HPC Comes Alive in Southern Africa

By Elizabeth Leake, STEM-Trek

April 13, 2015

South Africa’s Kruger National Park was the perfect setting for the conservation-themed, Ninth Annual Center for High Performance Computing’s (CHPC) National Meeting titled “Towards an Energy-Efficient HPC System.” Additional meetings were co-located Dec. 1-5, 2014, including the Southern African Development Community (SADC) HPC Forum, HPC Advisory Council, and the Industrial HPC Advisory Forum.

CHPC Director Happy Sithole opened the conference by thanking conference sponsors, especially its diamond sponsor, Intel, and welcoming 305 HPC enthusiasts from 19 countries and 12 research arenas, including SADC delegates, system administrators, researchers, computational scientists, and industry affiliates. Ninety-two South African students presented posters, or competed for a chance to represent South Africa in July at the HPC Advisory Council International Supercomputing Conference (HPCAC-ISC) Student Cluster Competition in Frankfurt, Germany.

Kruger is one of South Africa’s largest national parks, and home to 336 native trees, 49 fish, 34 amphibians, 114 reptiles, 507 birds, and more than 140 mammalian species that roam freely in a sanctuary the size of Slovenia (or New Jersey-U.S.). Summer had just begun and Kruger’s “Big Five” were active, including rhino, elephant, buffalo, lion, and leopard. The most dangerous animal in South Africa isn’t among the Big Five. Hippos are responsible for the most human deaths and are consequently killed by people who feel threatened, or poached for their tusks, fat and meat.

The Skukuza rest camp features an elegant airport with daily Airlink service from Johannesburg. Its Cattle Baron restaurant serves a Madagascar Peppercorn Steak that would impress the most discerning human carnivore. Additional amenities include a new conference center, air-conditioned bungalows, and paved roads where guests view wildlife from the safety of ranger-driven safari trucks.

Africa CHPC 2014 lions
Wildlife photos by Filippo Spiga (University of Cambridge-UK)

Pre-conference workshops, tutorials, plenary talks by international experts, and breakaway sessions spoke to the very heart of HPC. The program was thoughtfully selected to explore energy-efficient HPC architectural concepts, strategies for software optimization, advances in middleware, international cyberinfrastructure (CI) policy, industry expectations, and a road map for pan-African human capital development (HCD). A conference help desk was available for attendees with questions about CHPC resources. Students engaged in collegial competition, and a less friendly, but highly entertaining, HPC Vendor Crossfire was chaired by Addison Snell (Intersect360 Research).

HPC-Africa-2014-graphic
Bob Sinkovits (SDSC-US)

The intimacy of the conference venue was quite a change for those who attended SC14 one month prior with more than 10,000 attendees in New Orleans’ mile-long urban convention center.

“It was actually a refreshing change to have limited Internet access,” observed attendee and presenter Robert Sinkovits (San Diego Supercomputer Center-U.S.). “This encouraged everyone to close his or her laptop and focus on the conference. It was the first time I experienced a power outage while giving a presentation. I used the ten minutes of semi-darkness to answer questions and to discuss my research.”

“Overall, it was one of the best conference experiences I can remember—just the right size and with a great bunch of culturally-diverse attendees, fantastic poster sessions, top-notch plenary speakers and a phenomenal venue. What’s more, it was great to see African speakers focusing on locally-important research problems, such as detailed studies of southern ocean currents,” said Sinkovits.

SADC HPC Forum

Delegates from Botswana, Zimbabwe, Zambia, Lesotho, Tanzania, and South Africa attended the third annual SADC HPC Forum. On behalf of the SADC Secretariat, the two-day session was called to order by Senior Technical Adviser Anneline Morgan (SADC Science, Technology and Innovation, Social and Human Development and Special Programs), and presided over by SADC Forum Chair Willie Ganda (Zimbabwe) who will represent the forum at the June, 2015 SADC ministerial meeting in Zimbabwe. Sithole and Ms. Mmampei Chaba (Dept. of Science and Technology, South Africa) welcomed 30 SADC delegates and international advisers.

Morgan framed SADC’s mission and strategies toward a shared vision of peace, security, international trade, and HCD. Ganda expressed the importance of SADC’s continued progress toward a fully-functional, shared CI.

“Through education and research excellence, SADC member-states can uplift citizens from poverty and enable Africa to compete in global research and industrial theaters,” said Ganda. “SADC’s collective research will be a key enabler for success in a range of high-value industries.”

