Supercomputing Helps Ecologists Overturn Popular Theory

October 13, 2015

Oct. 13 — With an estimated 350,000 plant species on earth, one of the greatest challenges facing ecologists is quantifying plant diversity and understanding its relationship to plant survival. To make matters more difficult, even with all of the observation data collected by independent botanists and researchers for the last 500 years it has been nearly impossible to organize all of these data without the appropriate computational power.

Recent access, however, to Big Data supercomputing resources is revolutionizing the field. This research has been recently published in a series of papers in journals including EcologyEcographyEcology and Evolution, and the Proceedings of the National Academy of Sciences.

The Botanical Information and Ecology Network (BIEN) is an international group that leads collectors of botanical data, ecologists, and computer scientists worldwide to categorize and analyze plant species in the Americas. Using high performance computing (HPC) and data resources through the iPlant Collaborative and the Texas Advanced Computing Center (TACC), the researchers combined data — from some of the very earliest plant collections, to modern day herbarium specimens, to ecological surveys and measurements of plant traits to answer important questions on plant diversity.

The group found that in all of North and South America there were approximately 120,000 plant species. But mapping and determining the hotspots of species richness requires computationally intensive geographic range estimates. These methods can precisely track where plant species tend to grow and develop. They also give ecologists the ability to document continental scale patterns of species diversity that show where any species of plant could be found — such maps have never been made before.

“As you move along a gradient, such as a gradient in latitude or temperature or precipitation, we see changes in diversity,” said Brian Enquist, principal investigator of the BIEN group and professor at the University of Arizona. “As ecologists, an important question we want to understand is what determines the total number of species we see in a given location.”

A firm grasp on plant diversity also allows ecologists to understand how diversity is related to species’ survival or functioning in different environments and how species diversity can influence the functioning of ecosystems. The prevailing school of thought is that locations that contain a fewer number of species will then have lower ecosystem functioning. According to Enquist, ecologists commonly think of species diversity and ecosystem functioning as similar to investing in stocks.

“In general, you want to diversify your portfolio, so that you invest in a lot of different things,” Enquist said. “We have the same analogy in thinking about ecosystems. If there are fewer ways species can make a living by having a smaller number of traits or functions, it’s thought that ecosystems are less resilient. They tend to be more susceptible to big changes and crashes.”

High Performance Ecology

To investigate these claims further, the BIEN group had to first run algorithms that incorporate botanical observation records and observation data from numerous ecological and museum sources for each species. In 2011 the group first turned to the iPlant Collaborative, a biotechnology project that allows researchers to access HPC and to manage their data.

“Running geographic range estimation algorithms one species at a time is not that challenging, but once you scale it up to more than 100,000 species, it becomes computationally limiting with our standard set of resources,” Enquist said.

Working with iPlant gave the group access to TACC’s Stampede supercomputer, one of the most powerful in the world, enabling them to dramatically scale up their algorithms and workflow.

With supercomputing, and for the first time, the BIEN group could generate and store geographic range estimates for plant species in the Americas. These data and the corresponding geographic ranges, are now available via the groups’ geoportal. After analyzing this data, they were able to map and visualize the plant diversity of the New World. The group found that there is no relationship between the diversity of species and the range of ecological functioning, overturning a popular theory in ecology.

“We’ve discovered something that no one has hit upon,” Enquist said. “Not only are we able to visualize the distribution of plant diversity for the first time but our findings have also completely changed the way we think about the potential functioning of ecosystems and the role that biodiversity has to play.”

Martha Narro, senior projects coordinator for iPlant, facilitated the group’s interactions with resources at iPlant and TACC.

“The effort it took for the BIEN group to pull all of this data together by networking with scientists in North, Central and South America is an incredible accomplishment,” Narro said. “It shows what can happen if researchers collaborate to accomplish something they could never do with their own small datasets or by working piecemeal.”

These findings advance basic science and public understanding of the wealth of ecological diversity in North and South America.

From Theory to the Masses

One practical application of the BIEN group’s efforts is the new smartphone application, Plant-O-Matic, which was developed using TACC resources. The free app offers users the opportunity to explore and discover plants found in a localized region. “Even if you are in the middle of the Amazon, the top of a mountain in Colorado, or your backyard, we can deliver a personalized plant species guide to you,” Enquist said.

The group is also examining the distribution of plant species in light of climate change. By integrating data from their geographic range estimates with available climate change predictions from the Intergovernmental Panel on Climate Change (IPCC), the BIEN group developed the website Forest Forecasts. The site provides an interactive visualization of the best and worst-case scenarios of how distinct species and forests will be affected by climate change up to year 2080.

Enquist was recently invited to speak at the Aspen Ideas Festival to unveil the first of these visualizations and to show how access to high performance computing gives researchers new ways to visualize and personalize the potential impacts of climate change. Although Forest Forecasts is currently in its infancy stage, the group plans to use this data to inform policymakers and the public of the effects of climate change on forest diversity in the western United States.

