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DTSTART;TZID=America/Detroit:20180806T083000
DTEND;TZID=America/Detroit:20180806T163000
DTSTAMP:20260606T162026
CREATED:20230905T171419Z
LAST-MODIFIED:20260401T200727Z
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SUMMARY:Single-Cell Data Analytics Symposium 2018
DESCRIPTION:Please join us for the second annual Single-cell Genomic Data Analytics Symposium. The day long symposium will highlight researchers from U-M and around the world whose work is on the leading edge of innovation and discovery. This symposium is organized by the Michigan Center for Single-Cell Genomic Data Analytics and sponsored by the Michigan Institute for Data Science. \n\n\n\n\n  \nFEATURED SPEAKERS\n\nPeter Kharchenko\, Assistant Professor of Biomedical Informatics Harvard Medical School\nJohn Marioni\, Research Group Leader\, European Bioinformatics Institute\nDana Pe’er\, Scientific Director\, GMTEC; Chair\, Computational and Systems Biology Program\, Memorial Loan Kettering Cancer Center\nChristina Kendziorski\, Professor\, Biostatistics and Medical Informatics\, University of Wisconsin
URL:https://micde.umich.edu/event/single-cell-data-analytics-symposium-2018/
LOCATION:Palmer Commons\, Great Lakes Central Room\, 100 Washtenaw Ave.\, Ann Arbor\, MI\, United States
CATEGORIES:Conference,Seminar
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180622T130000
DTEND;TZID=America/Detroit:20180622T163000
DTSTAMP:20260606T162026
CREATED:20230905T171420Z
LAST-MODIFIED:20230905T171420Z
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SUMMARY:Spatial point process models
DESCRIPTION:This is the first workshop in a series of three workshops that will cover spatial modeling of three broad classes of data: (i) spatial point pattern\, (ii) discrete spatial variation on areal units\, and (iii) continuous spatial variation. \nSpatial point (and marked point) process models help us analyze the geometrical pattern of points in space and find application in a variety of fields including image processing\, public health\, forestry\, ecology\, and business. This workshop will provide an introduction to the point process model focusing on the conceptual aspects and implementation in R.
URL:https://micde.umich.edu/event/spatial-point-process-models/
LOCATION:Modern Languages Building (MLB)\, Room 2001B
CATEGORIES:Workshops
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180604T110000
DTEND;TZID=America/Detroit:20180607T170000
DTSTAMP:20260606T162026
CREATED:20230905T171420Z
LAST-MODIFIED:20230905T171420Z
UID:10000145-1528110000-1528390800@micde.umich.edu
SUMMARY:XSEDE HPC Summer Bootcamp
DESCRIPTION:ARC-TS and the Scientific Computing Student Club are hosting a satellite site for XSEDE hands-on workshops during this summer. These workshops provide a convenient way for researchers to learn about the latest techniques and technologies of current interest in HPC. \nThis 4 day event will include MPI\, OpenMP\, OpenACC and accelerators. \nOfficial registration is done through the XSEDE portal. Please follow this link to read about the workshop (including the full agenda) and to register https://portal.xsede.org/course-calendar/-/training-user/class/611/session/1609 \nNote: you will need to create and XSEDE account if you don’t have one already \n 
URL:https://micde.umich.edu/event/xsede-hpc-summer-bootcamp/
LOCATION:NCRC B16 B003E\, 2800 Plymouth Rd.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:Featured Events,SC2,Workshops
GEO:42.3016367;-83.7054664
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180531T090000
DTEND;TZID=America/Detroit:20180531T163000
DTSTAMP:20260606T162026
CREATED:20230905T171420Z
LAST-MODIFIED:20230905T171420Z
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SUMMARY:Introduction to SPSS
DESCRIPTION:Audience: Never before SPSS users who will be using SPSS for Windows.  Those using SPSS for Unix or Macintosh should email the instructor at cpow@umich.edu before enrolling. \nNote: Topic order is subject to change.  Participants must sign up for the entire series. \nFundamentals \nThis portion introduces SPSS for Windows\, the menu and the help systems\, the three main types of files used\, and printing from within SPSS.  It then addresses defining variables\, attaching labels\, defining missing values\, and various ways to enter data into SPSS.  Finally\, it covers a brief introduction to obtaining frequency distributions\, descriptive statistics\, and cross tabulations of variables. \nWithin-Case Transformations \nThis portion introduces data management capabilities\, including recoding variables (manual and automatic)\, computing new variables using formulas\, and counting occurrences of values within subjects.  Attention then turns to temporary transformations\, conditional processing of transformations\, and repetitive transformations.  SPSS syntax is also introduced. \nData Management with Multiple Files \nThis portion begins with a discussion of subsetting data files by drawing samples\, selecting groups and excluding groups from analysis.  Then\, the two main methods of merging SPSS data files are covered: adding additional variables and adding additional cases.  Next\, creating aggregated data sets and applying aggregated data to individuals is covered.  Lastly\, importing and exporting data between SPSS and other statistical programs (Excel\, dBase\, SAS) is demonstrated. \nBasic Statistics and Graphics\nThis portion covers basic exploratory procedures\, including obtaining percentiles\, frequencies\, descriptive statistics\, and cross tabulations. Basic comparative procedures including two-sample t-tests\, paired t-tests\, and one-way analysis of variance are also covered.  Then\, simple bivariate correlation analysis is introduced.  Participants are given a basic introduction to commonly used graphical procedures for displaying data\, including scatter plots\, bar graphs\, histograms\, and boxplots. \nRegistration\nTo register for CSCAR Workshops\, call the CSCAR front desk at (734) 764-7828 or come to the office in person with cash or check or a UM department shortcode: \nOFFICE HOURS\n9:00 a.m. – 5:00 p.m.\, Monday through Friday\nClosed 12pm – 1:00 p.m. every Tuesday for staff meeting.\nVoice: (734) 764-7828 (4-STAT from a campus phone)\nFax: (734) 647-2440 \nADDRESS\nCenter for Statistical Consultation and Research (CSCAR)\nThe University of Michigan\n3550 Rackham\n915 E. Washington St.\nAnn Arbor\, MI 48109-1070 \n 
URL:https://micde.umich.edu/event/introduction-to-spss-2-2/
LOCATION:Modern Languages Building (MLB)\, Room 2001B
CATEGORIES:Workshops
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180524T140000
DTEND;TZID=America/Detroit:20180524T170000
DTSTAMP:20260606T162026
CREATED:20230905T171420Z
LAST-MODIFIED:20230905T171420Z
UID:10000143-1527170400-1527181200@micde.umich.edu
SUMMARY:Geospatial analysis with Google Earth Engine
DESCRIPTION:Google Earth Engine (GEE) combines a multi-petabyte catalog of satellite imagery and geospatial datasets with planetary-scale analysis capabilities. This workshop will provide an introduction to GEE. We will cover data models in GEE\, basic vector and raster operations\, and classification in both feature and image space. \nYou should be familiar with vector and raster data\, GIS and remote sensing. We will use the web-based IDE for the Earth Engine JavaScript API. You will need to register (free) at signup.earthengine.google.com with Google to use the Earth Engine.
URL:https://micde.umich.edu/event/geospatial-analysis-with-google-earth-engine/
LOCATION:Modern Languages Building (MLB)\, Room 2001B
CATEGORIES:Workshops
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180516T140000
DTEND;TZID=America/Detroit:20180516T160000
DTSTAMP:20260606T162026
CREATED:20230905T171420Z
LAST-MODIFIED:20230905T171420Z
UID:10000147-1526479200-1526486400@micde.umich.edu
SUMMARY:Intro to Natural Language Processing with Python
DESCRIPTION:This workshop will provide a quick overview of natural language processing using Python. We’ll cover the basics. Segmenting text into tokens\, assigning part-of-speech\, assigning dependency labels\, detecting and labeling named-entities. We’ll also cover sentiment analysis\, topic modelling and maybe some visualizations. The workshop will be conducted in Python and is intended for users with basic Python programming knowledge. Anaconda Python 3.5 and a Jupyter Notebook will be used.
