Skip to content


CryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a state of the art software to process cryo-electron microscopy (cryo-EM) data. It is designed as a dispatcher for cryo-EM workloads on a group of servers and workstations. RCC provides support for CryoSPARC on the Beagle3 cluster.

Installation and Setup

In order to use CryoSPARC on Beagle3, you need to request for a license from CryoSPARC and send it to RCC via this form. RCC will then setup your account and provide you with your account details. Each user will also recieve a dedicated base port for their account, usually ranging from 39100-39300, and a host machine name.

Getting Started

CryoSPARC's GUI can be accessed via Thinlinc or via your local machine's web browser.

To start CryoSPARC, firstly, log into the host machine provided to you by RCC at the time of account creation and then run:

cryosparcm start

You may check the status of CryoSPARC at any point to learn CryoSPARC's status by using:

cryosparcm status
Now, to access the GUI, open a browser within Thinlinc or on your local machine and type the host machine name (beagle3-login3) in the address bar along with the port number assigned to you. The hostmachine name is provided in the file in the master folder of your installation directory.


You may type something like http://beagle3-login3.rcc.local:39190/ in the address bar of the Thinlinc browser.


You are required to use this host machine name provided at all times to avoid possible disruptions in service.


Sock Error

If the error message looks like, unix:///tmp/cryosparc-supervisor–6410667835282660811.sock refused connection (already shut down?), follow the steps mentioned below.

  1. Run cryosparcm stop

  2. Delete /tmp/*.sock file that belongs to your user account. The exact name of the the *.sock file will be in the error message.

  3. Kill any interfering zombie processes that are still running. You can find the process IDs using:

    ps -ax | grep "supervisord"
    ps -ax | grep "cryosparc"
    ps -ax | grep "mongod"
    kill <PID>

  4. Run cryosparcm start to start CryoSPARC again.

Database Failure:

  1. Kill the mongo processes. You can find the process IDs using:

ps -ax | grep “mongod” kill <PID>

  1. Delete the .lock file at <cryosparc-install-dir>/db

  2. Start CryoSPARC again using:

cryosparcm start

Database Spawn Error

If the error message looks like,

Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: ERROR (spawn error)

then follow the steps mentioned below

  1. Make a complete copy of your db directory as a backup and keep it safe

    cp -rav db db_backup

  2. Stop CryoSPARC

    cryosparcm stop

  3. Remove the original folder

    rm -rf db

  4. Kill zombie processes

    ps -ax | grep "supervisord" (kill only the process that is running from your cryosparc install)
    ps -ax | grep "cryosparc_command" (kill all the matching processes related to your cryosparc instance)
    ps -ax | grep "mongod" (kill only the process running your cryosparc database)

  5. Start cryosparc which will recreate the database

    cryosparcm start

  6. Stop cryosparc

    cryosparcm stop

  7. Run

    cp -rav db_backup db

  8. cd into the db directory that has all your original database files and run the following bash commands

    eval $(cryosparcm env)
    mongod --dbpath ./ --repair

  9. Start cryoSPARC again

    cryosparcm start