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Source repo: sdsc-summer-institute-2025 | Branch: main | Last synced: 2026-04-24 10:27:17.425 UTC

# Preparing for the SDSC Summer Institute 2025​

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 the event. Feel free to ask questions or if you have any problems with the start-up tasks.

Preparation Checklist​

Here is a summary of tasks to be completed before the institute begins:

Contents

Expanse User Guide​

We will cover the basics of using Expanse during the institute. However, the Expanse User Guide is a comprehensive resource that you should keep handy for reference. After the institute, you may need to review details about specific configurations. Here are some key points from the guide that you may find useful:

  • System Architecture: Expanse has different types of nodes for various computational needs, including standard compute nodes, GPU nodes with NVIDIA V100s, and large-memory nodes.
  • File Systems: You will have access to different file systems:
    • $HOME (/home): 100GB for source code and configuration files (backed up). Do not run jobs from here.
    • /expanse/lustre/scratch: Large, high-performance space for temporary job data. Not backed up, and files are purged after 90 days.
    • /expanse/lustre/projects: Project-specific storage space.
    • /scratch/$USER/job_$SLURM_JOB_ID: Fast, temporary local storage on compute nodes, available only during job execution.
  • Connecting: Connect to Expanse via SSH with two-factor authentication (2FA).
  • Software Environment: Manage software with module. Use module spider package_name`` to find available packages.
  • Running Jobs: Submit jobs to the Slurm scheduler with sbatch. Use srun for interactive sessions. Example scripts are in /cm/shared/examples/sdsc/ on Expanse.

Please keep the link to the full guide ready. It will be a valuable resource for you.

HPC Systems Accounts​

You will need a training account to access SDSC’s Expanse HPC system for the HPC & Data Science Summer Institute. This account will be created for you by our team.

An email will be sent from consult@sdsc.edu with the subject line "HPC & Data Science 2025 Summer Institute: Account Set-Up" that will include your training account username and password and instructions. We will send this email in time for "Prep Day," where we will be covering how to manage your training account, along with other useful information.

As a reminder, we are asking all attendees to use the training accounts that we are providing, even if you already have your own account. This will minimize problems related to custom configurations (e.g. environment variables, choice of shell, etc.) that may cause some of the hands-on examples to break.

This training account may be used:

Computer Requirements​

  • Laptop Required: The HPC and Data Science Summer Institute is designed as a hands-on program and does require that you bring a laptop with administrative privileges and wireless connectivity.
  • WiFi will be available throughout the SDSC building
  • Remember your charger. There will be extension cords throughout the room for charging devices.

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​

There are several methods for launching a secure Jupyter Notebook on Expanse:

Software Requirements​

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

GitHub, Slack, and Zoom​

Github​

  • Training material will be located on the SDSC Summer Institute GitHub repo and one of the Wednesday sessions will require a GitHub account.
  • If you do not already have one, you can create a free personal GitHub account here.
  • For basic GitHub usage on SDSC systems, see here

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 during the preparation day. Make sure to turn on your Slack notifications to receive alerts.
  • See "Preparation Information | HPC & Data Science Summer Institute 2025" email received for the link to join the Slack workspace for this institute.

Zoom​

  • We will be using Zoom for preparation day on Tuesday, July 29, 2025, from 9am-11am (Pacific Time).
  • 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 would have received an invite for the preparation day on Tuesday, July 29, 2025, from 9am - 11am (Pacific Time) early in July.

note

While Prep Day is a virtual event, the main HPC & Data Science Summer Institute sessions (Monday, August 4 - Friday, August 8) will be held in person and will not be available remotely.