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Winning posters announced for MICDE 2018 Symposium

By | Events, General Interest, Happenings, News

Approximately 50 posters from post-docs and graduate students across campus entered the Poster Competition at the 2018 MICDE Symposium on March 22, 2018. We’re proud to announce the winners:

  • First Place ($500): “Modeling and Enhanced Sampling of Protein-Protein Recognition,” Yanmin Wang, Chemistry
  • Second Place ($300): “Non-Newtonian Computational Model of Thrombosis Initiation,” Sabrina Lynch, Biomedical Engineering
  • Third Place ($200): “Computational Modeling of Particle-Laden Flows,” Gregory Shallcross, Sarah Beetham, and Yuan Yao, Mechanical Engineering
  • Honorable Mention:UM/LISA: Efficient Linear and Nonlinear Guided Wave Simulation,” Hui Zhang, Aerospace Engineering
  • Honorable Mention:Temperature-Dependent Green’s Function Methods for Electronic Structure Calculations,” Alicia Welden, Chemistry
  • Honorable Mention:Non-invasive Diagnostics of Coronary Artery Disease using Machine Learning and Computational Fluid Dynamics,” Kritika Iyer, Biomedical Engineering
  • Honorable Mention:Automated Diagnosis and Prognosis System for Traumatic Brain Injury Patients with Subdural Hematoma,” Negar Farzaneh

The 2018 MICDE Symposium: Summary by Bradley Dice, Ph.D student in Physics and Computational Science

By | Uncategorized

This piece was first published in LinkedIn by Bradley Dice, U-M Ph.D student in Physics and Computational Science.

MICDE Symposium 2018: Computation, A Pillar of Science and a Lens to the Future

High-performance computing (HPC) is becoming an increasingly powerful tool in the hands of scientists, driving new discoveries in physical sciences, life sciences, and social sciences. The development of new (frequently domain-specific) approaches to machine learning and faster, smarter processing of sets of Big Data allows us to explore questions that were previously impossible to study. Yesterday, I presented a poster at the Michigan Institute for Computational Discovery & Engineering (MICDE) annual Symposium and attended a number of talks by researchers working at the intersection of high-performance computing and their domain science. The theme for the symposium was “Computation: A Pillar of Science and a Lens to the Future.”

Collaborative Computational Science with signac

My scientific work, and the work of my colleagues in the Glotzer lab, has been made vastly more efficient through the use of tools for collaborative science, particularly the signac framework. I presented a poster about how the signac framework (composed of open-source Python packages signacsignac-flow, and signac-dashboard) enables scientists to rapidly simulate, model, and analyze data. The name comes from painter Paul Signac, who, along with Georges Seurat, founded the style of pointillism. This neo-impressionist style uses tiny dots of color instead of long brushstrokes, which collectively form a beautiful image when the viewer steps back. This metaphor fits the way that a lot of science works: given only points of data, scientists aim to see the whole picture and tell its story. Since our lab studies materials, our “points” of data fit into a multidimensional parameter space, where quantities like pressure and temperature, or even particles’ shapes, may vary. Using this data, our lab computationally designs novel materials from nanoparticles and studies the physics of complex crystalline structures.

The core signac package, which acts as a database on top of the file system, helps organize and manage scientific data and metadata. Its companion tool signac-flow enables users to quickly define “workflows” that run on supercomputing clusters, determining what operations to perform and submitting the jobs to the cluster for processing. Finally, signac-dashboard (which I develop) provides a web-based data visualization interface that allows users to quickly scan for interesting results and answer scientific questions. These tools include tutorials and documentation, to help users acquaint themselves and get on to doing science as quickly as possible. Importantly, the tools are not specific to materials science. Many scientific fields have similar questions, and the toolkit can easily be applied in fields where exploration or optimization within parameter spaces are common, ranging from fluid mechanics to machine learning.

During the symposium, I learned a lot about how others are using scientific computing in their own work. The symposium speakers came from a wide range of fields, including biology, mathematics, and fluid dynamics. Some of my favorite talks are described below.

The Past: Phylogeny and Uncovering Life’s Origins

High-performance computing is enabling scientists to look in all sorts of directions, including into the past. Stephen Smith, Assistant Professor of Ecology and Evolutionary Biology at the University of Michigan, talked about his lab’s research in detecting evolutionary patterns using genomic data. From the wealth of genetic data that scientists have collected, the Smith lab aims to improve our understanding of the “tree of life”: the overarching phylogenetic tree that can explain the progress of speciation over time. Projects like Open Tree of Life and PHLAWD, an open-source C++ project to process data from the National Center for Biotechnology Information’s GenBank data source, are just two of the ways that open science and big data are informing our understanding of life itself.

The Present: From Algebra to Autonomy

Cleve Moler, the original author of the MATLAB language and chief mathematician, chairman, and cofounder of MathWorks, spoke about his career and how the tools MATLAB has provided for numerical linear algebra (and many other computational tasks) have been important for the development of science and engineering over the last 34 years. MATLAB is taught to STEM students in many undergraduate curricula, and is used widely across industry to simulate and model the behavior of real systems. Features like the Automated System Driving Toolbox are poised to play a role in autonomous vehicles and the difficult computational tasks inherent in their operation.

