Michigan Institute for Computational Discovery and Engineering

Software Development For Research: Team-Based Programming Practices
2021-03-24 13:00 - 15:00 (America/Detroit) | Your Desktop
Software development and computer programming is increasingly a major part of scientific research. When small or large teams are involved in coding the same project, it’s a good idea to adopt team-based practices, such as “pair programming” or “code review” meetings, to ensure quality is maintained in the code. This hands-on workshop will provide examples of these topics in action, and attendees will leave prepared to use these skills in their own work groups.
This is part of a series of workshops focused on software and coding from a research perspective.

PhD Seminar: Chanese Forte and Hyeon Joo
2021-03-25 16:00 - 17:00 | Zoom Event, MI, United States
CHANESE FORTE, GRADUATE STUDENT, ENVIRONMENTAL HEALTH SCIENCES & SCIENTIFIC COMPUTING
Bio: Chanese is a Dual PhD student pursuing a degree in the Environmental Health Sciences and Scientific Computing. Chanese’s research interests lie in chemical exposure in agriculture workers and cellular alteration.
ASCERTAINING PESTICIDE EXPOSURE AND BIOACTIVITY USING OPEN SOURCE DATA: Pesticides are known to be harmful chemicals to human health, however, they are still heavily used in agriculture. Using large publicly available datasets, this study aims to quantify pesticide exposure levels of the US general population in comparison to farmworkers. The National Health and Nutrition Examination Survey (NHANES) is a cross-sectional study representative of the US population. NHANES was used to quantify pesticide exposure among US farmworkers and the general population who responded to NHANES. It compares and analyzes, using regression, the US pesticide exposure levels to the bioactivity of these same pesticides within the human body. By comparing population-level data with toxicological assay data in future projects, we hope to create a more overarching idea of how pesticides may be affecting the body and the human population level.
HYEON JOO, GRADUATE STUDENT, HEALTH INFRASTRUCTURES AND LEARNING SYSTEMS & SCIENTIFIC COMPUTING
Bio: Hyeon Joo is a second year PhD student in the Health Infrastructures and Learning Systems program of the Department of Health Learning Systems (Michigan Medical School). He completed his MS in Computer Science and Engineering, and Master of Health Informatics from the University of Michigan, Ann Arbor. His research focuses on developing and implementing computational data-driven algorithms, systems or tools to help users identify gaps and make informed decisions. He loves working in the field of health care as a data scientist and a software engineer.
EARLY PREDICTION OF HEART FAILURE USING ATTENTION MODELS USING EHR DATA: Heart Failure (HF) is a severe and progressive chronic condition affecting over 5.8 million patients with a 5-year mortality rate of 45-60% in the United States. Despite significant efforts and advanced HF management, diagnosing HF in the early stages remains challenging due to its syndromic nature and non-specific disease presentation. In this seminar, I will present a single attention recurrent network and a hierarchical attention convolutional neural networks to detect the early stage of HF at a tertiary hospital. I will also describe various methods of feature selection to reduce the computation time and improve the performance of the models. Lastly, I will present the challenges of adopting models in clinical practice which leads to my next research steps.

Register via Zoom to immediately receive login information. Note: You may register and join after the event has started.
This event is part of MICDE’s Winter 2021 seminar series featuring Ph.D. students in the Scientific Computing program. This series is open to all. University of Michigan faculty and students interested in computational and data sciences are encouraged to attend.
Questions? Email MICDE-events@umich.edu

GIS Fundamentals – (PostGIS-II)
2021-03-29 15:00 - 16:30 | Your Desktop
This workshop will further develop the material covered on spatial databases in the first workshop a few weeks back. PostGIS is the most widely used spatial database and is built on top of PostgreSQL, a powerful open source relational database. The focus of this workshop is to exploit PostGIS to deal with big vector data, and use familiar tools in R to reduce the burden to learn SQL.

This is a hands-on workshop. Please make sure that you have PostgreSQL installed along with pgAdmin.
Participants should be familiar with vector data processing in R.

GIS Fundamentals – (Map visualization - II)
2021-04-09 14:00 - 15:30 | Your Desktop
This workshop will further develop the material covered on mapping in the first workshop a few weeks back. We will focus on basic cartography principles for map-making and explore the functionalities of R and QGIS for making production-quality bi-variate static and dynamic choropleth maps. We will also explore the functionalities of leaflet, a powerful library, to create web maps and add extra information about more than two variables.
Participants should have some familiarity with R, but exposure to QGIS is not required.

NVidia GTC 2021 Conference
2021-04-12 - 2021-04-16
NVIDIA has their GTC technical conference April 12-16. It is free to attend and all online so no travel. Making you aware of this opportunity to hear from a global community of developers, researchers, engineers, and innovators who are delivering over a 1000 sessions, interactive panels, demos, and research posters. Registration is now open and the session catalog is published. Register HERE
Keynote
You will want to attend NVIDIA CEO Jensen Huang’s keynote. Traditionally NVIDIA uses Jensen’s keynote to make important announcements.