URL:https://micde.umich.edu/event/intro-to-natural-language-processing-with-python/
LOCATION:Modern Languages Building (MLB)\, Room 2001B
CATEGORIES:Workshops
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180416T160000
DTEND;TZID=America/Detroit:20180416T170000
DTSTAMP:20260606T162026
CREATED:20230905T171419Z
LAST-MODIFIED:20230905T171419Z
UID:10000127-1523894400-1523898000@micde.umich.edu
SUMMARY:MICDE Seminar: Vladimir Druskin\, Scientific Advisor\, Schlumberger Doll Research
DESCRIPTION:Bio: Vladimir Druskin is an applied mathematician with expertise in several areas including numerical algorithms\, large scale numerical simulations\, computational linear algebra\, inverse problems\, model reduction\, computational geophysics\, subsurface and medical imaging\, electrical engineering and financial mathematics. Dr. Druskin got his Ph.D. from Lomonosov Moscow State University (MSU) focused on applied mathematics. He is currently a scientific advisor at Schlumberger Doll Research working in energy research and development with demonstrated successful history of leading large collaborative industrial-academic projects in mathematical modeling and data-processing. \nReduced order models\, networks\, and applications to modeling and imaging with waves\nGeophysical seismic exploration\, as well as radar and sonar imaging require the solution of large-scale forward and inverse problems for hyperbolic systems of equations.  In this talk\, I will show how model order reduction can be used to address some intrinsic difficulties of these problems.  In model order reduction\, one approximates the response (transfer function) of a large-scale dynamical system using a smaller system\, called the reduced order model (ROM).  We consider ROMs that capture properties of the large problem that are essential for imaging and that can be realized via sparse graph-Laplacian networks.  The ROMs are data-driven\, i.e.\, they learn the underlying PDE problem from the transfer function.  One of the better-known applications of our ROMs is the efficient discretization of PDE problems in unbounded domains.  Here I will focus on two recent applications: (i) Multiscale modeling of elastic wave propagation via network approximations\, with low communication and computational cost; (ii) A direct\, nonlinear acoustic imaging algorithm in strongly heterogeneous media\, where the ROM is used to manipulate the data in such a way that multiply scattered waves are separated from the single scattered ones. \nDr. Druskin is being hosted by Prof. Borcea (Mathematics) and Prof. Schotland (Mathematics & Physics). If you would like to meet him\, please send an email to micde-contact@umich.edu
URL:https://micde.umich.edu/event/micde-seminar-vladimir-druskin-schlumberger-doll-research/
LOCATION:1360 East Hall\, 530 Church St.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:Featured Events,MICDE Seminar Series
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180410T143000
DTEND;TZID=America/Detroit:20180410T163000
DTSTAMP:20260606T162026
CREATED:20230905T171419Z
LAST-MODIFIED:20230905T171419Z
UID:10000140-1523370600-1523377800@micde.umich.edu
SUMMARY:Open Source GIS Tools
DESCRIPTION:This workshop will provide a fast paced introduction to open source GIS tools\, especially QGIS (but also R). We will explore QGIS’s power and functionalities for manipulating and analyzing vector GIS data. The workshop will be especially useful for students and researchers who use ArcGIS\, but would like to learn about open source GIS tools. Participant should have at least one semester or equivalent exposure to GIS.
URL:https://micde.umich.edu/event/open-source-gis-tools/
LOCATION:Angell Hall\, Classroom A
CATEGORIES:Workshops
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180410T143000
DTEND;TZID=America/Detroit:20180410T153000
DTSTAMP:20260606T162026
CREATED:20230905T171419Z
LAST-MODIFIED:20230905T171419Z
UID:10000128-1523370600-1523374200@micde.umich.edu
SUMMARY:MICDE Seminar: Raul Radovitzky\, Department of Aeronautics and Astronautics\, Massachusetts Institute of Technology
DESCRIPTION:Bio: Raul Radovitzky is the Raymond L. Bisplinghoff Professor of Aeronautics and Astronautics at the Massachusetts Institute of Technology. He also serves as the Associate Director of the MIT Institute for Soldier Nanotechnologies\, where he also leads research efforts on Blast and Ballistic Protection. He received a Civil Engineer degree from the University of Buenos Aires in 1991\, A S. M. in Applied Mathematics from Brown University in 1995 and a Ph.D. in Aeronautical Engineering from the California Institute of Technology in 1998. His research interests are in the development of numerical methods for multi-scale modeling of complex material response as well as in the formulation and implementation of algorithms for large-scale simulation of the dynamic response of materials to extreme loading conditions with emphasis on material and structural failure. The methods his group has developed have led to significant advances in our understanding of the physical effects of blast waves on the brain. This has helped to develop strategies to protect against Traumatic Brain Injury. Dr. Radovitzky is an Associate Fellow of the American Institute of Aeronautics and Astronautics and a member of the National Football League Head\, Neck and Spine Injury Research Committee. \nExtension of the peridynamic theory of solids for the simulation of materials under extreme loadings\nThe prediction of material and structural failure remains one of the most difficult challenges in structural and solid mechanics. Complexity emerges from the fundamental multiscale aspect of the mechanics of fracture\, where the small-scale response is usually responsible for large-scale system damage and failure. In addition\, significant algorithmic challenges remain\, including the difficulty in representing fracture\, some fundamental numerical convergence issues in the presence of material damage; and computational robustness and scalability enabling large-scale simulations.\nIn this presentation\, I will describe our efforts on the investigation of the theory of peridynamics and its numerical implementation\, as a promising alternative approach for simulating extreme material response. Peridynamics is a relatively new\, nonlocal formulation of continuum mechanics based on integral equations. It includes a physical length scale and naturally supports the presence of discontinuities in the solution field. As part of our work in this area\, we have proposed an extended formulation of the state theory of peridynamics addressing some fundamental issues present in the original theory. Specifically\, we have found that unphysical energy modes that do not contribute to the strain energy are allowed in the original formulation\, which\, in turn\, are responsible for the numerical instabilities commonly observed in peridynamic particle discretizations. In order to address this issue\, we introduce an extension of the constitutive correspondence framework based on bond-level nonlinear strain measures of the Seth-Hill type\, in direct analogy to local measures of deformation in continuum mechanics. We show that the numerical instabilities are eliminated when the numerical discretization is based on the extended theory.\nIn addition\, we have explored different approaches for incorporating material damage and fracture within the context of peridynamics formulations. I will describe one approach based on continuum damage models and another one particularly suited for brittle fracture.\nThe algorithms resulting from a particle discretizations of the proposed extended peridynamics framework have been implemented in our research code ΣMIT. I will provide examples illustrating the key numerical properties of the method. In addition\, I will show numerical results that demonstrate the ability of the method to capture experimentally observed ballistic limit curves for ductile materials\, as well as realistic fracture patterns in brittle materials subjected to projectile impact loadings. \nProf. Radovitzky is being hosted by Prof. Garikipati (Mechanical Engineering). If you would like to meet with him\, please send an email to micde-contact@umich.edu
URL:https://micde.umich.edu/event/micde-seminar-raul-radovitzky-mit/
LOCATION:Johnson Rooms\, Lurie Engineering Center\, 3rd Floor LEC 3213ABC\, 1221 Beal Ave.\, Ann Arbor\, MI\, United States
CATEGORIES:MICDE Seminar Series
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GEO:42.2914823;-83.7138452
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180406T150000
DTEND;TZID=America/Detroit:20180406T160000
DTSTAMP:20260606T162026
CREATED:20230905T171419Z
LAST-MODIFIED:20230905T171419Z
UID:10000138-1523026800-1523030400@micde.umich.edu
SUMMARY:CEE/MICDE Seminar: Khachik Sargsyan\, Sandia National Laboratories
DESCRIPTION:Bio: Khachik Sargsyan is a Principal Member of Technical Staff at Sandia National Laboratories (SNL) in Livermore\, CA. Before staff and postdoctoral positions at SNL\, he received his Ph.D. in Applied and Interdisciplinary Mathematics from University of Michigan\, Ann Arbor\, in 2007. His Bachelors degree\, awarded in 2002\, is in Applied Math and Physics from Moscow Institute of Physics and Technology. Dr. Sargsyan’s research evolves around uncertainty quantification (UQ) and predictability analysis of physical and computational models. He has developed and applied methods for model reduction\, UQ and data assimilation\, targeting fundamental challenges such as structural errors\, intrinsic stochasticity\, high-dimensionality\, limited data\, discontinuities and rare events\, with applications in climate modeling\, chemical kinetics\, hardware architecture simulators and turbulent combustion. He is one of the lead developers of UQTk (www.sandia.gov/uqtoolkit)\, a lightweight C++/Python software toolkit for quantification of uncertainties in model predictions.\n \nDr. Sargsyan is being hosted by Prof. Ivanov (Civil and Env. Engineering). If you would like to meet him\, please send an email to Chase Dwelle at dwellem@umich.edu \nProbabilistic Methods for Uncertainty Quantification in Computational Models\nOver the last decade\, improved measurement capabilities and computational resources have led to significant algorithmic developments toward efficient uncertainty quantification (UQ) for computational models. Such models of physical systems often involve input parameters that exhibit certain degree of uncertainty. Estimation and propagation of these uncertainties are crucial for model validation\, computational/experimental design and decision making. ​This talk will focus on probabilistic methods with emphasis on Polynomial Chaos (PC) expansions as a means for functional representation of random variables. The talk will highlight the use of PC methods both for forward propagation of uncertainties and for inverse problems\, such as parameter estimation via Bayesian inference. I will list associated major challenges\, including the curse of dimensionality and model structural error estimation\, in the context of computationally expensive models of physical systems. Both fundamental and more recent methods will be introduced and demonstrated\, impacting a wide range of applications\, such as climate modeling\, turbulent combustion and chemical kinetics.
