Knowledge Base Resources

• Dask Tutorial Github Page
• Video Recording of Tutorial - Part 1
• Video Recording of Tutorial - Part 2

A tutorial on the effective use of Dask on HPC resources. The four-hour tutorial will be split into two sections, with early topics focused on novice Dask users and later topics focused on intermediate usage on HPC and associated best practices. The knowledge areas covered include (but are not limited to): Beginner section High-level collections including dask.array and dask.dataframe Distributed Dask clusters using HPC job schedulers Earth Science data analysis using Dask with Xarray Using the Dask dashboard to understand your computation Intermediate section Optimizing the number of workers and memory allocation Choosing appropriate chunk shapes and sizes for Dask collections Querying resource usage and debugging errors

• Onshape Onboarding

This contains documentation for getting started with using OnShape for CAD. OnShape cloud-hosted CAD software that lets you work with others like on a Google Doc, with the power and capabilities of any other software like Solidworks or Inventor.

5 Days of recordings of Python data analysis and visualization training.

• Jetstream2 Status

Jetstream2 makes cutting-edge high-performance computing and software easy to use for your research regardless of your project’s scale—even if you have limited experience with supercomputing systems.Cloud-based and on-demand, the 24/7 system includes discipline-specific apps. You can even create virtual machines that look and feel like your lab workstation or home machine, with thousands of times the computing power.

• Github Wiki

This is a resource for researchers and students looking to on-board onto the c3ddb cluster at MGHPCC. In the code section, there are example job submission scripts for the different queues on c3ddb.

• Building the ArduPilot environment for Linux

This article provides instructions for building AirSim, an open-source simulator for autonomous vehicles, on Linux. It outlines the steps to build Unreal Engine, clone and build the AirSim repository, and set up the Unreal environment. It also includes information on how to use AirSim and optional setups such as remote control for manual flight.

• https://snakemake.readthedocs.io/en/stable/

Snakemake is a powerful and versatile workflow management system that simplifies the creation, execution, and management of data analysis pipelines. It uses a user-friendly, Python-based language to define workflows, making it particularly valuable for automating and reproducibly managing complex computational tasks in research and data analysis.

• GROMACS - MDTutorials.com
• OpenMM - Making It Rain
• NAMD - UIUC

Links to MD tutorials for beginner's across various simulation platforms.

• https://r4ds.had.co.nz/index.html

R for Data Science is a comprehensive resource for individuals looking to harness the power of the R programming language for data analysis, visualization, and statistical modeling. Whether you're a beginner or an experienced data scientist, this guide will help you unlock the full potential of R in the realm of data science.

• Termius

**Termius: The Modern SSH Client for 2023** Termius is the future-facing SSH client that's redefining remote server access in 2023. Designed for ease and efficiency, Termius offers a seamless connection experience across all devices, be it mobile or desktop. Gone are the days of re-inputting IP addresses, ports, and passwords; with Termius, one-click connectivity is the new norm. **How Termius Elevates Remote Server Access:** 1. **One-Click Connectivity:** Save the hassle of remembering and re-entering connection details. Termius provides an immediate connection to your infrastructure with a single click. 2. **Synchronized Across Devices:** Termius ensures that your data, connection settings, and preferences are consistent across all your devices, from mobile to desktop. 3. **Unparalleled Security:** With the Cloud Vault feature, users can securely store their data in an encrypted environment, accessible only from their specific devices. Shared vaults allow for safe connection sharing within teams. 4. **AI-Powered Terminal Experience:** Advanced AI-driven autocomplete means users can input command descriptions, and Termius will swiftly convert them into accurate bash commands, simplifying and enhancing the terminal interaction. 5. **Collaborative Troubleshooting:** Share terminal sessions with teammates, facilitating cooperative problem-solving or knowledge sharing. No additional server-side installations needed. 6. **Automation and Snippets:** Streamline routine processes with the ability to save and run frequently used shell scripts. Sharing these Snippets with your team can lead to increased productivity and fewer manual errors. 7. **All-Device Compatibility:** Whether on iPad, iPhone, Android, macOS, Windows, or Linux, Termius ensures a consistent and fluid experience. The platform's synchronization capability means you're always ready to respond swiftly, irrespective of the device in use. For professionals and businesses aiming for top-notch server access efficiency, Termius is the gold standard in 2023. Experience the revolution in SSH connectivity and optimize your workflow with Termius.

• Anvil Home Page

Purdue University is the home of Anvil, a powerful supercomputer that provides advanced computing capabilities to support a wide range of computational and data-intensive research spanning from traditional high-performance computing to modern artificial intelligence applications.