These findings have been the result of the group’s first attempts to analyze plant data. Enquist anticipates making additional waves in the field with future data outputs and high-impact research papers. But the researchers are just at the tip of the iceberg of ecological understanding.

Said Enquist: “We only have rudimentary knowledge in terms of what sets diversity of species and functioning. As ecologists and evolutionary biologists we’re still at the starting point and just getting our first glimpses.”

Source: Makeda Easter, TACC

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!

A Behind-the-Scenes Look at the Hardware That Powered the Black Hole Image

June 24, 2019

Two months ago, the first-ever image of a black hole took the internet by storm. A team of scientists took years to produce and verify the striking image – and now, Tom Coughlin (on behalf of Supermicro) has provided a Read more…

By Oliver Peckham

U.S. Blacklists Sugon, 4 Others from Access to Advanced Technology

June 21, 2019

Just as ISC19 wrapped up yesterday, showcasing the latest in supercomputing technology, the U.S. added five Chinese entities including Sugon to its blacklist prohibiting them from access to advanced technology vital to s Read more…

By John Russell

Is Weather and Climate Prediction the Perfect ‘Pilot’ for Exascale?

June 21, 2019

At ISC 2019 this week, Peter Bauer – deputy director of research for the European Centre for Medium-Range Weather Forecasts (ECMWF) – outlined an ambitious vision for the future of weather and climate prediction. For Read more…

By Oliver Peckham

HPE Extreme Performance Solutions

HPE and Intel® Omni-Path Architecture: How to Power a Cloud

Learn how HPE and Intel® Omni-Path Architecture provide critical infrastructure for leading Nordic HPC provider’s HPCFLOW cloud service.

For decades, HPE has been at the forefront of high-performance computing, and we’ve powered some of the fastest and most robust supercomputers in the world. Read more…

IBM Accelerated Insights

Avoid AI Redo’s by Starting with the Right Infrastructure

Do you know if you have the right infrastructure for AI? Many organizations don’t have it. In a recent IDC survey, “77.1% of respondents say they ran into one or more limitations with their AI infrastructure on-premise and 90.3% ran into compute limitations in the cloud.” Read more…

ISC Keynote: Thomas Sterling’s Take on Whither HPC

June 20, 2019

Entertaining, insightful, and unafraid to launch the occasional verbal ICBM, HPC pioneer Thomas Sterling delivered his 16th annual closing keynote at ISC yesterday. He explored, among other things: exascale machinations; quantum’s bubbling money pot; Arm’s new HPC viability; Europe’s... Read more…

By John Russell

Is Weather and Climate Prediction the Perfect ‘Pilot’ for Exascale?

June 21, 2019

At ISC 2019 this week, Peter Bauer – deputy director of research for the European Centre for Medium-Range Weather Forecasts (ECMWF) – outlined an ambitious Read more…

By Oliver Peckham

ISC Keynote: Thomas Sterling’s Take on Whither HPC

June 20, 2019

Entertaining, insightful, and unafraid to launch the occasional verbal ICBM, HPC pioneer Thomas Sterling delivered his 16th annual closing keynote at ISC yesterday. He explored, among other things: exascale machinations; quantum’s bubbling money pot; Arm’s new HPC viability; Europe’s... Read more…

By John Russell

IBM Claims No. 1 Commercial Supercomputer with Total Oil & Gas System 

June 20, 2019

IBM can now boast not only the two most powerful supercomputers in the world, it also has claimed the top spot for a supercomputer used in a commercial setting. Read more…

By Staff Report

HPC on Pace for 5-Year 6.8% CAGR; Guess Which Hyperscaler Spent $10B on IT Last Year?

June 20, 2019

In the neck-and-neck horse race for HPC server market share, HPE has hung on to a slim, shrinking lead over Dell EMC – but if server and storage market shares Read more…

By Doug Black

ISC 2019 Research Paper Award Winners Announced

June 19, 2019

At the 2019 International Supercomputing Conference (ISC) in Frankfurt this week, the ISC committee awarded the event's top prizes for outstanding research pape Read more…

By Oliver Peckham

ISC Keynote: The Algorithms of Life – Scientific Computing for Systems Biology

June 19, 2019

Systems biology has existed loosely under many definitions for a couple of decades. It’s the notion of describing living systems using first-principle physics Read more…

By John Russell

Summit Achieves 445 Petaflops on New ‘HPL-AI’ Benchmark

June 19, 2019

Summit -- the world's top-ranking supercomputer -- has been used to test-drive a new mixed-precision Linpack benchmark, which for now is being called HPL-AI. Traditionally, supercomputer performance is measured using the High-Performance Linpack (HPL) benchmark, which is the basis for the Top500 list that biannually ranks world's fastest supercomputers. Read more…

By Oliver Peckham

By the Numbers: For the HPC Industry, These Are the Good Old Days

June 18, 2019

For technology vendors in HPC and HPC-related markets driven by increased demand for AI, enterprise and exascale solutions, this is the best of times – with better times likely in the offing. HPC analyst firm Hyperion Research took the occasion of its semi-annual HPC market update breakfast today in Frankfurt... Read more…

