cryoSPARC

cryoSPARC is a software platform for obtaining 3D structural information from single particle cryo-EM data.

Installation

cryoSPARC is installed per-user under group directories:

/resnick/groups/<groupname>/<username>/cryosparc

Tip

Group directories offer 20 TB vs. 50 GB in home directories.

Requesting Access

Email help-hpc@caltech.edu with the list of accounts that need cryoSPARC access.

Connecting

Via Open OnDemand

Navigate to interactive.hpc.caltech.edu
Select Interactive Apps → Web Browser
Click Launch noVNC in New Tab
Access your assigned URL from ~/.cryosparc-creds:

cat ~/.cryosparc-creds
# Output: https://vislogin1.cm.cluster:<port>

Note

Requires campus network or Caltech VPN.

Management Commands

SSH directly to your configured hostname (login3/login4/vislogin3/vislogin4.hpc.caltech.edu).

General

# Check status
cryosparcm status

# Stop/Start/Restart
cryosparcm stop
cryosparcm start
cryosparcm restart

# Reset password
cryosparcm resetpassword --email your@email.com --password

# Connect cluster
cryosparcm cluster connect

Diagnostics

cryosparcm log command_cor
cryosparcm log webapp

Backups

cryosparcm backup --dir=/resnick/groups/<groupname>/<username>/cryosparc_backup

Job Submission

Jobs are submitted via SLURM to compute and GPU nodes. See Resources for available GPU configurations.