• Harnessing the Power of Cloud and Machine Learning for Climate and Ocean Advances
• Github for Outputs of Presentation

Documentation and presentation on how to use machine learning and deep learning framework using TensorFlow, Keras and sci-kit learn for Climate and Ocean Advances

• Beautiful Soup Docs

This package lets you easily scrape websites and extract information based on html tags and various other metadata found in the page. It can be useful for large-scale web analysis and other tasks requiring automated data gathering.

• Managing and Optimizing Your Jobs on HPC

An overview of tools and methods to manage and optimize jobs and HPC workflows

• Trusted CI

The mission of Trusted CI is to lead in the development of an NSF Cybersecurity Ecosystem with the workforce, knowledge, processes, and cyberinfrastructure that enables trustworthy science and NSF’s vision of a nation that is a global leader in research and innovation.

• Apache HTTP Server 2.4 Security Best Practices

The webpage provides guidelines for securing an Apache HTTP Server (version 2.4). It covers best practices such as minimizing module usage, restricting access with permissions, hiding server information, using secure configurations for authentication and encryption, and mitigating common threats like directory traversal and DoS attacks. The page serves as a resource for administrators to strengthen their web server’s security posture.

• Flexible and Robust Machine Learning Using mlr3 in R

The free online book for the mlr3 machine learning framework for R. Gives a comprehensive overview of the package and ecosystem, suitable from beginners to experts. You'll learn how to build and evaluate machine learning models, build complex machine learning pipelines, tune their performance automatically, and explain how machine learning models arrive at their predictions.

• Texas A&M Research Computing Training Resources

Training Resources and Courses offered by Texas A&M's Research Computing Group

• DAGMan
• DAGMan Workflows

DAGMan (Directed Acyclic Graph Manager) is a meta-scheduler for HTCondor. It manages dependencies between jobs at a higher level than the HTCondor Scheduler. It is a workflow management system developed by the High-Throughput Computing (HTC) community, specifically for managing large-scale scientific computations and data analysis tasks. It enables users to define complex workflows as directed acyclic graphs (DAGs). In a DAG, nodes represent individual computational tasks, and the directed edges represent dependencies between the tasks. DAGMan manages the execution of these tasks and ensures that they are executed in the correct order based on their dependencies. The primary purpose of DAGMan is to simplify the management of large-scale computations that consist of numerous interdependent tasks. By defining the dependencies between tasks in a DAG, users can easily express the order of execution and allow DAGMan to handle the scheduling and coordination of the tasks. This simplifies the development and execution of complex scientific workflows, making it easier to manage and track the progress of computations.

• Handwritten Digits PyTorch

This tutorial is essentially the "hello world" of image recognition and feed-forward neural network (using PyTorch). Using the MNIST database (filled within images of handwritten digits), the tutorial will instruct how to build a feed-forward neural network that can recognize handwritten digits. A solid understanding of feed-forward and back-propagation is recommended.

• Application Fundamentals

The provided text discusses various aspects of Android app development fundamentals. It covers key concepts related to app components, the AndroidManifest.xml file, and app resources. Android apps are built using various components, including Activities, Services, Broadcast Receivers, and Content Providers. These components serve different purposes and have distinct lifecycles. Activities are used for user interaction, services for background tasks, broadcast receivers for system-wide event handling, and content providers for managing shared data.The AndroidManifest.xml file is essential for declaring app components, permissions, and other settings. It informs the Android system about the app's components and capabilities. For instance, it specifies the minimum API level, declares hardware and software requirements, and defines intent filters to enable components to respond to specific actions.It's crucial to declare app requirements, such as device features and minimum Android API levels, to ensure compatibility with different devices and configurations. These declarations help in filtering the app's availability on Google Play for users with compatible devices.Android apps rely on resources separate from code, including images, layouts, strings, and more. These resources are stored in various directories and can be tailored for different device configurations. Providing alternative resources allows for optimization across different languages, screen sizes, orientations, and other factors. Understanding these fundamentals is essential for developing Android applications effectively, ensuring compatibility, and providing a consistent user experience across a wide range of devices and configurations.

• Neurostars

A question and answer forum for neuroscience researchers, infrastructure providers and software developers.

• CS224N: NLP with Deep Learning

CS244N is a renowned natural language processing course offered by Stanford University and taught by Christopher Manning. It covers a wide range of topics in NLP, including language modeling, machine translation, sentiment analysis, and more. It teaches both foundational concepts and cutting-edge research to gain a comprehensive understanding of NLP techniques and applications.

• What is VPN? How It Works, Types of VPN

A VPN, or Virtual Private Network, is a technology that creates a secure tunnel between your device and a VPN server. This tunnel encrypts all of your traffic, making it unreadable to anyone who tries to intercept it.

• The Plank Center Mentorship Guide

Backed by collegiate white papers, top industry professionals, and researchers, The Plank Center’s Mentorship Guide offers basic tips and tricks on how to get the most out of a mentorship relationship. This easy-to-follow guide supplements mentorship programs, lesson plans, and professional relationships.