Happy Sithole CHPC
Dr. Happy Sithole, CHPC

Dr. Sithole shared constructive feedback from the June 2014 SADC ministerial meeting. “The ministers expressed appreciation for our having established high-level objectives and timelines, and are pleased that we are as concerned with HCD and research as we are with the technology,” he said. “They would like us to spend our time together this week developing an implementation framework; we must determine how, when, and by whom each objective will be executed. With a well-defined plan, we will then be prepared to solicit industry partner and SADC ministerial support,” he added.

During this forum, SADC delegates presented national research priorities, progress made since last year and described what they will need to succeed in the future.

Infrastructure

The South African Department of Science and Technology’s Council for Scientific and Industrial Research (CSIR) first planted the seeds of a national CI in 2007 when CHPC was launched. Since then, Sithole has envisioned the build-out of a multinational high-performance regional network, a shared software stack, and digital trust fabric to provide the foundation for a productive and secure interfederated research and education CI for sub-Saharan Africa.

With the Square Kilometer Array (SKA) locating in the Karoo region of South Africa, and instrumentation planned in many SADC locations, there’s an emphasis on data-driven research. To advise on best practices relating to data-intensive research and multinational policy-making, Anwar Vahed (CSIR/Meraka Institute-SA) joined the SADC-HPC Forum discussions.

While some national HPC centers are further along and better funded than others, Sithole explained that all will benefit from the shared CI—especially where there are limited local resources. “While the Ranger installation was the catalyst for HPC engagement, it’s only the beginning. There’s an x86 system in Zimbabwe similar to Ranger, and more racks are promised by the University of Cambridge. Everything will be accessible, and shared,” said Sithole.

He also added that cloud-enabled, infrastructure-as-a-service is commercially available, and CyberSKA, a cloud-enabled portal for infrastructure located at CHPC, provides access to a variety of SKA-related test-bed systems. Advisers suggested that SADC researchers will benefit from U.S. and European-based innovation ecosystems and science gateways. “Not only are there resources earmarked for use by specific domains, they offer secure, data-transfer solutions to bridge technical and policy barriers between multinational collaborators,” shared Vahed.

SADC delegates
SADC 2014 HPC Forum delegates


Human Capital Development

SADC delegates are eager to learn the skills necessary to create a national point-of-presence for computational provisioning and workforce development. Adviser Dan Stanzione (Texas Advanced Computing Center, TACC-U.S.) expressed the importance of preparing multiple support communities, including systems builders, operators, trainers, and researchers. In addition to the training offered during the 2015 CHPC meeting, Sithole added that the student cluster competition is an excellent way to prepare young people to envision the possibility of pursuing high-tech careers. While it’s only sponsored by South Africa now, Sithole hopes it will be a SADC-wide competition in the future.

SKA contributed training resources to SADC HPC Forum institutions in South Africa, Mozambique, Botswana, Namibia, Mauritius, and Zambia, and non-SADC universities in Ghana and Kenya. Their training program requires 10 terabytes of local storage, which added to the Ranger rack implementation cost in some cases, according to CHPC’s Nick Thorne who is leading that effort.

In an effort to jump-start scientific and educational collaborations with SADC member nations, the U.S. National Science Foundation (NSF) is supporting local U.S. expenses for 16 visiting SADC scientists and system administrators so they can attend a Nov. 2015 training workshop at TACC prior to the SC15 conference. The first leg of their journey (16 African round-trip flights) is being donated by Airlink Airlines, and STEM-Trek hopes to find sponsors for the remaining 64 flights.

“NSF recognizes that HPC is a fundamental enabler of agricultural research and plant biology which are priorities for TACC and SADC, alike,” said Stanzione. “Through their investment, NSF hopes to foster future U.S./pan-African collaborations,” he added.

Throughout the HCD discussion, advisers volunteered knowledge of a variety of free or low-cost HPC training resources. The list is available on the STEM-Trek site.