Keynote: April 12, 11:30am-12:30pm Eastern Time

Sessions
Sessions ranging from very technical developer and researcher-focused talks, to business and implementation focused topics from leaders in their field. Below are a few examples of the sessions available at GTC 2021. (abstracts and details in the Session Catalog)

Accelerating Ray Tracing for the IceCube Neutrino Observatory with CUDA

Benedikt Reidel, Computing Manager, University of Wisconsin-Madison and IceCube Particle Astrophysics Center

Using Molecular Simulations to Help Drive Pharmaceutical Drug Discovery

David Mobley, Professor University of California, Irvine

Convergence of AI and HPC to Solve Grand Challenge Science Problems

Rommie Amaro, Professor University of California, Irvine

Toward a One-Hour Genomic Workup

Tychele Turner, Assistant Professor Washington University in St Louis

GPU-Accelerated Quantum Chemistry and Molecular Dynamics

NVIDIA Engineers
Register today, it only take a minute or two!

Object Detection using Deep Learning with TorchVision
2021-04-13 10:00 - 12:00 | Your Desktop
Like many image processing problems, deep learning has brought many effective solutions to the task of object detection. The TorchVision library is part of the PyTorch project, and it offers well-established and successful methods for object detection (as well as many other problems). This workshop will demonstrate the process of preparing your own image dataset and training it using TorchVision with one of Google Colab’s free-to-use GPUs. The workshop will be done online via Zoom. Some experience with Python is helpful, but no previous experience with PyTorch is needed. Google Colab requires a Google account (e.g. your umich account).

MCAIM Colloquium: Sheperd S. Doeleman, Harvard University, Founding Director of the Event Horizon Telescope
2021-04-14 16:00 - 17:00 | Zoom Event, MI, United States
Talk Title: Black Hole Imaging: First Results and Future Vision
Abstract: In April 2017, the Event Horizon Telescope (EHT) carried out a global Very Long Baseline Interferometry (VLBI) observing campaign at a wavelength of 1mm that led to the first resolved image of a supermas- sive black hole. For the 6.5 billion solar mass black hole in the giant elliptical galaxy M87, the EHT estimated the spin orientation and constrained models of accretion on Schwarzschild radius scales. This work relied on two decades of technical advances in ultra-high resolution interferometry and theoretical General Relativistic Magnetohydrodynamic (GRMHD) simulations. This talk will review these advances and recent new EHT results.
We will also look to the next decade when a next-generation EHT (ngE-HT) that doubles the number of participating radio dishes in the VLBI net-work will enable time-lapse movies of M87 that link the black hole to the relativistic jet it powers. For SgrA*, the Galactic Center black hole that evolves on time scales 1000 times faster, ngEHT will produce real-time video.
Bio: Sheperd S. Doeleman is an Astrophysicist at the Center for Astrophysics | Harvard & Smithsonian and Founding Director of the Event Horizon Telescope (EHT), a synchronized global array of radio observatories designed to examine the nature of black holes. He is also a Harvard Senior Research Fellow and a Project Co-Leader of Harvard’s recently established Black Hole Initiative (BHI). The BHI is a first-of-its-kind interdisciplinary program at the University that brings together the disciplines of Astronomy, Physics, Mathematics, Philosophy, and History of Science to define and establish black hole science as a new field of study.
As one of the founding members of the BHI, Doeleman leads a team studying supermassive black holes with sufficient resolution to directly observe the event horizon itself. Using Very Long Baseline Interferometry (VLBI) methods, the EHT telescope networks observe astronomical radio sources at 1.3 millimeter (mm) wavelengths. These sources include the supermassive black holes at the centers of our own Milky Way, called Sagittarius A* (SgrA*), as well as in Messier 87 (M87), the supergiant elliptical galaxy in the constellation Virgo.
Doeleman is a Guggenheim Fellow (2012) and was the recipient of the DAAD German Academic Exchange grant for research at the Max Planck Institute für Radioastonomie. He serves as a peer reviewer for the Astrophysical Journal, Science, and Nature, among others. Doeleman leads and co-leads research programs supported by grants from the National Science Foundation, the National Radio Astronomy Observatory (NRAO) ALMA-NA Development Fund, the Smithsonian Astrophysical Observatory, the MIT International Science & Technology Initiatives (MISTI), the Gordon and Betty Moore Foundation, and the John Templeton Foundation. He has taught at MIT and mentors students and post-doctoral fellows at MIT and Harvard.
Doeleman received his B.A. from Reed College in 1986, and left soon after for a year in Antarctica where he conducted multiple space-science experiments at McMurdo Station on the Ross Ice Shelf. With an appreciation for the challenges and rewards of instrumental work in difficult circumstances, he returned to complete a Ph.D. in astrophysics at MIT. After visiting the Max Planck Institute as a recipient of the DAAD, he came back to MIT in 1995 for a postdoctoral fellowship, eventually serving as assistant director of the MIT Haystack Observatory.
Doeleman’s interests focus on problems in astrophysics that require ultra-high resolving power—the ability to observe fine details of cosmic objects. His research employs the technique of Very Long Baseline Interferometry (VLBI), in which widely separated radio dishes are combined to form an Earth-sized virtual telescope. He has used this technique to study the atmospheres of dying stars, as well as stars that are just being born. His group at MIT pioneered development of instrumentation that enables VLBI to achieve the greatest resolving power possible from the surface of the Earth. He carried out the first global experiments using these new systems that successfully measured the size of the supermassive black hole at the center of the Milky Way Galaxy and in the galaxy M87. He now directs the international Event Horizon Telescope project, whose goal is to image the event horizon of a black hole, the boundary where gravity is so strong that even light cannot escape. This project addresses several fundamental questions about the Universe: Do event horizons exist? Does Einstein’s theory of gravity hold near a black hole? How do black holes affect the evolution of galaxies?

Join Zoom Meeting: https://umich.zoom.us/j/98619190605
Meeting ID: 986 1919 0605
Passcode: [REDACTED]
This event is hosted by the Michigan Center for Applied and Interdisciplinary Mathematics.

Computing our way out of a pandemic: modeling in the face of COVID-19
2021-05-06 09:00 - 16:30 | Zoom Event, MI, United States
The COVID-19 pandemic has produced massive amounts of information that require an accurate analysis to predict outcomes and design solutions rapidly. It also has required experts from many different backgrounds to rally around in the quest for rapid responses in the race to save lives.
Many of the most prominent of these researchers are from Michigan, and a significant number of them are computational scientists who addressed questions such as: What measures should be taken to minimize contagion? Is it safe to ride a bus? How are supply and demand chains being affected?
This virtual symposium will bring together researchers from the State of Michigan to share their past and future insights into the pandemic.

View additional event details.
View event agenda.
This is a free Zoom event, open to the general public. Please register to attend.

Advanced ML topics: Algorithms, writing ML code, comparing implementations
2021-05-07 10:00 - 12:00 | Your Desktop
OVERVIEW

This workshop is designed as a follow-up to the basic introduction to machine learning earlier in this series. We will cover several examples in Python and compare different implementations. We will also look at advanced topics in machine learning, such as GPU optimization, parallel processing, and deep learning. A basic understanding of Python is required.
INSTRUCTORS
Meghan Richey
Machine Learning Specialist
Information and Technology Services – Advanced Research Computing – Technology Services
Meghan Richey is a machine learning specialist in the Advanced Research Computing- Technology Services department at the University of Michigan. She consults on several faculty and student machine learning applications and research studies, specializing in natural language processing and convolutional neural networks. Before her position at the university, Ms. Richey worked for a defense contractor as a software engineer to design and implement software solutions for DoD-funded artificial intelligence efforts.

A Zoom link will be provided to the participants the day before the class. Registration is required.

Instructor will be available at the Zoom link, to be provided, from 9-10 AM for computer setup assistance.
Please note, this session will be recorded.

Register here
If you have questions about this workshop, please send an email to the instructor at richeym@umich.edu

Software Development For Research: Best Practices for Coding Styles
2021-05-10 13:00 - 15:00 | Your Desktop
Software development and computer programming is increasingly a major part of scientific research. Having a consistent coding style and following basic best practices used in the industry can help make your code easier to read and manage, both internally in your teams and for public code projects available to other researchers. This workshop will cover some general guidelines and suggestions to clean up your coding style. Attendees will learn helpful tips for computer coding and how to make their code readable to other collaborators.
Registrants will receive a Zoom link within 24 hours of event. Please register at least 24 hours in advance.

SRTI: Software For Cross-Language Real-Time Data Communication
2021-05-24 13:00 - 15:00 | Your Desktop
Computer software simulation is used in virtually every discipline. These programs virtually represent small components of real-world events and behaviors, and allow scientists to test different models to guide real-world research. However, these can be individually complex, and written in different computer languages and programs. It’s a difficult task to combine simulators from different parts of a research team to represent larger systems.
The “Simple Run-Time Infrastructure” is an open-source, free-to-use software tool, developed at the University of Michigan. It was built to simplify the process of sharing data between multiple live simulators, using a “publish/subscribe” model with messages rather than directly to specific programs. This workshop will present the background of the SRTI’s development, what it is capable of, and will provide a step-by-step example for participants.
Java will be required to run the SRTI. The live example will use an optional mixture that includes simulators written in Java, Matlab, and Python.
This special-track workshop (provided as a “seminar-style”) is open to researchers both inside and outside the University of Michigan. Up to 300 attendees can attend through Zoom.
We ask attendees to “register” by filling out the following Google Forms survey. The survey will provide a Zoom link for you to copy into your calendar.
The Google Forms survey link is: https://docs.google.com/forms/d/e/1FAIpQLSeMyniPQs7G1iuohuvSAdU4KE64-BQrCgrZRnC6YzxeCLFv7g/viewform?usp=sf_link
Please register at least 48 hours in advance.

GIS Fundamentals – Spatial Database, PostGIS
2021-05-26 15:30 - 17:00 | Your Desktop
PostGIS, built on top of PostgreSQL, is the most powerful open-source relational database for managing spatial data. In this workshop we will cover the basic concept of spatial databases, learn about setting PostGIS, and understand how PostGIS can help us manage large volumes of vector data spread over multiple tables and geometries efficiently. We will also touch upon topics such as spatial indexing and the capabilities of PostGIS for other data models for 2-D GIS such as the network and raster data model.

Marc Henry de Frahan Webinar
2021-06-04 10:00 - 11:00 | Zoom Event, MI, United States
Title: Leveraging modeling hierarchies in the Exascale era: applications to combustion technologies
Abstract: As we approach the confluence of widespread use of machine learning techniques and simulations running at exascale, several important challenges will need to be addressed. In this talk, we explore some of these challenges, with a specific focus on combustion applications. We discuss a combustion simulation code, PeleC, and its performance characteristics on the fastest supercomputers available today. We look at leveraging the resulting high-fidelity simulations to construct data-driven models for lower-fidelity simulations. We then examine how to adapt reinforcement learning methods to explore a modeling hierarchy and determine adequate control strategies for combustion technologies.
Bio: Marc Henry de Frahan is a computational scientist at the National Renewable Energy Laboratory, where he works on improving next-generation wind and combustion processes. As part of the Exascale Computing Project, Marc develops high-fidelity turbulence models to enhance simulation accuracy and efficient numerical algorithms for future high-performance computing hardware architectures. In addition to traditional physics-based modeling, he is integrating deep neural networks into modeling and reinforcement learning into advanced control strategies. Marc obtained his PhD in Mechanical Engineering in 2016 from the University of Michigan.

Zoom information to connect:
Link: https://umich.zoom.us/j/98133041706
Passcode: [REDACTED]

GIS Fundamentals - Height and Vertical Datum
2021-06-04 15:30 - 16:30 | Your Desktop
Understanding how heights are measured and recorded in GIS systems are essential for many applied tasks such as modeling flood risk due to sea level rise. In this workshop we will understand vertical datums, the concept of height, and what do terms like orthometric height and ellipsoid height mean. This will be a lecture-style workshop with a focus on conceptual details.
Participants should know basic GIS and should be familiar with horizontal datums.

XSEDE HPC HPC Summer Boot Camp
2021-06-08 11:00 - 2021-06-11 17:00 | Your Desktop
OVERVIEW
XSEDE, along with the Pittsburgh Supercomputing Center is pleased to present a Hybrid Computing workshop.
This 4 day event will include MPI, OpenMP, GPU programming using OpenACC and accelerators.
This workshop will be remote to desktop only due to the COVID-19 pandemic. When the registration has filled, there will be no more students added due to our current limits.
Questions
Please address any questions to Tom Maiden at tmaiden@psc.edu.

Image Segmentation using Deep Learning with FastAI
2021-06-15 10:00 - 12:00 | Your Desktop
Like other image processing problems, deep learning has brought many effective solutions to the task of image segmentation. This workshop will introduce you to the methods used in image segmentation, demonstrate how to prepare your own segmentation masks using Matlab, and guide you through performing image segmentation using the FastAI [fast.ai] Python library, which is built on the deep learning library PyTorch. Some familiarity with Python is expected, but no previous experience with FastAI or PyTorch is needed. The workshop will be done online via Zoom. We will run the code using Google Colab (with free-to-use GPUs), which requires a Google account.

GIS Fundamentals – Understanding and manipulating elevation data
2021-06-16 15:30 - 16:30 | Your Desktop
Elevation data can come in the form of point (e.g. from LiDAR), digital elevation model (DEM), or triangulated irregular network (TIN). In this workshop we will focus on DEM and TIN. We will learn about each model and related data structure, their relative strengths, the kind of information they provide, and how to obtain downstream derived information. This is a lecture-style workshop and the primary focus will be about understanding the two models. However, we will also see examples in ArcGIS or QGIS

Participants should know GIS and be familiar with vector and raster data.

Introduction to the Linux Command Line
2021-06-21 13:00 - 16:00 | Your Desktop
OVERVIEW
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.
​
PRE-REQUISITES
None.
INSTRUCTOR
Kenneth Weiss
IT Project Senior Manager
HITS Academic IT – HPC team
Ken is a High Performance Computing Consultant with the Health Information Technology & Services (HITS) Academic IT – HPC team 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.
MATERIALS

Lecture Notes
Reference text: William E Shotts, Jr., “The Linux Command Line: A Complete Introduction,” No Starch Press, January 2012 .http://linuxcommand.org/tlcl.php
Download Creative Commons Licensed version at http://downloads.sourceforge.net/project/linuxcommand/TLCL/13.07/TLCL-13.07.pdf

COURSE PREPARATION
You will need VPN software to access the U-M network. If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions. You will need VPN to be able to use the ssh client to connect to training host. Please use the ‘Campus All traffic’ profile in the Cisco client.
You will need an ssh client to connect to the training host. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:

Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer. This document describes how to download and use this software. A demonstration of this software will be given during class. You must have administrative authority over your computer to install this software.
Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application. You do not need administrative authority over your computer to use this software.

