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Research Computing Seminars

Summer 2023 Seminars

For the summer session, the research computing group will offer a single High-Performance Computing Quickstart training session, designed for small groups to learn more about completing their research computing projects on Lehigh University high-performance computing infrastructure.

This seminar reviews the minimum essential ingredients required to build research computing projects on Linux platforms. Students will learn the basics of Linux, use shell scripts, Python, and the scheduler on our high-performance computing (HPC) cluster to perform simple calculations. This course will outline the best practices for scaling and repeating many kinds of calculations. All students, faculty, and staff with an interest in learning more about HPC and Linux are welcome to attend.

Registration is available here for any one of the following dates.

  1. Tuesday, 6/13/23 from 1-2:30PM (in person, location TBD)
  2. Wednesday, 6/21/23 1-2:30PM (Zoom)
  3. Tuesday, 6/27/23 from 1-2:30PM (in person, location TBD)
  4. Wednesday, 7/5/23 from 1-2:30PM (Zoom)

Spring 2023 Seminars

The research computing seminars offered in the Spring semester are designed to lead participants through a survey of the wide range of available research computing techniques that they can apply to their training and research. Over the course of this seminar series, students will be expected to imagine how their projects can be formulated to take advantage of both small and large scale computation. We will begin with the end in mind, by first creating a map of the high-performance computing (HPC) resources available to the research community at Lehigh. After this introduction we will study the Linux basics required to effectively work with code and data, and then tackle the scheduler (SLURM) that we use to share a large HPC platform among many users. The final three sessions will provide a deeper dive into interactive computing with the Open OnDemand portal, building your own highly-portable software containers, and using Python for advanced computation on the cluster. Attendees are welcome to bring their own research problems and questions to these sessions.

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DateTitle

February 3


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titleResearch Computing resources at Lehigh

Description: This seminar provides an overview of Research Computing resources available to the Lehigh research community.

Instructor: Alex Pacheco


SlidesRecordings
February 10


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titleLinux: Basic Commands & Environment

Description: Linux is a free and open source operating system that is the OS of choice of the world's leading supercomputers as well as LTS HPC clusters and some computer labs at Lehigh. This session will provide an introduction to the linux/unix environment, command line basics, logging in to remote system, transferring data, vi/emacs editors etc to get started with using a Linux/Unix based computer. This seminar is geared towards researchers who want to learn or need to learn how to use a linux/unix based resource.

Instructor: Sachin Joshi


SlidesRecordings
February 17


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titleUsing SLURM scheduler on Lehigh's HPC cluster

Description: This seminar provides a hands on introduction to using the SLURM scheduler to submit and monitor jobs. SLURM is the scheduler on Lehigh's HPC resources, Sol and Hawk, and national supercomputing resources including XSEDE and NERSC.

Prerequisites: An HPC account or an account on national supercomputing resources (XSEDE, DOE, etc) that uses SLURM.

Familiarity with Linux/Unix environment, basic command and *nix editors such as vi or emacs is mandatory.

Instructor: Alex Pacheco


SlidesRecordings
February 24



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titlePython Programming

Description: In this seminar, you will learn the basics of Python, including language fundamentals and basic programming.

Prerequisites: Programming background is beneficial but not required.

Instructor: Sachin Joshi


SlidesRecordings
March 3


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titleR Programming

Description: In this seminar, you will learn the basics of R, including language fundamentals, data types, functions and basic programming including File I/O.

Prerequisites: Programming background is beneficial but not required.

Instructor: Jeremy Mack


SlidesRecordings
March 10


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titleIntroduction to Open OnDemand

DescriptionOpen OnDemand (OOD) is an NSF-funded open-source HPC portal developed by the Ohio Supercomputing Center. The goal of OOD is to provide an easy way for system administrators to provide web access to their HPC resources. This seminar introduces OOD to access interactive applications such as MATLAB, Jupyter Lab/Notebooks, and RStudio on Lehigh's HPC cluster.

