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Technology supports researchers’ quest to understand parental discipline behaviors

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

Image by Rajesh Balouria from Pixabay

How do different types of parental discipline behaviors affect children’s development in low- and middle-income countries (LMICs)? A group of researchers set out to understand that question. They used a large data set from UNICEF of several hundred thousand families. The data came from the fourth (2009–2013) and fifth (2012–2017) rounds of the UNICEF Multiple Indicator Cluster Surveys. 

“The majority of parenting research is conducted in higher income and Westernized settings. We need more research that shows what types of parenting behaviors are most effective at promoting children’s development in lower resourced settings outside of the United States. I wanted to conduct an analysis that provided helpful direction for families and policymakers in LMICs regarding what parents can do to raise healthy, happy children,” said Kaitlin Paxton Ward, People Analytics Researcher at Google and Research Affiliate at the University of Michigan.

Dr. Paxton Ward is the lead author on the recently-released paper, “Associations between 11 parental discipline behaviors and child outcomes across 60 countries.” Other authors are also cited in the article: Andrew Grogan-Kaylor, Julie Ma, Garrett T. Pace, and Shawna Lee.

Together, they tested associations between 11 parental discipline behaviors and outcomes (aggression, distraction, and prosocial peer relations) of children under five years in 60 LMICs:

  • Verbal reasoning (i.e., explaining why the misbehavior was wrong)
  • Shouting
  • Name calling
  • Shaking
  • Spanking
  • Hitting/slapping the body
  • Hitting with an object 
  • Beating as hard as one could
  • Removing privileges 
  • Explaining
  • Giving the child something else to do

Results

Verbal reasoning and shouting were the most common parental discipline behaviors towards young children. Psychological and physical aggression were associated with higher child aggression and distraction. Verbal reasoning was associated with lower odds of aggression, and higher odds of prosocial peer relations. Taking away privileges was associated with higher odds of distraction, and lower odds of prosocial peer relations. Giving the child something else to do was associated with higher odds of distraction. The results indicated that there was some country-level variation in the associations between parenting behaviors and child socioemotional outcomes, but also that no form of psychological or physical aggression benefitted children in any country.

Conclusion 

Parental use of psychological and physical aggression were disadvantageous for children’s socioemotional development across countries. Only verbal reasoning was associated with positive child socioemotional development. The authors suggest that greater emphasis should be dedicated to reducing parental use of psychological and physical aggression across cultural contexts, and increasing parental use of verbal reasoning.

The technology used to analyze the data

The researchers relied on a complicated Bayesian multilevel model. This type of analysis incorporated knowledge from previous studies to inform the current analysis, and also provided a way for the researchers to look in more detail at variation across countries. To accomplish this task, the team turned to ITS Advanced Research Computing (ARC) and the Great Lakes High-Performance Computing Cluster. Great Lakes is the largest and fastest HPC service on U-M’s campus. 

“I know for me as a parent of young children, you want the best outcome. I have known people to grow up with different forms of discipline and what the negative or positive influence of those are,” said Brock Palen, ARC director. 

The researchers also created a visual interpretation of their paper for public outreach using a web app called ArcGIS StoryMaps. This software helps researchers tell the story of their work. With no coding required, StoryMaps combine images, text, audio, video, and interactive maps in a captivating web experience. StoryMaps can be shared with groups of users, with an organization, or with the world. 

All students, faculty, and staff have access to ArcGIS StoryMaps. Since 2014, U-M folks have authored over 7,500 StoryMaps, and the number produced annually continues to increase year-over-year. Explore examples of how people around the world are using this technology in the StoryMaps Gallery.

“This intuitive software empowers the U-M community to author engaging, multimedia, place-based narratives, without involving IT staff,” said Peter Knoop, research consultant with LSA Technology Services. 

Correspondence to Dr. Kaitlin Paxton Ward, kpward@umich.edu.

Related article

Gordon Bell Prize winning team also leverages ITS services

By | Feature, General Interest, Great Lakes, HPC, News, Systems and Services

A U-M College of Engineering team led by Vikram Gavini was recently awarded the prestigious ACM Gordon Bell Prize. The honor was presented in recognition of their outstanding achievement for developing and demonstrating an approach that brought near-quantum mechanical accuracy for large systems consisting of tens of thousands of atoms into the range of today’s supercomputers. 

The ACM Gordon Bell Prize is awarded each year to recognize outstanding achievement in high-performance computing.

Dr. Gavini and team carried out their largest calculation on the fastest known computer in the world, the U.S. Department of Energy’s Frontier, and they sustained 660 petaflops. 