URL:https://micde.umich.edu/event/cee-micde-seminar-khachik-sargsyan-sandia-national-laboratories/
LOCATION:1311 EECS\, 1301 Beal Ave.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:MICDE Seminar Series,Seminar
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GEO:42.292322;-83.713272
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180406T150000
DTEND;TZID=America/Detroit:20180406T160000
DTSTAMP:20260606T162026
CREATED:20230905T171419Z
LAST-MODIFIED:20230905T171419Z
UID:10000139-1523026800-1523030400@micde.umich.edu
SUMMARY:AIM Seminar: Christoph Börgers\, Mathematics\, Tufts University
DESCRIPTION:Bio: Christoph Börgers is a Professor of Mathematics at Tufts University. He got his Ph.D. under Prof. Charles Peskin at the Courant Institute of Mathematical Sciences\, in 1985. Prof. Börgers was a professor in the University of Michigan department of Mathematics until 1996 when he moved to Tufts. His expertise is in mathematical neuroscience\, applied dynamical systems\, numerical analysis\, scientific computing\, and during the past decade\, most of his work has been in the area of Computational Neuroscience. \nRhythms in neuronal networks with recurrent excitation\nInteracting excitatory and inhibitory neuronal populations often generate oscillations in electrical fields in the brain. I will briefly review this mechanism and the reasons to believe that it is important in brain function. Most of the talk will be focused on the effects of recurrent excitation\, i.e.\, of the neurons of a local network in the brain exciting each other. Recurrent excitation can sustain activity in a network that would otherwise be quiescent; this is believed to be the basis of working memory. It can also lead to a runaway process\, with excitation generating more excitation etc.\, much as the presence of a quadratic term on the right-hand side of a differential equation can lead to blow-up in finite time; this may be related to epileptic seizures. For model problems\, we prove that abrupt transitions to runaway activity require recurrent excitation with fast kinetics\, while working memory activity is more robust with recurrent excitation with slow kinetics. \nProf. Börgers is being hosted by Prof. Robert Krasny (Mathematics).
URL:https://micde.umich.edu/event/aim-seminar-christoph-borgers-mathematics-tufts-university/
LOCATION:1084 East Hall\, 530 Church St.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:Featured Events,MICDE Seminar Series,Seminar
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180402T140000
DTEND;TZID=America/Detroit:20180402T150000
DTSTAMP:20260606T162026
CREATED:20230905T171419Z
LAST-MODIFIED:20230905T171419Z
UID:10000126-1522677600-1522681200@micde.umich.edu
SUMMARY:MICDE Seminar: Amanda Randles\, Department of Biomedical Engineering\, Duke University
DESCRIPTION:Bio: Amanda Randles is an assistant professor of Biomedical Engineering at Duke University. She has courtesy appointments in the departments of Mechanical Engineering and Material Science\, Computer Science and Mathematics\, and is a member of the Duke Cancer Institute. She got her Ph.D. from Harvard University in 2013\, and has been the recipient of the Lawrence Fellowship (Lawrence Livermore National Lab.)\, the Anita Borg Memorial Scholarship (Google)\, and the George Michael Memorial High Performance Computing Fellowship (ACM/IEEE) among many accomplishments in her early career. Her research in biomedical simulation and high performance computing focuses on the development of new computational tools that she uses to provide insight into the localization and development of human diseases ranging from atherosclerosis to cancer. \nMassively Parallel Simulations of Hemodynamics in the Human Vasculature\nThe recognition of the role hemodynamic forces have in the localization and development of disease has motivated large-scale efforts to enable patient-specific simulations. When combined with computational approaches that can extend the models to include physiologically accurate hematocrit levels in large regions of the circulatory system\, these image-based models yield insight into the underlying mechanisms driving disease progression and inform surgical planning or the design of next generation drug delivery systems. Building a detailed\, realistic model of human blood flow\, however\, is a formidable mathematical and computational challenge. The models must incorporate the motion of fluid\, intricate geometry of the blood vessels\, continual pulse-driven changes in flow and pressure\, and the behavior of suspended bodies such as red blood cells. In this talk\, I will discuss the development of HARVEY\, a parallel fluid dynamics application designed to model hemodynamics in patient-specific geometries. I will cover the methods introduced to reduce the overall time-to-solution and enable near-linear strong scaling on up to 1\,572\,864 core of the IBM Blue Gene/Q supercomputer. Finally\, I will present the expansion of the scope of projects to address not only vascular diseases\, but also treatment planning and the movement of circulating tumor cells in the bloodstream. \nProf. Randles is being hosted by Dr. Carrasco-Teja (MICDE). If you would like to meet her during her visit please send an email to mcteja@umich.edu
URL:https://micde.umich.edu/event/micde-seminar-amanda-randles-duke-university/
LOCATION:Johnson Rooms\, Lurie Engineering Center\, 3rd Floor LEC 3213ABC\, 1221 Beal Ave.\, Ann Arbor\, MI\, United States
CATEGORIES:Featured Events,MICDE Seminar Series
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180330T140000
DTEND;TZID=America/Detroit:20180330T163000
DTSTAMP:20260606T162026
CREATED:20230905T171419Z
LAST-MODIFIED:20230905T171419Z
UID:10000136-1522418400-1522427400@micde.umich.edu
SUMMARY:Parallel Processing with Python
DESCRIPTION:Modern computers have a CPU with multiple cores (usually between 4-8). Come learn how to take advantage of them to parallelize and speed up your code. We’ll show you how to structure your code so you can parallelize it in 5 lines or less. We will also cover some theory\, a few practical considerations along with some basic exercises. We’ll be using the multiprocessing module in Python. The workshop is intended for users with basic Python knowledge. The workshop assumes you know how to do the following in Python: i) write a for loop\, ii) write a function that has inputs and outputs.  Anaconda Python 3.5 will be used.
