Servers Headed to Junkyard Find 2nd Life Fighting Cancer in Clusters

By Tiffany Trader

March 20, 2020

Ottawa-based charitable organization Cancer Computer is on a mission to stamp out cancer and other life-threatening diseases, including coronavirus, by putting to good use discarded high-end computer hardware that would otherwise end up in landfills. Their tagline is “a cure could be waiting in line,” and their objective is to point as many cycles as possible at eliminating computational wait times that impede medical advances.

Since its founding five years ago, Cancer Computer has amassed 14,300 cores, in-line with the computing capacity of a mid-sized university, for researchers across the United States and Canada. In a typical scenario, Cancer Computer gets hardware from a corporate partner that’s upgrading their own hardware and supports the mission of helping advance omics-based research.

Founder and CTO Roy Chartier – who also started a for-profit company, Canada HPC Corp., earlier this year – said the inspiration for Cancer Computer came to him when he realized there was a dearth of resources for research computing, and as the need for computing grows, the gap was only getting worse. He chose cancer as a focus because of its lethality and because much of the research lends itself to high-throughput and high-performance computing. It’s a disease with broad impact – one-quarter of people will get a diagnosis in their lifetime. (Chartier himself told us he lost two people close to him to cancer).

But Cancer Computer doesn’t just focus on cancer, it also supports neuroscience research, contributing spare cycles for protein structure prediction via the Rosetta@home project (for which it is the #1 supporting org). And now Cancer Computer has joined in the global fight against the coronavirus pandemic by directing all available cycles to Rosetta’s COVID-19 project that assists scientists at the University of Washington’s Institute for Protein Design in Seattle. Similar to the Folding@home crowdsourcing coronavirus research project (see related story), Rosetta@home is modeling SARS-CoV2 protein interactions with potential drug targets.

When I spoke with Chartier in February, he was excited about a recent large donation, a tranche of 400 servers from the Canadian government. Chartier rattled off a number of sites where Cancer Computer has deployed its donated hardware: the University of Illinois at Urbana-Champaign, Indiana University, the University of Utah, Queens University in Kingston, ON, and McGill University, Montreal, to name a few. There are a number of private sites as well. As you’d expect, having been in production a few years, most of the donated hardware is Intel-based, but among the thousand-or-so nodes put into service, there are a couple dozen AMD servers and several GPU racks. Chartier said he’s interested in getting more AMD gear, which he says has demonstrated good results on some of the bio-benchmarks, like GROMACS.

Typically, Cancer Computer allocates 75 percent of its donated resources to the host institution with the remaining 25 percent dedicated specifically for the organization’s charitable goals through a number of projects. These include Open Science Grid, XSEDE, as well as Boinc-based distributed research networks, the World Community Grid and Rosetta@home. Cancer Computer also fields specific requests for researchers who do not have other resources available to them.

Cancer Computer’s donated servers are deployed either at a host institution or in a colocation facility operated by Cancer Computer or a partner. As the organization scales, Chartier would like to grow the colo side, with an eye to sites in green-power regions, including Quebec and Ontario, rich in hydro-electric power, and possibly geo-thermal powered Iceland. Certain workloads, such as ones involving clinical data, mandate the need to comply with HIPAA or PHIPA (Canada’s version of HIPAA), which can only be guaranteed in a commercial datacenter.

As a charity, funding is a constant challenge. Although the computers are donated and the staff are volunteers, there are still expenses: replacement hard drives, SSDs, RAM, switches and rails, as well as travel expenses for on-site installations. There is right now a concerted effort at Cancer Computer to build up their board and secure corporate sponsorships in order to scale and be more sustainable. A near-term goal is to employ one or two full-time techs and to implement cost recovery measures.

“We find people that we ask [to be involved] and they’re very passionate about it; they’re willing to help where they can, so it’s just a matter of finding the right people, the right institutions, the right projects, and the right donors, you know, the people who want to support you,” said Chartier.

Supercomputing has a history of giving decommissioned systems a new lease on life. This includes the high-profile donation of TACC’s Ranger system to universities in South Africa, as well as the UCSD Gordon system put into service at Simons Foundation’s Flatiron Institute in New York. But some donations you probably haven’t heard of. For various reasons, the partners may not want to make it public; often because they don’t want to ruffle the feathers of vendors in the business of selling the next-generation of gear. But with so many good causes needing processing power and the importance of reducing e-waste, there is growing support in the community – vendors included – for extending the life of systems that would otherwise end up in a landfill.

“The whole thing comes down to open science, right?” said Chartier. “Open science and sharing of data, sharing of research. If we get, let’s say, two or three more sites, and we had a constant inflow of gear, and we had enough money to be able to have technicians clean it, update the firmware and ship it to these locations, we continue to develop this international e-infrastructure, and make it sustainable and much bigger – I mean, no matter how much money you throw at a problem, particularly like cancer, you know, there’s always room for more.”

