SDSC Supercomputers, CIPRES Gateway Help Define New “Tree of Life”

April 27, 2016

April 27 — An outline for a new tree of life, depicting the evolution of life on this planet that included more than 1,000 new types of bacteria and Archaea lurking in the Earth’s nooks and crannies, was made possible with the help of supercomputing resources and a phylogenetics “gateway” created at the San Diego Supercomputer Center (SDSC), based at the University of California San Diego.

“The CIPRES Science Gateway was critical to our work,” said Laura Hug, who computed the trees at the University of California Berkeley and is now a biology faculty member at the University of Waterloo, Canada.  “Previous attempts to infer the trees presented severe problems with run time, memory allocation and a lack of parallelized implementation of the RAxML (for Randomized Axelerated Maximum Likelihood, a popular program for phylogenetic analysis of large datasets).”

“No run had successfully finished prior to our introduction to CIPRES,” she added. CIPRES, which stands for Cyberinfrastructure for Phylogenetic Research, is a web-based portal, or gateway, that allows researchers to explore evolutionary relationships between species using supercomputers provided by the National Science Foundation’s XSEDE (eXtreme Science and Engineering Discovery Environment) project.

The new tree, published online April 11 in the new journal Nature Microbiology and widely publicized, reinforced once again that the life we see around us – plants, animals, humans and other so-called eukaryotes – represents a tiny percentage of the world’s biodiversity.

“The tree of life is one of the most important organizing principles in biology,” said Jill Banfield, a UC Berkeley professor of earth and planetary science, policy, and management, and the study’s principal investigator. “The new depiction will be of use not only to biologists who study microbial ecology, but also biochemists searching for novel genes and researchers studying evolution and earth history.”

Charles Darwin first sketched a tree of life in 1837 as he sought ways to show how animals and plants are related to one another. The idea took root in the 19th century, with the tips of the twigs representing life on Earth today, while the branches connecting them to the trunk implied evolutionary relationships among these creatures. A branch that divides into two twigs near the tips of the tree implies that these organisms have a recent common ancestor, while a forking branch close to the trunk implies an evolutionary split in the distant past.

Since then, researchers have built on Darwin’s initial sketch, gradually adding twigs and branches to the original, including bacteria and Archaea — microbes that live in extreme environments such as hot springs and oxygen-free wetlands. Our current view of the tree of life consists of three major branches: eukaryotes, including animals, plants, fungi and protozoans; familiar bacteria like Escherchia coli; and the Archaea.

The revolution in DNA sequencing during the past couple of decades has led to an explosion of data offering yet more complete descriptions of the genetic relationships among species. Researchers began sequencing whole communities or organisms at once and picking out the individual groups based on their genes alone. This metagenomic sequencing revealed whole new groups of bacteria and Archaea, many of them from extreme environments, such as the toxic puddles in abandoned mines, the dirt under toxic waste sites, and the human gut. Some of these had been detected before, but nothing was known about them because they wouldn’t survive when isolated in a lab dish.

For the new paper, Banfield and Hug, along with more than a dozen other researchers who have sequenced new microbial species, gathered 1,011 previously unpublished genomes to add to already known genome sequences of organisms representing the major groups of life on Earth.

Counting on SDSC’s Comet and Gordon supercomputers

Access to supercomputers was a key part of this study, helping researchers to investigate relationships by comparing DNA sequences information between species. This type of analysis is becoming more powerful as the number of DNA sequences available is increasing rapidly, with new, larger data sets requiring higher levels of computational power.

For their supercomputer resources, the researchers reached out to the CIPRES gateway, which initially allowed them access to SDSC’s Gordon, the first high-performance supercomputer to use massive amounts of flash-based SSD (solid state drive) storage. The final trees were generated by SDSC’s latest system, Comet, a petascale supercomputer designed to transform advanced scientific computing by expanding access and capacity among traditional as well as non-traditional research domains. The two jobs ran for a total of about five days, using 48 cores.

“The CIPRES Gateway allows scientists to conduct their research in significantly shorter times without having to understand how to operate supercomputers,” said Mark Miller, principal investigator of the CIPRES gateway and an SDSC researcher.

Added Hug: “I spent over a month attempting to conduct these jobs on other servers with no success – the jobs always failed prior to finishing. Also, Mark (Miller) with customer assistance (from CIPRES) was invaluable in troubleshooting our analyses on CIPRES.”

