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Knowledge Base Resources

These resources are contributed by researchers, facilitators, engineers, and HPC admins. Please upvote resources you find useful!
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Topics

  • machine-learning (50)
  • ai (45)
  • training (41)
  • data-analysis (40)
  • deep-learning (28)
  • documentation (28)
  • big-data (26)
  • neural-networks (24)
  • workforce-development (21)
  • professional-development (18)
  • visualization (18)
  • parallelization (16)
  • community-outreach (14)
  • programming (14)
  • 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)

Topics

  • machine-learning (50)
  • ai (45)
  • training (41)
  • data-analysis (40)
  • deep-learning (28)
  • documentation (28)
  • big-data (26)
  • neural-networks (24)
  • workforce-development (21)
  • professional-development (18)
  • visualization (18)
  • parallelization (16)
  • community-outreach (14)
  • programming (14)
  • 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)

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RMACC Systems Administrator Workshop Slides
0
  • RMACC Sys Admin Workshop '24 Slides
A compilation of the slides from this year's RMACC Sys Admin Workshop. RMACC Sys Admin Workhop Schedule: Tuesday 12:00 PM Sign-in 1:00 PM Introductions 1:30 PM Lightning Talk - HPC Survival guide 2:00 PM Node Management - Scott Serr 2:30 PM Lightning Talk - Warewulf 3:00 PM Urgent HPC - Coltran Hophan-Nichols and Alexander Salois Wednesday 9:00 AM Breakfast 10:00 AM Round table Sites - BYU, INL, UMT, ASU, MSU 11:00 AM Open OnDemand setup - Dean Anderson 11:30 AM Lightning talk - Long term hardware support 12:00 PM Lunch 1:00 PM HPC Security - Matt Bidwell 2:00 PM Lightning talk- Security 2:30 PM ACCESS resources - Couso 3:00 PM Easybuild tutorial - Alexander Salois 3:30 PM General Q & A Thursday 9:00 AM Breakfast 10:00 AM Lightning Talk- Containers and Virtual Machines 11:00 AM University of Montana - Hellgate Site Tour 11:30 AM Closing Remarks
administering-hpchpc-toolscluster-supporthardwarehpc-cluster-architecturehpc-operationshpc-storagenetworkingserverless-hpcprofessional-development
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Type
presentation
Level
Intermediate, 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
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
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
Numba: Compiler for Python
0
  • Numba Compiler
Numba is a Python compiler designed for accelerating numerical and array operations, enabling users to enhance their application's performance by writing high-performance functions in Python itself. It utilizes LLVM to transform pure Python code into optimized machine code, achieving speeds comparable to languages like C, C++, and Fortran. Noteworthy features include dynamic code generation during import or runtime, support for both CPU and GPU hardware, and seamless integration with the Python scientific software ecosystem, particularly Numpy.
vectorizationoptimizationperformance-tuningparallelization
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Type
documentation
Level
Intermediate, Advanced
Introductory Python Lecture Series
0
  • Python Handbook Series
A lecture and notes with the goal of teaching introductory python. Starting by understanding how to download and start using python, then expanding to basic syntax for lists, arrays, loops, and methods.
documentationprogrammingpython
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Type
learning
Level
Beginner
RMACC Website
0
  • RMACC.org
Rocky Mountain Advanced Computing Consortium Website
community-outreach
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Type
website
Level
Beginner, Intermediate, Advanced
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
GDAL Multi-threading
0
  • GDAL Multi-threading
Multi-threading guidance when using GDAL.
parallelizationgis
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Type
learning
Level
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
GPU Acceleration in Python
0
  • GPU Acceleration in Python
This tutorial explains how to use Python for GPU acceleration with libraries like CuPy, PyOpenCL, and PyCUDA. It shows how these libraries can speed up tasks like array operations and matrix multiplication by using the GPU. Examples include replacing NumPy with CuPy for large datasets and using PyOpenCL or PyCUDA for more control with custom GPU kernels. It focuses on practical steps to integrate GPU acceleration into Python programs.
machine-learningbig-datadata-analysisoptimizationparallelizationgpucudapython
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Type
learning
Level
Beginner, Intermediate
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
MPI Resources
0
  • Easy MPI Tutorial
  • Open MPI documentation
Workshop for beginners and intermediate students in MPI which includes helpful exercises. Open MPI documentation.
parallelizationmpi
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Type
learning
Level
Beginner, Intermediate
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
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
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
Big Data Research at the University of Colorado Boulder
0
  • Big Data Research at the University of Colorado Boulder
Background: Big data, defined as having high volume, complexity or velocity, have the potential to greatly accelerate research discovery. Such data can be challenging to work with and require research support and training to address technical and ethical challenges surrounding big data collection, analysis, and publication. Methods: The present study was conducted via a series of semi-structured interviews to assess big data methodologies employed by CU Boulder researchers across a broad sample of disciplines, with the goal of illuminating how they conduct their research; identifying challenges and needs; and providing recommendations for addressing them. Findings: Key results and conclusions from the study indicate: gaps in awareness of existing big data services provided by CU Boulder; open questions surrounding big data ethics, security and privacy issues; a need for clarity on how to attribute credit for big data research; and a preference for a variety of training options to support big data research.
big-data
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Type
documentation
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
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
ACCESS Events and Training
0
  • Events and Training
Listing of upcoming ACCESS related events and training activities.
professional-developmenttrainingworkforce-development
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Type
website
Level
Beginner
Workshop on LangChain and GPT
0
  • Zoom Recording of Workshop on LangChain and GPT
  • Code
  • Data

This interactive workshop introduces participants to the power of GPT and LangChain for solving domain-specific scientific challenges. Participants will learn how to use these tools to address real research problems, such as predicting molecular properties or analyzing large-scale datasets in genomics. Through guided tutorials and hands-on project development, attendees will leave with a working application tailored to their own research needs.

aillmdata-analysispython
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Type
video_link
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
Master's in Data Science Program Guide - TechGuide
0
  • Masters in Data Science Program Guide
A master’s degree in data science helps prepare professionals to take the next career step. This article will focus primarily on data science, a graduate degree in this field, and a data scientist or data analyst career. With many employers preferring a master’s degree in data science for those seeking to fill roles as data scientists or analysts, we will discuss the data science master’s degree in detail.
big-datadata-analysisdata-science
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Type
website
Level
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

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