“We don’t want to compete with the vendors,” he added. “But if there’s usable, secondhand gear that’s being thrown out, my goodness, that’s definitely something that that really shouldn’t happen.”

A number of prominent organizations agree. At the University of Illinois at Urbana-Champaign, Cancer Computer’s deployment of 300 servers supports the work of more than 500 researchers per year. Cancer Computer is in the process of installing a high-throughput cluster at McGill comprised of some 400 servers. Indiana University is another high-profile site; the partners recently extended a three-year relationship.

For donations, Cancer Computer only accepts gear that’s less than 10 years old. On the compute side, Cancer Computer looks for Ivy Bridge processors or better; for storage it can go back a generation or two. The better equipment gets put into production, and the charity is also building an internal system with plans to assist partner universities with code development and the building of in-house applications.

In most cases, the hardware that Cancer Computer gets is at the end of its support contract. “We can give it a second life. Outside of a DMZ, the servers can run lots of workloads if there’s no personal data, and you don’t typically need the same levels of security that you would require with warrantied gear. Even if 10-20-30 percent of your drives are dead, you can set up your storage to be distributed and you can run, no problem. HPC can be engineered and architected in such a way to do that. It’s not a five-nines scenario,” he said.

Canada HPC

Chartier also updated us on Canada HPC, formed when some of the volunteers from Cancer Computer saw a commercial opportunity for workloads outside the cancer research space, as Cancer Computer’s mission is to provide compute resources to researchers either free where possible, or heavily discounted on a cost-recovery basis.

Earlier this month, Canada HPC signed a partnership agreement with Dell. As a solutions provider for Dell, Canada HPC will do everything from the rack-and-stack, configuration, deploying the scheduling tools, up to and including support. Chartier explained that Dell saw a need and reached out to them – and Canada HPC had the necessary Canadian federal government security clearances.

Subscribe to HPCwire's Weekly Update!

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

MLPerf Inference 4.0 Results Showcase GenAI; Nvidia Still Dominates

March 28, 2024

There were no startling surprises in the latest MLPerf Inference benchmark (4.0) results released yesterday. Two new workloads — Llama 2 and Stable Diffusion XL — were added to the benchmark suite as MLPerf continues Read more…

Q&A with Nvidia’s Chief of DGX Systems on the DGX-GB200 Rack-scale System

March 27, 2024

Pictures of Nvidia's new flagship mega-server, the DGX GB200, on the GTC show floor got favorable reactions on social media for the sheer amount of computing power it brings to artificial intelligence.  Nvidia's DGX Read more…

Call for Participation in Workshop on Potential NSF CISE Quantum Initiative

March 26, 2024

Editor’s Note: Next month there will be a workshop to discuss what a quantum initiative led by NSF’s Computer, Information Science and Engineering (CISE) directorate could entail. The details are posted below in a Ca Read more…

Waseda U. Researchers Reports New Quantum Algorithm for Speeding Optimization

March 25, 2024

Optimization problems cover a wide range of applications and are often cited as good candidates for quantum computing. However, the execution time for constrained combinatorial optimization applications on quantum device Read more…

NVLink: Faster Interconnects and Switches to Help Relieve Data Bottlenecks

March 25, 2024

Nvidia’s new Blackwell architecture may have stolen the show this week at the GPU Technology Conference in San Jose, California. But an emerging bottleneck at the network layer threatens to make bigger and brawnier pro Read more…

Who is David Blackwell?

March 22, 2024

During GTC24, co-founder and president of NVIDIA Jensen Huang unveiled the Blackwell GPU. This GPU itself is heavily optimized for AI work, boasting 192GB of HBM3E memory as well as the the ability to train 1 trillion pa Read more…

MLPerf Inference 4.0 Results Showcase GenAI; Nvidia Still Dominates

March 28, 2024

There were no startling surprises in the latest MLPerf Inference benchmark (4.0) results released yesterday. Two new workloads — Llama 2 and Stable Diffusion Read more…

Q&A with Nvidia’s Chief of DGX Systems on the DGX-GB200 Rack-scale System

March 27, 2024

Pictures of Nvidia's new flagship mega-server, the DGX GB200, on the GTC show floor got favorable reactions on social media for the sheer amount of computing po Read more…

NVLink: Faster Interconnects and Switches to Help Relieve Data Bottlenecks

March 25, 2024

Nvidia’s new Blackwell architecture may have stolen the show this week at the GPU Technology Conference in San Jose, California. But an emerging bottleneck at Read more…

Who is David Blackwell?

