Maintenance on May 3: Great Lakes, Armis2, and Lighthouse 

By | Uncategorized

On Tuesday, May 3, from 7-7:30 a.m., ARC will perform a vendor upgrade to Slurm on Great Lakes, Armis2, and Lighthouse HPC Clusters and their storage systems. ARC apologizes for the inconvenience.

Impact

  • This maintenance will cause a Slurm outage from 7-7:30 a.m.

  • Access to the cluster file systems will be available during the update.

  • Jobs not able to complete prior to 7 a.m. May 3 will not be able to start until after maintenance has ended. These jobs will be eligible to start once maintenance has been completed.

Status updates

Check the ITS Service Status page and follow ARC on Twitter for progress updates.

How can we help you?

For assistance or questions, please contact ARC at arc-support@umich.edu, or visit Virtual Drop-in Office Hours (CoderSpaces) for hands-on help, available 9:30-11 a.m. and 2-3:30 p..m. on Tuesdays; 1:30-3 p.m. on Wednesdays; and 2-3:30 p.m. on Thursdays.

For other topics, contact the ITS Service Center:

Understanding the strongest electromagnetic fields in the universe

By | Data, Great Lakes, HPC, Research, Uncategorized

Alec Thomas is part of the team from the U-M College of Engineering Gérard Mourou Center for Ultrafast Optical Science that is building the most powerful laser in the U.S.

Dubbed “ZEUS,” the laser will be 3-petawatts of power. That’s a ‘3’ with 15 zeros. All the power generated in the entire world is 10-terawatts, or 1000 times less than the ZEUS laser. 

The team’s goal is to use the laser to explore how matter behaves in the most extreme electric and magnetic fields in the universe, and also to generate new sources of radiation beams, which may lead to developments in medicine, materials science, and national security. 

A simulation of a plasma wake.

This simulation shows a plasma wake behind a laser pulse. The plasma behaves like water waves generated behind a boat. In this image, the “waves” are extremely hot plasma matter, and the “boat” is a short burst of powerful laser light. (Image courtesy of Daniel Seipt.)

“In the strong electric fields of a petawatt laser, matter becomes ripped apart into a `plasma,’ which is what the sun is made of. This work involves very complex and nonlinear physical interactions between matter particles and light. We create six-dimensional models of particles to simulate how they might behave in a plasma in the presence of these laser fields to learn how to harness it for new technologies. This requires a lot of compute power,” Thomas said. 

That compute power comes from the Great Lakes HPC cluster, the university’s fastest high-performance computing cluster. The team created equations to solve a field of motion for each six-dimensional particle. The equations run on Great Lakes and help Thomas and his team to learn how the particle might behave within a cell. Once the field of motion is understood, solutions can be developed. 

“On the computing side, this is a very complex physical interaction. Great Lakes is designed to handle this type of work,” said Brock Palen, director of Advanced Research Computing, a division of Information and Technology Services. 

Thomas has signed up for allocations on the Great Lakes HPC cluster and Data Den storage. “I just signed up for the no-cost allocations offered by the U-M Research Computing Package. I am planning to use those allocations to explore ideas and concepts in preparation for submitting grant proposals.”

Learn more and sign up for the no-cost U-M Research Computing Package (UMRCP).

Prof. Thomas’ work is funded by a grant from the National Science Foundation.

Yottabyte (Blue) to retire April 2022  

By | Uncategorized

The Yottabyte Research Cloud (YBRC), powered by Verge.io, provides U-M researchers with high-performance, secure, and flexible computing environments enabling the analysis of data sets, and hosting of databases for research purposes. Yottabyte (Blue) will retire on April 4, 2022. Yottabyte (Maize) for sensitive data will continue to be offered as a service. 

To determine if a virtual server is hosted in YBRC ‘Blue,’ check the hostname for the word ‘blue’ in its name, such as ‘yb-hostname.blue.ybrc.umich.edu.’

Members of the ARC Yottabyte team or Unit IT Support staff members will reach out to customers before the end of 2021 to determine customer needs and develop migration plans. Customers should review their data and projects that are currently utilizing Yottabyte (Blue), and  delete anything not needed.  

Visit the YBRC webpage on the ARC website for additional information about the retirement

Leveraging technology to improve education outcomes

By | Uncategorized

Nicole Wagner LamResearchers from U-M campuses and all across the country are using education data provided by the State of Michigan to study a wide variety of topics ranging from the effects of COVID-19 on public school enrollment to the role of neighborhood instability on student educational outcomes to exploring the ways that financial assets can change youth’s lives.

An arm of the Education Policy Initiative (EPI), the Michigan Education Data Center (MEDC) is a secure data clearinghouse that helps researchers use the State of Michigan’s education data to answer critical questions that improve outcomes for students. 

“Improving public education is one of the most pressing challenges facing our country today,” stated Kyle Kwaiser, EPI data architect and manager. “We’re using tools meant for research support, but using them as the foundation of a data clearinghouse serving researchers nationwide, and they’re working well.”

“Our researchers cover a breadth of topics for which Michigan education data are being used across all campuses. We think that the findings of these projects are powerful or will be very useful to policymakers,” said Nicole Wagner Lam, associate director for the Education Policy Initiative, the MEDC sponsor. 

Lam goes on to say that there are currently about 60 active research projects, about half of which are being conducted by U-M researchers. Researchers affiliated with U-M or Michigan State University leverage this restricted data stored on Turbo Research Storage that is provided by ARC.

Researchers also need a secure way to transfer, store, and analyze restricted data. MEDC affiliates also use Globus File Transfer and Yottabyte Research Cloud (YBRC) along with Turbo. Together, these three services enable productive and impactful research. 

Steve Wolodkin, ARC research cloud designer, says that, as a private cloud environment, YBRC gives researchers both good data protection and a familiar desktop environment. It also provides an easy mechanism to give multiple users access to the same desktop. Further, it is easy to add and remove users, which benefits this group particularly, as many of the people using it are students and change regularly. 

Jeremy Hallum, ARC research computing manager, explains how it all works together. YBRC provides a Windows virtual machine pool with various statistical software, configured in a way that supports this group’s research. User profiles and shared storage are integrated with Turbo storage, which allows researchers to access their data on any machine that they use. Globus is designed to move many large files, ranging from tens of gigabytes to tens of terabytes.

Lam said, “We are lucky to be at U-M and to work with researchers from all over the country. There are a lot of low- or no-cost resources at U-M to leverage, and many units that provide support.”

Kwaiser says that they worked closely with ARC two years ago when they were getting started. ARC helped create the structure, ensure security, and train MEDC how to use the services. It was a lot of work to get started. Now, everything is running smoothly. When needed, staff will attend one of four weekly office hours or attend an Office of Research training session. 

Several other ITS services have also been valuable for database hosting, access control, security, and VPN network connections. MiDatabase, a hosting service that provides campus with a centrally managed, on-premise cloud environment that reduces the cost, risk, and overhead involved in running services independently. MCommunity APIs are used to monitor and control access, know who’s logging on when, revoke access, control access to ARC resources. ARC is core but the MEDC team is also using ITS services. ITS Information Assurance was instrumental during the startup up, particularly when gaining data access approvals from the State of Michigan. ITS worked with MEDC and the State of Michigan to set up a standing Virtual Private Network (VPN) connection.

“I knew we could make solid progress with these ITS experts on board. I appreciate being able to work directly with them. It took months to gain trust from all parties when we were setting up, and now the resulting research is amazing,” Kwaiser said. “We’ve been able to get really far with resources at U-M.”

No-cost research computing allocations now available

By | HPC, News, Research, Systems and Services, Uncategorized

U-M Research Computing PackageResearchers on all university campuses can now sign up for the U-M Research Computing Package, a new package of no-cost supercomputing resources provided by Information and Technology Services.

As of Sept. 1, university researchers have access to a base allocation for 80,000 CPU hours of high-performance computing and research storage services at no cost. This includes 10 terabytes of high-speed and 100 terabytes of archival storage.

These base allocations will meet the needs of approximately 75 percent of current high-performance-computing users and 90 percent of current research storage users. Researchers must sign up on ITS’s Advanced Research Computing website to receive the allocation.

“With support from President (Mark) Schlissel and executive leadership, this initiative provides a unified set of resources, both on campus and in the cloud, that meet the needs of the rich diversity of disciplines. Our goal is to encourage the use, support and availability of high-performance computing resources for the entire research community,” said Ravi Pendse, vice president for information technology and chief information officer.

The computing package was developed to meet needs across a diversity of disciplines and to provide options for long-term data management, sharing and protecting sensitive data, and more competitive cost structures that give faculty and research teams more flexibility to procure resources on short notice.

“It is incredibly important that we provide our research community with the tools necessary so they can use their experience and expertise to solve problems and drive innovation,” said Rebecca Cunningham, vice president for research and the William G. Barsan Collegiate Professor of Emergency Medicine. “The no-cost supercomputing resources provided by ITS and Vice President Pendse will greatly benefit our university community and the countless individuals who are positively impacted by their research.”

Ph.D. students may qualify for their own UMRCP resources depending on who is overseeing their research and their adviser relationship. Students should consult with their Ph.D. program administrator to determine their eligibility. ITS will confirm this status when a UMRCP request is submitted.

Undergraduate and master’s students do not currently qualify for their own UMRCP, but they can be added as users or administrators of another person’s UMRCP. Students can also access other ITS programs such as Great Lakes for Course Accounts, and Student Teams.

“If you’re a researcher at Michigan, these resources are available to you without financial impact. We’re going to make sure you have what you need to do your research. We’re investing in you as a researcher because you are what makes Michigan Research successful,” Brock Palen, Advanced Research Computing director.

Services that are needed beyond the base allocation provided by the UMRCP are available at reduced rates and are automatically available for all researchers on the Ann Arbor, Dearborn, Flint and Michigan Medicine campuses.

More Information

Global research uses computing services to advance parenting and child development

By | General Interest, Great Lakes, HPC, News, Research, Uncategorized

Andrew Grogan-Kaylor, professor of Social Work, has spent the past 15 years studying the impact of physical discipline on children within the United States. 

Working with a team of other researchers at the School of Social Work, co-led by professors Shawna Lee and Julie Ma, he recently expanded his research to include children from all over the world, rather than exclusively the U.S. Current data for 62 low- and middle-income countries has been provided by UNICEF, a United Nations agency responsible for providing humanitarian and developmental aid to children worldwide. This data provides a unique opportunity to study the positive things that parents do around the world.

a group of smiling children

(Image by Eduardo Davad from Pixabay)

“We want to push research on parenting and child development in new directions. We want to do globally-based, diversity-based work, and we can’t do that without ARC services,” said Grogan-Kaylor. “I needed a bigger ‘hammer’ than my laptop provided.” 

The “hammer” he’s referring to is the Great Lakes HPC cluster. It can handle processing the large data set easily. When Grogan-Kaylor first heard about ARC, he thought it sounded like an interesting way to grow his science, and that included the ability to run more complicated statistical models that were overwhelming his laptop and department desktop computers. 

He took a workshop led by Bennet Fauber, ARC senior applications programmer/analyst, and found Bennet to be sensible and friendly. Bennet made HPC resources feel within reach to a newcomer. Typically, Grogan-Kaylor says, this type of resource is akin to learning a new language, and he’s found that being determined and persistent and finding the right people are key to maximizing ARC services. Bennet has explained error messages, how to upload data, and how to schedule jobs on Great Lakes. He also found a friendly and important resource at the ARC Help Desk, which is staffed by James Cannon. Lastly, departmental IT director Ryan Bankston has been of enormous help in learning about the cluster.

“We’re here to help researchers do what they do best. We can handle the technology, so they can solve the world’s problems,” said Brock Palen, ARC director. 

“Working with ARC has been a positive, growthful experience, and has helped me contribute significantly to the discussion around child development and physical punishment,” said Grogan-Kaylor. “I have a vision of where I’d like our research to go, and I’m pleased to have found friendly, dedicated people to help me with the pragmatic details.” 

More information

ARC, LSA support groundbreaking global energy tracking

By | General Interest, Great Lakes, HPC, News, Research, Uncategorized

How can technology services like high-performance computing and storage help a political scientist contribute to more equal access to electricity around the world? 

Brian Min, associate professor of political science and research associate professor with the Center for Political Studies, and lead researcher Zachary O’Keeffe have been using nightly satellite imagery to generate new indicators of electricity access and reliability across the world as part of the High-Resolution Electricity Access (HREA) project. 

The collection of satellite imagery is unique in its temporal and spatial coverage. For more than three decades, images have captured nighttime light output over every corner of the globe, every single night. By studying small variations in light output over time, the goal is to identify patterns and anomalies to determine if an area is electrified, when it got electrified, and when the power is out. This work yields the highest resolution estimates of energy access and reliability anywhere in the world.

A satellite image of Kenya in 2017

This image of Kenya from 2017 shows a model-based classification of electrification status based upon all night statistically recalibrated 2017 VIIRS light output. (Image courtesy Dr. Min. Sources: NOAA, VIIRS DNB, Facebook/CIESIN HRSL).

LSA Technology Services and ARC both worked closely with Min’s team to relieve pain points and design highly-optimized, automated workflows. Mark Champe, application programmer/analyst senior, LSA Technology Services, explained that, “a big part of the story here is finding useful information in datasets that were created and collected for other purposes. Dr. Min is able to ask these questions because the images were previously captured, and then it becomes the very large task of finding a tiny signal in a huge dataset.”

There are more than 250 terabytes of satellite imagery and data, across more than 3 million files. And with each passing night, the collection continues to grow. Previously, the images were not easily accessible because they were archived in deep storage in multiple locations. ARC provides processing and storage at a single place, an important feature for cohesive and timely research. 

The research team created computational models that run on the Great Lakes High-Performance Computing Cluster, and that can be easily replicated and validated. They archive the files on the Locker Large-File Storage service

One challenge Min and O’Keeffe chronically face is data management. Images can be hundreds of megabytes each, so just moving files from the storage service to the high-performance computing cluster can be challenging, let alone finding the right storage service. Using Turbo Research Storage and Globus File Transfer, Min and O’Keeffe found secure, fast, and reliable solutions to easily manage their large, high-resolution files.

Brock Palen, director of ARC, said that top speeds were reached when moving files from Great Lakes to Turbo at 1,400 megabytes per second. 

Min and team used Globus extensively in acquiring historical data from the National Oceanic and Atmospheric Administration (NOAA). Champe worked with the research team to set up a Globus connection to ARC storage services. The team at NOAA was then able to push the data to U-M quickly and efficiently. Rather than uploading the data to later be downloaded by Min’s team, Globus streamlined and sped up the data transfer process. 

Champe noted, “Over 100TB of data was being unarchived from tape and transferred between institutions. Globus made that possible and much less painful to manage.”

“The support we’ve gotten from ARC and LSA Technology has been incredible. They have made our lives easier by removing bottlenecks and helping us see new ways to draw insights from this unique data,” said Min. 

Palen added, “We are proud to partner with LSA Technology Services and ITS Infrastructure networking services to provide support to Dr. Min’s and O’Keeffe’s work. Their work has the potential to have a big impact in communities around the world.” 

“We should celebrate work such as this because it is a great example of impactful research done at U-M that many people helped to support,” Champe continued.

Min expressed his gratitude to the project’s partners. “We have been grateful to work with the World Bank and NOAA to generate new insights on energy access that will hopefully improve lives around the world.”

These images are now available via open access (free and available to all)

This is made possible by a partnership between the University of Michigan, the World Bank, Amazon Web Services, and NOAA

Using machine learning and the Great Lakes HPC Cluster for COVID-19 research

By | General Interest, Great Lakes, HPC, News, Research, Uncategorized

A researcher in the College of Literature, Science, and the Arts (LSA) is pioneering two separate, ongoing efforts for measuring and forecasting COVID-19: pandemic modeling and a risk tracking site

The projects are led by Sabrina Corsetti, a senior undergraduate student pursuing dual degrees in honors physics and mathematical sciences, and supervised by Thomas Schwarz, Ph.D., associate professor of physics. 

The modeling uses a machine learning algorithm that can forecast future COVID-19 cases and deaths. The weekly predictions are made using the ARC-TS Great Lakes High-Performance Computing Cluster, which provides the speed and dexterity to run the modeling algorithms and data analysis needed for data-informed decisions that affect public health. 

Each week, 51 processes (one for each state and one for the U.S.) are run in parallel (at the same time). “Running all 51 analyses on our own computers would take an extremely long time. The analysis places heavy demands on the hardware running the computations, which makes crashes somewhat likely on a typical laptop. We get all 51 done in the time it would take to do 1,” said Corsetti. “It is our goal to provide accurate data that helps our country.”

The predictions for the U.S. at the national and state levels are fed into the COVID-19 Forecasting Hub, which is led by the UMass-Amherst Influenza Forecasting Center of Excellence based at the Reich Lab. The weekly predictions generated by the hub are then read out by the CDC for their weekly forecast updates Center for Disease Control (CDC) COVID-19 Forecasting Hub

The second project, a risk tracking site, involves COVID-19 data-acquisition from a Johns Hopkins University repository and the Michigan Safe Start Map. This is done on a daily basis, and the process runs quickly. It only takes about five minutes, but the impact is great. The data populates the COVID-19 risk tracking site for the State of Michigan that shows by county the total number of COVID-19 cases, the average number of new cases in the past week, and the risk level.

“Maintaining the risk tracking site requires us to reliably update its data every day. We have been working on implementing these daily updates using Great Lakes so that we can ensure that they happen at the same time each day. These updates consist of data pulls from the Michigan Safe Start Map (for risk assessments) and the Johns Hopkins COVID-19 data repository (for case counts),” remarked Corsetti.

“We are proud to support this type of impactful research during the global pandemic,” said Brock Palen, director of Advanced Research Computing – Technology Services. “Great Lakes provides quicker answers and optimized support for simulation, machine learning, and more. It is designed to meet the demands of the University of Michigan’s most intensive research.”

ARC is a division of Information and Technology Services (ITS). 

Related information 

Beta tool helps researchers manage IT services

By | General Interest, News, Research, Uncategorized

Since August 2019, ARC-TS has been developing a tool that would give researchers and their delegates the ability to directly manage the IT research services they consume from ARC-TS, such as user access and usage stats.

The ARC-TS Resource Management Portal (RMP) beta tool is now available for U-M researchers.

The RMP is a self-service-only user portal with tools and APIs for research managers, unit support staff, and delegates to manage their ARC-TS IT resources. Common activities such as managing user access (adding and removing users), viewing historical usage to make informed decisions about lab resource needs, and determining volume capacity at a glance are just some of the functionality the ARC-TS RMP provides.

The portal currently provides tools for use with Turbo Research Storage, a high-capacity, reliable, secure, and fast storage solution. Longer-term, RMP will scale to include the other storage and computing services offered by ARC-TS. It is currently read-view only.

To get started or find help, contact arcts-support@umich.edu.

Modular Data Center Electrical Work

By | Flux, Systems and Services, Uncategorized

[Update 2019-05-17 ] The MDC electrical work was completed successfully and Flux has been returned to full production.

 

The Modular Data Center (MDC), which houses Flux, Flux Hadoop, and other HPC resources, has an electrical issue which requires us to bring the power usage below 50% for the some racks in order to resolve the problem.  In order to do this, we have put reservations on some of the nodes to reduce the power draw so the issue can be fixed by ITS Data Centers.  Once we hit the target power level and the issue is resolved, we will remove the reservations and return Flux and Flux Hadoop back into full production level.