Atlantic Canada

Preparing for Climate Change’s Effects with Geophysics

As climate change causes ever increasing fears of flooding, Dr. Peter Lelievre’s work in geophysical imaging becomes ever more important in the province of New Brunswick and beyond.

An assistant professor in Mount Allison University’s department of mathematics and computer science, Dr. Lelievre is an applied geophysicist who images what’s underground. Earlier in his career, that pursuit was tied to mineral exploration or “trying to help people find the materials such as metals that our society uses for basic building materials.” More recently, he’s become interested in imaging and understanding what happens with flood infrastructure.

“With climate change and rising sea levels, we need to understand more about how water moves through these flood barriers,” Lelievre explains. “Geophysical imaging can help us better understand these things, and also to try and find any erosional issues that could cause a breach.”

Lelievre walks on the fields and marshes near Sackville, N.B. — which are the same places his research now takes place. Being at Mount Allison means he’s surrounded by the dike land and he, his wife, and his dog walk on it frequently.

“It’s far more at the forefront of my mind in my daily life,” he says. “It’s been really nice to be able to shift and connect my research to that part of the local community and my daily life.”

Lelievre uses tools that measure electrical and electromagnetic fields and then he uses heavy mathematical methods and computational power to process the data.

“We run the data through these algorithms that we develop and this creates an image of what’s underground,” he says of his use of the Digital Research Alliance of Canada’s high-performance computing tools. “That’s where the heavy computational part fits in. These are tremendously large computational problems.”

For his heavier research, an imaging task could require 600 central processing units (CPUs), consume roughly two terabytes of random access memory (RAM) and take over four-days to finish. He and his research team use the modern Fortran programming language and create their own software to process their electrical and electromagnetic data and generate images of the Earth.

With the help of his students, postdocs and colleagues, he develops data processing methods that could be used in the field, and he collects field data to help test those methods.

“Eventually we’d like to be able to create data processing methods we can use in the field on a laptop, and so you’d just have a small, everyday laptop, where you get a result in effectively real time,” he says, and adds that the history of computing tells us that could well happen in the near future.

Making Data Meaningful

Whether it be for a community project to determine which water is safe for drinking, or a hospital-based project to determine the most efficient and effective ways to treat mental illness, Trishla Shah is an expert in taking the data we collect so easily today, and making them meaningful.

As the IT research scientist at the Nova Scotia Community College and a PhD candidate in computer science at Dalhousie University, Shah focuses on designing solutions by analyzing massive amounts of data. For example, Nova Scotia’s water comes from various places, including freshwater lakes, but also possibly from contaminated lakes, she says.

“We want to educate the organizations taking care of our water resources so we can see how we can preserve the well water and how we can make sure the water from the fresh lakes is not contaminated,” Shah says, adding that many of her projects come to her after receiving funding from a national social innovation fund.

Private IT companies that want to design and test a product from scratch also often approach the research scientist.

“We are being approached by startups, by midsize companies and by large-scale companies,” Shah says. “We are being approached by organizations that take care of Indigenous communities. One project we’re working on involves artificial intelligence, Indigenous communities and Halifax’s storied Bluenose ship.”

For another project, Shah is helping small- and medium-sized enterprises identify the right clean technology investments for their business. Her lab is building a data repository to provide solutions to scale access to low-carbon emissions for businesses in the agri-food, construction and manufacturing industries. The repository is integrated from various sources using web-scraping and text-mining techniques. The parameters of the data repository will be set to allow an algorithm to forecast carbon emission reductions and analyze the return-on-investment of various interventions.

Shah and her team get involved from the beginning, first collecting the data, then building a database, preprocessing, storing and managing the data in a way that ensures they’re secure and making sure there’s no breach. From there, they can make models of the data so they don’t have to analyze them manually.

Shah hasn’t used the services of ACENET directly, but she has circulated its many programs among the information technology students at the college.

“We have a lot of academic programs that have IT in them,” she says. “And students might want extra practice, or students might need to have something like a prerequisite. With ACENET, the courses are really applicable and I like to circulate them among students who need additional practice on that topic. So that’s my interest with ACENET. I’m a fan.”

In addition, Shah is in the process of designing her own student training module that has an online portal where students can enrol themselves in training that is focused on real-time projects.

“I have proposed to the committee that’s approving my student training module and funding that ACENET’s courses be prerequisites.”

Curbing Sea Lice in Salmon Farming

Gregor McEwan wants to help salmon farmers manage sea lice on their farms, and he’s using supercomputing to do it. It seems odd to think of research into aquatic life involving high-powered computing, but that’s what McEwan, a research scientist, is doing. He works under the supervision of Professor Crawford Revie in Revie’s lab in the Atlantic Veterinary College’s Department of Health Management at the University of Prince Edward Island. Salmon farming is an industry worth more than $16 billion worldwide, and Canada is the industry’s fourth-largest producer after Norway, Chile and Scotland. Farmed salmon is raised from eggs on land facilities and, when large enough, moved to cages in the sea. The fish are kept in the cages until they reach harvest weight — typically three to five kilograms. After that, they’re sent to processing plants to eventually become fillets available through retail. But often, in the sea cages, sea lice, among the most pervasive problems facing salmon farmers, invade. They attach to the salmon and feed off the fish’s mucus, flesh and blood, causing discomfort and reduced immunity for the salmon. “Usually, [due to immunity issues], they then get sick from something else, but enough sea lice will also kill the salmon,” McEwan says. “It’s a major issue for salmon farmers and they’re especially interested in using treatment methods they have — whether chemicals or mechanical treatments such as warm water baths — to solve it.” McEwan is trying to determine how they can use existing treatments most effectively and in what kind of patterns they should use them. “I build computer simulations to try out different strategies,” McEwan says. “It’s expensive to try them on the salmon farm in real time, so it makes sense to simulate them on computers.” To make the simulation work, he must set parameters — such as ‘how many lice are flowing on to the farm?’ — which is tricky. Such information is unknown because it’s not feasible to count lice in the open sea around each farm. “I take all the historical information I can get about the environment and the farmers’ weekly count records of sea lice on the salmon,” McEwan says. “I train the model with that information and extract the relevant parameters. I use machine-learning algorithms to get the correct parameters for the model. I can use the trend model to create predictions for the future. We can run scenarios where we say, ‘okay, what if this happens, or what if we use this kind of strategy?’” One of the things McEwan must consider is the ability of the lice to evolve a genetic resistance to the chemical treatments. For example, past research investigated the repercussions of wild salmon coming near the farm cages. Wild salmon carry lice, but McEwan’s discovered that, because their lice are genetically naïve to the chemical treatments, they bring what he calls a “genetic cleaner” to the equation. “Yes, you end up with a few more lice in the short term, but whatever treatments you’re using are more effective and work a lot longer because the genetic resistance is being cleaned out of the population,” he says. “It’s actually a net positive.” For McEwan’s simulations, ACENET’s resources are vital. His lab has powerful computers, but nothing on the scale of ACENET. He says without ACENET, everything he’s doing would take months instead of weeks. “We’d never be finished.”

