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CryoSPARC

A state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.

Homepage Version(s): 4.6.2

This application is available in Open OnDemand.

Note

In order to install the CryoSPARC Single Workstation edition in your home directory, you must have a valid License ID from CryoSPARC. If you need assistance installing CryoSPARC in your home directory, please include this License ID in your support ticket to RCC staff.

Accessing Single-Workstation CryoSPARC on the RCC Systems#

Before you begin, CryoSPARC must be installed in your home directory. RCC staff can assist with installation if needed.

Step 1: Log in to Open OnDemand#

  1. Open a Web Browser and navigate to Open OnDemand
  2. Enter your RCC Username and Password.

Step 2: Start an RCC Desktop Session on the cryosparc_q GPU Server#

  1. Select "Interactive Apps" in the top bar.
  2. Choose "RCC Desktop" from the drop-down list.
  3. Configure the Job Setup Screen:
    • SLURM Account: Select a GPU-Capable SLURM Account
    • Number of Hours: Estimate generously (Maximum is dependent on SLURM Account).
    • Amount of Memory: Leave blank.
    • Number of Nodes: 1
    • Number of Cores: Maximum of 16
    • Number of GPUs: Maximum of 2
  4. Click "Launch" to submit the job. When the job turns green, click "Launch RCC Desktop."

Step 4: Accessing CryoSPARC from the RCC Desktop Application#

  1. Click the Terminal Emulator icon from the bottom bar.
  2. In the terminal, type: 
    1
    $ cryosparcm start
  3. If the server was previously running, use: 
    1
    $ cryosparcm restart
  4. Once running, the terminal will display a URL similar to: 
    1
    http://localhost:39000
    Note: Each user will have a unique port number.
  5. Open the web browser inside the RCC desktop and enter the URL provided.
  6. Log in to the CryoSPARC interface using your credentials.

Step 5: Closing a Session#

  1. Once you are done with your session, log out from the CryoSPARC server.
  2. Close the web browser.
  3. Run the following command in the terminal to stop the server: 
    1
    $ cryosparcm stop
  4. Exit the Open OnDemand session by closing its tab.

CryoSPARC Cluster Beta Instructions#

Note

If you are interested in setting up a new CryoSPARC Cluster Version account, you will need an initial login token from RCC admins. Submit a ticket to support@rcc.fsu.edu to request access. Approval may take up to one week.

When submitting your ticket, please include the SLURM Accounts with GPU Nodes that you and your group have access to that you would like to run CryoSPARC on.

Warning

Access to the CryoSPARC Cluster Version is limited to groups with an active GPU Queue and Storage Purchase due to the intensive memory and compute requirements of CryoSPARC.

Step 1: Log in to Open OnDemand#

  1. Open a Web Browser and navigate to Open OnDemand
  2. Enter your RCC Username and Password.

Step 2: Job Setup Screen Configuration#

  1. Select "Interactive Apps" in the top bar.
  2. Choose "RCC Desktop" from the drop-down list.
  3. Configure the Job Setup Screen:
    • SLURM Account: backfill2
    • Number of Hours: Estimate generously (maximum limit: 2140 hours).
    • Amount of Memory: 32
    • Number of Nodes: 1
    • Number of Cores: 8
    • Number of GPUs: 0
  4. Click "Launch" to submit the job. When the job turns green, click "Launch RCC Desktop."

Note

These values are for the web interface session, not for CryoSPARC jobs themselves.

Step 3: RCC Desktop Session#

Step 4: Log in or Create a New Account#

  • Use your CryoSPARC account credentials.
  • If new, click "New Account" and follow the instructions.

Step 5: Begin using CryoSPARC#

Warning

When saving a project in CryoSPARC cluster, do not save to the $HOME directory. Due to CryoSPARC's Architecture this is not your home directory, this is a global "cryosparc user" home directory. Please save your projects to Scratch Space or your research group's shared storage space on /gpfs/research.