Cryosparc-cluster

Example

To start Cryosparc, first you need to have a license ID. You need a license ID for every unique instance of Cryosparc you start.

You don't need multiple license ID's if you only have one Cryosparc session running at a time. To obtain a license ID, go to Cryosparc

Go to Open OnDemand and fill in the following fields:

  • License ID — Enter your License ID. License ID field

  • Email address — This will be your CryoSPARC login. Email field

  • Password — Set a password for your user account. Password field

  • Slurm resource requirements — Configure the following: Slurm fields

    • Hours — Must be long enough for all CryoSPARC jobs to complete.
    • CPU cores — 8 is a good starting point.
    • RAM (GB) — 64 GB is a good starting point.

Once configured, press Launch. A CryoSPARC master will be launched. You will then be able to submit Cryosparc jobs to the Slurm cluster.

Note

You can only run a single CryoSPARC instance at a time, as all instances share the same database in your home directory. If you need to run multiple instances simultaneously, contact HPC Support.

When the Launch CryoSPARC Desktop - Cluster button appears, click the blue link next to Session ID: Session ID link

This opens the OnDemand working directory. Click the cryosparc-port.txt file to find the URL you'll use to connect to CryoSPARC from within the job. Session ID link

Then click My Interactive Sessions → Launch CryoSPARC Desktop - Cluster. A blank Linux desktop will open.

  1. Launch Firefox via Applications → Internet → Firefox.
  2. Navigate to the URL from cryosparc-port.txt (e.g. http://localhost:39000).
  3. Log in with the email address and password you set above.
  • In Cryosparc, click Queue Job in Patch Motion Correction

  • Then, select spartan and fill project_mem, project_partition, project_qos and project_time, then click Queue