March 22, 2024

During GTC24, co-founder and president of NVIDIA Jensen Huang unveiled the Blackwell GPU. This GPU itself is heavily optimized for AI work, boasting 192GB of HB Read more…

Nvidia Looks to Accelerate GenAI Adoption with NIM

March 19, 2024

Today at the GPU Technology Conference, Nvidia launched a new offering aimed at helping customers quickly deploy their generative AI applications in a secure, s Read more…

The Generative AI Future Is Now, Nvidia’s Huang Says

March 19, 2024

We are in the early days of a transformative shift in how business gets done thanks to the advent of generative AI, according to Nvidia CEO and cofounder Jensen Read more…

Nvidia’s New Blackwell GPU Can Train AI Models with Trillions of Parameters

March 18, 2024

Nvidia's latest and fastest GPU, codenamed Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from Read more…

Nvidia Showcases Quantum Cloud, Expanding Quantum Portfolio at GTC24

March 18, 2024

Nvidia’s barrage of quantum news at GTC24 this week includes new products, signature collaborations, and a new Nvidia Quantum Cloud for quantum developers. Wh Read more…

Alibaba Shuts Down its Quantum Computing Effort

November 30, 2023

In case you missed it, China’s e-commerce giant Alibaba has shut down its quantum computing research effort. It’s not entirely clear what drove the change. Read more…

Nvidia H100: Are 550,000 GPUs Enough for This Year?

August 17, 2023

The GPU Squeeze continues to place a premium on Nvidia H100 GPUs. In a recent Financial Times article, Nvidia reports that it expects to ship 550,000 of its lat Read more…

Shutterstock 1285747942

AMD’s Horsepower-packed MI300X GPU Beats Nvidia’s Upcoming H200

December 7, 2023

AMD and Nvidia are locked in an AI performance battle – much like the gaming GPU performance clash the companies have waged for decades. AMD has claimed it Read more…

DoD Takes a Long View of Quantum Computing

December 19, 2023

Given the large sums tied to expensive weapon systems – think $100-million-plus per F-35 fighter – it’s easy to forget the U.S. Department of Defense is a Read more…

Synopsys Eats Ansys: Does HPC Get Indigestion?

February 8, 2024

Recently, it was announced that Synopsys is buying HPC tool developer Ansys. Started in Pittsburgh, Pa., in 1970 as Swanson Analysis Systems, Inc. (SASI) by John Swanson (and eventually renamed), Ansys serves the CAE (Computer Aided Engineering)/multiphysics engineering simulation market. Read more…

Choosing the Right GPU for LLM Inference and Training

December 11, 2023

Accelerating the training and inference processes of deep learning models is crucial for unleashing their true potential and NVIDIA GPUs have emerged as a game- Read more…

Intel’s Server and PC Chip Development Will Blur After 2025

January 15, 2024

Intel's dealing with much more than chip rivals breathing down its neck; it is simultaneously integrating a bevy of new technologies such as chiplets, artificia Read more…

Baidu Exits Quantum, Closely Following Alibaba’s Earlier Move

January 5, 2024

Reuters reported this week that Baidu, China’s giant e-commerce and services provider, is exiting the quantum computing development arena. Reuters reported � Read more…

Leading Solution Providers

Contributors

Comparing NVIDIA A100 and NVIDIA L40S: Which GPU is Ideal for AI and Graphics-Intensive Workloads?

October 30, 2023

With long lead times for the NVIDIA H100 and A100 GPUs, many organizations are looking at the new NVIDIA L40S GPU, which it’s a new GPU optimized for AI and g Read more…

Shutterstock 1179408610

Google Addresses the Mysteries of Its Hypercomputer 

December 28, 2023

When Google launched its Hypercomputer earlier this month (December 2023), the first reaction was, "Say what?" It turns out that the Hypercomputer is Google's t Read more…

AMD MI3000A

How AMD May Get Across the CUDA Moat

October 5, 2023

When discussing GenAI, the term "GPU" almost always enters the conversation and the topic often moves toward performance and access. Interestingly, the word "GPU" is assumed to mean "Nvidia" products. (As an aside, the popular Nvidia hardware used in GenAI are not technically... Read more…

Shutterstock 1606064203

Meta’s Zuckerberg Puts Its AI Future in the Hands of 600,000 GPUs

January 25, 2024

In under two minutes, Meta's CEO, Mark Zuckerberg, laid out the company's AI plans, which included a plan to build an artificial intelligence system with the eq Read more…

Google Introduces ‘Hypercomputer’ to Its AI Infrastructure

December 11, 2023

Google ran out of monikers to describe its new AI system released on December 7. Supercomputer perhaps wasn't an apt description, so it settled on Hypercomputer Read more…

China Is All In on a RISC-V Future

January 8, 2024

The state of RISC-V in China was discussed in a recent report released by the Jamestown Foundation, a Washington, D.C.-based think tank. The report, entitled "E Read more…

Intel Won’t Have a Xeon Max Chip with New Emerald Rapids CPU

December 14, 2023

As expected, Intel officially announced its 5th generation Xeon server chips codenamed Emerald Rapids at an event in New York City, where the focus was really o Read more…

IBM Quantum Summit: Two New QPUs, Upgraded Qiskit, 10-year Roadmap and More

December 4, 2023

IBM kicks off its annual Quantum Summit today and will announce a broad range of advances including its much-anticipated 1121-qubit Condor QPU, a smaller 133-qu Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire