insight. The judges initially evaluated each poster independently, then compared notes and made a group decision on the winners.

Winners

 

In third place there were four winners:

  1. Sesham Srinu (UCT) – HPC and Computer Science: Optimal Approximate Entropy Detection for Dynamic Spectrum Access in Cognitive Radio
  2. Jean-Paul Fouche (CUBIC) – Health and Life Sciences: The ENIGMA-HIV working group: Association of CD4 with subcortical volume in HIV-positive adults
  3. Mofuti Mehlape (UL) – Material Science: Computational Modelling Studies of Pentladite Minerals: Atomistic Simulators Study
  4. David Tshwane (UL) – Material Science: Generation of MnO2 Nanotubes using Computer Simulation Strategy
 
Second Place
 
Elumalai Pavadai (UCT) – Computational Chemistry: (IN ABSENTIA) New Human Malaria Parasite Dihydroortate Dehydrogenase Inhibitors by Pharmacophore and Structure-based Virtual Screening.
 
First Place
 
Arodola Olayide (UKZN) -- Health and Life Sciences: Flap Dynamics Study of Human Cathespin D in the Treatment of Breast Cancer using Multidimensional Computational Analysis
 

Last Updated on Thursday, 07 January 2016 13:42

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CHPC in the News

Documentation for users:

Tsessebe Cluster Unavailable

Graphical Processing Unit Cluster Unavailable

CHPC SAGrid Cluster Available

Dirisa Storage Unit Unavailable

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