Tag

computational science

Designing optimal shunts for newborns with heart defects using computational modeling

By | General Interest, Happenings, News, Research

shuntFor babies born with hypoplastic left heart syndrome, several open-heart surgeries are required. During Stage I, a Norwood procedure is performed to construct an appropriate circulation to both the systemic and the pulmonary arteries. The pulmonary arteries receive flow from the systemic circulation, often by using a Blalock-Taussig (BT) shunt between the innominate artery and the right pulmonary artery. This procedure causes significantly disturbed flow in the pulmonary arteries.

A group of researchers led by U-M Drs. Ronald Grifka and Alberto Figueroa used computational hemodynamic simulations to demonstrate its capacity for examining the properties of the flow through and near the BT shunt. Initially, the researchers constructed a computational model which produces blood flow and pressure measurements matching the clinical magnetic resonance imaging (MRI) and catheterization data. Achieving this required us to determine the level of BT shunt occlusion; because the occlusion is below the MRI resolution, this information is difficult to recover without the aid of computational simulations. The researchers determined that the shunt had undergone an effective diameter reduction of 22% since the time of surgery. Using the resulting geometric model, they showed that we can computationally reproduce the clinical data. The researchers then replaced the BT shunt by with a hypothetical alternative shunt design with a flare at the distal end. Investigation of the impact of the shunt design revealed that the flare can increase pulmonary pressure by as much as 7%, and flow by as much as 9% in the main pulmonary branches, which may be beneficial to the pulmonary circulation.

Read more in Frontiers in Pediatrics.

HPC User Meetup

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Users of high performance computing resources are invited to meet ARC-TS HPC operators and support staff in person.

There is not a set agenda; come at anytime and stay as long as you please. You can come and talk about your use of any sort of computational resource, Flux, Armis, Hadoop, XSEDE, Amazon, or other.

Ask any questions you may have. The ARC-TS staff will work with you on your specific projects, or just show you new things that can help you optimize your research.

This is also a good time to meet other researchers doing similar work.

This is open to anyone interested; it is not limited to Flux users.

Examples of potential topics:

  • What ARC-TS services are there, and how to access them?
  • I want to do X, do you have software capable of it?
  • What is special about GPU/Xeon Phi/Accelerators?
  • Are there resources for people without budgets?
  • I want to apply for grant X, but it has certain limitations. What support can ARC-TS provide?
  • I want to learn more about the compiler and debugging?
  • I want to learn more about performance tuning, can you look at my code with me?
  • Etc.

MICDE Seminar: Ann Almgren, Lawrence Berkeley National Lab

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AnnAlmgrenBio: Ann S. Almgren is an applied mathematician who works as a staff scientist and acting group leader of the Center for Computational Sciences and Engineering at the Lawrence Berkeley National Laboratory. Her research interests involve the computational simulation of problems in astrophysics including the behavior of supernovae and white dwarfs. She earned a bachelor’s degree in physics from Harvard University in 1984 and master’s and doctoral degrees in mechanical engineering from the University of California, Berkeley in 1987 and 1991 respectively. After visiting the Institute for Advanced Study, she joined the applied mathematics group of the Lawrence Livermore National Laboratory in 1992, and moved to the Lawrence Berkeley Lab in 1996.

In 2015 she became a fellow of the Society for Industrial and Applied Mathematics “for contributions to the development of numerical methods for fluid dynamics and applying them to large-scale scientific and engineering problems.”[1]

 

[1] Biographical information taken from https://en.wikipedia.org/wiki/Ann_S._Almgren

HPC User Meetup

By |

Users of high performance computing resources are invited to meet ARC-TS HPC operators and support staff in person.

There is not a set agenda; come at anytime and stay as long as you please. You can come and talk about your use of any sort of computational resource, Flux, Armis, Hadoop, XSEDE, Amazon, or other.

Ask any questions you may have. The ARC-TS staff will work with you on your specific projects, or just show you new things that can help you optimize your research.

This is also a good time to meet other researchers doing similar work.

This is open to anyone interested; it is not limited to Flux users.

Examples of potential topics:

  • What ARC-TS services are there, and how to access them?
  • I want to do X, do you have software capable of it?
  • What is special about GPU/Xeon Phi/Accelerators?
  • Are there resources for people without budgets?
  • I want to apply for grant X, but it has certain limitations. What support can ARC-TS provide?
  • I want to learn more about the compiler and debugging?
  • I want to learn more about performance tuning, can you look at my code with me?
  • Etc.

MICDE Seminar: Andrea Lodi, Ecole Polytechnique, Montreal

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AndreaLodiBio: Dr. Andrea Lodi is a professor in the department of Mathematical and Industrial Engineering at the Polytechnique Montreal. He is the Canada Excellence Research Chair in Data Science for Real-Time Decision-Making at Polytechnique Montréal, Canada’s main chair in operations research.

Before joining the Polytechnique, Lodi was a professor in operations research in the faculty of electrical and information engineering at Italy’s University of Bologna. He earned his doctorate in systems engineering from this same university in 2000.

Lodi is interested in developing new models and algorithms that would make it possible to process a large quantity of data from multiple sources both rapidly and effectively. Through his research, he is looking for solutions designed to improve the electricity market, rail transport logistics, and health-care planning.

Lodi’s innovative work has earned him several awards, including the Google Faculty Research Award in 2010 and the IBM Faculty Award in 2011. In 2005 and 2006, he was a fellow in the prestigious Herman Goldstine program at the IBM Thomas J. Watson Research Center in New York.

In addition to co-ordinating several large-scale European projects in operations research, Lodi has also acted as a consultant for the IBM CPLEX research and development team since 2006. He has authored more than 70 publications in top mathematical programming journals; and has served as associate editor for several of these journals.[1]

 

This seminar is co-sponsored by the U-M Department of Industrial Operations & Engineering

 

[1] Biographical information taken from http://www.cerc.gc.ca/chairholders-titulaires/lodi-eng.aspx

HPC User Meetup

By |

Users of high performance computing resources are invited to meet ARC-TS HPC operators and support staff in person.

There is not a set agenda; come at anytime and stay as long as you please. You can come and talk about your use of any sort of computational resource, Flux, Armis, Hadoop, XSEDE, Amazon, or other.

Ask any questions you may have. The ARC-TS staff will work with you on your specific projects, or just show you new things that can help you optimize your research.

This is also a good time to meet other researchers doing similar work.

This is open to anyone interested; it is not limited to Flux users.

Examples of potential topics:

  • What ARC-TS services are there, and how to access them?
  • I want to do X, do you have software capable of it?
  • What is special about GPU/Xeon Phi/Accelerators?
  • Are there resources for people without budgets?
  • I want to apply for grant X, but it has certain limitations. What support can ARC-TS provide?
  • I want to learn more about the compiler and debugging?
  • I want to learn more about performance tuning, can you look at my code with me?
  • Etc.

MICDE Seminar: Anthony Wachs, University of British Columbia

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cropped-Anthony_Wachs_photo2Bio: Anthony Wachs is an assistant professor with a joint appointment in the departments of Mathematics and of Chemical and Biological Engineering at the University of British Columbia, Vancouver, Canada.

He received his B. Sc. and M. Sc. from the University Louis Pasteur of Strasbourg and his PhD from the Institut National Polytechnique of Grenoble in 2000. Right after, he was hired in 2001 as a Fluid Mechanics research engineer at IFP Energies nouvelles (IFPEN, at that time Institut Français du Pétrole) in Paris.

In 2009, he spent a one-year sabbatical at the nuclear research center of Cadarache in the south of France, where he worked for IRSN (the french national safety administration for nuclear energy). In 2010, he got his HDR (French Habilitation to Supervise Research) and was later promoted Scientific Advisor at IFPEN in Multiphase Flows and Scientific Computing. He then moved to IFPEN-Lyon where he supervised a group of researchers (including PhD and post-doc students) on the numerical simulation of reactive particulate flows (www.peligriff.com).

His main research interests are non-Newtonian Flows, Multiphase Flows and High Performance Computing. He collaborates extensively with academic groups in Canada, Brazil, France and Germany.

Research highlights: Running climate models in the cloud

By | General Interest, News, Research

Xianglei Huang

Can cloud computing systems help make climate models easier to run? Assistant research scientist Xiuhong Chen and MICDE affiliated faculty Xianglei Huang, from Climate and Space Sciences and Engineering (CLASP), provide some answers to this question in an upcoming issue of Computers & Geoscience (Vol. 98, Jan. 2017, online publication link: http://dx.doi.org/10.1016/j.cageo.2016.09.014).

Teaming up with co-authors Dr. Chaoyi Jiao and Prof. Mark Flanner, also in CLASP, as well as Brock Palen and Todd Raeker from U-M’s Advanced Research Computing – Technology Services (ARC-TS), they compared the reliability and efficiency of Amazon’s Web Service – Elastic Compute 2 (AWS EC2) with U-M’s Flux high performance computing (HPC) cluster in running the Community Earth System Model (CESM), a flagship climate model in the U.S. developed by the National Center for Atmospheric Research.

The team was able to run the CESM in parallel on an AWS EC2 virtual cluster with minimal packaging and code compiling effort, finding that the AWS EC2 can render a parallelization efficiency comparable to Flux, the U-M HPC cluster, when using up to 64 cores. When using more than 64 cores, the communication time between virtual EC2 exceeded the distributed computing time.