“The ACM Gordon Bell Prize is the most prestigious prize available for high-performance computing,” said Brock Palen, Advanced Research Computing (ARC) director, a division of Information and Technology Services (ITS). 

“This is so exciting because it is more than 660 times faster than our entire Great Lakes cluster at perfect efficiency. Their calculation was 10 times the improvement of any prior density-functional theory (DFT) calculation.” 

DFT is a method used in physics and chemistry to investigate the electronic structure of many-body systems. These systems can include atoms, molecules, or solids.  

“Dr. Gavini is a major user of ARC’s Great Lakes HPC Cluster, and we are so proud of this astonishing achievement.” 

Gavini said that any development needs to be carefully tested. “We use ARC’s Great Lakes to test smaller scale systems before moving to larger-scale, production-ready calculations. This testing is critical, and we need the accessibility and speed of Great Lakes to run calibrations and debug our implementations.”

“We use Great Lakes to actively test our implementations.”

For quick-access storage, Gavini and his team use Turbo Research Storage and Data Den Research Archive for longer-term storage. “We generate a lot of data, and storage is important to our work.”

The U-M Research Computing Package was also helpful in defraying some of their HPC and storage costs. 

“Thank you to ARC for providing their continual assistance for group members who have been in trenches. This has been a decade-long effort, and ITS/ARC was crucial along the journey,” said Gavini. 

Dr. Gavini is a professor of Mechanical Engineering and professor of Materials Science and Engineering, College of Engineering.

You’re invited: Parallel programming with MATLAB webinar on Dec. 4 

By | Events, HPC, News

We invite you to join us for an engaging virtual session on Parallel Computing with MATLAB, scheduled for December 4 from 1-4 p.m. EST. This session promises to equip you with valuable insights and knowledge. Here’s a glimpse of what you can expect to learn during the session.

Parallel Computing Hands-On Workshop:

Join us for an immersive hands-on workshop where we will introduce you to the world of parallel computing using MATLAB®. This workshop aims to equip you with the skills to tackle computationally and data-intensive problems by harnessing the power of multicore processors, GPUs, and computer clusters. Through practical exercises and real-world examples, you will gain a comprehensive understanding of parallel computing and learn best practices for its implementation.

Highlights:

  • Explore a range of exercises and examples, varying in difficulty from fundamental parallel usage concepts to more advanced techniques.
  • Learn how to optimize MATLAB applications by leveraging parallel computing capabilities.
  • Discover the benefits of running multiple Simulink simulations in parallel and enhance your simulation efficiency.
  • Dive into the world of GPU computing and unlock the potential for accelerated computations.
  • Explore the concept of offloading computations and delve into the realm of cluster computing.
  • Master the art of working with large data sets and efficiently process them using parallel computing techniques.

Don’t miss out on this opportunity to enhance your parallel computing skills with MATLAB. Join us for this exciting workshop and unlock the potential of parallel computing for your computational challenges.

Register soon to guarantee your spot and receive the Webex link before the workshop.

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.

Secure Enclave Service rate approved, shortcode needed by July 25 

By | Data, News, Systems and Services, Uncategorized

The Yottabyte Research Cloud (YBRC) migrated to the Secure Enclave Services (SES) in 2022. The new system provides improved performance for researcher workloads. Due to this transition, ARC began billing researchers who consume more than 16 gigabytes (GB) of RAM (memory) per month on July 1, 2023. 

The first 16 GB of RAM (memory) is covered by the U-M Research Computing Package (UMRCP). If you have not already requested or been granted the UMRCP, learn more and request it on the UMRCP service page on the ARC website.

Approved rate 

The approved rate for a Secure Enclave Services machine is $7.00 per GB of RAM (memory) per machine, per month. Visit the Rates page on the ARC website for information about billing for all ARC services. 

Action requested: Submit a shortcode 

A shortcode is needed to accommodate billing for any resources consumed that are not covered by the UMRCP. Please submit a shortcode no later than July 25, 2023. Access to your machine will be removed or reduced if a shortcode is not on file by July 25. Contact us at arc-support@umich.edu to submit your shortcode, or make any changes to the configuration or use of your machines. 

Some schools and colleges (including the U-M Medical School) are subsidizing the use of Secure Enclave Services beyond the 16 GB of RAM (memory). Talk to your unit’s IT staff or email ARC to learn more. 

Contact ARC (arc-support@umich.edu) if you would like to meet with the ARC storage manager to ask questions or get clarification.

