U-M plans participation at SC17 conference in Denver

By | General Interest, Happenings, HPC, News

Several University of Michigan researchers and professional IT staff will attend the Supecomputing 17 (SC17) conference in Colorado from Nov. 12-17, and participate in a number of different ways, including demonstrations, presentations and tutorials.

In addition to the events and presentations listed below, Amy Liebowitz, a network architect at ITS, is working on SCINet, a high-capacity network created every year for the conference. Liebowitz is on the routing team, which is responsible for installing, configuring and supporting the high performance conference network. The Routing Team also coordinates external connectivity with commodity Internet and R&E WAN service providers.

Please visit us at Booth 471 on the exhibit floor, or at one of the following events:

Sunday, Nov. 12

8:30 a.m. – 5 p.m.: Quentin Stout (EECS) and Christiane Jablonowski (CLASP) will teach the “Parallel Computing 101” tutorial.

Tuesday, Nov. 14

10:30 a.m.:  Research Networking at the University of Michigan
Eric Boyd, Director of Research Networks, U-M
U-M Booth #471

11 a.m.: The OSiRIS Project: Open Storage Research Infrastructure
Ben Meekhof, HPC Storage Administrator, Advanced Research Computing – Technology Services (ARC-TS)
U-M Booth #471

12:30 p.m.: GPU-Accelerated Predictive Material Design
Simon Adorf, Ph.D. Candidate, Chemical Engineering Department, U-M
U-M Booth #471

1:30 p.m.: Simple Data and Workflow Management with Signac
Simon Adorf, Ph.D. Candidate, Chemical Engineering Department, U-M
U-M Booth #471

1:30 – 3 p.m.: Matt McLean, a Big Data systems administrator with ARC-TS, will serve as a panelist at a presentation titled “The ARM Software Ecosystem: Are We There Yet?

2 p.m.: The Michigan Institute for Computational Discovery and Engineering
Mariana Carrasco-Teja, Assistant Director, MICDE
U-M Booth #471

5:15 – 7 p.m.: Jeff Sica, a research database administrator with ARC-TS, will help lead a Birds of a Feather session titled “Containers in HPC.”

6:15 – 8:30 p.m.: ARC at U-M is a sponsor of a networking and career networking reception put on by Women in HPC. ARC Director Sharon Broude Geva will speak at the event.

Wednesday, November 15

10 a.m.: The OSiRIS Project: Open Storage Research Infrastructure
Shawn McKee, U-M Department of Physics, OSiRIS Principal Investigator
U-M Booth #471

11 a.m.: Research Networking at the University of Michigan
Eric Boyd, Director of Research Networks, U-M
U-M Booth #471

3 p.m.: The New Cavium ThunderX Big Data Cluster at U-M
Matt McLean, Big Data Systems Administrator, ARC-TS
U-M Booth #471

Thursday, November 16

11 a.m.: The New Cavium ThunderX Big Data Cluster at U-M
Matt McLean, Big Data Systems Administrator, ARC-TS
U-M Booth #471

 

 

U-M partners with Cavium on Big Data computing platform

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

A new partnership between the University of Michigan and Cavium Inc., a San Jose-based provider of semiconductor products, will create a powerful new Big Data computing cluster available to all U-M researchers.

The $3.5 million ThunderX computing cluster will enable U-M researchers to, for example, process massive amounts of data generated by remote sensors in distributed manufacturing environments, or by test fleets of automated and connected vehicles.

The cluster will run the Hortonworks Data Platform providing Spark, Hadoop MapReduce and other tools for large-scale data processing.

“U-M scientists are conducting groundbreaking research in Big Data already, in areas like connected and automated transportation, learning analytics, precision medicine and social science. This partnership with Cavium will accelerate the pace of data-driven research and opening up new avenues of inquiry,” said Eric Michielssen, U-M associate vice president for advanced research computing and the Louise Ganiard Johnson Professor of Engineering in the Department of Electrical Engineering and Computer Science.

“I know from experience that U-M researchers are capable of amazing discoveries. Cavium is honored to help break new ground in Big Data research at one of the top universities in the world,” said Cavium founder and CEO Syed Ali, who received a master of science in electrical engineering from U-M in 1981.

Cavium Inc. is a leading provider of semiconductor products that enable secure and intelligent processing for enterprise, data center, wired and wireless networking. The new U-M system will use dual socket servers powered by Cavium’s ThunderX ARMv8-A workload optimized processors.

The ThunderX product family is Cavium’s 64-bit ARMv8-A server processor for next generation Data Center and Cloud applications, and features high performance custom cores, single and dual socket configurations, high memory bandwidth and large memory capacity.

Alec Gallimore, the Robert J. Vlasic Dean of Engineering at U-M, said the Cavium partnership represents a milestone in the development of the College of Engineering and the university.

“It is clear that the ability to rapidly gain insights into vast amounts of data is key to the next wave of engineering and science breakthroughs. Without a doubt, the Cavium platform will allow our faculty and researchers to harness the power of Big Data, both in the classroom and in their research,” said Gallimore, who is also the Richard F. and Eleanor A. Towner Professor, an Arthur F. Thurnau Professor, and a professor both of aerospace engineering and of applied physics.

Along with applications in fields like manufacturing and transportation, the platform will enable researchers in the social, health and information sciences to more easily mine large, structured and unstructured datasets. This will eventually allow, for example, researchers to discover correlations between health outcomes and disease outbreaks with information derived from socioeconomic, geospatial and environmental data streams.

U-M and Cavium chose to run the cluster on Hortonworks Data Platform, which is based on open source Apache Hadoop. The ThunderX cluster will deliver high performance computer services for the Hadoop analytics and, ultimately, a total of three petabytes of storage space.

“Hortonworks is excited to be a part of forward-leading research at the University of Michigan exploring low-powered, high-performance computing,” said Nadeem Asghar, vice president and global head of technical alliances at Hortonworks. “We see this as a great opportunity to further expand the platform and segment enablement for Hortonworks and the ARM community.”

Potential service disruption for Value Storage maintenance — Dec. 2

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

The ITS Storage team will be applying an operating system patch on the MiStorage Silver environment, which provides home directories for both Flux and Flux Hadoop.  The ITS maintenance window will be from December 2nd 11:00pm to December 3rd 7:00am (8 hours total).  This update might be potentially disruptive to the stability of the nodes and jobs running on them.

The ITS status page for this incident is here:  http://status.its.umich.edu/report.php?id=141155

For Flux users: we have created a reservation on Flux so no jobs will be running or impacted.  We will remove the reservation after we receive the update from the ITS storage team of a successful update.

For Flux Hadoop users:  The scheduler and user logins will be deactivated when the outage starts, and any user currently logged into the cluster will be logged out for the duration of the outage.  We will reactivate access when we have received the all-clear from the ITS storage team of a successful update.

Status updates will be posted on the ARC-TS Twitter feed: https://twitter.com/arcts_um  and if you have any questions, please email us at hpc-support@umich.edu.

CSCAR provides walk-in support for new Flux users

By | Data, Educational, Flux, General Interest, HPC, News

CSCAR now provides walk-in support during business hours for students, faculty, and staff seeking assistance in getting started with the Flux computing environment.  CSCAR consultants can walk a researcher through the steps of applying for a Flux account, installing and configuring a terminal client, connecting to Flux, basic SSH and Unix command line, and obtaining or accessing allocations.  

In addition to walk-in support, CSCAR has several staff consultants with expertise in advanced and high performance computing who can work with clients on a variety of topics such as installing, optimizing, and profiling code.  

Support via email is also provided via hpc-support@umich.edu.  

CSCAR is located in room 3550 of the Rackham Building (915 E. Washington St.). Walk-in hours are from 9 a.m. – 5 p.m., Monday through Friday, except for noon – 1 p.m. on Tuesdays.

See the CSCAR web site (cscar.research.umich.edu) for more information.

University of Michigan researcher contributes to NASA findings on carbon in the atmosphere showcased in the journal Science

By | General Interest, Happenings, News

 

High-resolution satellite data from NASA’s Orbiting Carbon Observatory-2 are revealing the subtle ways that carbon links everything on Earth – the ocean, land, atmosphere, terrestrial ecosystems and human activities. Scientists using the first 2 1/2 years of OCO-2 data have published a special collection of five papers today in the journal Science that demonstrates the breadth of this research. In addition to showing how drought and heat in tropical forests affected global carbon dioxide levels during the 2015-16 El Niño, other results from these papers focus on ocean carbon release and absorption, urban emissions and a new way to study photosynthesis. A final paper by OCO-2 Deputy Project Scientist Annmarie Eldering of NASA’s Jet Propulsion Laboratory in Pasadena, California, and colleagues gives an overview of the state of OCO-2 science.

Manish Verma, a Geospatial/Data Science Consultant at the University of Michigan’s Consulting for Statistics, Computing and Analytics Research (CSCAR) unit, contributed as a coauthor to an article on a new way to measure photosynthesis over time and space.

Using data from the OCO-2, Verma’s analysis helped expand the utility of measurements of solar induced fluorescence (SIF), which indicates active photosynthesis in plants. Verma’s work showed that SIF data collected from the OCO-2 satellite provides reliable information on the variability of photosynthesis at a much smaller scale — down to individual ecosystems.

This can, in turn, “lead to more reliable estimates of carbon sources — that is, when, where, why and how carbon is exchanged between land and atmosphere — as well as a deeper understanding of carbon-climate feedbacks,” according to the Science article.

For more, see the NASA press release (https://www.nasa.gov/feature/jpl/new-insights-from-oco-2-showcased-in-science) and the Science article (http://science.sciencemag.org/content/358/6360/eaam5747.full)

Real estate dataset available to researchers

By | Data, Data sets, Educational, General Interest, Happenings, News

The University of Michigan Library system and the Data Acquisition for Data Sciences program (DADS) of the U-M Data Science Initiative (DSI) have recently joined forces to license a major data resource capturing parcel-level information about the property market in the United States.  

