Introducing Lengau, The Fastest Computer In Africa


By: Mandy J Watson
Posted: 26 August 2016
Category: Features
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The CSIR has developed Africa's fastest supercomputer for the use of academics and industrial researchers. We got to go inside (twice) to find out more about the technology and how the supercomputer was planned and built. You can get a glimpse too with our quick video showcase.

The fastest computer in Africa, a one petaflop (1000 teraflop) machine custom built by South African engineers, scientists, and students is installed in the CSIR offices in the tiny, largely nondescript suburb of Rosebank in Cape Town near the Liesbeek River, down the road from the large Southern Suburbs school cluster, and not too far from the University Of Cape Town.

Introducing Lengau, The Fastest Computer In Africa

The high performance computer (HPC), which is named Lengau (Setswana for "cheetah"), is a project of the Centre For High Performance Computing (CHPC) at the CSIR's (Council For Scientific And Industrial Research) Meraka Institute. It's not the CSIR's first supercomputer, however. I discovered all of this in June when I was invited to attend the unveiling of Lengau and learn more about how it came about and what it will be used for. I subsequently interviewed the director of the CHPC, Dr Happy Sithole, for Tech, which should be published soon.

First, however, some history, as Lengau isn't the CSIR's first high performance computer - the CHPC has been dabbling in supercomputers for 10 years. Its first HPC, iQudu (Xhosa for "kudu"), was unveiled in 2007 and was a 2.5 teraflop machine.

Next was Tsessebe (an antelope that can run up to 80 kilometres an hour) in 2009, which managed 25.4 teraflops and was ranked 313 on the Top500 supercomputer list at the time, and number one in Africa. This HPC was upgraded in 2013 to 64.44 teraflops.


YouTube link ]

Now we have Lengau, which operates at speeds of one petaflop. It was ranked 121 in the world in June. It's the fastest computer in Africa and the third fastest in the Southern Hemisphere. (The fastest in the Southern Hemisphere, and number 79 in the world, is Magnus in Australia, which is rated at 1485.6 petaflops and comprises Cray components, and the second fastest is another HPC in Australia, rated at 1112.9 petaflops and comprising Fujitsu components, which reached a worldwide rank of 99.)

Lengau currently comprises 1039 Dell PowerEdge servers based on Intel Xeon processors, 24 192 cores processing cores, five petabytes of Dell Storage, Dell Networking Ethernet switches, and Mellanox EDR InfiniBand switches with a maximum interconnect speed of 56 gigabytes per second.

Introducing Lengau, The Fastest Computer In Africa


Building A Supercomputer

The project was spearheaded by the director of the CHPC, Dr Happy Sithole, who joined the CHPC when it formed in 2007. The funding was provided by the Department Of Science And Technology and the CSIR worked with technology providers to form mutually beneficial partnerships. Dell, for example, initially came on board by way of a student-cluster competition but then offered a long term investment after seeing the success of the student programme.

Introducing Lengau, The Fastest Computer In Africa
Above: Dr Happy Sithole (left) shows guests around the supercomputer during the launch.
The CSIR worked with local scientists and industry partners (the industry partners help to generate revenue by paying to use the equipment) to see what they would require in a supercomputer and set about building and testing components in its advanced computer engineering laboratory to devise architecture that would be relevant to their needs. This had an added benefit of reducing costs because they knew exactly what components they needed to buy that would be most beneficial for its users before they went out and bought them. It also meant that local engineers acquired hands-on experience in building the computer and their skills and knowledge are therefore in demand in other African countries where we are now helping various organisations to assemble their own HPCs.

Lengau continues to be a work in progress, however. Dr Sithole told me that the current format of the HPC is the first phase of the system and it's about 70% of what is required. The CSIR's engineers continue to test components and configurations and, over time, more components will be added, replaced, and upgraded to make the machine more powerful.

