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Source repo: ciml-summer-institute-2021 | Branch: main | Last synced: 2026-04-24 10:27:17.425 UTC

Preparing for the CIML Summer Institute 2021

You will get the most out of the CIML Summer Institute if you are prepared prior to the event. By brushing up on your knowledge of Linux and installing all necessary software on your laptop before to the event, you’ll be able to focus your attention on the skills and topics that are most relevant to high performance and data intensive computing.

To help you get the most out of this workshop, this section contains a set of detailed start-up instructions, beginning with setting up your account and connecting to Expanse, to configuring your laptop for running visualization software. Please read the documents and exercises carefully, and complete all necessary steps before event. Feel free to ask questions or if you have any problems with the start-up tasks

Contents​

Prep Day Schedule (6/18/2021, 9-11 am):​

TIME (PST)TOPICPRESENTER
9:00 AM - 9:10 AMWelcomepresenter
9:10 AM – 9:40 AMAccounts, Login, Environment, Running Jobspresenter
9:40 AM – 10:10 AMInstalling miniconda, Running Jupyter Notebookspresenter
10:10 AM – 10:40 AMHands-on - Confirm conda installation (mini-conda)presenter
10:40 AM – 11:00 AMQ&A, Wrap-upall
note

if you have any difficulties getting set up, please contact Institute staff at consult@sdsc.edu.

Expanse User Guide​

Please read the Expanse user guide and familiarize yourself with the hardware, file systems, batch job submission, compilers and modules. The guide can be found here:

Accounts:​

Logging onto Expanse training account:​

  • You will be given an account on the SDSC Expanse computer. Information on the account will be sent to you via email. Please complete the process of activating your account before the institute begins.

Logging onto the Expanse Portal:​

  • This section will be covered on day 1 (1.3 Expanse & Expanse User Portal).
  • XSEDE training accounts to access the Expanse portal have already been created for you. Please do not create a new one on your own.
  • Once you have received your expanse account information, please go to https://portal.expanse.sdsc.edu, to confirm your login.

Computer and Laptop Set-up:​

  • We recommend a second screen for the hands-on sessions. The first to view the presentation, the second for hands-on.
  • After you access your account information, confirm that you can login (SSH) to Expanse using the device you plan to use during the CIML Summer Institute (laptop, workstation, etc...). Detailed instructions on connecting to Expanse using SSH can be found here.

It has been suggested that a second monitor may be helpful during online instruction. While one monitor could be used to follow instruction, the other for the hands-on. Additionally, the use of a mouse may be beneficial as well during some sessions.

Remote access via Zoom, Slack, and GitHub​

  • For the institute, we will coordinate our remote access via Zoom, Slack, and GitHub
  • When setting up your “display name” on Zoom & Slack, please list your FIRST name, LAST name, and institution (i.e., Jane Doe (SDSC))

Zoom:​

You will need to install the latest Zoom client, which is available for Windows, MacOS and Linux, Once installed, you can test your microphone and camera interface with Zoom here. You can find more information on Zoom system requirements, including bandwidth requirements here.

To ensure the security of our Zoom links, details will be sent to all participants just prior to preparation day (June 18) and again prior to CIML Summer Institute week (June 22-24). Zoom details for all sessions will be unique.

Slack:​

  • We will also be using Slack as our main platform for announcements, where participants can communicate and ask for help. Download (Windows, MacOS, or Linux) and get started. Zoom chat will be disabled. Make sure to turn on your notifications to receive alerts.
  • When setting up your “display name” on Zoom & Slack, please list your FIRST name, LAST name, and institution (i.e., Jane Doe (SDSC))

Github:​

Using GitHub​

Software Requirements:​

The document below contains a list of software being used at the institute and installation instructions:

Basic Skills​

See the Basic HPC Skills repo https://github.com/sdsc-hpc-training-org/basic_skills/tree/master/basic_linux_skills