Ranger Implementation

Eighty-four racks of TACC’s Ranger system were donated by the University of Texas at Austin-U.S. (UT). CHPC shipped one fourth of the racks to South Africa (SA) in late 2013 with the intention of distributing them among SA universities to create mid-level HPC services. Additional SADC regions received racks directly from TACC, namely Tanzania (16), and Botswana (4). CHPC augmented the SA racks with additional hardware that allows them to function as stand-alone clusters, and distributed them to the University of Fort Hare (Eastern Cape), University of KwaZulu Natal), University of Venda (Limpopo), and University of the Witwatersrand (Gauteng). Two racks will be hosted by the Zambia Research and Education Network group. During the meeting, Lesotho expressed an interest in hosting resources, too.

“It wasn’t as easy as we thought it would be to create many, small clusters from a large system,” said CHPC’s Thorne. “There were unforeseen costs and physical challenges, but it has been highly successful, nevertheless.”

“There has been surprising demand for upcycled systems,” he continued. “In Africa, hardware is more expensive, but energy and personnel are less costly than they are in the U.S. or Europe, so there’s a stronger case to keep systems in production longer.” Since UT donated Ranger, others have offered their decommissioned hardware, including Cambridge University.

zimbabwe-data-center-blue-skirts2-e1423872915297
Zimbabwe Center for High Performance Computing 2014 dedication

Zimbabwe’s effort first began in 2011, and a recently- renovated building houses their new datacenter. Their X86-class system (similar to Ranger) will be shared with the SADC-CI, and they have plans to expand. Next to CHPC in South Africa, Zimbabwe’s center is the second brightest point-of-presence on the regional CI front. With redundant data and power, plus three 120 kw back-up generators, Zimbabwe’s datacenter will be able to support up to 36 teraflops of processing power.

To establish Zimbabwe’s HPC center, Ganda lobbied and appealed to e-government agencies and regional industries (mining and agriculture). He helped them understand how a local HPC center will impact economic, research and educational outcomes. A similar funding strategy (with cross-functional private and public support) has been effective in South Korea, according to SADC HPC Forum Adviser Cynthia McIntyre (Council on Competitiveness-U.S.).

Port_Elizabeth_1_ashxTenth CHPC National Meeting,
Port Elizabeth, South Africa, Nov. 30 to
Dec. 4, 2015

Sithole thanked conference sponsors Intel, Dell, Altair, HP, Huawei, Data Direct Networks, Seagate, Amazon Web Services, Mellanox, Eclipse Holdings, and Rectron. He hopes everyone will return next year for their tenth national meeting at the Boardwalk Hotel in beautiful Port Elizabeth, known as the “Friendly City.”

Watch for updates about the HPCAC-ISC Student Cluster Competition, SC15 TACC Workshop and the 2015 conference on the CHPC site.

Africa CHPC 2014 tree-bird
Wildlife photos by Filippo Spiga (University of Cambridge-UK)

About the Author

ElizabethLeake-headshotElizabeth Leake is the president and founder of STEM-Trek Nonprofit, a global, grassroots organization that supports scholarly travel for science, technology, engineering, and mathematics scholars from underrepresented groups and regions. Since 2011, she has worked as a communications consultant for a variety of education and research organizations, and served as correspondent for activities sponsored by the eXtreme Science and Engineering Discovery Environment (TeraGrid/XSEDE), the Partnerhip for Advanced Computing in Europe (DEISA/PRACE), the European Grid Infrastructure (EGEE/EGI), South African Center for High Performance Computing (CHPC), the Southern African Development Community (SADC), and Sustainable Horizons, Inc.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Digging into the Atos-Nimbix Deal: Big US HPC and Global Cloud Aspirations. Look out HPE?

August 2, 2021

Behind Atos’s deal announced last week to acquire HPC-cloud specialist Nimbix are ramped-up plans to penetrate the U.S. HPC market and global expansion of its HPC cloud capabilities. Nimbix will become “an Atos HPC c Read more…

Berkeley Lab Makes Strides in Autonomous Discovery to Tackle the Data Deluge

August 2, 2021

Data production is outpacing the human capacity to process said data. Whether a giant radio telescope, a new particle accelerator or lidar data from autonomous cars, the sheer scale of the data generated is increasingly Read more…

Verifying the Universe with Exascale Computers

July 30, 2021

The ExaSky project, one of the critical Earth and Space Science applications being solved by the US Department of Energy’s (DOE’s) Exascale Computing Project (ECP), is preparing to use the nation’s forthcoming exas Read more…