During class you will be given the name of the training host to be able to participate in the hands-on activities.
A Zoom link will be provided to the participants the day before the class. Registration is required. Please note, this session will be recorded.
If you have questions about this workshop, please send an email to the instructor at kgweiss@umich.edu

Register at https://ttc.iss.lsa.umich.edu/ttc/sessions/introduction-to-the-linux-command-line-30/register/

Introduction to Research Computing on the Great Lakes Cluster
2021-06-22 13:00 - 16:00 | Your Desktop
OVERVIEW
This workshop will introduce you to high performance computing on the Great Lakes cluster. After a brief overview of the components of the cluster and the resources available there, the main body of the workshop will cover creating batch scripts and the options available to run jobs, and hands-on experience in submitting, tracking, and interpreting the results of submitted jobs. By the end of the workshop, every participant should have created a submission script, submitted a job, tracked its progress, and collected its output. Additional tools including high-performance data transfer services and interactive use of the cluster will also be covered.
PRE-REQUISITES
This course assumes familiarity with the Linux command line as might be obtained from the 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, and be able to create and remove files and folders. Some exposure to shell input and output redirection and pipes would also be useful.
INSTRUCTORS
Dr. Charles J Antonelli
Research Computing Services
LSA Technology Services
Charles is a member of the LSA Technology Services Research team at the University of Michigan, where he is responsible for high performance computing support and education, and was 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.
MATERIALS

Lecture Notes
Great Lakes Slurm HPC cluster
Great Lakes User Guide
Two-page Cheat Sheet

COURSE PREPARATION
In order to participate successfully in the workshop exercises, you must have a user login, a Slurm account, and be enrolled in Duo. The user login allows you to log in to the cluster, create, compile, and test applications, and prepare jobs for submission. The Slurm account allows you to submit those jobs, executing the applications in parallel on the cluster and charging their resource use to the account. Duo is required to help authenticate you to the cluster.
USER LOGIN
If you already have a Great Lakes user login, you don’t need to do anything. Otherwise, go to the Great Lakes user login application page at: http://arc-ts.umich.edu/login-request/
Please note that obtaining a user account requires human processing, so be sure to do this at least two business days before class begins.
SLURM ACCOUNT
We create a Slurm account 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 job account 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 Slurm account, you can use that, though if there are any issues with that account, we will ask you to use the workshop account.
DUO AUTHENTICATION
Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH (AKA Level 1) password as well as authenticate through Duo in order to access Great Lakes.
If you need to enroll in Duo, follow the instructions at Enroll a Smartphone or Tablet in Duo.
Please enroll in Duo before you come to class.
LAPTOP PREPARATION
You will need VPN software to access the U-M network on which Great Lakes is located. If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions. Please use the ‘Campus All traffic’ profile in the Cisco client.
You will need an ssh client to connect to the Great Lakes cluster. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:
Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer. This document describes how to download and use this software, except please note you will be connecting to greatlakes.arc-ts.umich.edu instead of the cited host. You must have administrative authority over your computer to install this software.
Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application. You do not need administrative authority over your computer to use this software.
Our Great Lakes User Guide in Section 1.2 describes in more detail how to use PuTTY to connect to Great Lakes.
Please prepare and test your computer’s ability to make remote connections before class; we cannot stop to debug connection issues during the class.
A Zoom link will be provided to the participants the day before the class. Registration is required. Please note this session will be recorded.

If you have questions about this workshop, please send an email to the instructors at hpc-course@umich.edu
Please register at https://ttc.iss.lsa.umich.edu/ttc/sessions/introduction-to-research-computing-on-the-great-lakes-cluster-6/register/

Introduction to the Linux Command Line
2021-06-23 13:00 - 16:00 | Your Desktop
OVERVIEW
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.
​
PRE-REQUISITES
None.
INSTRUCTOR
Kenneth Weiss
IT Project Senior Manager
HITS Academic IT – HPC team
Ken is a High Performance Computing Consultant with the Health Information Technology & Services (HITS) Academic IT – HPC team 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.
MATERIALS

Lecture Notes
Reference text: William E Shotts, Jr., “The Linux Command Line: A Complete Introduction,” No Starch Press, January 2012 .http://linuxcommand.org/tlcl.php
Download Creative Commons Licensed version at http://downloads.sourceforge.net/project/linuxcommand/TLCL/13.07/TLCL-13.07.pdf

COURSE PREPARATION
You will need VPN software to access the U-M network. If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions. You will need VPN to be able to use the ssh client to connect to training host. Please use the ‘Campus All traffic’ profile in the Cisco client.
You will need an ssh client to connect to the training host. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:

Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer. This document describes how to download and use this software. A demonstration of this software will be given during class. You must have administrative authority over your computer to install this software.
Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application. You do not need administrative authority over your computer to use this software.