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 can now be used with Armis2 

By | Armis2, HPC, News, Uncategorized

Researchers who have an Armis2 High-Performance Computing account can now move data to and from other Protected Health Information (PHI)-approved systems using Globus File Transfer. (The endpoint is umich#armis2.) 

To learn more about your responsibility and approved services, visit the Sensitive Data Guide and the Protected Health Information (PHI) webpage on the Safe Computing Website. Send an email to ARC at arc-support@umich.edu to get started using Globus with PHI on your own system (this is not needed for researchers using ARC services including Armis2, and Data Den and Turbo with Sensitive Data).

“With the addition of Globus on Armis2, researchers using ITS ARC services can use the same Globus tools and processes to securely and reliably move their data on all ARC systems and across the university and beyond,” said Matt Britt, ARC HPC systems manager.

Globus allows the transfer and collaborative access of data between different storage systems, lab computers, and personal desktops and laptops. Globus enables researchers to use a web browser to submit transfer and data synchronization requests between destinations. 

As a robust, cloud-based, file transfer service, Globus is designed to securely move your data, ranging from megabytes to petabytes. ARC is a Globus Subscription Provider for the U-M community, which allows U-M resources to serve as endpoints or collections for file transfers.

“There are many interesting research collaborations happening at U-M, as well as nationally and internationally. Globus can facilitate all of those interactions securely,” said Brock Palen, ARC director. “Globus is the go-to tool we recommend for data transfer.”

Learn more 

How can we help you?

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

PFAS research in the Michigan mother-infant pairs study, supported by ITS, SPH, MM, AGC

By | News

Three mothers holding their infants. Everyone is sitting on a couch..PFAS (per- and polyfluoroalkyl substances) are a class of chemicals that have been around since the 1940s and became more broadly used in the post-war 1960s era. PFAS are in our homes, offices, water, and even our food and blood. PFAS break down slowly and are difficult to process, both in the environment and our bodies. 

Scientific studies have shown that exposure to some PFAS in the environment may be linked to harmful health effects in humans and animals. Because there are thousands of PFAS chemicals found in many different consumer, commercial, and industrial products, it is challenging to study and assess the human health and environmental risks. 

Fortunately, some of the most persistent PFAS are being phased out. The EPA has been working on drinking water protections, scientists are working on ways to break down and eliminate PFAS, and PFAS are being addressed at a national level

A team of University of Michigan researchers from the School of Public Health DoGoodS-Pi Environmental Epigenetics Lab and Michigan Medicine are working to understand how behaviors and environments during pregnancy can cause changes to the way genes work in offspring. This emerging field is known as toxicoepigenetics. 

Jackie Goodrich, Ph.D., research associate professor at the U-M School of Public Health, led the team. “PFAS may impact the development of something we all have called the epigenome. The epigenome is a set of modifications on top of our DNA that controls normal development and function. Environmental exposures like PFAS can alter how the epigenome forms, and this impacts development and health. Our study expands on current knowledge about PFAS and the epigenome by focusing on a type of epigenetic mark that is not usually measured.”

Vasantha Padmanabhan, Ph.D., M.S., professor emerita (in service), Department of Pediatrics, Michigan Medicine, built the Michigan Mother-Infant Pairs study over the past decade with an emphasis on identifying harmful exposures during pregnancy that impact women and their newborns. “I am so grateful to those who engaged in this study. PFAS are complex, and mothers’ and infants’ involvement helped us work toward a solution that impacts us all. I want to acknowledge the contributions of the U-M Department of Obstetrics and Gynecology, Michigan Institute for Clinical & Health Research (MICHR), and the Von Voigtlander Women’s Hospital that made this study possible.” 

Rebekah Petroff, Ph.D., a research fellow with Environmental Health Sciences, led the computation portion of the research. She said that using Turbo for storing the raw data and Great Lakes for high-performance computing (HPC) enabled a much faster analysis that was needed for the study with so much data to analyze. 

Turbo and Great Lakes are services provided by Advanced Research Computing, a division of Information and Technology Services (ITS). ARC facilitates powerful approaches to complex research challenges in fields ranging from physics to linguistics, and from engineering to medicine.

Petroff said, “This analysis would have taken over a month straight of computing time on a regular desktop computer. The first job we submitted to Great Lakes ran so fast—I had results the next morning! Great Lakes made this research possible, and I believe that our study results can be broadly impactful to public health and toxicoepigenetics going forward.”

Support for using this complex technology also came from Dan Barker, a UNIX systems admin with the U-M School of Public Health Biostatistics Department. Barker assisted with the code needed to use Great Lakes. “We started with a test run of a few hundred pairs of genomes. Once we were successful with that, we ran the entire nearly 750,000 epigenetic marks across 141 people and seven different PFAS.”