Their investigation, representing the total diversity among all sequenced genomes, produced a tree with branches dominated by bacteria, especially by uncultivated bacteria. A second view of the tree grouped organisms by their evolutionary distance from one another rather than current taxonomic definitions, making clear that about one-third of all biodiversity comes from cultivated bacteria, one-third from uncultivated bacteria and one-third from Archaea and Eukaryotes.

“The two main take-home points I see in this tree are the prominence of major lineages that have no cultivable representatives, and the great diversity in the bacterial domain, most importantly, the prominence of candidate phyla radiation,” Banfield said. “The candidate phyla radiation has as much diversity within it as the rest of the bacteria combined.”

About SDSC

As an Organized Research Unit of UC San Diego, SDSC is considered a leader in data-intensive computing and cyberinfrastructure, providing resources, services, and expertise to the national research community, including industry and academia. Cyberinfrastructure refers to an accessible, integrated network of computer-based resources and expertise, focused on accelerating scientific inquiry and discovery. SDSC supports hundreds of multidisciplinary programs spanning a wide variety of domains, from earth sciences and biology to astrophysics, bioinformatics, and health IT. SDSC’s Comet joins the Center’s data-intensive Gordon cluster, and are both part of the National Science Foundation’s XSEDE (eXtreme Science and Engineering Discovery Environment) program, the most advanced collection of integrated digital resources and services in the world.


Source: SDSC, Written by Robert Sanders (UC Berkeley) and Warren Froelich (SDSC)

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!

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

March 18, 2024

Nvidia's latest and fastest GPU, code-named Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from its predecessors, including the red-hot H100 and A100 GPUs. 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. While Nvidia may not spring to mind when thinking of the quant Read more…

2024 Winter Classic: Meet the HPE Mentors

March 18, 2024

The latest installment of the 2024 Winter Classic Studio Update Show features our interview with the HPE mentor team who introduced our student teams to the joys (and potential sorrows) of the HPL (LINPACK) and accompany Read more…

Houston We Have a Solution: Addressing the HPC and Tech Talent Gap

March 15, 2024

Generations of Houstonian teachers, counselors, and parents have either worked in the aerospace industry or know people who do - the prospect of entering the field was normalized for boys in 1969 when the Apollo 11 missi Read more…

Apple Buys DarwinAI Deepening its AI Push According to Report

March 14, 2024

Apple has purchased Canadian AI startup DarwinAI according to a Bloomberg report today. Apparently the deal was done early this year but still hasn’t been publicly announced according to the report. Apple is preparing Read more…

Survey of Rapid Training Methods for Neural Networks

March 14, 2024

Artificial neural networks are computing systems with interconnected layers that process and learn from data. During training, neural networks utilize optimization algorithms to iteratively refine their parameters until Read more…

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

March 18, 2024

Nvidia's latest and fastest GPU, code-named 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…

Houston We Have a Solution: Addressing the HPC and Tech Talent Gap

March 15, 2024

Generations of Houstonian teachers, counselors, and parents have either worked in the aerospace industry or know people who do - the prospect of entering the fi Read more…

Survey of Rapid Training Methods for Neural Networks

March 14, 2024

Artificial neural networks are computing systems with interconnected layers that process and learn from data. During training, neural networks utilize optimizat Read more…

PASQAL Issues Roadmap to 10,000 Qubits in 2026 and Fault Tolerance in 2028

March 13, 2024

Paris-based PASQAL, a developer of neutral atom-based quantum computers, yesterday issued a roadmap for delivering systems with 10,000 physical qubits in 2026 a Read more…

India Is an AI Powerhouse Waiting to Happen, but Challenges Await

March 12, 2024

The Indian government is pushing full speed ahead to make the country an attractive technology base, especially in the hot fields of AI and semiconductors, but Read more…

Charles Tahan Exits National Quantum Coordination Office

March 12, 2024

(March 1, 2024) My first official day at the White House Office of Science and Technology Policy (OSTP) was June 15, 2020, during the depths of the COVID-19 loc Read more…

AI Bias In the Spotlight On International Women’s Day

March 11, 2024

What impact does AI bias have on women and girls? What can people do to increase female participation in the AI field? These are some of the questions the tech 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…

Analyst Panel Says Take the Quantum Computing Plunge Now…

November 27, 2023

Should you start exploring quantum computing? Yes, said a panel of analysts convened at Tabor Communications HPC and AI on Wall Street conference earlier this y 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…

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…

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…

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

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…

Training of 1-Trillion Parameter Scientific AI Begins

November 13, 2023

A US national lab has started training a massive AI brain that could ultimately become the must-have computing resource for scientific researchers. Argonne N 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…

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…

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…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire