2015-2016 Education Snapshot

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XSEDESummerBootCamp2016

Students at the U-M satellite site of the XSEDE 2016 Summer Bootcamp

We have over 80 students between our Ph.D. in Scientific Computing and the Graduate Certificate in Computational Discovery and Engineering. The students come from five different schools and colleges, and 30 percent are women. We also have partnered with the Multidisciplinary Design Program to offer our Masters students the experience to work on industrial projects and gain practicum credits.

Our faculty have designed two courses that are being offered for the first time: Methods and Practices of Scientific Computing in Fall 2016 and Data-Driven Analysis and Modeling of Complex Systems in Winter 2017. Methods and Practices of Scientific Computing has gathered a tremendous amount of interest, and very quickly was over-subscribed. Data-Driven Analysis and Modeling of Complex Systems is a fast paced research area that combines scientific computing with big data to improve the existing models’ accuracy and representation of physical and biological systems.

Scientific Computing Student Club social gathering

Scientific Computing Student Club social gathering

We have brought a large community of students together by sponsoring and helping found the Scientific Computing Student Club. Its goal is to become a place for all students that use or want to use high performance computing to meet, share ideas, and find peer-to-peer help. It started in February, with social gatherings, talks from expert speakers, and more. The club has nearly 200 members, including undergraduates, graduate students, and postdocs from six U-M schools and colleges.

Graduate programs in computational and data science — informational sessions Sept. 19 & 21

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Students interested in computational and data science are invited to learn about graduate programs that will prepare them for success in computationally intensive fields. Pizza and pop will be provided.

Two sessions are scheduled:

Monday, Sept. 19, 5 – 6 p.m.
Johnson Rooms, Lurie Engineering Center (North Campus)

Wednesday, Sept. 21, 5 – 6 p.m.
2001 LSA Building (Central Campus)

The sessions will address:

  • The Ph.D. in Scientific Computing, which 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, which 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. This year we will offer a new practicum option through the Multidisciplinary Design Program.
  • The Graduate Certificate in Data Science, which 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.

MICDE Fall 2016 Seminar Series speakers announced

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The Michigan Institute for Computational Discovery and Engineering (MICDE) is proud to announce its fall lineup of seminar speakers. In cooperation with academic departments across campus, the seminar series brings nationally recognized speakers to campus.

This fall’s speakers are:

Sept. 13: Nathan Kutz, Professor of Applied Mathematics, University of Washington

Sept. 22: Rob Gardner, Senior Scientist at the Computation Institute, University of Chicago

Sept. 29: Jeremy Lichstein, Assistant Professor of Biology, University of Florida

Oct. 6: Jonathan Freund, Professor of Mechanical Science and Engineering and of Aerospace Engineering, University of Illinois, Urbana-Champaign

Oct. 14: Anthony Wachs, Assistant Professor of Mathematics and of Chemical and Biological Engineering, University of British Columbia

Oct. 26: Andrea Lodi, Professor of Mathematical and Industrial Engineering, Polytechnique Montreal

Nov. 11: David Higdon, Professor of the Biocomplexity Institute, Virginia Tech

Dec. 9: Ann Almgren, Staff Scientist at the Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratories

For more information, including links to bios and abstracts as available, please visit micde.umich.edu/seminar-series/.

Students in the Graduate Certificate in Computational Discovery and Engineering program are required to attend at least half of the seminars.

Registration open for on-campus telecast of XSEDE workshop on MPI — Sept. 7-8

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U-M is hosting a telecast of a workshop on MPI (message passing interface) presented by XSEDE and the Pittsburgh Supercomputing Center.

This workshop is intended to give C and Fortran programmers a hands-on introduction to MPI programming. Attendees will leave with a working knowledge of how to write scalable codes using MPI – the standard programming tool of scalable parallel computing.

Time/Date: 11 a.m. to 5 p.m. Eastern, Wednesday, Sept. 7 and Thursday, Sept. 8

Location: Room B003E, North Campus Research Complex (NCRC), Building 16, 2800 Plymouth Rd.

Registration: Registration is required through the XSEDE website (you must create an XSEDE user account to register). Space is limited.

More information: Class website.

Contact: Simon Adorf (csadorf@umich.edu)

miRcore’s high school biotechnology camp a success

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GIDAS Biotechnology camp’s high school students learning about microRNA targeted predictions using Flux, with support from MICDE and U-M’s Scientific Computing Student Club members.

