cryoSPARC

CryoSPARC is the state-of-the-art platform used globally for obtaining 3D structural information from single particle cryo-EM data.

cryosparc

We install cryoSPARC on a per-user basis as some installation parameters need to be managed by our support staff (i.e. port mapping, license keys, compiled in hostnames). The cryoSPARC graphical interface is accessed via our low latency web-based Open OnDemand console, providing very low latency access to the cryoSPARC's interface. Installations are preformed under the /central/groups/<groupname>/<hpc-username> as home directories are limited to 50GB of storage. (By comparison group directories are 10TB+)

cryoSPARC is configured in such a way to allow larger jobs to be submitted through the slurm interface to compute and gpu enabled node dependent on job requirements. See here for our currently available hardware. cryoSPARC runs a 'master' service on one of our login nodes which is responsible for dispatching jobs via the worker processes and providing the web server interface required for visualization.

If you or your group would like to start making use of cryoSPARC on the central hpc please email help-hpc@caltech.edu and be sure to including a list of accounts. We will provide you the proper URL (loginhost+assigned port) to navigate to in the OOD interface described below.

Once your installation has been completed by our staff you can visit the GUI by navigating to ondemand.hpc.caltech.edu while on-campus or VPN. Note the service is not available off-campus unless over Caltech's VPN service.

Connecting to the cryoSPARC interface

Navigate to our OnDemand site.

Click Interactive Apps at the top then 'Web Browser'

Once the Web Browser App is ready you'll be able to click 'Launch noVNC in New Tab'

In the Web Browser interface navigate to your assigned URL+port noted in your cluster home directory ~/.crysparc-creds (i.e. something like https://vislogin1.cm.cluster:<your assigned cryosparc port>) or (http://login1:<port> for older installations, the ~/.cryosparc-creds file will contain the proper URL information)

Basic Cryosparc Management Commands

Given that the cryoSPARC service runs under your own account you will have full control of the server processes. Below are a few basic management commands, other commands may be found in the official cryosparc documentation. Before running these commands, be sure you SSH directly to the hostname cryosparc was configured against otherwise the commands below will fail. (i.e. login1.hpc.caltech.edu, login2.hpc.caltech.edu, vislogin1.hpc.caltech.edu, vislogin2.hpc.caltech.edu)

General Commands

cryosparcm status

cryosparcm <stop> <start> <restart> (Note that the server will need to be restarted after reboot of the login nodes)

cryosparcm resetpassword --email <email> --password

cryosparcm cluster connect (Used after updating either the cluster_info or submission scripts)

Diagnostics

cryosparcm log command_cor

cryosparcm log webapp

Database Backups

cryosparcm backup --dir=/central/groups/voorheeslab/voorhees/cryosparc_backup