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Knowledge Base Resources

Contributed by cyberinfrastructure professionals (researchers, research computing facilitators, research software engineers and HPC system administrators), these resources are shared through the ConnectCI community platform. Add resources you find helpful!
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Topics

  • machine-learning (50)
  • ai (43)
  • training (40)
  • data-analysis (39)
  • deep-learning (28)
  • documentation (28)
  • big-data (26)
  • neural-networks (24)
  • workforce-development (20)
  • visualization (18)
  • professional-development (17)
  • parallelization (16)
  • programming (14)
  • community-outreach (13)
  • image-processing (13)
  • cybersecurity (12)
  • gpu (12)
  • r (12)
  • pytorch (11)
  • slurm (10)
  • c (9)
  • cloud-computing (9)
  • compiling (9)
  • mpi (9)
  • plotting (9)
  • administering-hpc (8)

Programming Language

  • python (48)
  • c++ (15)
  • bash (8)

Science Domain

  • data-science (16)

Skill Level

  • intermediate (191)
  • beginner (189)
  • advanced (111)

Content Type

  • learning (91)
  • website (64)
  • documentation (57)
  • tool (34)
  • video_link (19)
  • presentation (7)
  • mailing_list (2)
  • video (1)
Data visualization with Matplotlib
0
  • Guide to data visualization with matplotlib
Data visualization is a critical aspect of data analysis. It allows for a clear and concise representation of data, making it easier for users to understand and interpret complex datasets. One of the most popular libraries for data visualization in Python is Matplotlib. The included website aims to provide a brief overview of Matplotlib, its features, and examples/exercises to dive deeper into its functionalities.
plottingvisualization
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Type
website
Level
Beginner
ACES: Charliecloud Containers for Scientific Workflows (Tutorial)
0
  • ACES: Charliecloud Containers for Scientific Workflows (Video)
  • ACES: Charliecloud Containers for Scientific Workflows (Slides)
This tutorial introduces the use of Containers using the Charliecloud software suite. This tutorial will provide participants with background and hands-on experience to use basic Charliecloud containers for HPC applications. We discuss what containers are, why they matter for HPC, and how they work. We'll give an overview of Charliecloud, the unprivileged container solution from Los Alamos National Laboratory's HPC Division. Students will learn how to build toy containers and containerize real HPC applications, and then run them on a cluster. Exercises are demonstrated using the ACES cluster, a composable accelerator testbed at Texas A&M University. Students with an allocation on the ACES cluster can follow along with the ACES-specific exercises.
ACESTAMUscratchlammpstensorflowopen-ondemandgpunfsslurmbashtrainingpythoncontainers
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Type
learning
Level
Beginner
Python Data and Viz Training (CCEP Program)
0
5 Days of recordings of Python data analysis and visualization training.
data-sciencepython
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Type
learning
Level
Beginner, Intermediate
Python Tools for Data Science
0
  • Python Tools for Data Science
Python has become a very popular programming language and software ecosystem for work in Data Science, integrating support for data access, data processing, modeling, machine learning, and visualization. In this webinar, we will describe some of the key Python packages that have been developed to support that work, and highlight some of their capabilities. This webinar will also serve as an introduction and overview of topics addressed in two Cornell Virtual Workshop tutorials, available at https://cvw.cac.cornell.edu/pydatasci1 and https://cvw.cac.cornell.edu/pydatasci2
aimachine-learningbig-datadata-analysisdata-wranglingdata-sciencetrainingworkforce-developmentpythonscikit-learnsql
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Type
video_link
Level
Intermediate
Examples of Thrust code for GPU Parallelization
0
  • thrust_ex.txt
Some examples for writing Thrust code. To compile, download the CUDA compiler from NVIDIA. This code was tested with CUDA 9.2 but is likely compatible with other versions. Before compiling change extension from thrust_ex.txt to thrust_ex.cu. Any code on the device (GPU) that is run through a Thrust transform is automatically parallelized on the GPU. Host (CPU) code will not be. Thrust code can also be compiled to run on a CPU for practice.
parallelizationgpucuda
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Type
learning
Level
Intermediate, Advanced
Gaussian 16
0
  • Gaussian 16 HomePage
  • About Gaussian 16
Gaussian 16 is a computational chemistry package that is used in predicting molecular properties and understanding molecular behavior at a quantum mechanical level.
gaussiancomputational-chemistry
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Type
tool
Level
Intermediate, Advanced
Rockfish at Johns Hopkins University
0
  • Rockfish Resources and Documentation
Resources and User Guide available at Rockfish
rockfish
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Type
documentation
Level
Intermediate
Anvil Documentation
0
  • Anvil Documentation
Documentation for Anvil, a powerful supercomputer at Purdue University 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.
anvil
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Type
documentation
Level
Beginner, Intermediate, Advanced
HPCwire
0
  • HPCwire
HPCwire is a prominent news and information source for the HPC community. Their website offers articles, analysis, and reports on HPC technologies, applications, and industry trends.
documentationpytorchdata-sciencebioinformaticshpc-operationstrainingprogrammingprogramming-best-practicespython
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Type
website
Level
Beginner, Intermediate, Advanced
Official Documentation of VisIt
0
  • Vislt github
  • Writing a File Format Reader
VisIt is a prominent open-source, interactive parallel visualization and graphical analysis tool predominantly used for viewing scientific data. Its GitHub repository offers a detailed insight into the software's source code, documentation, and contribution guidelines. In particular, it offers useful examples on how it
visItnovel-acceleratorsparticle-physics
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Type
documentation
Level
Intermediate, Advanced
Docker Container Library
0
  • Docker Container Library
The Docker container library, commonly known as Docker Hub, is a vast repository that hosts a multitude of pre-configured container images, streamlining the deployment process. It can drastically speed up a workflow, and gives you a consistent starting point each time. Check it out, they might have exactly what you are looking for!
documentationcloud-computingcloud-open-sourcedata-access-protocolsdata-managementdata-reproducibilitycontainers