During class you will be given the name of the training host to be able to participate in the hands-on activities.
A Zoom link will be provided to the participants the day before the class. Registration is required. Please note, this session will be recorded.
If you have questions about this workshop, please send an email to the instructor at kgweiss@umich.edu

Register at https://ttc.iss.lsa.umich.edu/ttc/sessions/introduction-to-the-linux-command-line-31/register/

Advanced research computing on the Great Lakes Cluster
2021-06-24 09:00 - 12:00 | Your Desktop
OVERVIEW

This workshop will cover some more advanced topics in computing on the U-M Great Lakes Cluster. Topics to be covered include a review of common parallel programming models and basic use of Great Lakes; dependent and array scheduling; workflow scripting using bash; high-throughput computing using launcher; parallel processing in one or more of Python, R, and MATLAB; and profiling of parallel code using Allinea Performance Reports and Allinea MAP.
PRE-REQUISITES
This 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.
INSTRUCTORS
Dr. Charles J Antonelli
Research Computing Services
LSA Technology Services
Charles is a member of the LSA Technology Services Research team at the University of Michigan, where he is responsible for high performance computing support and education, and was 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.
John Thiels
Research Computing Services
LSA Technology Services
MATERIALS

Lecture Notes
Great Lakes Slurm HPC cluster
Great Lakes User Guide
Two-page Cheat Sheet
MPI Profiling with Allinea MAP

COURSE PREPARATION
In order to participate successfully in the workshop exercises, you must have a user login, a Slurm account, and be enrolled in Duo. The user login allows you to log in to the cluster, create, compile, and test applications, and prepare jobs for submission. The Slurm account allows you to submit those jobs, executing the applications in parallel on the cluster and charging their resource use to the account. Duo is required to help authenticate you to the cluster.
USER LOGIN
If you already have a Great Lakes user login, you don’t need to do anything. Otherwise, go to the Great Lakes user login application page at: http://arc-ts.umich.edu/login-request/ .
Please note that obtaining a user account requires human processing, so be sure to do this at least two business days before class begins.
SLURM ACCOUNT
We create a Slurm account 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 job account 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 Slurm account, you can use that, though if there are any issues with that account, we will ask you to use the workshop account.
DUO AUTHENTICATION
Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH (AKA Level 1) password as well as authenticate through Duo in order to access Great Lakes.
If you need to enroll in Duo, follow the instructions at Enroll a Smartphone or Tablet in Duo.
Please enroll in Duo before you come to class.

LAPTOP PREPARATION
You will need VPN software to access the U-M network. If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions. You will need VPN to be able to use the ssh client to connect to Great Lakes. Please use the ‘Campus All traffic’ profile in the Cisco client.
You will need an ssh client to connect to the Great Lakes cluster. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:

Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer. This document describes how to download and use this software, except please note you will be connecting to greatlakes.arc-ts.umich.edu instead of the cited host. You must have administrative authority over your computer to install this software.
Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application. You do not need administrative authority over your computer to use this software.

Our Great Lakes User Guide in Section 1.2 describes in more detail how to use PuTTY to connect to Great Lakes.
Please prepare and test your computer’s ability to make remote connections before class; we cannot stop to debug connection issues during the class.

A Zoom link will be provided to the participants the day before the class. Registration is required.Please note this session will be recorded.

Please register at https://ttc.iss.lsa.umich.edu/ttc/sessions/advanced-research-computing-on-the-great-lakes-cluster-9/register/

ME Special Webinar: Aditya Nair, Mechanical Engineering, University of Nevada
2021-06-25 12:00 - 13:00 | Zoom Event, MI, United States
Bio: Aditya G. Nair joined the Department of Mechanical Engineering at U. Nevada, Reno in August 2020. His research interests are in the areas of computational fluid dynamics, unsteady aerodynamics, high-performance computing, data science and control theory focused on modeling and control of high-dimensional fluid flow physics. He received his Ph.D. in mechanical engineering from the Florida State U. in 2018. Prior to this, he completed his M.S. in mechanical engineering from U. Michigan in 2013 and B.E in mechanical engineering from University of Mumbai in 2011. Following his Ph.D., he served as a post-doctoral research associate in the mechanical engineering department at U. of Washington till July 2020.
Physics-based and data-driven strategies for modeling and control of unsteady fluid flows
Data and network science offer novel perspectives to describe complex dynamics over a web of interactions. The last few years have seen an emergence of such techniques to characterize, model, and control fluid flows. The ability of these approaches to characterize vortical and modal interactions in unsteady fluid flows is essential to understand its complex behavior. Using a simple description of the flow physics on a mathematical graph with weights based on vortical interactions, modal interactions and probabilistic interactions, we can design feedback control techniques to alter flow behavior. We discuss some of the successes and challenges associated with applying this formalism for fluid dynamics.
Zoom information
link: umich.zoom.us/j/92859783250
passcode: [REDACTED]
Prof. Nair is being hosted by Prof. Johnsen (Mechanical Engineering).

Introduction to Research Computing on the Great Lakes Cluster
2021-06-25 13:00 - 16:00 | Your Desktop
OVERVIEW
This workshop will introduce you to high performance computing on the Great Lakes cluster. After a brief overview of the components of the cluster and the resources available there, the main body of the workshop will cover creating batch scripts and the options available to run jobs, and hands-on experience in submitting, tracking, and interpreting the results of submitted jobs. By the end of the workshop, every participant should have created a submission script, submitted a job, tracked its progress, and collected its output. Additional tools including high-performance data transfer services and interactive use of the cluster will also be covered.
PRE-REQUISITES
This course assumes familiarity with the Linux command line as might be obtained from the 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, and be able to create and remove files and folders. Some exposure to shell input and output redirection and pipes would also be useful.
INSTRUCTORS
Dr. Charles J Antonelli
Research Computing Services
LSA Technology Services
Charles is a member of the LSA Technology Services Research team at the University of Michigan, where he is responsible for high performance computing support and education, and was 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.
MATERIALS