URL:https://micde.umich.edu/event/parallel-processing-with-python/
LOCATION:Modern Languages Building (MLB)\, Room 2001B
CATEGORIES:Workshops
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180330T140000
DTEND;TZID=America/Detroit:20180330T150000
DTSTAMP:20260606T162026
CREATED:20230905T171419Z
LAST-MODIFIED:20230905T171419Z
UID:10000125-1522418400-1522422000@micde.umich.edu
SUMMARY:MICDE Seminar: Michael Falk\, Department of Materials Science and Engineering\, Johns Hopkins University
DESCRIPTION:Bio: Michael Falk is a professor of Materials Science and Engineering at Johns Hopkins University where he also serves as the Vice Dean for Undergraduate Education. He holds a bachelor’s degree in physics and a master’s degree in Computer Science from Johns Hopkins. He completed his Ph.D. in physics at the University of California\, Santa Barbara and then launched his academic career as a computational materials scientist at the University of Michigan in 2000. In 2008 he returned to Johns Hopkins as an associate professor of Materials Science and Engineering with joint appointments in Mechanical Engineering and Physics. Prof. Falk’s research focuses on utilizing computer simulation on the atomic scale to understand the processes by which materials are pushed out of equilibrium by processes such as bending\, breaking\, charging and undergoing frictional sliding. His research has had an abiding focus on the ways glass structures accommodate plastic flow\, deformation and fracture. These investigations have involved developing new methodologies for deploying molecular dynamics simulations and the development of thermodynamically motivated constitutive theories. Prof. Falk also engages in educational research and is a strong advocate for diversity and inclusion\, engaging in outreach to Baltimore City elementary schools and advocating for a welcoming climate for LGBTQ people within the engineering and physics professions. \nConnecting atomistic simulations\, defect-based theories and continuum plasticity in amorphous solids\nGlasses\, and the more general category of materials known as amorphous solids\, lack crystal structure and find wide application from consumer goods to photovoltaics. Yet\, issues quantifying disorder have stymied the construction of physically grounded mechanical constitutive laws for these materials suitable for failure prediction. Atomistic simulation methods can provide some insight regarding the mechanisms of plastic deformation and strain localization. Recent investigations have aimed at quantifying the defects that control plastic flow by quantifying a yield stress field at the nanometer scale. Analysis of these fields have confirmed some of the assumptions built into the shear transformation zone theory of amorphous plasticity\, most notably the orientational nature of the defect and their pre-existence in the structure. I will further discuss methods for quantitatively predicting strain localization\, a limiting failure process in high-strength metallic glasses and other amorphous materials by parameterizing the effective-temperature shear transformation zone theory from molecular dynamics simulations. We have directly cross-compared molecular dynamics simulations and continuum representations of these same materials in order to test and validate our constitutive theories. The role of coarse graining in the linkage of continuum and atomistic methods is crucial\, and convergence only arises above a critical length scale on the order of tens of angstroms. The investigation makes clear the need to separate out the relevant fluctuations in material structure from the shorter wavelength fluctuations that serve to obscure them. It is\, in the end\, the interactions between these larger-scale relevant fluctuations via the material’s mechanical response that controls the failure process during strain localization. \nProf. Falk is being hosted by Prof. Yue Fan (Mechanical Engineering). If you would like to meet him during his visit please email micde-contact@umich.edu
URL:https://micde.umich.edu/event/micde-seminar-michael-falk-hopkins/
LOCATION:1303 EECS\, 1301 Beal Ave\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:Featured Events,MICDE Seminar Series
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180323T143000
DTEND;TZID=America/Detroit:20180323T170000
DTSTAMP:20260606T162026
CREATED:20230905T171417Z
LAST-MODIFIED:20230905T171417Z
UID:10000137-1521815400-1521824400@micde.umich.edu
SUMMARY:Intro to GPU & CUDA Programming
DESCRIPTION:This workshop is an introduction to GPU programing for scientific and engineering applications. The basics of GPU architecture will be presented. Parallel programing strategies will be discussed followed by actual programing examples. \nPlease bring a laptop if would like to try the examples during the session\, but it is not necessary\, since the examples will be available for you to try later on the Flux computing cluster. Participants should be familiar with programming and how to use Flux.
URL:https://micde.umich.edu/event/intro-to-gpu-cuda-programming/
LOCATION:1180 Duderstadt Center\, 2281 Bonisteel Blvd\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:Workshops
GEO:42.291072;-83.715734
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180322T180000
DTEND;TZID=America/Detroit:20180322T200000
DTSTAMP:20260606T162026
CREATED:20230905T171417Z
LAST-MODIFIED:20230905T171417Z
UID:10000134-1521741600-1521748800@micde.umich.edu
SUMMARY:[SC2] Social After the Symposium
DESCRIPTION:After the MICDE symposium join us at the Ann Arbor Brewing Co. – Tap Room. We will provide the appetizers and non-alcoholic drinks.\nHope to see you there! \nPlease RSVP here
URL:https://micde.umich.edu/event/sc2-social-after-the-symposium/
LOCATION:Arbor Brewing Co – Tap Room\, 114 E Washington St\, Ann Arbor\, MI\, 48104\, United States
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180322T080000
DTEND;TZID=America/Detroit:20180322T170000
DTSTAMP:20260606T162026
CREATED:20230905T171418Z
LAST-MODIFIED:20230905T171418Z
UID:10000131-1521705600-1521738000@micde.umich.edu
SUMMARY:Computation: A Pillar of Science and a Lens to the Future — the 2018 MICDE Symposium
DESCRIPTION:The Michigan Institute for Computational Discovery and Engineering 2018 Symposium will feature eminent scientists from around the world and the U-M campus. The symposium this year will show how computational science is leading the research at all scales in our lives\, from the molecular level to the sky. \nVisit the Symposium page for more details. \nPlease register if you plan to attend. \n\n\n\n\n\n\n\n\n\n\n\n\n\n\nSPEAKERS\n\n\n\n\n\n\n\n\n\n\nGuruduth Banavar\nChief Technology Officer\nViome \n\n\n\n\n\n\n\n\n\n\n\nCynthia Chestek\nAssistant Professor\, Biomedical Engineering and EECS\nUniversity of Michigan \n\n\n\n\n\n\n\n\n\n\n\nAlison Marsden\nPrincipal Investigator\, Cardiovascular Biomechanics Computation Lab\nStanford University \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nCleve Moler\nCofounder and Chief Mathematician\nMathWorks \n\n\n\n\n\n\n\n\n\n\n\nRaju Namburu\nChief\, Computational and Information Sciences Directorate\nArmy Research Lab \n\n\n\n\n\n\n\n\n\n\n\nStephen Smith\nAssistant Professor\, Ecology and Evolutionary Biology\nUniversity of Michigan \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nBeth Wingate\nProfessor\, Mathematics\nUniversity of Exeter \n\n\n\n\n\n\n\n\n\nPOSTER COMPETITION\nThe symposium will include a poster competition highlighting outstanding computational work from U-M students and postdocs. First place is awarded $500\, and second and third places win $250.
URL:https://micde.umich.edu/event/computation-a-pillar-of-science-and-a-lens-to-the-future-the-2018-micde-symposium/
LOCATION:Rackham Amphitheatre\, 915 E. Washington St.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:Conference,Featured Events,MICDE Seminar Series
GEO:42.2807892;-83.7381556
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180320T140000
DTEND;TZID=America/Detroit:20180320T160000
DTSTAMP:20260606T162026
CREATED:20230905T171418Z
LAST-MODIFIED:20230905T171418Z
UID:10000132-1521554400-1521561600@micde.umich.edu
SUMMARY: Deep Neural Networks with TensorFlow: A Quick Start Introduction
DESCRIPTION:Deep Neural Networks (DNNs) are used as a machine learning method for both regression and classification problems. TensorFlow is a popular software library that is often used to construct and train DNNs. In this workshop\, participants will learn how to quickly use the high-level TensorFlow Estimator module to perform nonlinear regression and classification with standard fully connected DNNs. We will also show how the Estimator module can be used to perform image classification using Convolutional Neural Networks (CNNs). All examples will use Python; some familiarity with Python is recommended. You are encouraged but not required to bring a laptop with TensorFlow already installed.
