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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)
RMACC Website
0
  • RMACC.org
Rocky Mountain Advanced Computing Consortium Website
community-outreach
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Type
website
Level
Beginner, Intermediate, Advanced
MATLAB with other Programming Languages
0
  • Using MATLAB with Other Programming Languages
MATLAB is a really useful tool for data analysis among other computational work. This tutorial takes you through using MATLAB with other programming languages including C, C++, Fortran, Java, and Python.
cc++fortranjavamatlabpython
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Type
tool
Level
Beginner, Intermediate, Advanced
Vulkan Support Survey across Systems
0
  • OSF hosted knowledge base submission
It's not uncommon to see beautiful visualizations in HPC center galleries, but the majority of these are either rendered off the HPC or created using programs that run on OpenGL or custom rasterization techniques. To put it simply the next generation of graphics provided by OpenGL's successor Vulkan is strangely absent in the super computing world. The aim of this survey of available resources is to determine the systems that can support Vulkan workflows and programs. This will assist users in getting past some of the first hurdles in using Vulkan in HPC contexts.
big-datacomputer-graphicsworkflow
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Type
learning
Level
Intermediate
GDAL Multi-threading
0
  • GDAL Multi-threading
Multi-threading guidance when using GDAL.
parallelizationgis
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Type
learning
Level
Intermediate
Ultimate guide to Unix
0
  • unix list of basic commands
Unix is incredibly common and useful. This website provides all the common commands and explanations for one to get started with a unix system.
bash
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Type
website
Level
Beginner
Using Dask on HPC Systems
0
  • 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
trainingjupyterhubpython
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Type
learning
Level
Beginner, Intermediate
Implementing Markov Processes with Julia
0
  • Markov Decision Processes in Julia
The following link provides an easy method of implementing Markov Decision Processes (MDP) in the Julia computing language. MDPs are a class of algorithms designed to handle stochastic situations where the actor has some level of control. For example, used at a low level, MDPs can be used to control an inverted pendulum, but applied in higher level decision making the can also decide when to take evasive action in air traffic management. MDPs can also be extended to the partially observable domain to form the Partially Observable Markov Decision Process (POMDP). This link contains a wealth of information to show one can easily implement basic POMDP and MDP algorithms and apply well known online and offline solvers.
aimachine-learningjulia
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Type
tool
Level
Intermediate, Advanced
Learn Python Online
0
  • Python Courses Online
Learn Python online with these distance learning courses.
professional-developmenttrainingpython
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Type
website
Level
Beginner
Language models and using HPC resources
0
  • AI-Generated Text Detection In 2023
Documentation and research based on the latest NLP text generation detection methods for 2023.
natural-language-processing
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Type
learning
Level
Intermediate
CyberAmbassadors: Professional Skills for Interdisciplinary Work
0
  • CyberAmbassador Program
The CyberAmbassadors project was funded through a workforce development grant from the National Science Foundation (Award #1730137). Starting in 2017, the initial focus of this project was to develop, test, and refine new curriculum to help CyberInfrastructure (CI) Professionals strengthen their communications, teamwork and leadership skills. With support and collaboration from a number of academic and professional organizations, the CyberAmbassadors project was expanded to offer professional skills training to college students and professionals working across STEM (science, technology, engineering, math) disciplines.
mentorshipprofessional-developmentresearch-facilitationtrainingworkforce-development
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Type
learning
Level
Beginner, Intermediate, Advanced
Samtools Documentation
0
  • https://www.htslib.org/doc/
Samtools is a suite of programs for interacting with high-throughput sequencing data, especially in the SAM/BAM format. It offers various utilities for processing, analyzing, and managing sequence data generated from next-generation sequencing (NGS) experiments. Samtools is widely used in bioinformatics and genomics research for tasks such as read alignment, variant calling, and data manipulation.
documentationdata-analysisbioinformaticsdata-sciencegenomics
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Type
documentation
Level
Beginner, Intermediate, Advanced
Charliecloud User Group
0
  • Charliecloud User Group
Announcements for for users and developers of Charliecloud, which provides lightweight user-defined software stacks for high-performance computing.