Lecture Notes
Great Lakes Slurm HPC cluster
Great Lakes User Guide
Two-page Cheat Sheet

COURSE PREPARATION
In order to participate successfully in the workshop exercises, you must have a user login, a Slurm account, and be enrolled in Duo. The user login allows you to log in to the cluster, create, compile, and test applications, and prepare jobs for submission. The Slurm account allows you to submit those jobs, executing the applications in parallel on the cluster and charging their resource use to the account. Duo is required to help authenticate you to the cluster.
USER LOGIN
If you already have a Great Lakes user login, you don’t need to do anything. Otherwise, go to the Great Lakes user login application page at: http://arc-ts.umich.edu/login-request/
Please note that obtaining a user account requires human processing, so be sure to do this at least two business days before class begins.
SLURM ACCOUNT
We create a Slurm account 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 job account 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 Slurm account, you can use that, though if there are any issues with that account, we will ask you to use the workshop account.
DUO AUTHENTICATION
Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH (AKA Level 1) password as well as authenticate through Duo in order to access Great Lakes.
If you need to enroll in Duo, follow the instructions at Enroll a Smartphone or Tablet in Duo.
Please enroll in Duo before you come to class.
LAPTOP PREPARATION
You will need VPN software to access the U-M network on which Great Lakes is located. If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions. Please use the ‘Campus All traffic’ profile in the Cisco client.
You will need an ssh client to connect to the Great Lakes cluster. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:
Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer. This document describes how to download and use this software, except please note you will be connecting to greatlakes.arc-ts.umich.edu instead of the cited host. You must have administrative authority over your computer to install this software.
Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application. You do not need administrative authority over your computer to use this software.
Our Great Lakes User Guide in Section 1.2 describes in more detail how to use PuTTY to connect to Great Lakes.
Please prepare and test your computer’s ability to make remote connections before class; we cannot stop to debug connection issues during the class.
A Zoom link will be provided to the participants the day before the class. Registration is required. Please note this session will be recorded.

If you have questions about this workshop, please send an email to the instructors at hpc-course@umich.edu
Please register at https://ttc.iss.lsa.umich.edu/ttc/sessions/introduction-to-research-computing-on-the-great-lakes-cluster-8/register/

Advanced research computing on the Great Lakes Cluster
2021-06-29 13:00 | Your Desktop
OVERVIEW

This workshop will cover some more advanced topics in computing on the U-M Great Lakes Cluster. Topics to be covered include a review of common parallel programming models and basic use of Great Lakes; dependent and array scheduling; workflow scripting using bash; high-throughput computing using launcher; parallel processing in one or more of Python, R, and MATLAB; and profiling of parallel code using Allinea Performance Reports and Allinea MAP.
PRE-REQUISITES
This 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.
INSTRUCTORS
Dr. Charles J Antonelli
Research Computing Services
LSA Technology Services
Charles is a member of the LSA Technology Services Research team at the University of Michigan, where he is responsible for high performance computing support and education, and was 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.
John Thiels
Research Computing Services
LSA Technology Services
MATERIALS

Lecture Notes
Great Lakes Slurm HPC cluster
Great Lakes User Guide
Two-page Cheat Sheet
MPI Profiling with Allinea MAP

COURSE PREPARATION
In order to participate successfully in the workshop exercises, you must have a user login, a Slurm account, and be enrolled in Duo. The user login allows you to log in to the cluster, create, compile, and test applications, and prepare jobs for submission. The Slurm account allows you to submit those jobs, executing the applications in parallel on the cluster and charging their resource use to the account. Duo is required to help authenticate you to the cluster.
USER LOGIN
If you already have a Great Lakes user login, you don’t need to do anything. Otherwise, go to the Great Lakes user login application page at: http://arc-ts.umich.edu/login-request/ .
Please note that obtaining a user account requires human processing, so be sure to do this at least two business days before class begins.
SLURM ACCOUNT
We create a Slurm account 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 job account 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 Slurm account, you can use that, though if there are any issues with that account, we will ask you to use the workshop account.
DUO AUTHENTICATION
Duo two-factor authentication is required to log in to the cluster. When logging in, you will need to type your UMICH (AKA Level 1) password as well as authenticate through Duo in order to access Great Lakes.
If you need to enroll in Duo, follow the instructions at Enroll a Smartphone or Tablet in Duo.
Please enroll in Duo before you come to class.

LAPTOP PREPARATION
You will need VPN software to access the U-M network. If you do not have VPN software already installed, please download and install the Cisco AnyConnect VPN software following these instructions. You will need VPN to be able to use the ssh client to connect to Great Lakes. Please use the ‘Campus All traffic’ profile in the Cisco client.
You will need an ssh client to connect to the Great Lakes cluster. Mac OS X and Linux platforms have this built-in. Here are a couple of choices for Windows platforms:

Download and install U-M PuTTY/WinSCP from the Compute at the U website. This includes both the PuTTY ssh client and terminal emulator and a graphical file transfer tool in one installer. This document describes how to download and use this software, except please note you will be connecting to greatlakes.arc-ts.umich.edu instead of the cited host. You must have administrative authority over your computer to install this software.
Download PuTTY directly from the developer. Download the putty.exe application listed under “Alternative binary files,”, then execute the application. You do not need administrative authority over your computer to use this software.