URL:https://micde.umich.edu/event/deep-neural-networks-with-tensorflow-a-quick-start-introduction/
LOCATION:Modern Languages Building (MLB)\, Room 2001B
CATEGORIES:Workshops
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180316T140000
DTEND;TZID=America/Detroit:20180316T163000
DTSTAMP:20260606T162026
CREATED:20230905T171418Z
LAST-MODIFIED:20230905T171418Z
UID:10000135-1521208800-1521217800@micde.umich.edu
SUMMARY:Intro to SQL
DESCRIPTION:Ever want to know how to communicate with a database? You need to know SQL\, a standard programming language for working with relational database management systems in data warehouses or just Microsoft Access. This workshop will cover the basic syntax of SQL. Material will focus mainly on how to query databases. A web-based tool will be used for the tutorial.
URL:https://micde.umich.edu/event/intro-to-sql-2/
LOCATION:Modern Languages Building (MLB)\, Room 2001B
CATEGORIES:Workshops
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180316T120000
DTEND;TZID=America/Detroit:20180316T133000
DTSTAMP:20260606T162026
CREATED:20230905T171418Z
LAST-MODIFIED:20230905T171418Z
UID:10000133-1521201600-1521207000@micde.umich.edu
SUMMARY:[SC2 & MICDE] Lunch with alumni: Lois K. Smith
DESCRIPTION:Lois graduated from Michigan in the Fall 2016 with a PhD from the AOSS (now Climate and Space Sciences and Engineering) department and was an MICDE fellow and is Certificate in Computational Discovery & Engineering alumni. Since graduating\, she has been in industry working as a data scientist (iSpot\, Microsoft). She is back on campus and will join the SC2 to talk about her transition to industry and how MICDE and her training in computational sciences helped on the way. \nRSVP please.
URL:https://micde.umich.edu/event/sc2-micde-lunch-with-alumni-lois-k-smith/
LOCATION:1180 Duderstadt Center\, 2281 Bonisteel Blvd\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:Education,SC2
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GEO:42.291072;-83.715734
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180309T150000
DTEND;TZID=America/Detroit:20180309T160000
DTSTAMP:20260606T162026
CREATED:20230905T171418Z
LAST-MODIFIED:20230905T171418Z
UID:10000120-1520607600-1520611200@micde.umich.edu
SUMMARY:MICDE Seminar: Michael Shelley\, Courant Institute\, New York University
DESCRIPTION:Bio: Michael J. Shelley is an American applied mathematician who works on the modeling and simulation of complex systems arising in physics and biology. He holds a BA in Mathematics from the University of Colorado (1981) and a PhD in Applied Mathematics from the University of Arizona (1985). He was a postdoctoral researcher at Princeton University\, and then joined the faculty of mathematics at the University of Chicago. In 1992 he joined the Courant Institute of Mathematical Sciences at New York University where he is the George and Lilian Lyttle Professor of Applied Mathematics. He is also a Professor of Neuroscience (NYU) and Professor of Mechanical Engineering (NYU-Poly). \nProfessor Shelley’s work includes free-boundary problems in fluids and materials science\, singularity formation in partial differential equations\, modeling visual perception in the primary visual cortex\, dynamics of complex and active fluids\, cellular biophysics\, and fluid-structure interaction problems such as the flapping of flags\, stream-lining in nature\, and flapping flight. He is also the co-founder and co-director of the Courant Institute’s Applied Mathematics Lab. \nSource https://en.wikipedia.org/wiki/Michael_Shelley_(mathematician) \nModeling and Simulating Active Mechanics in the Cell\nMany fundamental phenomena in eukaryotic cells — nuclear migration\, spindle positioning\, chromosome segregation — involve the interaction of (often transitory) cellular structures with boundaries and fluids. Understanding the consequences of these interactions require specialized numerical methods for their large-scale simulation\, as well as mathematical modeling and analysis. In this context\, I will discuss the recent interactions of mathematical modeling and large-scale\, detailed simulations with experimental measurements of activity-driven Biomechanical processes within the cell.
URL:https://micde.umich.edu/event/micde-seminar-michael-shelley-courant-institute-new-york-university/
LOCATION:1084 East Hall\, 530 Church St.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:MICDE Seminar Series
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180306T130000
DTEND;TZID=America/Detroit:20180306T160000
DTSTAMP:20260606T162026
CREATED:20230905T171418Z
LAST-MODIFIED:20260522T153159Z
UID:10000005-1520341200-1520352000@micde.umich.edu
SUMMARY:Introduction to the Flux cluster and batch computing
DESCRIPTION:Overview\nThis workshop will provide a brief overview of the components of the Flux Cluster. The main body of the workshop will cover the resource manager and scheduler\, creating submissions scripts to run jobs and the options available in them\, and hands-on experience. By the end of the workshop\, every participant should have created a submission script\, submitted a job\, tracked its progress\, and collected its output. Participants will have several working examples from which to build their own submissions scripts in their own home directories. \nPrerequisites\nObtain a user account on Flux. If you do not have a Flux user account\, click here to go to the account application page at: https://arc-ts.umich.edu/fluxform/ \nRegister for Duo authentication. See below for details. \nThis course assumes familiarity with the Linux command line as might be got from the CSCAR/ARC-TS workshop Introduction to the Linux Command Line. In particular\, participants should understand how files and folders work\, be able to create text files using the nano editor\, be able to create and remove files and folders\, and understand what input and output redirection are and how to use them. \n \nInstructor\nBennet Fauber\nScientific Applications Analyst\nAdvanced Research Computing — Technology Services \nBennet Fauber is a member of the technical team that administers the Flux cluster. \nMaterials\nIn-class handouts\n\nOutput from qstat\nOutput from checkjob\nOutput from mdiag\nOutput from showq\n\nSupplementary materials\n\nFlux in Ten Easy Steps\nUsing PBS\nUsing software modules\nLinking libraries with applications\nEstablishing and managing a Flux project allocation\n\n\nCourse Preparation\nIn order to participate successfully in the workshop exercises\, you must have a Flux user account and be registered for the Duo authentication service. The user account allows you to log in to the cluster\, create\, compile\, and test applications\, and prepare Flux jobs for submission. Information about registering for Duo is at the ITS Two Factor Authentication web page. \nFlux user account\nA single Flux user account can be used to prepare and submit jobs using various allocations. If you already already possess a user account\, you can use it for this course\, you can skip to “Flux allocation” below. If not\, please visit https://arc-ts.umich.edu/fluxform to obtain one. A user account is free to members of the University community. Please note that obtaining an account requires human processing\, so be sure to do this at least two business days before class begins. \nFlux allocation\nWe create an allocation for the workshop so you can run jobs on the cluster during the workshop and for one day after for those who would like additional practice. The workshop allocation is quite limited and is intended only to run examples to help you cement the details of job submission and management. If you already have an existing Flux allocation\, you can use that\, though if there are any issues with that allocation\, we will ask you to use the workshop allocation. \nLaptop Preparation\nThe classroom contains Windows computers\, which require your uniqname and UMICH password to login\, and which have all necessary software preloaded. \nIf you want to use a laptop for the course\, you are welcome to do so. However\, if there are problems connecting your laptop\, you will be asked to switch to the provided computer for the class. We will try to help resolve issues after the workshop. \nIf you want to try to prepare your laptop for use in the class\, please see our web page on Preparing your laptop to use Flux. If you have a Windows computer\, we recommend that you install PuTTY/WinSCP from the Blue Disc web site. Macintosh computers typically have the minimum requirements installed as part of the system. \nMore help\nPlease use our class mailing list hpc101course@umich.edu for questions\, comments\, or to seek further assistance.