Prerequisites: An HPC account with an active allocation and a web browser. A Lehigh IP or VPN required.

Instructor: Alex Pacheco


SlidesRecordings
March 17


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titleData Visualization with Python

Description: This seminar provides a hands on introduction to Data Visualization using the Python programming language.

Prerequisites: Programming background in Python is required.

Instructor: Sachin Joshi


SlidesRecordings
March 24


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titleData Visualization with R

Description: This seminar provides a hands on introduction to Data Visualization using the R programming language

Prerequisites: Programming background in R is required.

Instructor: Jeremy Mack


SlidesRecordings
March 31


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titleBring Your Own Software: Containers on HPC Resources

Description: Singularity is an open-source container engine designed to bring operating system-level virtualization to scientific and high-performance computing. In this seminar, we’ll provide an overview of Singularity and how you can Build Your Own Software in a singularity container for use in your research on Sol.

Prerequisites: A Linux system with singularity installed (check your package manager if your distribution provides singularity or see installation instructions).  

Instructor: Alex Pacheco


SlidesRecordings
April 7


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titleObject-Oriented Programming with Python

Description:  Object Oriented Programming or OOP is a programming paradigm which provides a means of structuring programs (combining data and functionality) so that properties and behaviors are bundled into individual objects. In this seminar, you’ll learn the basic concepts of OOP in Python: Python Classes, Object Instances, Defining and Working with Methods and OOP Inheritance.

Prerequisites:  Programming background in Python is required. Knowledge of OOP’s concepts is beneficial but not required.

Instructor: Sachin Joshi


SlidesRecordings
April 14


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titleShiny Apps in R

Description: Shiny Apps, interactive web applications built using R programming language, have grown in popularity. This session will provide attendees experience using the Shiny package and the idea of reactive programming, which forms the basis of building an interactive web application.

Prerequisites: Programming background in R is required.

Instructor: Jeremy Mack


SlidesRecordings

...

TitleDownloads


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titleResearch Computing resources at Lehigh

Description: This training provides an overview of Research Computing resources available to the Lehigh research community.


SlidesRecordings

Writing an Allocation Proposal

SlidesRecordings


Expand
titleUsing SLURM scheduler on Sol

Description: This training provides a hands on introduction to using the SLURM scheduler to submit and monitor jobs. SLURM is the scheduler on Lehigh's HPC resource, Sol, and national supercomputing resources including XSEDE and NERSC.

Prerequisites: An account on Sol or an account on national supercomputing resources (XSEDE, DOE, etc) that uses SLURM.

Familiarity with Linux/Unix environment, basic command and *nix editors such as vi or emacs is mandatory.


SlidesRecordings


Expand
titleIntroduction to Open OnDemand

DescriptionOpen OnDemand (OOD) is an NSF-funded open-source HPC portal developed by the Ohio Supercomputing Center. The goal of OOD is to provide an easy way for system administrators to provide web access to their HPC resources. This tutorial introduces OOD to access Lehigh's Sol cluster.

Prerequisites: An account on Sol with an active allocation and a web browser. A Lehigh IP or VPN required.


SlidesRecordings


Expand
titleBring Your Own Software

Description: This seminar is geared towards users who wish to bring or build their own software stack to use on Sol and Hawk (or even local linux systems). Topics to be covered include best practices for installing packages using make, cmake and configure, SPACK package manager, and Singularity. 

Prerequisites: Some familiarity with compilers, and linux environment is required.


Slides
A Brief Introduction to LinuxSlidesRecordings


Expand
titleLinux: Basic Commands & Environment

Description: Linux is a free and open source operating system that is the OS of choice of the world's leading supercomputers as well as LTS HPC clusters and some computer labs at Lehigh. This session will provide an introduction to the linux/unix environment, command line basics, logging in to remote system, transferring data, vi/emacs editors etc to get started with using a Linux/Unix based computer. This training is geared towards researchers who want to learn or need to learn how to use a linux/unix based resource.