Until now, climate and earth systems simulations had relied on numerical model suites that run on thousands of dedicated HPC cores for hours, days or weeks, depending on the size and scale of each model. Although these HPC resources have the advantage of being supported and maintained by trained IT support staff, making them easier to use them, they are expensive and not readily available to every investigator that needs them.

Furthermore, the systems within reach are sometimes not large enough to run simulations at the desired scales. Commercial cloud systems, on the other hand, are cheaper and accessible to everyone, and have grown significantly in the last few years. One potential drawback of cloud systems is that the user needs to provide and install all the software and the IT expertise needed to run the simulations’ packages.

Chen and Huang’s work represents an important firstxiangleihuangpost2016 step in the use of cloud computing in large-scale climate simulations. Now, cloud computing systems can be considered a viable alternate option to traditional HPC clusters for computational research, potentially allowing researchers to leverage the computational power offered by a cloud environment.

This study was sponsored by the Amazon Climate Initiative through a grant awarded to Prof. Huang. The local simulation in U-M was made possible by a DoE grant awarded to Prof. Huang.

Top image: http://www.cesm.ucar.edu/

MICDE Seminar: Jonathan Freund, University of Illinois at Urbana-Champaign

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Bio: Jonathan Freund is the Donald Biggar Willett Professor of Mechanical Science & Engineering and Aerospace at the University of Illinois at Urbana-Champaign.   He is a Fellow of the American Physical Society, and a winner of the 2008 Frenkiel Prize from its Division of Fluid Dynamics where he currently serves as the division secretary/treasurer.  He is an associate editor of Physical Review Fluids and on the editorial board of Annual Review of Fluid Mechanics.  Computational science has been central to his research, which has included simulations of turbulent jet noise and its control, the dynamics of molecularly thin liquid films, nanostructure formation by ion-bombardment of semiconductor materials, and most recently the dynamics of red blood cells flowing in the narrow confines of the microcirculation.  He co-directs the DOE-funded Center for Exascale Simulation of Plasma-Coupled Combustion at the University of Illinois.

Adjoint-based optimization for understanding and reducing flow noise

Advanced simulation tools, particularly large-eddy simulation techniques, are becoming capable of making quality predictions of jet noise for realistic nozzle geometries and at engineering relevant flow conditions.  Increasing computer resources will be a key factor in improving these predictions still further.  Quality prediction, however, is only a necessary condition for the use of such simulations in design optimization.  Predictions do not of themselves lead to quieter designs.  They must be interpreted or harnessed in some way that leads to design improvements.  As yet, such simulations have not yielded any simplifying principals that offer general design guidance. The turbulence mechanisms leading to jet noise remain poorly described in their complexity.  In this light, we have implemented and demonstrated an aeroacoustic adjoint-based optimization technique that automatically calculates gradients that point the direction in which to adjust controls in order to improve designs.  This is done with only a single flow solutions and a solution of an adjoint system, which is solved at computational cost comparable to that for the flow. Optimization requires iterations, but having the gradient information provided via the adjoint accelerates convergence in a manner that is insensitive to the number of parameters to be optimized.  The talk will review the formulation of the adjoint of the compressible flow equations for optimizing noise-reducing controls and present examples of its use.  We will particularly focus on some mechanisms of flow noise that have been revealed via this approach.

This seminar is co-sponsored by U-M Aerospace Engineering

MICDE Seminar: Jeremy Lichstein, University of Florida

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JeremyLichsteinBio: Jeremy Lichstein is an assistant professor of Biology at the University of Florida. Professor Lichstein got his Ph. D. from Princeton University and was a postdoctoral research fellow at Princeton’s department of Ecology and Evolutionary Biology. He was the recipient of the University of Florida Excellence Award for Assistant Professor, and was named a Florida Climate Institute Fellow for 2016-2017. His research interests are forest dynamics, biodiversity, carbon cycle and climate change.

Biodiversity and the changing Earth System: computational challenges and new answers to old questions

Terrestrial ecosystems currently offset roughly 25% of global annual anthropogenic fossil fuel emissions. However, the fate of this carbon sink is highly uncertain, in large part because global models diverge in their predictions of ecosystem responses to climate change, drought, and other perturbations. Although there is little agreement on how terrestrial ecosystems will respond to global change on decadal and longer time-scales, there is wide consensus that current global models are overly simplistic in their representation of important ecological processes. I will discuss our current understanding of how tree functional diversity is maintained in forests, the consequences of including more realistic levels of functional diversity in global models, and the computational challenges that need to be overcome in order to introduce ecological realism into the Earth System Models that the scientific and policy communities rely on for climate projections. A key result that is emerging from empirical and theoretical studies is that shifts in species composition across time or space (beta diversity) have different (and sometimes opposite) effects on ecosystem stability as local (alpha) diversity.

This seminar is co-sponsored by the U-M department of Ecology and Evolutionary Biology