Introducing Lengau, The Fastest Computer In Africa

"We do some technology refreshers at entry level," Dr Sithole says. "We look at what the new technologies are that are coming up and we implement part of our upgrade just with some of the technologies just to introduce our users to the technology. Once there is good uptake on those test beds that determines what we need to take. Normally we would make a major upgrade after four years or five years but in between we have got some technology evaluation that we do. [The HPC is constantly evolving] with a major shift every four to five years."

This process might also be accelerated faster than the intended timeframe because projects such as the Square Kilometre Array, one of the heavy users of the HPC, need more computing power than was initially anticipated.

Introducing Lengau, The Fastest Computer In Africa

You may be wondering why Lengau was built in Cape Town when the CSIR has campuses all over the country. The answer is a very practical one. It just so happened that the Cape Town offices had the space at the time that the HPC projects were first getting started and had been assigned to the CSIR.

It took the place of the Fishing Industry Research Institute that was being scaled down as the HPC project was being initiated. "We had to break down walk-in freezers in here, which were not being used," Dr Sithole says.

Introducing Lengau, The Fastest Computer In Africa


Inside Lengau's Lair

It is quite an experience to spend some time in the HPC room, which, even though it's no longer filled with freezers, features environmental factors that make it perfect for computing but unpleasant for humans.

The room is very loud, for instance, but it's soundproofed so that people working on the outside monitoring the systems and doing maintenance just hear a dull hum in the background. Much of the noise is actually due to the air conditioning and cooling systems, rather than the computer components, and it's not recommended to spend any time in the room without ear plugs or you can damage your hearing.

Introducing Lengau, The Fastest Computer In Africa
Above: Some of the ColdLogik cooling units that form part of Lengau.
The air conditioning and ColdLogik cooling systems from USystems serve to cool the components, which generate a lot of heat as they process and store data. (Think of the back of your computer or the bottom of your laptop, then think about that hardware physically multiplied to fill the space of a computer room and running at a petaflop speed and you'll have some idea of the heat that is generated by the components.)

Introducing Lengau, The Fastest Computer In Africa
Above: UPS unit number two, with one of the fire-suppression units mounted on the wall next to it.
There's also a lot of airflow in the room due to vents in the floor that push cold air in and help to keep the ambient temperature down. Should the worst happen and something causes a fire to start, there are giant fire-suppression units mounted on the wall, although they are so huge that I'm not sure how one operates them; I assume it's computer controlled. There's also more than one doorway in the room so there are options if people need to evacuate quickly.

Introducing Lengau, The Fastest Computer In Africa
Above: A computer in the room next to the supercomputer monitors the cooling systems.
The supercomputer comprises various racks and modules so engineers can pull out trays to change components that have either failed or need to be upgraded without affecting the overall system and the system is supported by two massive uninterruptible power supply banks, one on each side of the room, so it's protected from spikes and dips in the power grid, as well as power outages. A system administrator told me that Lengau utilises the electricity supply that is available to the suburban neighbourhood, which has the unfortunate consequence of constraining the maximum amount of power that the HPC can utilise so it can only grow to a certain size, unless the electricity supply is increased.

The components are very valuable and need to be protected but so does the data. The CSIR has a separate division in Pretoria that hosts data for safe keeping and disaster recovery in long-term storage but the data that is still being processed is housed within the supercomputer as scratch storage as it doesn't have significant value until the processing is finished. The policy with regards to the supercomputer is that when academics and researchers are finished processing they take the data with them but all the research that is funded through public funds must also be made available for open access as part of DIRISA's (Data Intensive Research Initiative Of South Africa) objectives.

Introducing Lengau, The Fastest Computer In Africa

The total cost has been a little over R100 million, which sounds like a lot until you think about security upgrades to homesteads, private planes for governmental VVIPs, and locomotives that are too tall for the infrastructure. An "off the shelf" (not that there is such as thing) HPC would have cost more but the expenses were reduced due to great planning and all the in house testing that the CSIR conducted, and continues to conduct, to determine the best components for our needs. As a result, this is a project we can be very proud of. It's impressive, it's well managed, and it's allowing our finest minds to operate at the same level as academics around the world - without having to leave the continent to do so.

Introducing Lengau, The Fastest Computer In Africa


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