The Future: Parallel-in-Time Predictions and Meteorology

A significant challenge in weather and climate modeling is that supercomputer architectures are highly parallel, while many simulations of fluids are inherently serial: each timestep must be computed before the next timestep can begin. Beth Wingate, Professor of Mathematics at the University of Exeter and published poet, is developing a powerful approach that may change the way that such models work. Called “parallel-in-time,” it separates the effects of slow dynamics and fast dynamics, enabling parallel architectures to take advantage of longer timesteps and separate the work across many processors.


Computational science is growing rapidly, improving our ability to address the most pressing questions and the mysteries of our world. As new supercomputing resources come online, such as Oak Ridge National Laboratories’ Summit, the promise of exascale computing is coming ever closer to reality. I look forward to what the next year of HPC will bring to our world.

[SC2 Jobs] Coding Institute Workshop for SGCI

By | SC2 jobs

The Science Gateways Community Institute will host a Summer 2018 workshop that will be a four-week Coding Institute for undergraduate students that will take place on the campus of Elizabeth City State University. The workshop will cover the core skills needed to be productive in the design and maintenance of science gateways. The program will be presented as short tutorials alternated with practical experiences, and all instruction will be done via live coding.

Eligible applicants are undergraduate students majoring in computer science or computer engineering (or related fields) who have an interest in the design and maintenance of science gateways. Ten participants will be selected for the Coding Institute. Participants of the Coding Institute will receive a weekly stipend of $500 plus funding for transportation and housing. All selected participants will be required to attend both the PEARC18 and Gateways 2018 conferences. Funding to attend both conferences will be provided by SGCI’s Workforce Development.

If you are an undergraduate student who would like to apply for the four-week Coding Institutecomplete this application form. The deadline for submitting this application form and supporting documents is April 27, 2018.


Minimum Requirements:
•Undergraduate majoring in Computer Science or Computer Engineering (or related fields) and have an interest in the design and maintenance of science gateways

Job category

Coding Institute Workshop


Elizabeth City, NC

Application deadline

April 27, 2018

[SC2 Jobs] Gateway Development Internship for SGCI

By | SC2 jobs

The Workforce Development team from SGCI offers eight-week summer internships for students interested in developing their gateway development skills. Participants will be placed at one of the seven universities that form the SGCI partnership, or a specific site can be suggested by an SGCI client, partner, or others who are interested in hosting a student intern.

Eligible applicants include graduate students majoring in computer science or computer engineering (or related fields) at any level and undergraduates majoring in computer science or computer engineering (or related fields) who have completed their junior year and who demonstrate strong programming and software engineering skills.

Participants will receive a stipend, plus housing and transportation. Interns will be required to attend the Gateways 2018 conference, for which Workforce Development will provide funding. Attending PEARC18 is recommended, but not required. Funding will be provided by Workforce Development to interns who decide to attend.

Learn more about the internship opportunity by reading these blog posts written by some of the students who worked as SGCI interns during summer of 2017:

Summer 2018 Gateway Development Internships

If you are a student and would like to apply for an internshipcomplete this application form. The deadline for submitting this application and supporting documents is April 27, 2018. We will begin to fill slots on March 9, 2018, and will continue the review process until all slots are filled.


Application deadline

April 27, 2018

ConFlux cluster expands

By | General Interest, Happenings, HPC, News

ARC-TS has installed 15 new compute nodes into the ConFlux cluster. These nodes have the same 20 cores CPU as the original set, but with 256 GB of RAM instead of 128 GB. Neither the original nodes nor the newly added ones contain any GPUs

As a result, jobs should spend less time in queue, and users can be more liberal in their memory requirements.

[SC2 Jobs] SLATE: A Platform for Scientific Cyberinfrastructure

By | SC2 jobs

We are looking for motivated individuals interested in learning cutting-edge technologies to help us develop, prototype and test SLATE: Service Layes At The Edge, a collaborative project between the University of Michigan, University of Chicago and the University of Utah.  The SLATE team is working to deliver a new platform for scientific cyberinfrastructure (see http://slateci.io/). Building upon container-based technologies (e.g. Docker, Kubernetes, Helm, …) we aim to create a distributed environment where scientific collaborations can create, deploy and operate the tools they need to manage their data collection, distribution, and processing.

The successful candidate will help to take existing applications and package them in a way that can be readily used within the platform so that the details of installation, configuration, and operations of the application are taken care of for the scientific user. The candidate will learn how to use the latest container technologies and how to use them to solve concrete problems. The position will pay 12-15$ an hour based on experience for 20-30 hours a week depending on availability of the candidate.


Minimum Requirements:

* Basic experience with Linux administration


Preferred Requirements:

* Experience with source control (e.g. git)

* Experience with virtual machine technology (e.g. VirtualBox)

* Experience with container technology (e.g. Docker)


If interested, please send your CV to Brock Palen brockp@umich.edu