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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

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/.

ARC-TS joins Cloud Native Computing Foundation

By | General Interest, Happenings, News

Advanced Research Computing – Technology Services (ARC-TS) at the University of Michigan has become the first U.S. academic institution to join the Cloud Native Computing Foundation (CNCF), a foundation that advances the development and use of cloud native applications and services. Founded in 2015, CNCF is part of the Linux Foundation.

CNCF announced ARC-TS’s membership at the KubeCon and CloudNativeCon event in Copenhagen. A video of the opening remarks by CNCF Executive Director Dan Kohn can be viewed on the event website.

“Our membership in the CNCF signals our commitment to bringing cloud computing and containers technology to researchers across campus,” said Brock Palen, Director of ARC-TS. “Kubernetes and other CNCF platforms are becoming crucial tools for advanced machine learning, pipelining, and other research methods. We also look forward to bring an academic perspective to the foundation.”

ARC-TS’s membership and participation in the group signals its adoption and commitment to cloud-native technologies and practices. Users of containers and other CNCF services will have access to experts in the field.

Membership gives the U-M research community input into in the continuing development of cloud-native applications, and within CNCF-managed and ancillary projects. U-M is the second academic institution to join the foundation, and the only one in the U.S.

ARC-TS begins work on new “Great Lakes” cluster to replace Flux

By | Flux, Happenings, HPC, News

Advanced Research Computing – Technology Services (ARC-TS) is starting the process of creating a new, campus-wide computing cluster, “Great Lakes,” that will serve the broad needs of researchers across the University. Over time, Great Lakes will replace Flux, the shared research computing cluster that currently serves over 300 research projects and 2,500 active users.

“Researchers will see improved performance, flexibility and reliability associated with newly purchased hardware, as well as changes in policies that will result in greater efficiencies and ease of use,” said Brock Palen, director of ARC-TS.

The Great Lakes cluster will be available to all researchers on campus for simulation, modeling, machine learning, data science, genomics, and more. The platform will provide a balanced combination of computing power, I/O performance, storage capability, and accelerators.

ARC-TS is in the process of procuring the cluster. Only minimal interruption to ongoing research is expected. A “Beta” cluster will be available to help researchers learn the new system before Great Lakes is deployed in the first half of 2019.

The Flux cluster is approximately 8 years old, although many of the individual nodes are newer. One of the benefits of replacing the cluster is to create a more homogeneous platform.

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. The cluster will consist of approximately 20,000 cores.

For more information, contact hpc-support@umich.edu, and see arc-ts.umich.edu/systems-services/greatlakes, where updates to the project will be posted.

Interdisciplinary Committee on Organizational Studies (ICOS) Big Data Summer Camp, May 14-18

By | Data, Educational, General Interest, Happenings, News
Social and organizational life are increasingly conducted online through electronic media, from emails to Twitter feed to dating sites to GPS phone tracking. The traces these activities leave behind have acquired the (misleading) title of “big data.” Within a few years, a standard part of graduate training in the social sciences will include a hefty dose of “using of big data,” and we will all be utilizing terms like API and Python.
This year ICOS, MIDAS, and ARC are again offering a one-week “big data summer camp” for doctoral students interested in organizational research, with a combination of detailed examples from researchers; hands-on instruction in Python, SQL, and APIs; and group work to apply these ideas to organizational questions.  Enrollment is free, but students must commit to attending all day for each day of camp, and be willing to work in interdisciplinary groups.

The dates of the camp are all day May 14th-18th.

https://ttc.iss.lsa.umich.edu/ttc/sessions/interdisciplinary-committee-on-organizational-studies-icos-big-data-summer-camp-3/ 

U-M launches Data Science Master’s Program

By | Educational, General Interest, Happenings, News

The University of Michigan’s new, interdisciplinary Data Science Master’s Program is taking applications for its first group of students. The program is aimed at teaching participants how to extract useful knowledge from massive datasets using computational and statistical techniques.

The program is a collaboration between the College of Engineering (EECS), the College of Literature Science and the Arts (Statistics), the School of Public Health (Biostatistics), the School of Information, and the Michigan Institute for Data Science.

“We are very excited to be offering this unique collaborative program, which brings together expertise from four key disciplines at the University in a curriculum that is at the forefront of data science,” said HV Jagadish, Bernard A. Galler Collegiate Professor of Electrical Engineering and Computer Science, who chairs the program committee for the program.

“MIDAS was a catalyst in bringing  faculty from multiple disciplines together to work towards the development of this new degree program,”  he added.

MIDAS will provide students in this program with interdisciplinary collaborations, intellectual stimulation, exposure to a broad range of practice, networking opportunities, and space on Central Campus to meet for formal and informal gatherings.

For more information, see the program website at https://lsa.umich.edu/stats/masters_students/mastersprograms/data-science-masters-program.html, and the program guide (PDF) at https://lsa.umich.edu/content/dam/stats-assets/StatsPDF/MSDS-Program-Guide.pdf.

Applications are due March 15.

HPC training workshops begin Tuesday, Feb. 13

By | Educational, Events, General Interest, Happenings, HPC, News

series of training workshops in high performance computing will be held Feb. 12 through March 6, 2018, presented by CSCAR in conjunction with Advanced Research Computing – Technology Services (ARC-TS).

Introduction to the Linux command Line
This course will familiarize the student with the basics of accessing and interacting with Linux computers using the GNU/Linux operating system’s Bash shell, also known as the “command line.”
Location: East Hall, Room B254, 530 Church St.
Dates: (Please sign up for only one)
• Tuesday, Feb. 13, 1 – 4 p.m. (full descriptionregistration)
• Friday, Feb. 16, 9 a.m. – noon (full description | registration)

Introduction to the Flux cluster and batch computing
This workshop will provide a brief overview of the components of the Flux cluster, including the resource manager and scheduler, and will offer students hands-on experience.
Location: East Hall, Room B254, 530 Church St.
Dates: (Please sign up for only one)
• Monday, Feb. 19, 1 – 4 p.m. (full description | registration)
• Tuesday, March 6, 1 – 4 p.m. (full description | registration)

Advanced batch computing on the Flux cluster
This course will cover advanced areas of cluster computing on the Flux cluster, including common parallel programming models, dependent and array scheduling, and a brief introduction to scientific computing with Python, among other topics.
Location: East Hall, Room B250, 530 Church St.
Dates: (Please sign up for only one)
• Wednesday, Feb. 21, 1 – 5 p.m. (full description | registration)
• Friday, Feb. 23, 1 – 5 p.m. (full description | registration)

Hadoop and Spark workshop
Learn how to process large amounts (up to terabytes) of data using SQL and/or simple programming models available in Python, R, Scala, and Java.
Location: East Hall, Room B250, 530 Church St.
Dates: (Please sign up for only one)
• Thursday, Feb. 22, 1 – 5 p.m. (full description | registration)

Video available from MIDAS Research Forum

By | General Interest, Happenings, News, Research

Video is now available from the MIDAS Research Forum held Dec. 1 in the Michigan League at http://myumi.ch/6vA3V

The forum featured U-M students and faculty showcasing their data science research; a workshop on how to work with industry; presentations from student groups; and a summary of the data science consulting and infrastructure services available to the U-M research community.

NOTE: The keynote presentation from Christopher Rozell of the Georgia Institute of Technology will be available in the near future.