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ARC Director Sharon Broude Geva elected Chair of the Coalition for Academic Scientific Computation

By | HPC, News

Dr. Sharon Broude Geva, Director of Advanced Research Computing at the University of Michigan, has been elected Chair of the Coalition for Academic Scientific Computation (CASC) for 2019.

Founded in 1989, CASC advocates for the use of advanced computing technology to accelerate scientific discovery for national competitiveness, global security, and economic success. The organization’s members represent 87 institutions of higher education and national labs.

The chair position is one of four elected CASC executive officers. The officers work closely as a team with the director of CASC. The Chair is responsible for arranging and presiding over general CASC meetings and acts as an official representative of CASC.

Geva served as CASC secretary in 2015 and 2016, and vice-chair in 2017 and 2018.

The other executive officers for 2019 are Neil Bright, Georgia Institute of Technology, Vice Chair; Craig Stewart, Indiana University, Secretary; Scott Yockel, Harvard University, Treasurer; Rajendra Bose, Columbia University, past chair. Lisa Arafune is CASC Director.

 

U-M prepares for SC18 conference in Dallas

By | General Interest, Happenings, News

University of Michigan researchers and IT staff are gearing up for extensive participation in the Supercomputing ‘18 conference (SC18) in Dallas from Nov. 11-16.

SC “Perennial” Quentin Stout, U-M professor of Electrical Engineering and Computer Science and one of only 19 people who have been to every Supercomputing conference, will once again co-present a tutorial titled Parallel Computing 101.

And with the recent announcement of a new HPC cluster on campus called Great Lakes, IT staff from Advanced Research Computing – Technology Services (ARC-TS) will be making multiple presentations around the conference on the details of the new supercomputer.

U-M will be at exhibit booth 1204A, adjacent to the Michigan State University booth, highlighting our computational and data-intensive research as well as the comprehensive set of tools and services we provide to our researchers. Representatives from all ARC units will be at the booth: ARC-TS, the Michigan Institute for Data Science (MIDAS), the Michigan Institute for Computational Discovery and Engineering (MICDE), and Consulting for Statistics, Computing and Analytics Research (CSCAR).

The booth will also feature two demonstrations: one will focus on the Open Storage Research Infrastructure or OSiRIS, the multi-institutional software-defined data storage system, and the Services Layer At The Edge (SLATE) project, both of which are supported by the NSF; the other will test conference-goers’ ability to detect “fake news” stories compared to an artificial intelligence system created by researchers supported by MIDAS.

U-M Activities

Sunday, Nov. 11

8:30 a.m. – 5 p.m.
Tutorial: Parallel Computing 101: Prof. Stout and Associate Professor Christiane Jablonowski of the U-M Department of Climate and Space Sciences and Engineering will provide a comprehensive overview of parallel computing.

8:30am – noon
Introduction to Kubernetes. Presented by Bob Killen, Research Cloud Administrator, and Scott Paschke, Research Cloud Solutions Designer, both from ARC-TS. Containers have shifted the way applications are packaged and delivered. Their use in data science and machine learning is skyrocketing with the beneficial side effect of enabling reproducible research. This rise in use has necessitated the need to explore and adopt better container-centric orchestration tools. Of these tools, Kubernetes – an open-source container platform born within Google — has become the de facto standard. This half-day tutorial will introduce researchers and sys admins who may already be familiar with container concepts to the architecture and fundamental concepts of Kubernetes. Attendees will explore these concepts through a series of hands-on exercises and leave with the leg-up in continuing their container education, and gain a better understanding of how Kubernetes may be used for research applications.

Tuesday, Nov. 13

Brock Palen, Director of ARC-TS, will speak about the new Great Lakes HPC cluster:

  • DDN booth (3123), 1:30 p.m.
  • Mellanox booth (3207), 3:30 p.m.
  • Dell booth (3218), 4:30 p.m.

11 a.m. – noon
Todd Raeker, Research Technology Consultant for ARC-TS, will be at the Globus booth (4201) to talk about U-M researchers’ use of the service.

12:15pm – 1:15pm
Birds of a Feather: Meeting HPC Container Challenges as a Community. Bob Killen, Research Cloud Administrator at ARC-TS, will give a lightning talk as part of this session that will present, prioritize, and gather input on top issues and budding solutions around containerization of HPC applications.

2 p.m.
Sharon Broude Geva, Director of ARC, will be live on the SC18 News Desk discussing ARC HPC services, Women in HPC, and the Coalition for Scientific Academic Computation (CASC). The stream will be available from the Supercomputing Twitter account: https://twitter.com/Supercomputing

5:15pm – 6:45pm
Birds of a Feather: Ceph Applications in HPC Environments: Ben Meekhof, HPC Storage Administrator at ARC-TS, will give a lightning talk on Ceph and OSiRIS as part of this session. More details at https://www.msi.umn.edu/ceph-hpc-environments-sc18

7 p.m.
ARC is a sponsor of the Women in HPC Reception. See the event description for more details and to register. Sharon Broude Geva, Director of ARC, will give a presentation.

Wednesday, Nov. 14

1 – 2 p.m.
Todd Raeker, Research Technology Consultant for ARC-TS, will be at the Globus booth (4201) to talk about U-M researchers’ use of the service.

1:30 p.m.
Brock Palen, Director of ARC-TS, will speak the SLURM booth (1242) about the new Great Lakes HPC cluster:

5:15 – 6:45 p.m.
Birds of a Feather: Cloud Infrastructure Solutions to Run HPC Workloads: Bob Killen, Research Cloud Administrator at ARC-TS, will present at this session aimed at architects, administrators, software engineers, and scientists interested in designing and deploying cloud infrastructure solutions such as OpenStack, Docker, Charliecloud, Singularity, Kubernetes, and Mesos.

Follow ARC on Twitter at https://twitter.com/ARC_UM for updates.

Beta cluster available for learning Slurm; new scheduler to be part of upcoming cluster updates

By | Flux, General Interest, Happenings, HPC, News

New HPC resources to replace Flux and updates to Armis are coming.  They will run a new scheduling system (Slurm). You will need to learn the commands in this system and update your batch files to successfully run jobs. Read on to learn the details and how to get training and adapt your files.

In anticipation of these changes, ARC-TS has created the test cluster “Beta,” which will provide a testing environment for the transition to Slurm. Slurm will be used on Great Lakes; the Armis HIPAA-aligned cluster; and a new cluster called “Lighthouse” which will succeed the Flux Operating Environment in early 2019.

Currently, Flux and Armis use the Torque (PBS) resource manager and the Moab scheduling system; when completed, Great Lakes and Lighthouse will use the Slurm scheduler and resource manager, which will enhance the performance and reliability of the new resources. Armis will transition from Torque to Slurm in early 2019.

The Beta test cluster is available to all Flux users, who can login via ssh at ‘beta.arc-ts.umich.edu’. Beta has its own /home directory, so users will need to create or transfer any files they need, via scp/sftp or Globus.

Slurm commands will be needed to submit jobs. For a comparison of Slurm and Torque commands, see our Torque to Slurm migration page. For more information, see the Beta home page.

Support staff from ARC-TS and individual academic units will conduct several in-person and online training sessions to help users become familiar with Slurm. We have been testing Slurm for several months, and believe the performance gains, user communications, and increased reliability will significantly improve the efficiency and effectiveness of the HPC environment at U-M.

The tentative time frame for replacing or transitioning current ARC-TS resources is:

  • Flux to Great Lakes, first half of 2019
  • Armis from Torque to Slurm, January 2019
  • Flux Operating Environment to Lighthouse, first half of 2019
  • Open OnDemand on Beta, which replaces ARC Connect for web-based job submissions, Jupyter Notebooks, Matlab, and additional software packages, fall 2018

MIDAS announces winners of 2018 poster competition

By | Educational, General Interest, Happenings, Research

The Michigan Institute for Data Science (MIDAS) is pleased to announce the winners of its 2018 poster competition, which is held in conjunction with the MIDAS annual symposium.

The symposium was held on Oct. 9-10, 2018, and the student poster competition had more than 60 entries. The winners, judged by a panel of faculty members, received cash prizes.

Best Overall

Arthur Endsley, “Comparing and timing business cycles and land development trends in U.S. metropolitan housing markets”

Most likely health impact

  • Yehu Chen, Yingsi Jian, Qiucheng Wu, Yichen Yang, “Compressive Big Data Analytics – CBDA: Applications to Biomedical and Health Studies”
  • Jinghui Liu, “An Information Retrieval System with an Iterative Pattern for TREC Precision Medicine”

Most likely transformative science impact

  • Prashant Rajaram, “Bingeability and Ad Tolerance: New Metrics for the Streaming Media Age”
  • Mike Ion, “Learning About the Norms of Teaching Practice: How Can Machine Learning Help Analyze Teachers’ Reactions to Scenarios?”

Most interesting methodological advancement

  • Nina Zhou and Qiucheng Wu, “DataSifter: Statistical Obfuscation of Electronic Health Records and Other Sensitive Datasets”
  • Aniket Deshmukh, “Simple Regret Minimization for Contextual Bandits”

Most likely societal impact

  • Ece Sanci, “Optimization of Food Pantry Locations to Address Food Scarcity in Toledo, OH”
  • Rohail Syed, “Human Perception of Surprise: A User Study”

Most innovative use of data

  • Lan Luo, “Renewable Estimation and Incremental Inference in Generalized Linear Models with Streaming Datasets”
  • Danaja  Maldeniya, “Psychological Response of Communities affected by Natural Disasters in Social Media”

U-M selects Dell EMC, Mellanox and DDN to Supply New “Great Lakes” Computing Cluster

By | Flux, General Interest, Happenings, HPC, News

The University of Michigan has selected Dell EMC as lead vendor to supply its new $4.8 million Great Lakes computing cluster, which will serve researchers across campus. Mellanox Technologies will provide networking solutions, and DDN will supply storage hardware.

Great Lakes will be available to the campus community in the first half of 2019, and over time will replace the Flux supercomputer, which serves more than 2,500 active users at U-M for research ranging from aerospace engineering simulations and molecular dynamics modeling to genomics and cell biology to machine learning and artificial intelligence.

Great Lakes will be the first cluster in the world to use the Mellanox HDR 200 gigabit per second InfiniBand networking solution, enabling faster data transfer speeds and increased application performance.

“High-performance research computing is a critical component of the rich computing ecosystem that supports the university’s core mission,” said Ravi Pendse, U-M’s vice president for information technology and chief information officer. “With Great Lakes, researchers in emerging fields like machine learning and precision health will have access to a higher level of computational power. We’re thrilled to be working with Dell EMC, Mellanox, and DDN; the end result will be improved performance, flexibility, and reliability for U-M researchers.”

“Dell EMC is thrilled to collaborate with the University of Michigan and our technology partners to bring this innovative and powerful system to such a strong community of researchers,” said Thierry Pellegrino, vice president, Dell EMC High Performance Computing. “This Great Lakes cluster will offer an exceptional boost in performance, throughput and response to reduce the time needed for U-M researches to make the next big discovery in a range of disciplines from artificial intelligence to genomics and bioscience.”

The main components of the new cluster are:

  • Dell EMC PowerEdge C6420 compute nodes, PowerEdge R640 high memory nodes, and PowerEdge R740 GPU nodes
  • Mellanox HDR 200Gb/s InfiniBand ConnectX-6 adapters, Quantum switches and LinkX cables, and InfiniBand gateway platforms
  • DDN GRIDScaler® 14KX® and 100 TB of usable IME® (Infinite Memory Engine) memory

“HDR 200G InfiniBand provides the highest data speed and smart In-Network Computing acceleration engines, delivering HPC and AI applications with the best performance, scalability and efficiency,” said Gilad Shainer, vice president of marketing at Mellanox Technologies. “We are excited to collaborate with the University of Michigan, Dell EMC and DataDirect Networks, in building a leading HDR 200G InfiniBand-based supercomputer, serving the growing demands of U-M researchers.”

“DDN has a long history of working with Dell EMC and Mellanox to deliver optimized solutions for our customers. We are happy to be a part of the new Great Lakes cluster, supporting its mission of advanced research and computing. Partnering with forward-looking thought leaders as these is always enlightening and enriching,” said Dr. James Coomer, SVP Product Marketing and Benchmarks at DDN.

Great Lakes will provide significant improvement in computing performance over Flux. For example, each compute node will have more cores, higher maximum speed capabilities, and increased memory. The cluster will also have improved internet connectivity and file system performance, as well as NVIDIA Tensor GPU cores, which are very powerful for machine learning compared to prior generations of GPUs.

“Users of Great Lakes will have access to more cores, faster cores, faster memory, faster storage, and a more balanced network,” said Brock Palen, Director of Advanced Research Computing – Technology Services (ARC-TS).

The Flux cluster was created approximately 8 years ago, although many of the individual nodes have been added since then. Great Lakes represents an architectural overhaul that will result in better performance and efficiency. Based on extensive input from faculty and other stakeholders across campus, the new Great Lakes cluster will be designed to deliver similar services and capabilities as Flux, including the ability to accommodate faculty purchases of hardware, access to GPUs and large-memory nodes, and improved support for emerging uses such as machine learning and genomics.

ARC-TS will operate and maintain the cluster once it is built. Allocations of computing resources through ARC-TS include access to hundreds of software titles, as well as support and consulting from professional staff with decades of combined experience in research computing.

Updates on the progress of Great Lakes will be available at https://arc-ts.umich.edu/greatlakes/.

MICDE announces 2018-2019 fellowship recipients

By | Educational, General Interest, Happenings, News

The Michigan Institute for Computational Discovery and Engineering (MICDE) is pleased to announce the 2018-2019 recipients of the MICDE Fellowships for students enrolled in the PhD in Scientific Computing or the Graduate Certificate in Computational Discovery and Engineering. The fellowships, which carry a $4,000 stipend, are meant to augment other sources of funding and are available to students in both programs. See our Fellowship page for more information.

