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Jan 19, 2012

SA’s supercomputer back in world top-500 after R9m upgrade

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South Africa’s Centre for High Performance Computing’s (CHPC’s) Tsessebe Sun Constellation System has regained its position as one of the world’s fastest 500 supercomputers, following a R9-million upgrade.

The CHPC is an initiative of the Department of Science and Technology, and is driven by the Council for Scientific and Industrial Research.

The South African supercomputer now takes the 329th place in the international top-500 list, says CHPC director Dr Happy Sithole.

This ranking was confirmed in November, at the Super Computing Conference in Seattle, in the US. This followed shortly after a three-week upgrade of the machine in October, which saw the performance, as measured by the LINPACK Benchmark system, improve from 25 teraflops to 61 teraflops.

A teraflop refers to operating speed – and not storage capacity, which uses the byte-scale – with one teraflop equal to one-trillion floating point operations per second. This is largely similar to the older term of instructions per second. (To put this in perspective, consider that standard household computers and laptops operate at between one and seven gigaflops, or one-billion floating point operations per second.)

Shortly after its launch by Science and Technology Minister Naledi Pandor, in September 2009, the Tsessebe Cluster was ranked at number 311 on the top-500 list. As a consequence of fast developments in the supercomputing arena, machines generally do not stay in the rankings for very long and by May 2010 the CHPC machine had already fallen to 461st.

The CHPC's Tsessebe system is made up of Oracle’s Sunblade X6275 blades with Intel Nehalem 8 core processors and Westmere 12 core processors, as well as Dell’s Poweredge C6100 servers with Intel Westmere 12 core processors.

The upgrade to this complex machine was performed by a CHPC team, in collaboration with the Cambridge High Performance Computing Centre, Dell and Eclipse Holdings.

The decision to upgrade the CHPC system was taken to cater for the increased demand for high performance computing by various universities and science council teams, bringing utilisation to nearly 100%, explains Sithole.

Having a world-class supercomputer is also part of South Africa’s commitment to host the Square Kilometre Array (SKA) project, in order to process the enormous data rates that will be produced by this project’s radio telescopes, should South Africa win the bid to host the E1.5-billion SKA project.

“Getting back in the top-500 was a bonus,” says Sithole.

The CHPC system is available to researchers across the country through the 10 gigabit-per-second South African National Research Network. Industry also has access to the supercomputer.

Supercomputers are typically used for high calculation-intensive tasks, such as problems around weather forecasting, climate research, molecular modeling and quantum physics.

For example, supercomputers have been used abroad to help understand certain diseases by computing the complex process behind protein folding. Proteins that fold incorrectly can cause illness. If scientists can understand what leads to misfolds, new treatments or cures might be possible. Supercomputers have also helped researchers improve the efficiency of combustion engines, especially for aircraft.


South Africa requires more supercomputers than the systems – some universities have small supercomputers – currently available, says Sithole.

“The availability of more supercomputers in South Africa and Africa as a whole is paramount to finding solutions to the problems that plague the region, such as climate change and the impact it has on Africa’s agriculture, HIV/Aids, malaria and the implementation of renewable energy.

“South Africa’s economy also exerts pressures on industry to continuously grow its business to maintain its edge in the market. Computational research, used together with conventional research, offers remarkably speedy research solutions that are neither labour intensive, nor exorbitant,” he notes.
The other African countries with known supercomputers are Tanzania (a 2.5 teraflop cluster) and Egypt.
The CHPC system has been Africa’s fastest supercomputer since its launch.
There are plans to expand South Africa’s supercomputer abilities, with CHPC to build a second supercomputer, starting in 2013.

“This will be a new system and not an upgrade, and it will ensure we can allow for more users around the country,” says Sithole.

One challenge with building any supercomputer is the fact that computer chips change every 18 months.

Supercomputers also require specific working environments.

This environment must be programmed and controlled by a building management system, especially in terms of temperature and relative humidity.

The optimal humidity operating range is between 45% and 55%. Room temperature has to be 20 ˚C.

Supercomputers have more than one brain, or processor. These processors run different parts of the same computer programme concurrently (parallel processing), resulting in significantly faster compute times.

Parallel processing is used when many complex calculations are required, such as in climate or earthquake modelling.

Supercomputers have ten times the speed and memory compared to a personal computer, and are made up of many smaller computers – sometimes thousands of them – connected via fast local network connections.

The fastest supercomputers currently operating do so on the petaflop scale – that is one quadrillion operations per second, explains Sithole.

The world’s fastest supercomputer is Japan’s K computer, running at 10 petaflops, he adds.

Talk is now of achieving a system capable of exaflop operation by around 2018. An exaflop is a quintillion floating point operations per second – that is a number with 18 zeros.
The first machine generally referred to as a supercomputer – though not officially designated as one – the IBM Naval Ordnance Research Calculator, was used at Columbia University from 1954 to 1963 to calculate missile trajectories.

The history of supercomputers is closely associated with Seymour Cray, who designed the first officially designated supercomputers in the late 1960s.

In the initial stages supercomputers were the entities of large government agencies and government-funded institutions. They were carefully controlled since they were used for nuclear weapons research. They were also a source of national pride, and symbolic of technical leadership, says Sithole.

Edited by: Creamer Media Reporter
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