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

Preparing for the SDSC Summer Institute 2022

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

This section contains a set of detailed start-up instructions for setting up your account, connecting to Expanse and configuring your laptop to run the 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:

HPC Systems Accounts:​

  • For the Summer Institute, we have created training accounts for you:
    • (1) For access for the Expanse portal, use your XSEDE portal username: trainXX
    • (2) For direct access to the system via ssh, use your SDSC local username: xdtrXX
  • 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 (portal.expanse.sdsc.edu):​

  • 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 "SDSC 2022 Summer Institute: Account Set-Up".
  • Use username "trainXX"
  • 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" (SSH/terminal):​

Computer Requirements:​

  • After you access your account information, confirm that you can login (SSH) to Expanse using the device you plan to use during the SDSC Summer Institute (laptop, workstation, etc...). Detailed instructions on connecting to Expanse using SSH can be found here.
  • We recommend a second screen for the hands-on sessions. The first to view the presentation, the second for hands-on.
  • For visualization tutorial a mouse with scroll wheel is highly recommended (laptop track pads are very difficult to use for 3D navigation).

Remote access via GitHub, Zoom, and Slack​

  • For the institute, we will coordinate our remote access using GitHub, Zoom, and Slack.
  • When setting up your “display name” on both Zoom & Slack, please use your FIRST name, LAST name, and institution (i.e., Harry Potter (SDSC)).

Github:​

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 as a calendar invite to all HPC/DS 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 have access to FOUR channels:

  • Main Room: Used for announcements, team-wide conversations, and any questions during sessions. For assistance with your account, go to #help-desk channel
  • Breakout Room: Used for instructions occurring in the Zoom “breakout room” during parallel sessions.
  • Help-desk: 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.

Software Requirements:​

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

Preparation Activities:​

The Summer Institute is a combination of in-depth lectures and hands-on learning. The following documents will guide you through the necessary steps needed to be prepared to get to work when you arrive at the Institute.

Basic HPC Skills:​

Launching Jupyter Notebooks:​