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Source repo: ciml-summer-institute-2022 | Branch: main | Last synced: 2026-04-24 10:27:17.425 UTC

Preparing for the CIML Summer Institute

SESSION: 0_preparation

Instructions:​

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​

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:

note

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

HPC Systems Accounts:​

  • For the CIML Institute, we have created TWO types of Training accounts for you:
    • (1) XSEDE and Expanse portal ID
    • (2) Local Expanse user account
  • Note: The two topics below will be covered on the Preparation day (1.2 Accounts, Login, Environment, Running Jobs and Logging into Expanse User Portal).

Logging onto the Expanse 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. See email sent from cwong@sdsc.edu for your XSEDE & Expanse acount with the subject link "CIML 2022 Summer Institute: Account Set-Up".
  • Once you have received your XSEDE and Expanse portal ID information, go to https://portal.expanse.sdsc.edu, to confirm your login.
  • For a short (18 min) video on using the Expanse portal, see here.

Logging onto Expanse using your "Local Expanse user account":​

Basic Skills​

There are several basic skills needed in order to access and run jobs on HPC systems. There are two GitHub repositories with several mini-tutorials that you can access:

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 both Zoom & Slack, please use your FIRST name, LAST name, and institution (i.e., Harry Potter (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.

Connection details were sent via as a calendar invite to all CIML participants. You should have received TWO invites (1) preparation day and (2) instruction days. If you did not receive this as noted, please contact cwong@sdsc.edu.

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 Slack notifications to receive alerts.

You should have access to THREE channels:

  • General: This channel will be used for announcements, team-wide conversations, and any questions during sessions. For assistance with your account, go to #help-desk channel
  • Help-desk: This channel will be used to troubleshoot any issues related to account access or login
  • Introduce-yourself: With everyone attending virtually, getting the opportunity to introduce each other is hard. Please use this space to introduce yourself, so we can get to know each other.

Github:​