 

From Aug. 8-12, 2016, MICDE and ARC-TS donated a Flux allocation and computational support to miRcore and its GIDAS’ Biotechnology Camp for high school students. All the students were able to log in the cluster, and use the command line to run RNAhybrid, a tool for finding the minimum free energy hybridization of a long and a short RNA. The students learned about microRNA target predictions that complemented the camp’s wet lab experiments. Scientific Computing Student Club members Joe Paki and Blair Winograd provided support to the students.

MICDE is partnered with miRcore, a non-profit organization whose mission is to democratize medical research by building funds for microgrants to support innovative genetic research.

New graduate course offering: “Methods and Practice of Scientific Computing”

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The Michigan Institute for Computational Discovery and Engineering (MICDE) is pleased to announce “Methods and Practice of Scientific Computing”, the first graduate course designed and organized by MICDE faculty. The course will be taught in Fall 2016, coordinated by Dr. Brendan Kochunas. This foundational course in scientific computing has been developed as a broad introduction to the subject, and has been designed to support research in all disciplines represented in MICDE. In addition to Brendan Kochunas, the course was developed by MICDE professors Bill Martin, Karthik Duraisamy, Vikram Gavini, and Shravan Veerapaneni, and MICDE Assistant Director Mariana Carrasco-Teja.

The details follow:

NERS 590
4 credits
Prerequisites: Graduate standing and permission of instructor.

This course is designed for graduate students who are developing the methods, and using the tools, of scientific computing in their research. With the increased power and availability of computers to do massively scaled simulations, computational science and engineering as a whole has become an integral part of research that complements experiment and theory. This course will teach students the necessary skills to be effective computational scientists and how to produce work that adheres to the scientific method. A broad range of topics will be covered including: software engineering best practices, computer architectures, computational performance, common algorithms in engineering, solvers, software libraries for scientific computing, uncertainty quantification, verification and validation, and how to use all the various tools to accomplish these things. The class will have lecture twice a week and have an accompanying lab component. Students will be graded on homeworks, lab assignments, and a course project.

A draft of the syllabus can be found here. Please contact MICDE at micde-contact@umich.edu with any questions.

Software Carpentry workshop at U-M — May 2-3

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A Software Carpentry workshop will be held at the U-M Medical School May 2 and 3. These workshops are free and open to anyone on campus; the sessions are suitable for researchers in the humanities and social sciences. Register here.

This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Who: The course is aimed at graduate students, postdocs, and other researchers across the University of Michigan. You don’t need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Furstenberg 2710 (2nd floor of Med Sci II).

Student groups can access Flux at no charge under Flux Academic Use program

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Undergraduate groups can now access Flux, U-M’s shared computing cluster, at no cost under the new Flux Academic Use program from Advanced Research Computing (ARC). Flux Academic Use aims to provide undergraduates with experience in high performance computing and access to computational resources for their projects; it is not meant for faculty-led research. Jobs submitted under Flux Academic Use will run only when unused cycles are available. To be most efficient, student groups should use short or checkpointed jobs to take advantage of these available cycles. Student groups can also purchase Flux allocations for jobs that are higher priority or time constrained; those allocations can also work in conjunction with the free Flux Academic Use jobs. Undergraduate groups must have a faculty sponsor to be eligible for Flux Academic Use. For more information, or to request time under Flux Academic Use, please email hpc-support@umich.edu.

Midwest Big Data Hub offers early career seed funding to improve data access — April 1, May 1 deadlines

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The Midwest Big Data Hub, an NSF-funded group including U-M’s Michigan Institute for Data Science (MIDAS), is seeking proposals from early career researchers to enhance collaborations with data-producing organizations to improve access to data. Senior researchers are also welcome to apply for funding for activities that bring together data producers and researchers with significant participation from early career researchers.

The goal of the funding, provided by the Computing Community Consortium, is to improve partnerships and collaboration between data producing organizations in industry, government, and academia and researchers. Activities can include workshops, internships, hackathons at universities, data-related competitions, travel grants and lecture series. Awards will range from between $10,000 and $40,000.

Deadlines for applications are April 1 and May 1.

For more information, including how to apply, read the proposal description on the MIDAS website.