AWARDEES

Zhitong Bai, Mechanical Engineering
Kyle Bushick, Materials Science and Engineering
Geunyeong Byeon, Industrial and Operations Engineering
Sehwan Chung, Civil and Environmental Engineering
Khoi Dang, Chemistry
Sicen Du, Materials Science and Engineering
Joseph Hollowed, Physics
Jia Li, Physics
Sabrina Lynch, Biomedical Engineering
Samar Minallah, Climate and Space Sciences and Engineering
Everardo Olide, Applied Physics
Shaowu Pan, Aerospace Engineering
Alicia Petersen, Climate and Space Sciences and Engineering
Vyas Ramasubramani, Chemical Engineering
Fabricio Vasselai, Political Science
Nathan Vaughn, Applied and Interdisciplinary Mathematics
Blair Winograd, Chemistry
Samuel Young, Chemical Engineering
Kexin Zhang, Chemistry
Bu Zhao, School of Environment and Sustainability

ARC-TS seeks pilot users for two new research storage services

By | General Interest, Happenings, HPC, News

Advanced Research Computing – Technology Services (ARC-TS) is seeking pilot users for two new research storage services.

The first, Locker, is group project storage focused on large data sets, and is available at a cost less than half that of current primary storage services. Locker still provides encryption, replication, snapshots, and workstation access. Example use cases for Locker are research projects in climate studies, genomics, imaging, and other data-intensive sciences.

The second service, Data Den, provides archive class storage for research data that is not actively used. As our lowest cost research storage offering, Data Den provides “cold storage” for massive amounts of data with 20 petabytes of encrypted and replicated capacity. Data Den allows researchers to preserve data between rounds of funding and management plans, and to free up space in more expensive primary storage by moving valuable, but not currently used, data.

Those interested in participating in the pilots should contact ARC-TS at hpc-support@umich.edu.

Eric Michielssen honored for paper describing new algorithm to solve Maxwell’s equations

By | General Interest, Happenings, News

Eric Michielssen, professor of Electrical Engineering and Computer Science, and Associate Vice President for Advanced Research Computing, has won the Sergei A. Schelkunoff Transactions Prize Paper Award for research impacting the ability to rapidly analyze electromagnetic phenomena.

This award is presented to the authors of the best paper published in the IEEE Transactions on Antennas and Propagation during the previous year.

The 2017 paper, “A Butterfly-Based Direct Integral-Equation Solver Using Hierarchical LU Factorization for Analyzing Scattering From Electrically Large Conducting Objects,“ co-authored by Han Guo (ECE doctoral student), Yang Liu (MSE PHD, EE, 2013 2015; Lawrence Berkeley National Lab), and Prof. Jun Hu (UESTC), describes a new algorithm for solving Maxwell’s equations that is orders of magnitude faster than prior algorithms, opening the door to its use for the design and optimization of electromagnetic devices.

For more, see the College of Engineering press release.

MICDE to provide data analysis and dissemination support for $18 million tobacco research center

By | General Interest, Happenings, News, Research

The University of Michigan School of Public Health will house a new, multi-institutional center focusing on modeling and predicting the impact of tobacco regulation, funded with an $18 million federal grant from the National Institutes of Health and the Food and Drug Administration.

The Center for the Assessment of the Public Health Impact of Tobacco Regulations will be part of the NIH and FDA’s Tobacco Centers of Regulatory Science, the centerpiece of an ongoing partnership formed in 2013 to generate critical research that informs the regulation of tobacco products.

The Michigan Institute for Computational Discovery and Engineering (MICDE) will support the center’s Data Analysis and Dissemination core by collecting national and regional survey data, conducting analysis of the use of tobacco products including vaping and e-cigarettes, and disseminate the resulting tobacco modeling parameters to other research centers and the Food and Drug Administration.

The center is led by MICDE affiliated faculty member Rafael Meza, associate professor of Epidemiology, and David Levy, professor of Oncology at Georgetown University.

For more on the center, see the press release from the U-M School of Public Health: https://sph.umich.edu/news/2018posts/tcors-091718.html

MDST group wins KDD best paper award

By | General Interest, Happenings, MDSTPosts, Research

A paper by members and faculty leaders of the Michigan Data Science Team (co-authors: Jacob Abernethy, Alex Chojnacki, Arya Farahi, Eric Schwartz, and Jared Webb) won the Best Student Paper award in the Applied Data Science track at the KDD 2018 conference in August in London.

The paper, ActiveRemediation: The Search for Lead Pipes in Flint, Michigan, details the group’s ongoing work in Flint to detect pipes made of lead and other hazardous material.

For more on the team’s work, see this recent U-M press release.