Barker also helped design and submit array jobs which are a series of identical, or near identical, tasks that are run multiple times. This is a common technique used by researchers when leveraging HPC. Array jobs allow for essential analytical comparisons among the test results. Petroff said, “In our study, we used an array job to split up our computations so that they ran much more efficiently!”

The U-M Advanced Genomics Core (AGC) performed the epigenetic assays, a kind of laboratory technique which measures marks on your DNA, for this project. AGC is part of the campus-wide laboratories that develop and provide state-of-the-art scientific resources to enable biomedical research known as Biomedical Research Core Facilities (BRCF). Other BRCF cores also worked on this project, including the Epigenomics Core and the Bioinformatics Core.

Genotyping is similar to reading a few words scattered on a page. This process gives researchers small packets of data to compare. Genotyping looks for information at a specific place in the DNA where we know important data will be. This project used a type of genotyping called microarrays (also known as “arrays”) and help researchers understand how regulation of DNA—including methylation and hydroxymethylation measured in this study—are impacted by exposures like PFAS.  

Brock Palen, ARC director, said, “This research is of human interest and impacts all of us. I’m pleased that ARC assisted their research with staff expertise, equipment, and no-cost allocations from the U-M Research Computing Package.”

Petroff said that follow up studies are needed to better understand if the results are universal or specific to this cohort of infants and parents. If the results hold steady, then a significant discovery has been made that will lead to more comprehensive PFAS mitigation solutions. “Although steps are being taken to mitigate PFAS, exposure is still prevalent, and a deeper understanding of how it impacts humans is needed,” said Dana Dolinoy, Ph.D., chair, NSF International Department Chair of Environmental Health Sciences and epigenetics expert.

Read the full article: Mediation effects of DNA methylation and hydroxymethylation on birth outcomes after prenatal per- and polyfluoroalkyl substances (PFAS) exposure in the Michigan mother–infant pairs cohort.

Funding was provided by grants from the National Institutes of Health, the U.S. Environmental Protection Agency, and the National Institute of Environmental Health Sciences Children’s Health Exposure Analysis Resource program.

ARC Summer 2023 Maintenance happening in June

By | HPC, News, Systems and Services

Summer maintenance will be happening earlier this year (June instead of August). Updates will be made to software, hardware, and operating systems to improve the performance and stability of services. ARC works to complete these tasks quickly to minimize the impact of the maintenance on research.

The dates listed below are the weeks the work will be occurring; the actual dates will be revised as planning continues.

HPC clusters and storage systems (/scratch) will be unavailable:

  • June 5-9: Great Lakes, Armis2, and Lighthouse

Storage systems will be unavailable:

  • June 6-7: Turbo, Locker, and Data Den

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.

Data Den now supports sensitive data

By | News, Uncategorized

Data Den Research Archive is a service for preserving electronic data generated from research activities. It is a low-cost, highly durable storage system and is the largest storage system operated by ARC. Storing of sensitive data (including HIPAA, PII, and FERPA) is now supported (visit the Sensitive Data Guide for full details). This service is part of the U-M Research Computing Package (UMRCP) that provides storage allocations to researchers. Most researchers will not have to pay for Data Den. 

A disk-caching, tape-backed archive, this storage service is best for data that researchers do not need regularly, but still need to keep because of grant requirements. 

“Data Den is a good place to keep research data past the life of the grant,” said Jeremy Hallum, ARC research computing manager. “ARC can store data that researchers need to keep for five to ten years.” 

Hallum goes on to say that Data Den is only available in a replicated format. “Volumes of data are duplicated between servers or clusters for disaster recovery so research data is very safe.”

Data Den can be part of a well-organized data management plan providing international data sharing, encryption, and data durability. Jerome Kinlaw, ARC research storage lead, said that the Globus File Transfer service works well for data management. “Globus is easy to use for moving data in and out of Data Den.”

The ITS U-M Research Computing Package (UMRCP) provides 100 terabytes (TB) of Data Den storage to qualified researchers. This 100 TB can be divided between restricted and non-restricted variants of Data Den for use as needed. (The ITS Data Storage Finder can help researchers find the right storage solutions to meet their needs.)

“I’m pleased that Data Den now offers options for sensitive data, and that researchers can take advantage of the UMRCP allocations,” said Brock Palen, ARC director. “We want to lighten the load so that researchers can do what they do best, and our services are now more cost effective than ever.”