URL:https://micde.umich.edu/event/introduction-to-the-flux-cluster-and-batch-computing-5-3/
LOCATION:East Hall B254\, 530 Church St.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:High Performance Computing,Workshops
GEO:42.2757302;-83.7351764
X-APPLE-STRUCTURED-LOCATION;VALUE=URI;X-ADDRESS=East Hall B254 530 Church St. Ann Arbor MI 48109 United States;X-APPLE-RADIUS=500;X-TITLE=530 Church St.:geo:-83.7351764,42.2757302
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180223T130000
DTEND;TZID=America/Detroit:20180223T170000
DTSTAMP:20260606T162026
CREATED:20230905T171418Z
LAST-MODIFIED:20230905T171418Z
UID:10000035-1519390800-1519405200@micde.umich.edu
SUMMARY:Advanced batch computing on the Flux cluster
DESCRIPTION:Overview\nThis course will cover some more advanced topics in cluster computing on the U-M Flux Cluster. Topics to be covered include a review of common parallel programming models and basic use of Flux; dependent and array scheduling; advanced troubleshooting and analysis using checkjob\, qstat\, and other tools; and parallel debugging and profiling of C and Fortran code\, including logging\, gdb (line-oriented debugging)\, ddt (GUI-based debugging) and map (GUI-based profiling) of MPI and OpenMP programs. We will issue you a temporary allocation to use for the course\, or you can use your existing Flux allocations\, if any. \nPrerequisites\nIntroduction to Batch Computing on Flux or equivalent. This course assumes familiarity with the Linux command line\, text editing on Linux\, and a basic understanding of Flux including how to submit and track jobs. \n \nInstructors\nDr. Charles J Antonelli\nAdvocacy and Research Support\nLSA Information Technology \nCharles is a High Performance Computing Consultant in the Advocacy and Research Support Group of LSAIT at the University of Michigan\, where he is responsible for high performance computing support and education\, and is an advocate to the Departments of History and Communications. Prior to this\, he built a parallel data ingestion component of a novel earth science data assimilation system\, a secure packet vault\, and worked on the No. 5 ESS Switch at Bell Labs in the 80s. He has taught courses in operating systems\, distributed file systems\, C++ programming\, security\, and database application design. \nMark Champe\nAdvocacy and Research Support\nLSA Information Technology \nMaterials\n\nLecture Notes (updated Feb. 2018)\nMPI Profiling with Allinea MAP\nFlux in Ten Easy Steps\nUsing PBS\nFlux configuration\n\n\nCourse Preparation\nIn order to participate successfully in the workshop exercises\, you must have a Flux user account\, a Flux allocation (one is created for each workshop)\, and be enrolled in Duo. The user account allows you to log in to the cluster\, create\, compile\, and test applications\, and prepare Flux jobs for submission. The allocation allows you to submit those jobs\, executing those applications in parallel on the cluster and charging their resource use against the allocation. Duo is required to help authenticate you to the cluster. \n\nFlux user account\nA single Flux user account can be used to prepare and submit jobs using various allocations. If you already already possess a user account\, you can use it for this course\, you can skip to “Flux allocation” below. If not\, please visit https://arc-ts.umich.edu/fluxform to obtain one. A user account is free to members of the University community. Please note that obtaining an account requires human processing\, so be sure to do this at least two business days before class begins. \n\nFlux allocation\nWe create an allocation for the workshop so you can run jobs on the cluster during the workshop and for one day after for those who would like additional practice. The workshop allocation is quite limited and is intended only to run examples to help you cement the details of job submission and management. If you already have an existing Flux allocation\, you can use that\, though if there are any issues with that allocation\, we will ask you to use the workshop allocation. \n\nDuo Authentication\nDuo two-factor authentication is required to log in to the cluster. When logging in\, you will need to type your UMICH password as well as authenticate through Duo in order to access Flux. \nIf you need to enroll in Duo\, follow the instructions at Getting Started: How to Enroll in Duo. \nPlease enroll in Duo before you come to class. \n\nLaptop Preparation\nYou do not need to bring your own laptop to class. The classroom contains Windows computers\, which require your uniqname and UMICH password to login\, and that have all necessary software pre-loaded. \nIf you want to use a laptop for the course\, you are welcome to do so:  please see our web page on Preparing your laptop to use Flux. However\, if there are problems connecting your laptop\, you will be asked to switch to the provided computer for the class. We cannot stop to debug connection issues with personal or departmental laptops during the class. \nMore help\nPlease use our class mailing list hpc201course@umich.edu for questions\, comments\, or to seek further assistance.
URL:https://micde.umich.edu/event/advanced-batch-computing-on-the-flux-cluster-5-3/
LOCATION:East Hall B250\, 530 Church St.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:High Performance Computing,Workshops
GEO:42.2757302;-83.7351764
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180222T130000
DTEND;TZID=America/Detroit:20180222T170000
DTSTAMP:20260606T162026
CREATED:20230905T171418Z
LAST-MODIFIED:20230905T171418Z
UID:10000034-1519304400-1519318800@micde.umich.edu
SUMMARY:Hadoop and Spark Workshop
DESCRIPTION:Overview\nLearn how to process large amounts (up to terabytes) of data using SQL and/or simple programming models available in Python\, R\, Scala\, and Java. Computers will be provided to follow along with hands-on examples; users can also bring laptops. \nPrerequisites\nIntro to the Linux Command Line or equivalent. This course assumes familiarity with the Linux command line. \nA user account on Flux. If you do not have a Flux user account\, click here to go to the account application page at: https://arc-ts.umich.edu/fluxform/ \nDuo authentication. \nDuo two-factor authentication is required to log in to the cluster. When logging in\, you will need to type your UMICH password as well as authenticate through Duo in order to access Flux. \nIf you need to enroll in Duo\, follow the instructions at Getting Started: How to Enroll in Duo. \n \nInstructor\nBrock Palen\nDirector\nARC-TS \nBrock has over 10 years of high performance computing and data intensive computing experience in an academic environment. He currently works with the team at ARC-TS to provide HPC\, Data Science\, storage\, and other research computing services to the University. Brock also is the NSF XSEDE projects Campus Champion representing the schools to this and other national computing infrastructures and organizations. \nMaterials\n\nThe presentation is at https://umarcts.bitbucket.io/presentations/hadoop/#/title (Visit our Version Control page for information on using Bit Bucket)\n\nCourse Preparation\nIn order to participate successfully in the class exercises\, you must have a Flux user account. The user account allows you to log in to the cluster\, create\, compile\, and test applications\, and transfer data into Hadoop’s filesystem for processing. \nFlux user account\nA single Flux user account can be used to prepare and submit jobs using various allocations. If you already already possess a user account\, you can use it for this course\, you can skip to “Flux allocation” below. If not\, please visit https://arc-ts.umich.edu/fluxform to obtain one. A user account is free to members of the University community. Please note that obtaining an account requires human processing\, so be sure to do this at least two business days before class begins. \nDuo Authentication\nDuo two-factor authentication is required to log in to the cluster. When logging in\, you will need to type your UMICH password as well as authenticate through Duo in order to access Flux. \nIf you need to enroll in Duo\, follow the instructions at Getting Started: How to Enroll in Duo. \nMore help\nPlease email hpc-support@umich.edu for questions\, comments\, or to seek further assistance.