What’s After Exascale? The Internet of Workflows Says HPE’s Nicolas Dubé

July 29, 2021

With the race to exascale computing in its final leg, it’s natural to wonder what the Post Exascale Era will look like. Nicolas Dubé, VP and chief technologist for HPE’s HPC business unit, agrees and shared his vision at Supercomputing Frontiers Europe 2021 held last week. The next big thing, he told the virtual audience at SFE21, is something that will connect HPC and (broadly) all of IT – into what Dubé calls The Internet of Workflows. Read more…

How UK Scientists Developed Transformative, HPC-Powered Coronavirus Sequencing System

July 29, 2021

In November 2020, the COVID-19 Genomics UK Consortium (COG-UK) won the HPCwire Readers’ Choice Award for Best HPC Collaboration for its CLIMB-COVID sequencing project. Launched in March 2020, CLIMB-COVID has now resulted in the sequencing of over 675,000 coronavirus genomes – an increasingly critical task as variants like Delta threaten the tenuous prospect of a return to normalcy in much of the world. Read more…

AWS Solution Channel

Data compression with increased performance and lower costs

Many customers associate a performance cost with data compression, but that’s not the case with Amazon FSx for Lustre. With FSx for Lustre, data compression reduces storage costs and increases aggregate file system throughput. Read more…

KAUST Leverages Mixed Precision for Geospatial Data

July 28, 2021

For many computationally intensive tasks, exacting precision is not necessary for every step of the entire task to obtain a suitably precise result. The alternative is mixed-precision computing: using high precision wher Read more…

Digging into the Atos-Nimbix Deal: Big US HPC and Global Cloud Aspirations. Look out HPE?

August 2, 2021

Behind Atos’s deal announced last week to acquire HPC-cloud specialist Nimbix are ramped-up plans to penetrate the U.S. HPC market and global expansion of its Read more…

How UK Scientists Developed Transformative, HPC-Powered Coronavirus Sequencing System

July 29, 2021

In November 2020, the COVID-19 Genomics UK Consortium (COG-UK) won the HPCwire Readers’ Choice Award for Best HPC Collaboration for its CLIMB-COVID sequencing project. Launched in March 2020, CLIMB-COVID has now resulted in the sequencing of over 675,000 coronavirus genomes – an increasingly critical task as variants like Delta threaten the tenuous prospect of a return to normalcy in much of the world. Read more…

What’s After Exascale? The Internet of Workflows Says HPE’s Nicolas Dubé

July 29, 2021

With the race to exascale computing in its final leg, it’s natural to wonder what the Post Exascale Era will look like. Nicolas Dubé, VP and chief technologist for HPE’s HPC business unit, agrees and shared his vision at Supercomputing Frontiers Europe 2021 held last week. The next big thing, he told the virtual audience at SFE21, is something that will connect HPC and (broadly) all of IT – into what Dubé calls The Internet of Workflows. Read more…

IBM and University of Tokyo Roll Out Quantum System One in Japan

July 27, 2021

IBM and the University of Tokyo today unveiled an IBM Quantum System One as part of the IBM-Japan quantum program announced in 2019. The system is the second IB Read more…

Intel Unveils New Node Names; Sapphire Rapids Is Now an ‘Intel 7’ CPU

July 27, 2021

What's a preeminent chip company to do when its process node technology lags the competition by (roughly) one generation, but outmoded naming conventions make it seem like it's two nodes behind? For Intel, the response was to change how it refers to its nodes with the aim of better reflecting its positioning within the leadership semiconductor manufacturing space. Intel revealed its new node nomenclature, and... Read more…

Will Approximation Drive Post-Moore’s Law HPC Gains?

July 26, 2021

“Hardware-based improvements are going to get more and more difficult,” said Neil Thompson, an innovation scholar at MIT’s Computer Science and Artificial Intelligence Lab (CSAIL). “I think that’s something that this crowd will probably, actually, be already familiar with.” Thompson, speaking... Read more…

With New Owner and New Roadmap, an Independent Omni-Path Is Staging a Comeback

July 23, 2021

Put on a shelf by Intel in 2019, Omni-Path faced a uncertain future, but under new custodian Cornelis Networks, OmniPath is looking to make a comeback as an independent high-performance interconnect solution. A "significant refresh" – called Omni-Path Express – is coming later this year according to the company. Cornelis Networks formed last September as a spinout of Intel's Omni-Path division. Read more…

Chameleon’s HPC Testbed Sharpens Its Edge, Presses ‘Replay’