SlidesRecordings
Basic Shell ScriptingSlidesRecordings
Advanced Shell ScriptingSlidesRecordings


Expand
titleR Programming

Description: In this tutorial, you will learn the basics of R, including language fundamentals, data types, functions and basic programming including File I/O.

Prerequisites: Programming background is beneficial but not required.


SlidesRecordings


Expand
titleData Visualization with R

Description: This tutorial provides a hands on introduction to Data Visualization using the R programming language

Prerequisites: Programming background in R is required.


SlidesRecordings


Expand
titleShiny Apps in R

Description: Shiny Apps, interactive web applications built using R programming language, have grown in popularity. This session will provide attendees experience using the Shiny package and the idea of reactive programming, which forms the basis of building an interactive web application.

Prerequisites: Programming background in R is required.


SlidesRecordings


Expand
titlePython Programming

Description: In this seminar, you will learn the basics of Python, including language fundamentals and basic programming.

Prerequisites: Programming background is beneficial but not required.


SlidesRecordings


Expand
titlePython Data Structures

Description: Data Structures are the fundamental constructs around which you build your programs. Python is a high-level, interpreted, interactive and object-oriented scripting language using which we can study the fundamentals of data structure in a simpler way as compared to other programming languages. In this seminar we are going to study a short overview of some frequently used data structures in general and how they are related to some specific python data types.

Prerequisites: Programming background in Python is required. Knowledge of data structure concepts is beneficial but not required.


SlidesRecordings


Expand
titleData Visualization with Python

Description: This seminar provides a hands on introduction to Data Visualization using the Python programming language.

Prerequisites: Programming background in Python is required.


SlidesRecordings


Expand
titleObject-Oriented Programming with Python

Description:  Object Oriented Programming or OOP is a programming paradigm which provides a means of structuring programs (combining data and functionality) so that properties and behaviors are bundled into individual objects. In this seminar, you’ll learn the basic concepts of OOP in Python: Python Classes, Object Instances, Defining and Working with Methods and OOP Inheritance.

Prerequisites:  Programming background in Python is required. Knowledge of OOP’s concepts is beneficial but not required.


SlidesRecordings


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titleMachine Learning

Description: Machine learning is a method of data analysis that automates analytical model building. It is a branch of artificial intelligence (AI) based on the idea that systems can learn from data, identify patterns and make decisions with minimal human intervention. In this two part seminar you’ll learn the basic machine learning concepts: supervised and unsupervised learning, classification and regression algorithms. This is a two part seminar.

Prerequisites: Basic knowledge of general CS concepts such as data structures, linear algebra and design of algorithm is required.


Slides (Part I, Part II)Recordings (Part I, Part II)


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titleText Mining 

Description: Text mining, also known as Text Analytics is the process of deriving high-quality information from text. It is the process of examining large collections of written resources to generate new information and to transform the unstructured text into structured data for use in further analysis. In this seminar you’ll learn the basic introduction to text analysis, different steps of text analysis: gathering textual data, cleaning and preparing textual data , analyzing the data (ETL) and visualizing textual data using tools from the HathiTrust Research Center (HTRC).

Prerequisites: Programming background is required. Basic knowledge of general CS concepts such as data structures, linear algebra and design of algorithms is required.


SlidesRecordings


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titleMATLAB

Description: MATLAB is a programming platform designed specifically for engineers and scientists. MATLAB is a special-purpose language that is an excellent choice for writing moderate-size programs that solve problems involving the manipulation of numbers. MATLAB is easy to learn, versatile and the design of the language makes it possible to write a powerful program in a few lines. Using MATLAB, you can: Analyze data, Develop algorithms and Create models and applications. In this seminar you’ll learn the basics of MATLAB, including language fundamentals and basic programming that will help you achieve the above functionalities.

Prerequisites: Programming background is beneficial but not required.


Slides
Version Control with GITSlides
Document Creation with LaTeXSlides
Using Virtualized Software at Lehigh

Storage Options at LehighSlides
Research Data ManagementSlides
Enhancing Research ImpactSlides

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