URL:https://micde.umich.edu/event/hadoop-workshop-2/
LOCATION:East Hall B250\, 530 Church St.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:High Performance Computing,Workshops
GEO:42.2757302;-83.7351764
X-APPLE-STRUCTURED-LOCATION;VALUE=URI;X-ADDRESS=East Hall B250 530 Church St. Ann Arbor MI 48109 United States;X-APPLE-RADIUS=500;X-TITLE=530 Church St.:geo:-83.7351764,42.2757302
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180221T130000
DTEND;TZID=America/Detroit:20180221T170000
DTSTAMP:20260606T162026
CREATED:20230905T171418Z
LAST-MODIFIED:20230905T171418Z
UID:10000033-1519218000-1519232400@micde.umich.edu
SUMMARY:Advanced batch computing on the Flux cluster
DESCRIPTION:Overview\nThis course will cover some more advanced topics in cluster computing on the U-M Flux Cluster. Topics to be covered include a review of common parallel programming models and basic use of Flux; dependent and array scheduling; advanced troubleshooting and analysis using checkjob\, qstat\, and other tools; and parallel debugging and profiling of C and Fortran code\, including logging\, gdb (line-oriented debugging)\, ddt (GUI-based debugging) and map (GUI-based profiling) of MPI and OpenMP programs. We will issue you a temporary allocation to use for the course\, or you can use your existing Flux allocations\, if any. \nPrerequisites\nIntroduction to Batch Computing on Flux or equivalent. This course assumes familiarity with the Linux command line\, text editing on Linux\, and a basic understanding of Flux including how to submit and track jobs. \n \nInstructors\nDr. Charles J Antonelli\nAdvocacy and Research Support\nLSA Information Technology \nCharles is a High Performance Computing Consultant in the Advocacy and Research Support Group of LSAIT at the University of Michigan\, where he is responsible for high performance computing support and education\, and is an advocate to the Departments of History and Communications. Prior to this\, he built a parallel data ingestion component of a novel earth science data assimilation system\, a secure packet vault\, and worked on the No. 5 ESS Switch at Bell Labs in the 80s. He has taught courses in operating systems\, distributed file systems\, C++ programming\, security\, and database application design. \nMark Champe\nAdvocacy and Research Support\nLSA Information Technology \nMaterials\n\nLecture Notes (updated Feb. 2018)\nMPI Profiling with Allinea MAP\nFlux in Ten Easy Steps\nUsing PBS\nFlux configuration\n\n\nCourse Preparation\nIn order to participate successfully in the workshop exercises\, you must have a Flux user account\, a Flux allocation (one is created for each workshop)\, and be enrolled in Duo. The user account allows you to log in to the cluster\, create\, compile\, and test applications\, and prepare Flux jobs for submission. The allocation allows you to submit those jobs\, executing those applications in parallel on the cluster and charging their resource use against the allocation. Duo is required to help authenticate you to the cluster. \n\nFlux user account\nA single Flux user account can be used to prepare and submit jobs using various allocations. If you already already possess a user account\, you can use it for this course\, you can skip to “Flux allocation” below. If not\, please visit https://arc-ts.umich.edu/fluxform to obtain one. A user account is free to members of the University community. Please note that obtaining an account requires human processing\, so be sure to do this at least two business days before class begins. \n\nFlux allocation\nWe create an allocation for the workshop so you can run jobs on the cluster during the workshop and for one day after for those who would like additional practice. The workshop allocation is quite limited and is intended only to run examples to help you cement the details of job submission and management. If you already have an existing Flux allocation\, you can use that\, though if there are any issues with that allocation\, we will ask you to use the workshop allocation. \n\nDuo Authentication\nDuo two-factor authentication is required to log in to the cluster. When logging in\, you will need to type your UMICH password as well as authenticate through Duo in order to access Flux. \nIf you need to enroll in Duo\, follow the instructions at Getting Started: How to Enroll in Duo. \nPlease enroll in Duo before you come to class. \n\nLaptop Preparation\nYou do not need to bring your own laptop to class. The classroom contains Windows computers\, which require your uniqname and UMICH password to login\, and that have all necessary software pre-loaded. \nIf you want to use a laptop for the course\, you are welcome to do so:  please see our web page on Preparing your laptop to use Flux. However\, if there are problems connecting your laptop\, you will be asked to switch to the provided computer for the class. We cannot stop to debug connection issues with personal or departmental laptops during the class. \nMore help\nPlease use our class mailing list hpc201course@umich.edu for questions\, comments\, or to seek further assistance.
URL:https://micde.umich.edu/event/advanced-batch-computing-on-the-flux-cluster-5-2/
LOCATION:East Hall B250\, 530 Church St.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:High Performance Computing,Workshops
GEO:42.2757302;-83.7351764
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180220T140000
DTEND;TZID=America/Detroit:20180220T150000
DTSTAMP:20260606T162026
CREATED:20230905T171418Z
LAST-MODIFIED:20230905T171418Z
UID:10000099-1519135200-1519138800@micde.umich.edu
SUMMARY:MICDE Seminar: Heather Mayes\, Chemical Engineering\, University of Michigan
DESCRIPTION:Bio: Heather Mayes is an Assistant Professor in the Department of Chemical Engineering. Her research group uses multi-scale modeling to discover protein-sugar interactions and to harness them for renewable energy and improved health. The study of carbohydrate-protein interactions is an important step to create renewable fuels and chemicals from non-food biomass\, and the results can be applied to several human diseases\, including cancer and autoimmune disorders. Prof. Mayes uses computational tools in her research\, including quantum mechanics\, molecular dynamics\, and rare-event sampling methods. She collaborates with experimental groups to understand past and guide future wet-lab studies to advance renewable chemicals and fuels\, as well as disease understanding. \nSimulating Protein-Carbohydrate Interactions to Bridge the Gap Between Human Chemical Intuition and Molecular Biophysics\nIn complex reacting systems\, it can be exceedingly difficult\, or even impossible\, to tease out elementary reaction mechanisms from wet-lab data alone\, due to data convolution resulting from the multiple reacting steps and competing reactions that simultaneously occur. The systems that the Mayes group studies (multiple types of protein-carbohydrate interactions) certainly fall into this category\, with understanding further hindered by the conformational\, stereochemical\, and regiochemical degrees of freedom key to chemical reactions in these systems. Yet\, understanding these elementary mechanisms would not only help answer fundamental questions in biology\, but also improve our ability to harness these systems for applications from renewable energy to pharmaceutical interventions. I will discuss several systems that we are studying\, and focus on our investigations of how enzymes break down plant biomass. I will share how our computational research rationalizes non-intuitive wet-lab observations by revealing mechanisms that do not conform to human intuition. In doing so\, we gather lessons from how nature has evolved efficient enzymes that we can then apply to rational enzyme design.
URL:https://micde.umich.edu/event/micde-seminar-heather-mayes-chemical-engineering-university-of-michigan/
LOCATION:NCRC10 ACR2\, 2800 Plymouth Rd\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:Featured Events,MICDE Seminar Series
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BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180219T130000
DTEND;TZID=America/Detroit:20180219T160000
DTSTAMP:20260606T162026
CREATED:20230905T171416Z
LAST-MODIFIED:20260522T142511Z
UID:10000004-1519045200-1519056000@micde.umich.edu
SUMMARY:Introduction to the Flux cluster and batch computing
DESCRIPTION:Overview\nThis workshop will provide a brief overview of the components of the Flux Cluster. The main body of the workshop will cover the resource manager and scheduler\, creating submissions scripts to run jobs and the options available in them\, and hands-on experience. By the end of the workshop\, every participant should have created a submission script\, submitted a job\, tracked its progress\, and collected its output. Participants will have several working examples from which to build their own submissions scripts in their own home directories. \nPrerequisites\nObtain a user account on Flux. If you do not have a Flux user account\, click here to go to the account application page at: https://arc-ts.umich.edu/fluxform/ \nRegister for Duo authentication. See below for details. \nThis course assumes familiarity with the Linux command line as might be got from the CSCAR/ARC-TS workshop Introduction to the Linux Command Line. In particular\, participants should understand how files and folders work\, be able to create text files using the nano editor\, be able to create and remove files and folders\, and understand what input and output redirection are and how to use them. \n \nInstructor\nBennet Fauber\nScientific Applications Analyst\nAdvanced Research Computing — Technology Services \nBennet Fauber is a member of the technical team that administers the Flux cluster. \nMaterials\nIn-class handouts\n\nOutput from qstat\nOutput from checkjob\nOutput from mdiag\nOutput from showq\n\nSupplementary materials\n\nFlux in Ten Easy Steps\nUsing PBS\nUsing software modules\nLinking libraries with applications\nEstablishing and managing a Flux project allocation\n\n\nCourse Preparation\nIn order to participate successfully in the workshop exercises\, you must have a Flux user account and be registered for the Duo authentication service. The user account allows you to log in to the cluster\, create\, compile\, and test applications\, and prepare Flux jobs for submission. Information about registering for Duo is at the ITS Two Factor Authentication web page. \nFlux user account\nA single Flux user account can be used to prepare and submit jobs using various allocations. If you already already possess a user account\, you can use it for this course\, you can skip to “Flux allocation” below. If not\, please visit https://arc-ts.umich.edu/fluxform to obtain one. A user account is free to members of the University community. Please note that obtaining an account requires human processing\, so be sure to do this at least two business days before class begins. \nFlux allocation\nWe create an allocation for the workshop so you can run jobs on the cluster during the workshop and for one day after for those who would like additional practice. The workshop allocation is quite limited and is intended only to run examples to help you cement the details of job submission and management. If you already have an existing Flux allocation\, you can use that\, though if there are any issues with that allocation\, we will ask you to use the workshop allocation. \nLaptop Preparation\nThe classroom contains Windows computers\, which require your uniqname and UMICH password to login\, and which have all necessary software preloaded. \nIf you want to use a laptop for the course\, you are welcome to do so. However\, if there are problems connecting your laptop\, you will be asked to switch to the provided computer for the class. We will try to help resolve issues after the workshop. \nIf you want to try to prepare your laptop for use in the class\, please see our web page on Preparing your laptop to use Flux. If you have a Windows computer\, we recommend that you install PuTTY/WinSCP from the Blue Disc web site. Macintosh computers typically have the minimum requirements installed as part of the system. \nMore help\nPlease use our class mailing list hpc101course@umich.edu for questions\, comments\, or to seek further assistance.