Recasting Residue Into Power

Kelly Hawboldt imagines a world where Atlantic Canadians can have their own energy sources or their own water filtration systems built entirely on the region’s own biomass residue. Hawboldt is a chemical engineer who works in Memorial University’s faculty of engineering. She focuses on converting biomass residue from the forestry and fishery sectors — sawmill and pulp and paper waste, sawdust, saw chips and shellfish residue, for example — into items of value. “There’s a lot of added value in those residues, so we try to recover that usefulness,” she says. “We’ve developed processes that are green and sustainable to extract value and then we try to develop by-products that have lifecycle — they either degrade to what they started with or can be used to make something else.” Pyrolysizing (burning without oxygen at high temperatures) such residue can result in three products: a gas that can be used for energy, a liquid that will also produce energy, or a solid in the form of carbon, which can be used as an absorbent for contaminants. She works with Stephanie MacQuarrie, an associate professor of chemistry at Cape Breton University. “She’s a chemist and I’m a chemical engineer, so it’s a nice mix,” Hawboldt says. “We mix the mussel shells and the forestry residue and it changes the quality of the by-products. They might, for example, have better absorption capacity for certain types of contaminants.” She focuses on Atlantic Canada because it’s a small place, with a small population and plenty of biomass. “Because of transport, it’s hard to get the biomass residues to a market,” she explains. “So we focus on developing products and processes that will build that community rather than trying to export everything. Forestry companies could be supplying their own energy or their own water-filtration source. That’s where we’d like to go.” Hawboldt has been working in this area for the past 15 years and uses high-powered computing through ACENET and Compute Canada to do her work. Once she establishes processes for her residue-revamping, she models them so she can modify the designs. “Experimentally, this kind of work would take a long time, but we can vary things within the model and once we’ve validated it, it’s much quicker and easier to change things,” she says. Along with with Dr. MacQuarrie, she creates biochar — the solid product of pyrolysis and a highly porous material with various functions that must be analyzed to get the best benefits. “With ACENET, we’ve modelled the surface of the char and then we see if there’s a tendency for various contaminants to absorb,” she says. “So, I might take hydrogen sulphide or a metal and the molecular model would do a series of calculations to see if, based on the surface of that char, there’s a tendency for our contaminant of interest to absorb. If it does, we can then do the more detailed experiment. It’s a very useful screening tool.” ACENET, she says, is essential for her work. “Some of these models can take days to run. Without ACENET, I don’t think we could run them. You’d be talking about months instead of days.”

A Crusade to Protect Crustaceans Against Climate Change

Fraser Clark is a man on a mollusc mission — or you could call it a crustacean crusade. The Dalhousie University animal science and aquaculture professor studies the immunology of crustaceans with a goal of understanding their health and what pathogens threaten them, particularly as East Coast waters warm, and the pH drops, as a result of climate change. He concentrates his research on the wild lobster, crab and shrimp fisheries, with a secondary focus on commercial shellfish, including scallops, oysters and mussels. “My work is on the health, disease and stress in these species,” Clark says. “I look at their immune response, their stress response and how they interact with pathogens.” His research aims to contribute to the health of the Atlantic Canadian fishery industry, helping fishers to have access to hardier and faster-growing products. “With the oysters, mussels and scallops, we find markers for disease and stress resilience, especially as it concerns the ocean’s response to climate change,” he says. When it comes to major wild fisheries, he says, only crustaceans remain. Lobster is the biggest, then crab and shrimp. “We’re finding some interesting differences between crustaceans in the same area, but I can’t say much about pathogens yet,” he says, stressing that none of the pathogens affects humans. “Some are new pathogens, some haven’t been studied before. We’re cataloguing what’s normal and what could come up the Eastern seaboard of the U.S. as waters warm. We know what’s down there, we know what’s up here and we’re able now to monitor it because we have baseline studies.” The differences in immune systems of crustaceans in the same habitat can be used as health-markers, something that currently doesn’t exist for crustaceans. Practically speaking, it’s useful to understand the immune systems of lobsters, for example, as they’re more valuable when alive. When they’re killed, cooked and processed, they are worth less on the market, but live ones that die before they’re sold aren’t worth anything at all, he notes. Surprisingly, he came to this work after doing a master’s in cancer research. “I didn’t feel I was having much of an impact in my local area,” says the Kensington, P.E.I.-born researcher. “So, I got involved in work at the Lobster Science Centre. Now there’s a local impact as I interact with fishers, industry, aquaculture associations and local governments. I can make a difference to their industry.” To do his work, Clark uses resources provided by Compute Canada. He uses its high-powered computing resources to sequence transcriptomes, which are similar to genomes. He then compares different immune genes in different species. He compares the different sequences and constructs models to see how closely related they are. “We’re really interested in how closely related the immune systems are of crab, lobster and shrimp all living in the same area,” he says. “They seem to get sick from different things even though they’ve all been growing in the same area for the last 150 million years.” To that end, the GenAp Galaxy web portal application hosted by Compute Canada has been helpful. “It allows biologists to use high-end computing resources without needing to do high-end coding,” he says. “As long as we understand the assumptions and limitations of the tests, we can get user-friendly data. My undergraduates and graduate students can learn to use these computing resources within days. It’s exceptionally helpful for biologists.”

