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Overview

Please check this page to see upcoming events and other important dates for planned outages, upgrades, scheduled training, and news.

HPC Bootcamp Fall 2024
UW ARCC will host a HPC Bootcamp titled Research Computing & HPC Essentials - (Getting started with ARCC's services). The bootcamp will be held in person only (no virtual attendees), and runs over the course of a full week. Attendees are encouraged to bring their own devices, but some lab computers will be available at the Bootcamp. Due to demand UW ARCC has scheduled the bootcamp to be held twice during late Summer/Early Fall 2024:
  • August Bootcamp (Monday August 12, 2024 through Friday August 16, 2024)

  • September Bootcamp (Monday September 9, 2024 through Friday September 13, 2024)

Interested parties may sign up for either bootcamp here.

Our bootcamp can help train new or intermediate users on ARCC HPC resources, and will cover the topics in modules listed in the table below:

Schedule

Topics/Modules (Expand for Description)

Monday AM

 Intro to Linux Command-Line: The File System

Introduce users to typing commands using the command line to work with the Linux operating system. Focusing on hands-on exercises, it will introduce the basic structure and use of the file system, and how to find help.

Monday PM

 Intro to Linux Command-Line: View, Find and Search Files

Introduce how to work with, view, find and search the content of text files. The workshop is aimed at beginners with basic command-line experience of the Linux file system and will focus on hands-on exercises.

Prerequisites: Basic command-line experience or attendance at Intro to Linux Command Line: The File System

 Text Editors in Linux

Introduce the various text editors available on our Services. Using emacs as a GUI via an OnDemand interactive desktop, and vim/nano from a terminal command line.

Prerequisites: Basic command-line experience or attendance at either Intro to Command Line module

Tuesday AM

 Intro to HPC

Introduce UW ARCC, our core services, and how we can help.
Introduce the core concepts behind High Performance Computing and clusters.

Tuesday PM

 Intro to Accessing the Cluster

Introduce users on how to remotely access the clusters

  • Over the web using OnDemand

  • Accessing Beartooth with traditional SSH and 2 factor authentication

  • Accessing MedicineBow using passwordless authentication

 Intro to using the Module System

 Introduce users on how to set up and personalize their environment for their computational needs. 

 Intro to Job Scheduling

Introduce users to job management using the Slurm system - demonstrating how to create interactive jobs and submit jobs to the cluster queue that follow a basic workflow.

Wednesday AM

 Using OnDemand (Access to ARCC HPCs in a web browser)

Navigating Remote web access to HPC Services

Wednesday PM

 Data Management

Introducing the concept of data management with a focus on some common best practices of working with data on ARCC systems.

 Data Transfers

The practical options for transferring data from onto HPC systems from local computers and remote servers.

Thursday AM

 Intro to Using Conda: Creating Python/R and other Application Environments

 Introduce what Conda is and how it can be used to create a variety of environments, such as Python/R and contained applications.

Thursday PM

 Using Python, Conda and Pip on the Cluster

Discuss how the various Python related tools work together on the cluster and introduce a series of best practices for managing these environments. (**Note: This is not an introduction to programming in Python. It covers how to use Python, Conda and Pip on an HPC cluster)

Prerequisites: Intermediate users of HPC or attendance at prior modules, and experience programming in Python

 Using R and RStudio on the Cluster

Discuss how the various R related tools and RStudio work together on the cluster and introduce a series of best practices for managing these environments. (**Note: This is not an introduction to programming in R. It covers how to use R and RStudio on an HPC cluster)

Prerequisites: Intermediate users of HPC or attendance at prior modules, and experience programming in R or RStudio

Friday AM

 Jupyter Notebooks with OnDemand
  • Demonstrate how to use the OnDemand Jupyter Service across a variety of available languages and kernels.

  • Demonstrate how to convert an existing Conda environment into a kernel that can be used within a notebook.

Prerequisites: Intermediate users of HPC or attendance at Using Python, Conda and Pip on the Cluster

 Intro to External HPC Resources

Introducing external HPC resources available to UW researchers including those hosted by NWSC/NCAR and ANL (Argonne National Labs). Provides information for how prospective users can request access and support. It will also cover how knowledge gained from using UW ARCC HPC resources that can be translated to resources provided by external centers.

Those who sign up for a bootcamp have the option to attend all modules, but are not required to attend all of them.

Please contact arcc-help@uwyo.edu with any questions, inquiries, or comments.

MedicineBow Go-Live Delayed and Beartooth Maintenance Scheduled
In response to some supply chain issues and equipment delays, ARCC is pushing back the go-live date of the MedicineBow cluster by 2 weeks. MedicineBow is now scheduled to be released to campus on Monday July 15th, 2024.

We have also scheduled Beartooth maintenance for the end of the month beginning Monday July 29th 2024. This maintenance is scheduled for completion at the end of that week, August 2nd, 2024.

We apologize for any inconvenience. Please reach out to us with any questions or concerns at arcc-help@uwyo.edu.

R Vulnerability
Please be aware of a vulnerability in the R language in all versions prior to R version 4.4.0. Here are several announcements about the vulnerability: 
https://www.cisa.gov/news-events/alerts/2024/05/01/certcc-reports-r-programming-language-vulnerability

https://kb.cert.org/vuls/id/238194  :   “A vulnerability in the R language that allows for arbitrary code to be executed directly after the deserialization of untrusted data has been discovered. This vulnerability can be exploited through RDS (R Data Serialization) format files and .rdx files. An attacker can create malicious RDS or .rdx formatted files to execute arbitrary commands on the victim's target device.”

We encourage all of our R users to migrate to R version 4.4.0, and off of prior versions of R (4.3.x or earlier) at your earliest convenience. To assist you with this migration we have installed modules for R version 4.4.0 on the Beartooth HPC Environment:

r/4.4.0
r-rmpi/0.7-1-ompi-r4.4

These modules are available via the “module …” commands as well as in OnDemand. The R/4.4.0 module is now the default R module on Beartooth, Loren and Wildiris HPC Clusters and will be the only R module available on MedicineBow. These modules include the R packages we typically include in our earlier R modules. If you have installed any libraries yourself you will need to re-install those libraries in R version 4.4.0, as those installations are version-specific.

We intend to disable ARCC’s older R modules on Beartooth by Friday June 28th, 2024.

If you have installed your own copy of R, via conda or some other method, you are welcome to use ARCC’s R modules. We encourage you to upgrade your personally installed version of R to 4.4.0.

Please let us know if you have any questions by writing to us at arcc-help@uwyo.edu


Announcements:

See Past ARCC Related Announcements Here

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