The data were licensed from the Corelogic corporation, who have assimilated deed, tax and foreclosure information on nearly all properties in the entire US. Coverage dates vary by county, some county records go back fifty years. Coverage is more comprehensive from the 1990s to the present.

These data will support a variety of research efforts into regional economies, economic disparities, trends in land-use, housing market dynamics, and urban ecology, among many other areas.

The data are available on the Turbo Research Storage system for users of the U-M High Performance Computing infrastructure, and via the University of Michigan Library.

To access the data, researchers must first sign a MOU; contact Senior Associate Librarian Catherine Morse cmorse@umich.edu for more information, or visit https://www.lib.umich.edu/database/corelogic-parcel-level-real-estate-data.

Mini-course: Introduction to Python — Sept. 11-14

By | Data, Educational, Events, General Interest, News

Asst. Prof. Emanuel Gull, Physics, is offering a mini-course introducing the Python programming language in a four-lecture series. Beginners without any programming experience as well as programmers who usually use other languages (C, C++, Fortran, Java, …) are encouraged to come; no prior knowledge of programming languages is required!

For the first two lectures we will mostly follow the book Learning Python. This book is available at our library. An earlier edition (with small differences, equivalent for all practical purposes) is available as an e-book. The second week will introduce some useful python libraries: numpyscipymatplotlib.

At the end of the first two weeks you will know enough about Python to use it for your grad class homework and your research.

Special meeting place: we will meet in 340 West Hall on Monday September 11 at 5 PM.

Please bring a laptop computer along to follow the exercises!

Syllabus (Dates & Location for Fall 2017)

  1. Monday September 11 5:00 – 6:30 PM: Welcome & Getting Started (hello.py). Location: 340 West Hall
  2. Tuesday September 12 5:00 – 6:30 PM: Numbers, Strings, Lists, Dictionaries, Tuples, Functions, Modules, Control flow. Location: 335 West Hall
  3. Wednesday September 13 5:00 – 6:30 PM: Useful Python libraries (part I): numpy, scipy, matplotlib. Location: 335 West Hall
  4. Thursday September 14 5:00 – 6:30 PM: Useful Python libraries (part 2): 3d plotting in matplotlib and exercises. Location: 335 West Hall

For more information: https://sites.lsa.umich.edu/gull-lab/teaching/physics-514-fall-2017/introduction-to-python/

 

Info sessions on graduate studies in computational and data sciences — Sept. 21 and 25

By | Educational, Events, General Interest, News, Research

Learn about graduate programs that will prepare you for success in computationally intensive fields — pizza and pop provided

  • The Ph.D. in Scientific Computing is open to all Ph.D. students who will make extensive use of large-scale computation, computational methods, or algorithms for advanced computer architectures in their studies. It is a joint degree program, with students earning a Ph.D. from their current departments, “… and Scientific Computing” — for example, “Ph.D. in Aerospace Engineering and Scientific Computing.”
  • The Graduate Certificate in Computational Discovery and Engineering trains graduate students in computationally intensive research so they can excel in interdisciplinary HPC-focused research and product development environments. The certificate is open to all students currently pursuing Master’s or Ph.D. degrees at the University of Michigan.
  • The Graduate Certificate in Data Science is focused on developing core proficiencies in data analytics:
    1) Modeling — Understanding of core data science principles, assumptions and applications;
    2) Technology — Knowledge of basic protocols for data management, processing, computation, information extraction, and visualization;
    3) Practice — Hands-on experience with real data, modeling tools, and technology resources.

Times / Locations:

HPC training workshops begin Thursday, Sept. 21

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

series of training workshops in high performance computing will be held Sept. 21 through Oct. 31, 2017, presented by CSCAR in conjunction with Advanced Research Computing – Technology Services (ARC-TS). All sessions are held at East Hall, Room B254, 530 Church St.

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.”
Dates: (Please sign up for only one)
• Thursday, Sept. 21, 9 a.m. – noon (full descriptionregistration)
• Thursday, Sept. 28, 9 a.m. – noon (full description | registration)
Location:
East Hall, Room B250, 530 Church St.

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.
Dates: (Please sign up for only one)
• Thursday, Sept. 28, 1 – 4 p.m. (full description | registration)
• Monday, Oct. 2, 9 a.m. – noon (full description | registration)
Location:
East Hall, Room B254, 530 Church St.

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, among other topics.
Dates: (Please sign up for only one)
• Tuesday, Oct. 10, 1 – 5 p.m. (full description | registration) Location: East Hall, Room B254, 530 Church St.
• Thursday, Oct. 12, 9 a.m. – noon (full description | registration) Location: East Hall, Room B254, 530 Church St.
• Friday, Oct. 13, 9 a.m. – noon (full description | registration) Location: East Hall, Room B250, 530 Church St.

Hadoop Workshop
Learn how to process large amounts (up to terabytes) of data using SQL and/or simple programming models available in Python, Scala, and Java.
Date:
• Tuesday, Oct. 31, 1 – 5 p.m. (full description | registration)
Location:
East Hall, Room B254, 530 Church St.