Predicting the Influence of the Ocean on Machines and Structures

Understanding how machines and structures perform in the ocean has important implications for everything from the way ships manoeuvre to how tidal power turbines respond to massive hydraulic forces. One University of New Brunswick scientist is working hard to increase that understanding and he’s employing some powerful computational tools. Andrew Gerber is a professor of mechanical engineering at UNB. He’s an expert in the field of computational fluid dynamics (CFD) and high performance computing, a discipline that focuses on solving the equations that govern fluid movement using supercomputers. Supercomputers are needed to study in detail how ocean turbulent fluid motion interacts with machines and structures situated within it. Oceans are extremely demanding environments. For man-made systems to survive requires detailed understanding, something that supercomputer simulations can provide. Gerber is involved with a number of important projects including a tidal power study in the Bay of Fundy and a project with Defence Research and Development Canada to study the performance of Canadian naval submarines. “We do a lot of work with submarines,” says Gerber. “We simulate extreme manoeuvres on the computer to see what’s happening to the forces and moments acting on the body of the submarine as it moves through the water. It’s very expensive for the navy to do experiments of this type so our simulations allow them to make predictions without the need for extensive experimentation”. Gerber’s work with tidal power focuses on making detailed fluid flow predictions to support tidal power turbine deployments in the Bay of Fundy. He and his colleagues at UNB are working with the Fundy Ocean Research Centre for Energy (FORCE), and with researchers at Acadia University and Dalhousie University, to measure tidal flow and energy potential in the Minas Passage near Parrsboro and in Grand Passage at Brier Island, Nova Scotia. This work will have a huge impact on where turbine arrays are deployed considering issues such as survivability and maximizing power output. The tidal study involves huge volumes of water requiring complex calculations. Twice each day 10 cubic kilometers of seawater are forced through the Minas Passage – 10 billion tons of water that represent an outflow more than 40 times the amount that flows from the Saint Lawrence River over the same period of time. With technical support from ACENET and funding from the Canada Foundation for Innovation, Gerber set up a “contributed system,” a computer cluster operated by Gerber’s UNB laboratory and managed by ACENET. Under the system, any unused cycles are turned over to ACENET for other researchers to use. The system is powered by the latest Graphical Processing Unit (GPU) hardware, and combined with a CFD simulation software (EXN/Aero) that can efficiently utilize the new hardware, the complex tidal simulations can be completed much more rapidly with high-resolution. In addition to his work at UNB, Gerber is also a partner in a spinoff company called Envenio Inc., a Fredericton-based firm that provides computational fluid mechanics services and engineering software development to engineers and companies. Its flagship product is EXN/Aero, which is specifically designed for next generation hardware. Gerber says that as climate change becomes more prevalent, understanding the movements of fluids in the oceans and atmosphere and their impact on infrastructure will become crucial. “One of the goals of Envenio is to help engineers build better designs for extreme weather events in the ocean or atmosphere and to provide the computational tools to do so.”

Acadia Professor Uses ACENET to Unlock Tidal Power Secrets

In Richard Karsten’s office at Acadia University the entire Bay of Fundy has been reduced to a grid made up of 100,000 triangles displayed on an oversized computer screen. The data points – tide height, current, water depth – have been carefully plotted by the mathematics professor and his graduate students to create a computer model that can pinpoint the nature of the tide at any spot on the bay, at any given second for the next 25 years. It’s a staggering amount of data. “At the basic level, what we’re studying is how fast the water is flowing at any given point,” he says. “Then we get into more detail and look at things like the variations in the direction and speed of flow.” The 270 kilometre-long bay Karsten is studying is one of the most unique places on Earth; a submerged rift valley where the world’s highest tides reach a daily height of 16 meters, moving 160 billion tonnes of seawater in the process and powering a dynamic ecosystem teaming with life. It’s a place often mentioned in the same breath as the Great Barrier Reef and the Amazon; where a dozen species of whales regularly congregate and millions of shore birds gather every year to fatten themselves up for their migration to South America. It could also be North America’s next great source of hydroelectric power. A number of projects are underway to harness those powerful tides. Most notable is the Fundy Ocean Research Centre for Energy or FORCE, a government and industry supported test centre for in-stream tidal energy located in Parrsboro, Nova Scotia. There are smaller projects as well, including one by Fundy Tidal Inc., a corporation headquartered on Brier Island Nova Scotia. Fundy Tidal is working with partner Clean Current Power Systems Inc. of British Columbia to develop five small community tidal projects to sell energy through Nova Scotia’s Community Feed-In Tariff (COMFIT) program. Karsten’s research, along with information provided by project partners Dalhousie University, the University of New Brunswick and Dynamic Systems Analysis, will provide information for those projects by locating the spots where engineers can best place underwater turbines, along with long term projections of just how profitable those turbines will be. “Numerical models are relatively cheap as opposed to testing,” he says. It is one reason his research has attracted funding support from Natural Resources Canada, the Offshore Energy and Research Association of Nova Scotia and NSERC. Charting terabytes of information presents a significant “big data” problem, but Karsten has a valuable tool in his arsenal – a computer network hundreds of times more powerful than the computer on his desk. By tapping into the ACENET system that links large computers located in a number of Atlantic Canadian universities, he has access to a super computer network capable of, in aggregate, computations of up to 68 Teraflops. “What would take years on a desktop takes us a few days or weeks with the ACENET supercomputer,” he says. The speed of the system allows him to run various “what if” scenarios, such as adding more turbines to a particular location or seeing what additional forces would be generated by a storm surge. “It means we are able to answer questions quickly.” Hydrographers have been maintaining accurate tidal charts for more than a century, but until recently no one was too concerned with information like flow direction and force – information that is vitally important to tidal power engineers. If, for example, the water doesn’t flow back and forth along the same direction with each tide, a turbine might have to be turned constantly to face the flow – a design feature that would increase the cost of the operation significantly. Karsten’s research provides critical support to the development of a tidal energy industry both in Nova Scotia and nationally. Such an industry would produce substantial amounts of sustainable, renewable electricity that would reduce Nova Scotia production of greenhouse gases and decrease its dependency on foreign fuels. Last year, some of his research activities included making extractable power estimates for all major Nova Scotia tidal resources. In total, the calculations estimated that the tidal resource could support over 1400 MW of installed capacity with only a minor impact on the tides. This is 55% of Nova Scotia generation capacity. “Tides are ultimately predictable,” says Karsten. “That’s what makes them so appealing as an energy source. But there are a lot of variables – rocks or seaweed on the bottom, deep channels or shoals within a passage – that affect the energy in the tidal currents.” There is a less pragmatic purpose for Karsten’s research as well. As biologists and oceanographers at Acadia and other universities scramble to unravel the delicate ecosystem of the Bay of Fundy, they are sharing data in an attempt to understand how tides affect the movements of fish and other sea life. “You would think we know a lot about Fundy but we really don’t yet,” he says. “It’s still very much a mysterious place.”

Digitizing History

Josh MacFadyen is the first MacFadyen in several centuries not to farm. And that, in a sense, is what’s led to his life’s work as an associate professor in the Applied Communication, Leadership and Culture (ACLC) program at the University of Prince Edward Island and a Canada Research Chair (Tier II) in geospatial humanities. MacFadyen studies the environmental history of Canada, with a focus on Atlantic Canada. He’s specifically interested in food systems and how humans, and even animals, have fed themselves over time and how they stayed warm in a world before fossil fuels. “And that could have some applications for how we might right [things] going forward,” he says, referring to perhaps novel ways to tackle climate change by learning from the past. MacFadyen was trained as an historian, but over time, because he was using a lot of technology in his work, he became a digital historian. “Digital historian is just a fancy way of saying we use spatial analysis, geographic information systems, and other digital tools related to large datasets such as historical Censuses to understand questions of how general land use and energy systems have changed, and how we’ve arrived at the modern world,” he says. He says Atlantic Canada is the right place to be for his studies as it still has large areas that are predominantly agricultural, though that is gradually changing. For example, the move away from farming isn’t limited to his family. In fact, it’s long been a trend on the island, which has seen a 20 per cent decrease in farmland in the last 20 years. It’s a fact he’s considering in his field of study. He uses Census data to get a granular look at such trends and he uses remote sensing — everything from aerial photos and satellite, to light detection and ranging (LiDAR) —to dig deeper. “The sources I’ve been able to use most consistently are aerial photos —we’ve got the whole province covered right back to 1935,” he says, and adds that he has used that data to develop products that would be useful to historians. His current is a portal for exploring maps, atlases, aerial photos and geospatial data related to the history of Prince Edward Island that resides at projects.upei.ca/geolab. To develop these tools, MacFadyen has used the services of the Digital Research Alliance of Canada through ACENET by participating in workshops and training modules for the humanities and social sciences. “They’re just tremendous,” he says of the workshops and networking. “I just thought ‘Wow, what a great way to join this regional, highly skilled and very active group of people who are trying to create resources for the humanities and social sciences in Atlantic Canadian universities.’ They’re offering these regular training modules, and some are specifically for us.”

Bringing Communities Together Through Music

Marcia Ostashewski’s ethnomusicology work brings together local communities through music and performance projects. At times, those communities stretch much further — one project connected people from Cape Breton, Alberta and Croatia. Ostashewski, an Associate Professor of Ethnomusicology, Tier 2 Canada Research Chair for Communities and Cultures and Director of the Centre for Sound Communities (soundcommunities.org) at Cape Breton University, brought the aforementioned group together through her work on diversitycapebreton.ca, a web portal that highlights the Eastern and Central European cultural contributions to Cape Breton. “There was a gap in the scholarship, public heritage interpretation and public school curriculum about the contributions of these Europeans,” Ostashewski says, “and to attend to this gap, we developed the portal.” She created it in partnership with the University of Prince Edward Island, along with a working group based at Cape Breton University, and received a grant from the Social Sciences and Humanities Research Council (SSHRC). She interviewed experts from Eastern Europe and worked with partners at the University of Alberta and Japan’s University of Aizu. The Croatia connection came when she invited a Croatian post-doctoral student to work on the project. The site has two major components. One is an archive and the other is an interactive section with display options such as virtual tours. The latter also features curriculum specifically written for students and teachers in Nova Scotia’s school system. “You can adjust them to meet your classroom’s needs,” Ostashewski says. “Those are very well received by teachers.” The archive also includes many digitized archival documents, as well as interviews and videos of public performances. In addition to Eastern and Central Europeans, the Whitney Pier and Glace Bay areas of Cape Breton once had a large Jewish community that now only numbers about 10 families. The archive also highlights their contributions. “There used to be several synagogues, but now many members of those communities have moved off-island,” she says. “So it’s nice to have this material available to the public. As a result of the portal, the Beit Hatfutsot, a high-profile museum of the Jewish diaspora in Israel, found out about the Jewish community in Cape Breton and asked us to write some information for them. We’ve also done exhibits and presentations in Toronto, where many of these families have moved.” This project was made possible with help from ACENET, a regional partner of Compute Canada that makes high-performance computing accessible to researchers in Atlantic Canada. Once the SSHRC grant ran out, it was vital to have ACENET house the portal. “ACENET is also training students, faculty and staff to take on the responsibility of managing, maintaining and growing this and other research sites,” Ostashewski says. Ostashewski has also studied the live music and poetry of bards (singingstorytellers.ca, songsoftruth.ca) from around the world, and, through a pilot project called iCreate Cape Breton, she works with at-risk youth and elders to foster resilience among youth facing environmental changes that lead to social justice issues. Her most significant recent work may be her collaborations with Membertou First Nation and other Cape Breton Island communities. Mi’kmaq Elders have described here work as “truth and reconciliation in action.” Ostashewski said ethnomusicology research is moving toward more intensive community-engaged research, which suits her fine, and which will continue to require plenty of high-powered computing.