Our Great Lakes User Guide in Section 1.2 describes in more detail how to use PuTTY to connect to Great Lakes.
Please prepare and test your computer’s ability to make remote connections before class; we cannot stop to debug connection issues during the class.

A Zoom link will be provided to the participants the day before the class. Registration is required.Please note this session will be recorded.

Please register at https://ttc.iss.lsa.umich.edu/ttc/sessions/advanced-research-computing-on-the-great-lakes-cluster-10/register/

Geostatistics – I
2021-06-29 15:00 - 16:00 | Your Desktop
Many environmental variables such as temperature, rainfall, air pollutants, and soil nutrients are measured at sparsely sampled point locations. We often need to estimate these variables at one of more unsampled locations. Geostatistics provide tools and techniques to carry out this task.

In a series of three workshops, we will cover the basics of Geostatistics. In this first workshop we will understand the idea of stationary random fields, positive definite functions, and the fundamental building blocks of Gaussian random fields. This is mainly a lecture style workshop, but we will also execute some examples in R. The material will also help you understand the foundations of Gaussian Process Regression, a commonly used technique in Machine Learning and AI.

Introduction to Deep Neural Networks with Keras/TensorFlow
2021-07-06 10:00 - 12:00 | Your Desktop
Deep Neural Networks (DNNs) are used as a machine learning method for both regression and classification problems. Keras is a high-level, Python interface running on top of multiple neural network libraries, including the popular library TensorFlow. In this workshop, participants will learn how to quickly use the Keras interface to perform nonlinear regression and classification with standard fully-connected DNNs, as well as image classification using Convolutional Neural Networks (CNNs). We will also look at regularization techniques and how to deal with under- and over-fitting. All examples will use Python; some familiarity with Python is recommended. The workshop will be done online via Zoom. We will run the models using Google Colab, which requires a Google account.

Geostatistics – II
2021-07-15 15:00 - 16:00 | Your Desktop
Many environmental variables such as temperature, rainfall, air pollutants, and soil nutrients are measured at sampled point locations. We often need to estimate these variables at one of more unsampled locations. Geostatistics provide tools and techniques to carry out this task.

In a series of three workshops, we are covering the basics of Geostatistics. In this second workshop, we will focus on covariance and variogram, and their estimation in the context of geostatistical modeling. This is mainly a lecture style workshop, but we will also execute some examples in R. The material will also help you understand the basics of Gaussian Process Regression, a commonly used modeling technique in Machine Learning.

R Short Course: Getting Started (Part 1)
2021-07-22 14:00 - 15:30 | Your Desktop
This is part 1 of a 5-part series of workshops on programming in R. This week, we’ll discuss the following topics: creation and naming of objects, R’s global environment, arithmetic operations, R’s package system, and reading and writing data. These workshops follow a hybrid format: a week before the scheduled meeting time participants will be given access to pre-recorded content and recommended readings to review at their own pace. The following week, we’ll meet at the posted time for 90 minutes over Zoom to answer questions and work on a collection of exercises. At the end of the course, we’ll gather for a 3-hour practicum, in which we’ll program a console version of the game “Mastermind”.

Android Application Development: An Overview
2021-07-26 10:00 - 12:00 | Your Desktop
Mobile app development is one of the biggest new industries of the last decade. As of 2017, Google and Apple (the creators of Android and iOS, respectively) confirmed a combined total of over 3 billion devices (including smartphones, smartwatches, and much more) around the globe using their mobile operating systems. The capabilities and built-in sensors on modern smartphones also provide a new avenue to collect data or engage with participants in a non-invasive manner. It might seem intimidating to write a mobile app for the first time, but the process is similar to writing software for a desktop computer, which in itself isn’t as hard as you might think!
We will present a brief overview on developing Android apps, the differences between Android and iOS development, and provide quick demonstrations on how you can use a variety of available programming environments and languages to create an app. A basic familiarity with computer programming is recommended to get the most out of the seminar. This is not a in-depth workshop with the intention to have its participants program code alongside the presentation, but meant to introduce available options for you to consider and to answer questions on the topic.
Please register at least 24 hours in advance. Event may be canceled if pre-registration is low.

Geostatistics – III
2021-07-27 15:00 - 16:00 | Your Desktop
Many environmental variables such as temperature, rainfall, air pollutants, and soil nutrients are measured at sampled point locations. We often need to estimate these variables at one of more unsampled locations. Geostatistics provide tools and techniques to carry out this task.

In a series of three workshops, we will cover the basics of Geostatistics. In this third workshop, we will combine the material we covered in the first two workshops and develop the geostatistical modeling approach. This is mainly a lecture style workshop, but will include an example in R. The material will also help you understand the basics of Gaussian Process Regression, a commonly used modeling technique in Machine Learning.