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Type
tool
Level
Managing and Optimizing Your Jobs on HPC
0
  • Managing and Optimizing Your Jobs on HPC
An overview of tools and methods to manage and optimize jobs and HPC workflows
memoryoptimizationbatch-jobsjob-accountingjob-submissionresourcesslurm
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Type
video_link
Level
Intermediate
GIS: What is a Geodetic Datums?
0
  • What are Geodetic Datums?
Often when working with GIS, or spatial data, one encounters the word "datum" and it may require that you choose a "datum" when doing GIS computation tasks. Below is a short video on what are datums from NOAA and UCAR.
arcgisgis
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Type
learning
Level
Beginner
Advanced Mathematical Optimization Techniques
0
  • https://scipy-lectures.org/advanced/mathematical_optimization/
Mathematical optimization deals with the problem of finding numerically minimums or maximums of a functions. This tutorial provides the Python solutions for the optimization problems with examples.
optimizationpython
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Type
learning
Level
Beginner, Intermediate, Advanced
ACCESS - Video for new ACCESS users
0
  • Using ACCESS at Duke
This is a short video on how to exchange ACCESS credits and connect to Jetstream 2 (please note this was created for Duke users but applies to all) .
ACCESS-accountACCESS-creditsexchange-requestjetstreamcloud-computinglogintrainingcilogon
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Type
video_link
Level
Beginner
Research Security Operations Center at IU
0
  • Research Security Operations Center
The NSF-funded ResearchSOC helps make scientific computing resilient to cyberattacks and capable of supporting trustworthy, productive research through operational cybersecurity services, training, and information sharing necessary to a community as unique and variable as research and education (R&E). ResearchSOC is a service offering from Indiana University's OmniSOC.
cybersecurity
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Type
website
Level
Beginner, Intermediate, Advanced
PetIGA, an open-source code for isogeometric analysis
0
  • github link
  • documentation link
This documentation provides an overview of the PetIGA framework, an open source code for solving multiphysics problems with isogeometric analysis. The documentation covers some simple tutorials and examples to help users get started with the framework and apply it to solve real-world problems in continuum mechanics, including solid and fluid mechanics.
finite-element-analysisdocumentationfluid-dynamicsc
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Type
documentation
Level
Beginner, Intermediate
Fairness and Machine Learning
0
  • Fairness and Machine Learning
The "Fairness and Machine Learning" book offers a rigorous exploration of fairness in ML and is suitable for researchers, practitioners, and anyone interested in understanding the complexities and implications of fairness in machine learning.
aidata-analysisdeep-learningmachine-learningdata-science
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Type
documentation
Level
Intermediate, Advanced
Containerization Explained
0
  • Containerization Explained
Containerization is a software development method in which applications are packaged into standard units for development, shipment, and deployment.
containers
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Type
video_link
Level
Beginner
United Nations Mentor Handbook
0
  • United National Mentor Handbook
The United Nations (UN) is an international organization comprising 193 Member States, including the United States. As a global organization, the UN is the one place on Earth where the world's nations can gather to discuss common problems and find shared solutions that benefit all humanity. This handbook has been produced for UN staff of all backgrounds and levels and provides an overview of how to approach your participation in a mentorship program. This resource is quickly digestible and provides a basic structure that will be helpful to review before the first meeting with your mentee.
mentorshipprofessional-developmenttrainingworkforce-development
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Type
documentation
Level
Beginner
Paraview UArizona HPC links (beginner)
0
  • University of Arizona Visualization homepage
  • Getting Started with Paraview
  • Paraview Cameras and Keyframes
  • Graphs and Data Exporting
  • Visualizing netcdf files
These links take you to visualization resources supported by the University of Arizona's HPC visualization consultant (rtdatavis.github.io). The following links are specific to the Paraview program and the workflows that have been used my researchers at the U of Arizona. Some of the pages linked are very beginner friendly: getting started, working with cameras and keyframes for rendering, visualizing external files (netcdf climate data), graphs and data exporting. Many of the workflows involve using remote desktops via the Open On Demand interface, but if this isn't set up at your university you can use paraview locally on a desktop. Feel free to post on access ci https://ask.cyberinfrastructure.org/ if you need assistance getting a paraview gui open for your work on HPC.
visualization
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Type
documentation
Level
Beginner
PyTorch Introduction
0
  • PyTorch Tutorial at Stanford University
This is a very barebones introduction to the PyTorch framework used to implement machine learning. This tutorial implements a feed-forward neural network and is taught completely asynchronously through Stanford University. A good start after learning the theory behind feed-forward neural networks.
deep-learningmachine-learningneural-networkspytorchpython
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Type
website
Level
Intermediate
Practical Machine Learning with Python
0
  • Regression forecasting and predicting - Practical Machine Learning Tutorial with Python p.5
This video series provides a holistic understanding of machine learning, covering theory, application, and inner workings of supervised, unsupervised, and deep learning algorithms. It covers topics such as linear regression, K Nearest Neighbors, Support Vector Machines (SVM), flat clustering, hierarchical clustering, and neural networks. Goes over the high level intuitions of the algorithms and how they are logically meant to work. Apply the algorithms in code using real world data sets along with a module, such as with Scikit-Learn.
machine-learningprogrammingpython
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Type
video_link
Level
Advanced
Bash shell tutorial
0
  • Bash shell tutorial
Training materials for using the bash (and zsh) shell.
bash
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Type
learning
Level
Intermediate

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