URL:https://micde.umich.edu/event/introduction-to-the-flux-cluster-and-batch-computing-5-2/
LOCATION:East Hall B254\, 530 Church St.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:High Performance Computing,Workshops
GEO:42.2757302;-83.7351764
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BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180216T090000
DTEND;TZID=America/Detroit:20180216T120000
DTSTAMP:20260606T162026
CREATED:20230905T171416Z
LAST-MODIFIED:20230905T171416Z
UID:10000058-1518771600-1518782400@micde.umich.edu
SUMMARY:Introduction to the Linux Command Line
DESCRIPTION: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 generically referred to as “the command line”. Topics include: a brief overview of Linux\, the Bash shell\, navigating the file system\, basic commands\, shell redirection\, permissions\, processes\, and the command environment. The workshop will also provide a quick introduction to nano a simple text editor that will be used in subsequent workshops to edit files. \n \nInstructor\nKenneth Weiss\nIT Project Senior Manager\nMedical School Information Services (MSIS) \nKen is a High Performance Computing Consultant in the Computational Research Consulting Division of MSIS at the University of Michigan. He works with a team of IT specialists to provide high performance computing support and training for the Medical School. Prior to this\, he spent 21 years managing research computing\, including an HPC cluster\, for Dr. Charles Sing in the Human Genetics Department. \nMaterials\n\nLecture Notes (updated Sept. 21\, 2017)\nReference text: William E Shotts\, Jr.\, “The Linux Command Line: A Complete Introduction\,” No Starch Press\, January 2012 .http://linuxcommand.org/tlcl.php\nDownload Creative Commons Licensed version at http://downloads.sourceforge.net/project/linuxcommand/TLCL/13.07/TLCL-13.07.pdf\n\n\nCourse Preparation\nYou must register at least three full days prior to the event so that we have time to insure you have proper UM credentials for the workshop. This allows enough time for you to get your account adjusted by ITS in case you do not have access to the Linux systems.
URL:https://micde.umich.edu/event/introduction-to-the-linux-command-line-2-3/
LOCATION:East Hall B254\, 530 Church St.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:High Performance Computing,Workshops
ORGANIZER;CN="Advanced Research Computing":MAILTO:arc-contact@umich.edu
GEO:42.2757302;-83.7351764
X-APPLE-STRUCTURED-LOCATION;VALUE=URI;X-ADDRESS=East Hall B254 530 Church St. Ann Arbor MI 48109 United States;X-APPLE-RADIUS=500;X-TITLE=530 Church St.:geo:-83.7351764,42.2757302
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180213T130000
DTEND;TZID=America/Detroit:20180213T160000
DTSTAMP:20260606T162026
CREATED:20230905T171417Z
LAST-MODIFIED:20230905T171417Z
UID:10000057-1518526800-1518537600@micde.umich.edu
SUMMARY:Introduction to the Linux Command Line
DESCRIPTION: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 generically referred to as “the command line”. Topics include: a brief overview of Linux\, the Bash shell\, navigating the file system\, basic commands\, shell redirection\, permissions\, processes\, and the command environment. The workshop will also provide a quick introduction to nano a simple text editor that will be used in subsequent workshops to edit files. \n \nInstructor\nKenneth Weiss\nIT Project Senior Manager\nMedical School Information Services (MSIS) \nKen is a High Performance Computing Consultant in the Computational Research Consulting Division of MSIS at the University of Michigan. He works with a team of IT specialists to provide high performance computing support and training for the Medical School. Prior to this\, he spent 21 years managing research computing\, including an HPC cluster\, for Dr. Charles Sing in the Human Genetics Department. \nMaterials\n\nLecture Notes (updated Sept. 21\, 2017)\nReference text: William E Shotts\, Jr.\, “The Linux Command Line: A Complete Introduction\,” No Starch Press\, January 2012 .http://linuxcommand.org/tlcl.php\nDownload Creative Commons Licensed version at http://downloads.sourceforge.net/project/linuxcommand/TLCL/13.07/TLCL-13.07.pdf\n\n\nCourse Preparation\nYou must register at least three full days prior to the event so that we have time to insure you have proper UM credentials for the workshop. This allows enough time for you to get your account adjusted by ITS in case you do not have access to the Linux systems.
URL:https://micde.umich.edu/event/introduction-to-the-linux-command-line-2-2/
LOCATION:East Hall B254\, 530 Church St.\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:High Performance Computing,Workshops
ORGANIZER;CN="Advanced Research Computing":MAILTO:arc-contact@umich.edu
GEO:42.2757302;-83.7351764
X-APPLE-STRUCTURED-LOCATION;VALUE=URI;X-ADDRESS=East Hall B254 530 Church St. Ann Arbor MI 48109 United States;X-APPLE-RADIUS=500;X-TITLE=530 Church St.:geo:-83.7351764,42.2757302
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Detroit:20180208T140000
DTEND;TZID=America/Detroit:20180208T150000
DTSTAMP:20260606T162026
CREATED:20230905T171417Z
LAST-MODIFIED:20230905T171417Z
UID:10000097-1518098400-1518102000@micde.umich.edu
SUMMARY:MICDE Seminar: Dominika Zgid\, Chemistry\, University of Michigan
DESCRIPTION:Bio: Dominika Zgid is an assistant professor of Chemistry at the University of Michigan. She received her Ph.D. from the University of Waterloo\, Canada\, in 2008. Since starting at Michigan\, she has received a DOE Early Career Award in 2013 and an NSF Career Award in 2015. \nHer main interests are at the interface of theoretical chemistry and condensed matter physics with a major focus on designing new\, systematically improvable and controlled computational methods that can be used to study strongly correlated molecules and materials. She has worked on a variety of topics\, such as a molecular version of density matrix renormalization group\, solvers for dynamical mean field theory using explicit bath formulation\, conserving Green’s function methods for weakly correlated systems and the development of the self-energy embedding theory. \nTowards Accurate Quantum-Mechanical Calculations beyond Density Functional Theory on Large Systems\nWe present a detailed discussion of self-energy embedding theory (SEET) which is a quantum embedding scheme allowing us to describe a chosen subsystem very accurately while keeping the description of the environment at a lower cost. We apply SEET to molecular examples where commonly our chosen subsystem is made out of a set of strongly correlated orbitals while the weakly correlated orbitals constitute an environment. Such a self-energy separation is very general and to make this procedure applicable to multiple systems a detailed and practical procedure for the evaluation of the system and environment self-energy is necessary. We list all the intricacies for one of the possible procedures while focusing our discussion on many practical implementation aspects such as the choice of best orbital basis\, impurity solver\, and many steps necessary to reach chemical accuracy. \nFinally\, on a set of carefully chosen molecular examples\, we demonstrate that SEET\, which is a controlled\, systematically improvable Green’s function method can be as accurate as established wavefunction quantum chemistry methods.
URL:https://micde.umich.edu/event/micde-seminar-dominika-zgid-chemistry-university-of-michigan/
LOCATION:CHEM 1706\, 930 N University\, Ann Arbor\, MI\, 48109\, United States
CATEGORIES:Featured Events,MICDE Seminar Series
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GEO:42.2780546;-83.7366011
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