New Hardware-Accelerated Visualization Partition 

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

We are excited to introduce a brand-new feature of Great Lakes to researchers who need hardware acceleration for their visualization requirements. ARC has created a specialized “viz” partition, consisting of four nodes equipped with NVIDIA P40 GPUs. These nodes are accessible through Open OnDemand’s Remote Desktop functionality.

Key details about this new feature:

  • Jobs utilizing the viz partition have a maximum walltime of 2 hours.
  • The charge rate for the viz partition is currently aligned with our standard partition. 

To make use of the viz partition, follow these steps:

  • Create a Remote Desktop job on Great Lakes via Open OnDemand.
  • Request the “viz” partition, specifying 1 node and 1 GPU (Please note that we have only one GPU available per node).
  • Prefix any application you intend to run with accelerated graphics with the command “vglrun.” (example: “vglrun glxgears”)

For questions or support requests, please contact our team at arc-support@umich.edu.

What DNA can tell us about dog evolution

By | General Interest, HPC, News, Research, Systems and Services

An excerpt from the Michigan Medicine Health Lab Podcast:

An international consortium of scientists, led by Jeff Kidd, Ph.D., of the University of Michigan, Jennifer R. S. Meadows of Uppsala University in Sweden, and Elaine A. Ostrander, Ph.D. of the NIH National Human Genome Research Institute, is using an unprecedentedly large database of canine DNA to take an unbiased look at how our furry friends evolved into the various breeds we know and love.

A paper, published in the journal Genome Biology, outlines what the Dog10K project discovered after sequencing the genomes of close to 2,000 samples from 321 different breed dogs, wild dogs, coyotes, and wolves, and comparing them to one reference sample—that of a German Shepherd named Mischka.

Analyzing more than 48 million pieces of genetic information, they discovered that each breed dog had around 3 million single nucleotide polymorphism differences.

These SNPs or “snips” are what account for most of the genetic variation among people and dogs alike.

They also found 26,000 deleted sequences that were present in the German Shepherd but not in the comparison breed and 14,000 that were in the compared breed but missing from Mischka’s DNA.

“We did an analysis to see how similar the dogs were to each other, and it ended up that we could divide them into around 25 major groups that pretty much match up with what people would have expected based on breed origin, the dogs’ type, size and coloration,” said Kidd.

Most of the varying genes, he added, had to do with morphology, confirming that the breed differences were driven by how the dogs look.

Relative to dogs, wolves had around 14% more variation. And wild village dogs—dogs that live amongst people in villages or cities but aren’t kept as pets—exhibited more genetic variation than breed dogs.

The data set, which was processed using the Great Lakes high-performing computing cluster at U of M, also revealed an unusual amount of retrogenes, a new gene that forms when RNA gets turned back into DNA and inserted back into the genome in a different spot.

Listen to the podcast or read the transcript on the Health Lab webpage.

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

2024 ARC Winter Maintenance

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

Winter maintenance is coming up! See the details below. Reach out to arc-support@umich.edu with questions or if you need help. 

HPC

Like last year, we will have a rolling update which, outside of a few brief interruptions, should keep the clusters in production, Here is the schedule: 

December 6, 11 p.m.

  • Update Slurm Controllers: Expect a brief 1-minute interruption when querying Slurm. All jobs will continue to run.
  • Update Open OnDemand Servers: Expect a few seconds of interruption if you are using Open OnDemand.
  • Login Servers Update: We will begin updating our login servers. This update is not expected to impact any users.

 December 7:

  • Compute Rolling Updates: We will start rolling updates across all clusters a few nodes at a time, so there should be minimal impact on access to resources.

December 19, 10:30a.m.:

  • Update Globus transfer (xfer) nodes: as these nodes are in pairs for each cluster. For the Globus transfer nodes, we will take one node of each pair down at a time, so all Globus services will remain working. If you are using scp/sftp, your jobs may be interrupted, so please schedule these transfers accordingly or use Globus. Total maintenance time should be approximately one hour.

January 3, 8 a.m.:

  • Reboot Slurm Controller Nodes: This will cause an approximately 10-minute Slurm outage. All running jobs will continue to run.
  • Armis2 Open OnDemand Node: We will reload and reboot the Armis2 Open OnDemand node. This will take approximately 1 hour.
  • Great Lakes and Lighthouse Open OnDemand Nodes: These nodes will be down approximately 10 to 15 minutes.
  • Globus Transfer (xfer) Nodes: These nodes will be rebooted. This will take approximately 15 minutes.
  • Sigbio Login Reload/Reboot: This will take approximately 1 hour.
  • Some Armis2 Faculty Owned Equipment (FOE) nodes will require physical and configuration updates. Expected downtime is 4 hours.

HPC Maintenance Notes:

  • Open OnDemand (OOD) users will need to re-login. Any existing jobs will continue to run and can be reconnected in the OOD portal.
  • Login servers will be updated, and the maintenance should not have any effect on most users. Those who are affected will be contacted directly by ARC. 
  • New viz partition : there will be a new partition called viz with 16 new GPUs, which can support exactly one GPU per job .
  • The –cpus-per-gpu Slurm bug has been fixed.

HPC Maintenance Details:

NEW version in BOLD

OLD version

Red Hat 8.6 EUS

  • Kernel 4.18.0-372.75.1.el8_6.x86_64

  • glibc-2.28-189.6

  • ucx-1.15.0-1.59056 (OFED provided)

  • gcc-8.5.0-10.1.el8

Red Hat 8.6 EUS

  • Kernel 4.18.0-372.51.1.el8_6.x86_64

  • glibc-2.28-189.6

  • ucx-1.15.0-1.59056 (OFED provided)

  • gcc-8.5.0-10.1.el8

Mlnx-ofa_kernel-modules

  • OFED 5.9.0.5.5.1

    • kver.4.18.0_372.51.1.el8_6

Mlnx-ofa_kernel-modules

  • OFED 5.9.0.5.5.1

    • kver.4.18.0_372.51.1.el8_6

Slurm 23.02.6 copiles 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 23.02.5 copiles 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

PMIx LD config /opt/pmix/3.2.5/lib

PMIx LD config /opt/pmix/3.2.5/lib

PMIx versions available in /opt :

  • 3.2.5

  • 4.2.6

PMIx versions available in /opt :

  • 3.2.5

  • 4.2.6

Singularity CE (Sylabs.io)

  • 3.10.4

  • 3.11.1

Singularity CE (Sylabs.io)

  • 3.10.4

  • 3.11.1

NVIDIA driver 545.23.06

NVIDIA driver 530.30.02

Open OnDemand 3.0.3

Open OnDemand 3.0.3

 

Storage

There is no scheduled downtime for Turbo, Locker, or  Data Den.

 

Secure Enclave Service (SES)

  • SES team to add details here

Maintenance notes:

  • No downtime for ARC storage systems maintenance (Turbo, Locker, and Data Den).
  • Open OnDemand (OOD) users will need to re-login. Any existing jobs will continue to run and can be reconnected in the OOD portal.
  • Login servers will be updated, and the maintenance should not have any effect on most users. Those who are affected will be contacted directly by ARC. 
  • Copy any data and files that may be needed during maintenance to your local drive using Globus File Transfer before maintenance begins. 

Status updates and additional information

  • Status updates will be available on the ARC Twitter feed and ITS service status page,  throughout the course of the maintenance.
  • ARC will send an email to all HPC users when the maintenance has been completed. 

How can we help you?

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