By Doug Black

High Performance (Potato) Chips

May 5, 2006

In this article, we focus on how Procter & Gamble is using high performance computing to create some common, everyday supermarket products. Tom Lange, a 27-year veteran of the company, tells us how P&G models products, processes and production systems for the betterment of consumer package goods. Read more…

By Michael Feldman

Cray, AMD to Extend DOE’s Exascale Frontier

May 7, 2019

Cray and AMD are coming back to Oak Ridge National Laboratory to partner on the world’s largest and most expensive supercomputer. The Department of Energy’s Read more…

By Tiffany Trader

Graphene Surprises Again, This Time for Quantum Computing

May 8, 2019

Graphene is fascinating stuff with promise for use in a seeming endless number of applications. This month researchers from the University of Vienna and Institu Read more…

By John Russell

Why Nvidia Bought Mellanox: ‘Future Datacenters Will Be…Like High Performance Computers’

March 14, 2019

“Future datacenters of all kinds will be built like high performance computers,” said Nvidia CEO Jensen Huang during a phone briefing on Monday after Nvidia revealed scooping up the high performance networking company Mellanox for $6.9 billion. Read more…

By Tiffany Trader

AMD Verifies Its Largest 7nm Chip Design in Ten Hours

June 5, 2019

AMD announced last week that its engineers had successfully executed the first physical verification of its largest 7nm chip design – in just ten hours. The AMD Radeon Instinct Vega20 – which boasts 13.2 billion transistors – was tested using a TSMC-certified Calibre nmDRC software platform from Mentor. Read more…

By Oliver Peckham

It’s Official: Aurora on Track to Be First US Exascale Computer in 2021

March 18, 2019

The U.S. Department of Energy along with Intel and Cray confirmed today that an Intel/Cray supercomputer, "Aurora," capable of sustained performance of one exaf Read more…

By Tiffany Trader

Deep Learning Competitors Stalk Nvidia

May 14, 2019

There is no shortage of processing architectures emerging to accelerate deep learning workloads, with two more options emerging this week to challenge GPU leader Nvidia. First, Intel researchers claimed a new deep learning record for image classification on the ResNet-50 convolutional neural network. Separately, Israeli AI chip startup Hailo.ai... Read more…

By George Leopold

TSMC and Samsung Moving to 5nm; Whither Moore’s Law?

June 12, 2019

With reports that Taiwan Semiconductor Manufacturing Co. (TMSC) and Samsung are moving quickly to 5nm manufacturing, it’s a good time to again ponder whither goes the venerable Moore’s law. Shrinking feature size has of course been the primary hallmark of achieving Moore’s law... Read more…

By John Russell

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

Nvidia Embraces Arm, Declares Intent to Accelerate All CPU Architectures

June 17, 2019

As the Top500 list was being announced at ISC in Frankfurt today with an upgraded petascale Arm supercomputer in the top third of the list, Nvidia announced its Read more…

By Tiffany Trader

The Case Against ‘The Case Against Quantum Computing’

January 9, 2019

It’s not easy to be a physicist. Richard Feynman (basically the Jimi Hendrix of physicists) once said: “The first principle is that you must not fool yourse Read more…

By Ben Criger

Top500 Purely Petaflops; US Maintains Performance Lead

June 17, 2019

With the kick-off of the International Supercomputing Conference (ISC) in Frankfurt this morning, the 53rd Top500 list made its debut, and this one's for petafl Read more…

By Tiffany Trader

Cray – and the Cray Brand – to Be Positioned at Tip of HPE’s HPC Spear

May 22, 2019

More so than with most acquisitions of this kind, HPE’s purchase of Cray for $1.3 billion, announced last week, seems to have elements of that overused, often Read more…

By Doug Black and Tiffany Trader

Intel Launches Cascade Lake Xeons with Up to 56 Cores

April 2, 2019

At Intel's Data-Centric Innovation Day in San Francisco (April 2), the company unveiled its second-generation Xeon Scalable (Cascade Lake) family and debuted it Read more…

By Tiffany Trader

Announcing four new HPC capabilities in Google Cloud Platform

April 15, 2019

When you’re running compute-bound or memory-bound applications for high performance computing or large, data-dependent machine learning training workloads on Read more…

By Wyatt Gorman, HPC Specialist, Google Cloud; Brad Calder, VP of Engineering, Google Cloud; Bart Sano, VP of Platforms, Google Cloud

In Wake of Nvidia-Mellanox: Xilinx to Acquire Solarflare

April 25, 2019

With echoes of Nvidia’s recent acquisition of Mellanox, FPGA maker Xilinx has announced a definitive agreement to acquire Solarflare Communications, provider Read more…

By Doug Black

Nvidia Claims 6000x Speed-Up for Stock Trading Backtest Benchmark

May 13, 2019

A stock trading backtesting algorithm used by hedge funds to simulate trading variants has received a massive, GPU-based performance boost, according to Nvidia, Read more…

By Doug Black

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This