containers
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Type
mailing_list
Level
Beginner
ACCESS Support Portal
0
  • ACCESS Support Portal
affinity-grouppegasusACCESS-websiteopen-ondemand
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Type
website
Level
Beginner, Intermediate, Advanced
Use Windows Subsystem for Linux for HPC Command Line Access from Windows
0
  • Install Linux on Windows with WSL
Windows Subsystem for Linux (WSL) provides a Linux environment for Windows users to access HPC resources fast and efficiently.
workflowssh
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Type
tool
Level
Beginner
TensorFlow for Deep Neural Networks
0
  • TensorFlow Docs
TensorFlow is a powerful framework for Deep Learning, developed by google. This specifically is their python package, which is easy to use and can be used to train incredibly powerful models.
documentationfastertensorflow
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Type
tool
Level
Intermediate, Advanced
Installing Rocky Linux Operating System
0
  • Installing Rocky Linux 9
Rocky Linux is an open-source enterprise operating system. It is compatible with Red Hat Enterprise Linux (RHEL). It is a community-driven project that provides a stable and reliable platform for production workloads. It is one of the best alternatives to Opensource CentOS, since Centos will be on end of life (EoL) soon in 2024 by shifting to CentOS Stream.
unix-environmentsoftware-installation
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Type
learning
Level
Beginner
Neurodesk
0
  • Neurodesk
Neurodesk provides a containerised data analysis environment to facilitate reproducible analysis of neuroimaging data. Analysis pipelines for neuroimaging data typically rely on specific versions of packages and software, and are dependent on their native operating system. These dependencies mean that a working analysis pipeline may fail or produce different results on a new computer, or even on the same computer after a software update. Neurodesk provides a platform in which anyone, anywhere, using any computer can reproduce your original research findings given the original data and analysis code.
psychologycontainerssoftware-installationversion-control
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Type
website
Level
Beginner, Intermediate, Advanced
Data Imputation Methods for Climate Data and Mortality Data
0
  • Data Imputation Methods for Climate Data and Mortality Data - Slices
  • Github repository
  • Data Imputation Methods for Climate Data and Mortality Data - Full Tutorial
This slices and videos introduced how to use K-Nearest-Neighbors method to impute climate data and how to use Bayesian Spatio-Temporal models in R-INLA to impute mortality data. The demos will be added soon.
allocation-valuedocumentationaiplottingvisualizationdata-analysismachine-learning
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Type
video_link
Level
Intermediate, Advanced
ACCESS KB Guide - DELTA
0
  • ACCESS KB Guide - DELTA
NCSA is the home of Delta, a computing and data resource that balances cutting-edge graphics processor and CPU architectures with a non-POSIX file system with a POSIX-like interface. Delta allows applications to reap the benefits of modern file systems without rewriting code.
delta
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Type
documentation
Level
Beginner, Intermediate, Advanced
Slurm Tutorials
0
  • Slurm Tutorials
Introduction to the Slurm Workload Manager for users and system administrators, plus some material for Slurm programmers.
administering-hpccluster-managementhpc-cluster-architecturetraining
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Type
learning
Level
Beginner
Ask.CI Q&A Platform for Research Computing
0
  • Ask.CI
resourcesprogramming-best-practices
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Type
website
Level
Beginner, Intermediate, Advanced
Weka
0
  • Weka Homepage
  • Weka Data Mining Tutorials
Weka is a collection of machine learning algorithms for data mining tasks. It contains tools for data preparation, classification, regression, clustering, association rules mining, and visualization.
big-datadata-analysismachine-learningwekadata-sciencejava
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Type
tool
Level
Intermediate, Advanced
ACCESS Video Learning Center
0
  • Video Learning Center
A library of short videos about ACCESS allocations, resources and support.
training
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Type
video_link
Level
Beginner
Campus Champions Home Page
0
  • Campus Champions Home
Campus Champions foster a dynamic environment for a diverse community of research computing and data professionals sharing knowledge and experience in digital research infrastructure.
community-outreachprofessional-development
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Type
website
Level
Beginner, Intermediate, Advanced

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