July 22, 2021

“One way of saying what I do for a living is to say that I develop scientific instruments,” said Kate Keahey, a senior fellow at the University of Chicago a Read more…

AMD Chipmaker TSMC to Use AMD Chips for Chipmaking

May 8, 2021

TSMC has tapped AMD to support its major manufacturing and R&D workloads. AMD will provide its Epyc Rome 7702P CPUs – with 64 cores operating at a base cl Read more…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

Berkeley Lab Debuts Perlmutter, World’s Fastest AI Supercomputer

May 27, 2021

A ribbon-cutting ceremony held virtually at Berkeley Lab's National Energy Research Scientific Computing Center (NERSC) today marked the official launch of Perlmutter – aka NERSC-9 – the GPU-accelerated supercomputer built by HPE in partnership with Nvidia and AMD. Read more…

Ahead of ‘Dojo,’ Tesla Reveals Its Massive Precursor Supercomputer

June 22, 2021

In spring 2019, Tesla made cryptic reference to a project called Dojo, a “super-powerful training computer” for video data processing. Then, in summer 2020, Tesla CEO Elon Musk tweeted: “Tesla is developing a [neural network] training computer called Dojo to process truly vast amounts of video data. It’s a beast! … A truly useful exaflop at de facto FP32.” Read more…

Google Launches TPU v4 AI Chips

May 20, 2021

Google CEO Sundar Pichai spoke for only one minute and 42 seconds about the company’s latest TPU v4 Tensor Processing Units during his keynote at the Google I Read more…

CentOS Replacement Rocky Linux Is Now in GA and Under Independent Control

June 21, 2021

The Rocky Enterprise Software Foundation (RESF) is announcing the general availability of Rocky Linux, release 8.4, designed as a drop-in replacement for the soon-to-be discontinued CentOS. The GA release is launching six-and-a-half months after Red Hat deprecated its support for the widely popular, free CentOS server operating system. The Rocky Linux development effort... Read more…

Iran Gains HPC Capabilities with Launch of ‘Simorgh’ Supercomputer

May 18, 2021

Iran is said to be developing domestic supercomputing technology to advance the processing of scientific, economic, political and military data, and to strengthen the nation’s position in the age of AI and big data. On Sunday, Iran unveiled the Simorgh supercomputer, which will deliver.... Read more…

HPE Launches Storage Line Loaded with IBM’s Spectrum Scale File System

April 6, 2021

HPE today launched a new family of storage solutions bundled with IBM’s Spectrum Scale Erasure Code Edition parallel file system (description below) and featu Read more…

Leading Solution Providers

Contributors

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

GTC21: Nvidia Launches cuQuantum; Dips a Toe in Quantum Computing

April 13, 2021

Yesterday Nvidia officially dipped a toe into quantum computing with the launch of cuQuantum SDK, a development platform for simulating quantum circuits on GPU-accelerated systems. As Nvidia CEO Jensen Huang emphasized in his keynote, Nvidia doesn’t plan to build... Read more…

Microsoft to Provide World’s Most Powerful Weather & Climate Supercomputer for UK’s Met Office

April 22, 2021

More than 14 months ago, the UK government announced plans to invest £1.2 billion ($1.56 billion) into weather and climate supercomputing, including procuremen Read more…

Quantum Roundup: IBM, Rigetti, Phasecraft, Oxford QC, China, and More

July 13, 2021

IBM yesterday announced a proof for a quantum ML algorithm. A week ago, it unveiled a new topology for its quantum processors. Last Friday, the Technical Univer Read more…

AMD-Xilinx Deal Gains UK, EU Approvals — China’s Decision Still Pending

July 1, 2021

AMD’s planned acquisition of FPGA maker Xilinx is now in the hands of Chinese regulators after needed antitrust approvals for the $35 billion deal were receiv Read more…

Q&A with Jim Keller, CTO of Tenstorrent, and an HPCwire Person to Watch in 2021

April 22, 2021

As part of our HPCwire Person to Watch series, we are happy to present our interview with Jim Keller, president and chief technology officer of Tenstorrent. One of the top chip architects of our time, Keller has had an impactful career. Read more…

Senate Debate on Bill to Remake NSF – the Endless Frontier Act – Begins

May 18, 2021

The U.S. Senate today opened floor debate on the Endless Frontier Act which seeks to remake and expand the National Science Foundation by creating a technology Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire