Category

Research

HPC Emergency 2023 Maintenance: September 15

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

Due to a critical issue which requires an immediate update, we will be performing updates to Slurm and underlying libraries which allow parallel jobs to communicate. We will be updating the login nodes and the rest of the cluster on the fly and you should only experience minimal impact when interacting with the clusters. 

  • Jobs that are currently running will be allowed to finish. 
  • All new jobs will only be allowed to run on nodes which have been updated. 
  • The login and Open OnDemand nodes will also be updated, which will require a brief interruption in service.

Queued jobs and maintenance reminders

Jobs will remain queued, and will automatically begin after the maintenance is completed. Any parallel using MPI will fail; those jobs may need to be recompiled, as described below. Jobs not using MPI will not be affected by this update.

Jobs will be initially slow to start, as compute nodes are drained of running jobs so they can be updated. We apologize for this inconvenience, and want to assure you that we would not be performing this maintenance during a semester unless it was absolutely necessary.

Software updates

Only one version of OpenMPI (version 4.1.6) will be available; all other versions will be removed. Modules for the versions of OpenMPI that were removed will warn you that it is not available, as well as prompt you to load openmpi/4.1.6. 

When you use the following command, it will default to openmpi/4.1.6:
module load openmpi 

Any software packages you use (provided by ARC/LSA/COE/UMMS or yourself) will need to be updated to use openmpi/4.1.6. The software package updates will be completed by ARC. The code you compile yourself will need to be updated by you.

Note that at the moment openmpi/3.1.6 will be discontinued and warned to update your use to openmpi/4.1.6.

Status updates

 

System software changes

Great Lakes, Armis2 and Lighthouse

NEW version in BOLD OLD version
Slurm 23.02.5 compiles with:
  • PMIx
    • /opt/pmix/3.2.5
    • /opt/pmix/4.2.6
  • hwloc 2.2.0-3 (OS provided)
  • ucx-1.15.0-1.59056 (OFED provided)
  • slurm-libpmi
  • slurm-contribs
Slurm 23.02.3 compiles with:
  • PMIx
    • /opt/pmix/2.2.5
    • /opt/pmix/3.2.3
    • /opt/pmix/4.2.3
  • hwloc 2.2.0-3 (OS provided)
  • ucx-1.15.0-1.59056 (OFED provided)
  • slurm-libpmi
  • slurm-contribs
PMIx LD config /opt/pmix/3.2.5/lib PMIx LD config /opt/pmix/2.2.5/lib
PMIx versions available in /opt :
    • 3.2.5
    • 4.2.6
PMIx versions available in /opt :
  • 2.2.5
  • 3.2.3
  • 4.1.2
OpenMPI
  • 4.1.6
OpenMPI
  • 3.1.6
  • others

 

How can we help you?

For assistance or questions, contact ARC at arc-support@umich.edu.

Summer 2023 Network Maintenance: HPC and storage unavailable August 21-22 

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

During the 2023 summer maintenance, a significant networking software bug was discovered and ARC was unable to complete the ARC HPC and Storage network updates at the MACC Data Center.

ITS has been working with the vendor on a remediation, and it will be implemented on August 21-22.  This will require scheduled maintenance for the HPC clusters Great Lakes, Armis2, and Lighthouse, as well as the ARC storage systems Turbo, Locker, and Data Den. The date was selected to minimize any impact during the fall semester. 

Maintenance dates:

HPC clusters and storage systems (/home and /scratch) and ARC storage systems (Turbo, Locker, and Data Den) will be unavailable August 21 starting at 7:00am.  Expected completion date is August 22nd.

Queued jobs and maintenance reminders

Jobs will remain queued, and will automatically begin after the maintenance is completed. The command “maxwalltime” will show the amount of time remaining until maintenance begins for each cluster, so you can size your jobs appropriately. The countdown to maintenance will also appear on the ARC homepage

Status updates

How can we help you?

For assistance or questions, contact ARC at arc-support@umich.edu.

U-M Research Computing Package automatic renewal begins July 1

By | News, Research, Uncategorized

** Looking for the LARCC Application?

____

The no-cost bundle of supercomputing resources known as the U-M Research Computing Package (UMRCP) automatically renews for most on July 1. 

Provided by Information and Technology Services, the UMRCP offers qualified researchers on all campuses (Ann Arbor, Dearborn, Flint, and Michigan Medicine) with allocations of high-performance computing, secure enclave, and research storage services. (Many units, including Michigan Medicine, provide additional resources to researchers. Be sure to check with your school or college.) 

If a faculty researcher has left the university (or is about to), and their research remains at the university, an alternative administrator must be assigned via the ARC Resource management Portal (RMP) so that the allocations can continue uninterrupted. ARC is available to help researchers make this transition. 

Don’t have the UMRCP? Here’s how to request resources 

Faculty, as well as staff and PhD students with their own funded research on all campuses (Ann Arbor, Dearborn, Flint, and Michigan Medicine), are welcome to request allocations. Full details are available on the Advanced Research Computing website

PhD researchers who do not have their own funded research can work with their advisor to be added to their allocations via the ARC Resource Management Portal (RMP).

“The UMRCP was launched in 2021 to meet the needs of a diversity of disciplines and to provide options for long-term data management, sharing, and protecting sensitive data,” said Brock Palen, director, ITS Advanced Research Computing. “The UMRCP alleviates a lot of the pressure that researchers feel in terms of managing the technology they need to achieve breakthroughs.”

More information

Globus maintenance happening at 9 a.m. on March 11

By | Armis2, Data, General Interest, Great Lakes, HPC, News, Research, Uncategorized

Due to planned maintenance by the vendor, Globus services will be unavailable for up to two hours beginning at 9 a.m. U.S. Eastern Time (10 a.m. Central Time) on Saturday, March 11, 2023.

Customers will not be able to authenticate or initiate any transfers during that time. Any transfers that have started before the outage will be stalled until the outage is over. Transfers will resume once maintenance is complete.

More details are available on the Globus blog.

For assistance or questions, please contact ARC at arc-support@umich.edu.

Dailey receives U-M Robotics’ first-ever alumni award 

By | General Interest, Happenings, News, Research, Uncategorized

Meghan Dailey will be presenting The Future of Machine Learning in Robotics on September 23 at 2 p.m., at FMCRB or Zoom

Meghan Dailey is the U-M Robotics department’s first Alumni Merit Award recipient!

Dailey is a member of the first-ever class in U-M Robotics. She earned a Masters of Science degree in 2015 with a focus in artificial intelligence. She is currently a machine learning specialist with Advanced Research Computing (ARC), a division of Information and Technology Service (ITS)

You’re invited 

In honor of the award, Dailey will be presenting “The Future of Machine Learning in Robotics” on Friday, September 23, 2 p.m., Ford Robotics Building (FMCRB) or on Zoom (meeting ID: 961 1618 4387, passcode: 643563). Machine learning is becoming widely prevalent in many different fields, including robotics. In a future where robots and humans assist each other in completing tasks, what is the role of machine learning, and how should it evolve to effectively serve both humans and robots? Dailey will discuss her past experiences in robotics and machine learning, and how she envisions machine learning contributing to the growth of the robotics field.

About Dailey

A member of the ARC Scientific Computing and Research Consulting Services team, Dailey helps researchers with machine learning and artificial intelligence programming. She has consulted with student and faculty teams to build neural networks for image analysis and classification. She also has extensive experience in natural language processing and has worked on many projects analyzing text sentiment and intent.

Image courtesy U-M Robotics

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.

Preserving Michigan’s musical history and culture

By | Feature, News, Research

From Kentucky bluegrass to Louisiana Zydeco to German hurdy-gurdy to East European Klezmer to Indian Manipuri dancing to Native American pow wows, and much more, these musical traditions from around the country and around the world have found their way to Michigan. Beginning in 2014, the Musical Heritage Project has been documenting Michigan’s folk music history.

Lester Monts

Lester Monts Lester Monts specializes in ethnomusicology and has been documenting Michigan’s folk cultural heritage since 2014. (Image courtesy Lester Monts)

The project is led by ethnomusicologist Dr. Lester P. Monts, Arthur F. Thurnau Professor Emeritus of Music, who began his musical journey as an orchestral trumpet player. He earned bachelor’s and master’s degrees in trumpet performance and teaching trumpet at the college level before completing the doctoral degree in ethnomusicology and embarking on a research career. In the mid-1970s, Monts began to focus his research on music and culture in Liberia and Sierra Leone in West Africa. The fourteen-year Liberian civil war thwarted his fieldwork in that region.

Noting that there has been no systematic effort to collect and archive Michigan’s rich folk music heritage, the Michigan Musical Heritage Project was launched. Monts has embraced the study of music from the cultural and social aspects of the people who make it. He notes that “music brings people together; it has the power to create community, and we witnessed this occurring throughout our many journeys around the state.”

Using his charm, passion, likeability, and keen musical knowledge to cultivate trust with his interviewees, Monts captured more than 400 hours of audio and video data over the years, amassing a total of 80 terabytes of data. He believes this to be the most extensive collection of Michigan folk music in the state and that U-M is the right place to house this collection.

The Michigan Musical Heritage Project crew.

The Michigan Musical Heritage Project crew wraps up at the end of recording session. (Image courtesy Lester Monts)

With a videography crew consisting primarily of former U-M students, Monts traveled all around the state to record performances at folk music festivals and cultural gatherings, such as the Celtic Festival (Saline), Irish Folk Music Festival (Muskegon) Hispanic Heritage Festival (Hart), Hiawatha Traditional Music Festival (Marquette), Port Sanilac Blues Festival (Port Sanilac), Africa World Festival (Detroit), Aura Jamboree (Aura), Oldtime Fiddlers Convention and Traditional Music Festival (Hillsdale).

He says, “The creative talents of the state’s outstanding musicians must be preserved, not only for my research but for that of others as well. If properly preserved, I’m confident that in the future, the ethnomusicology program and the American Cultures department will find these data provide important insights into Michigan’s diverse musical heritage.”

How technology supports this project 

Monts’ crew includes a strong partnership with Tom Bray, converging technologies consultant and adjunct assistant professor of Art and Design, Penny W. Stamps School of Art and Design. Bray has been instrumental in pairing the right technology for the long-term preservation of this collection, which includes converting older footage to digital media. 

Tom Bray

Tom Bray (image courtesy LSA)

Bray has collaborated with Monts to convert older technologies, such as VHS, 8mm, and high-8 video, to digital files. The files are both compressed and uncompressed and are very large and of high resolution.

All of this wonderful and important audio and video footage needs to be preserved somewhere. But where do you turn when you have 80 terabytes of data? Monts said, “I’ve been desperately searching for a way to archive the video data collected under the auspices of the Michigan Musical Heritage Project.” 

Enter the U-M Research Computing Package (UMRCP) and the team from Advanced Research Computing (ARC), a division of Information and Technology Services. The UMRCP offers researchers across all campuses several resources at no additional cost to researchers, including 100 terabytes of long-term storage.

Bray said, “I had to read the UMRCP email announcement twice because I couldn’t believe my eyes. I was so excited that ITS and the university are supporting researchers in this way. We jumped on this opportunity right away.” 

ARC Director Brock Palen is excited about this work, too. “This is super interesting, and not like the usual types of research ARC normally sees, like climate and genomics. We’re happy to help Dr. Monts and Mr. Bray, and anyone who needs it, anytime. The archive is intentionally built for holding large-volume, raw data such as 4k video, and we are proud to be their go-to for this important cultural preservation project.” 

Old media in Dr. Monts' office

Hours and hours of media is being converted to a digital format. (Photo by Stephanie Dascola)

ARC replicates and encrypts in two secure locations that are miles apart, so those who use ARC services will not have to worry about crashes that they might experience if they are using their own equipment. The UMRCP also includes technical expertise by talented ARC staff to further remove barriers so researchers can do what they do best.

Monts and Bray also leverage the university’s network and WiFi services to transfer the files from their studio in the Duderstadt Center to storage. The network is designed to minimize bottlenecks so that data transfers quickly and efficiently. 

Dr. Monts said, “Although the pandemic temporarily disrupted my plans to complete the video documentary, I take solace in knowing that the many hours of data we collected is in a much safer environment than we had. The UMRCP storage resource is truly a boon!”

Related links

An old reel-to-reel tape player.

A reel-to-reel tape player. (Photo by Stephanie Dascola)

Lester Monts plays footage from a special women's only dance in Iberia.

Dr. Monts shows footage from a special women-only dance in Iberia. He earned permission to record this rarely-documented group of women. (Photo by Stephanie Dascola)

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

Using tweets to understand climate change sentiment

By | HPC, News, Research, Systems and Services

A team from Urban Sustainability Research Group of the School for Environment and Sustainability (UM-SEAS) has been studying public tweets to understand climate change and global warming attitudes in the U.S. 

Dimitris Gounaridis, is a fellow with the study. The team is mentored by Joshua Newell, and combines work about perceptions on climate change by Jianxun Yang and proprietary level vulnerability assessment by Wanja Waweru

“This research is timely and urgent. It helps us identify hazards, and elevated risks of flooding and heat, for socially vulnerable communities across the U.S. This risk is exacerbated especially for populations that do not believe climate change is happening,” Dimitris stated. 

The research team used a deep learning algorithm that is able to recognize text and predict whether the person tweeting believes in climate change or not. The algorithm analyzed a total of 7 million public tweets from a combination of datasets from a dataset called the U-M Twitter Decahose and the George Washington University Libraries Dataverse. This dataset consists of an historical archive of Decahose tweets and an ongoing collection from the Decahose. The current deep learning model has an 85% accuracy rate and is validated at multiple levels.

The map below shows the prediction of specific users that believe or are skeptical of climate change and global warming. Dimitris used geospatial modeling techniques to identify clusters of American skepticism and belief to create the map.

A map of the United States with blue and red dots indicating climate change acceptance.

(Image courtesy Dimitris Gounaridis.)

The tweet stream is sampled in real-time. Armand Burks, a research data scientist with ARC, wrote the Python code that is responsible for continuously collecting the data and storing it in Turbo Research Storage. He says that many researchers across the university are using this data for various research projects as well as classes. 

“We are seeing an increased demand for shared community data sets like the Decahose. ARC’s platforms like Turbo, ThunderX, and Great Lakes, hold and process that data, and our data scientists are available, in partnership with CSCAR, to assist in deriving meaning from such large data. 

“This is proving to be an effective way to combine compute services, methodology, and campus research mission leaders to make an impact quickly,” said Brock Palen, director of ARC.

In the future, Dimitris plans to refine the model to increase its accuracy, and then combine that with climate change vulnerability for flooding and heat stress.

“MIDAS is pleased that so many U-M faculty members are interested in using the Twitter Decahose. We currently have over 40 projects with faculty in the Schools of Information, Kinesiology, Social Work, and Public Health, as well as at Michigan Ross, the Ford School, LSA and more,” said H.V. Jagadish, MIDAS director and professor of Electrical Engineering and Computer Science

The Twitter Decahose is co-managed and supported by MIDAS, CSCAR, and ARC, and is available to all researchers without any additional charge. For questions about the Decahose, email Kristin Burgard, MIDAS outreach and partnership manager.

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