List of known problems and issues
After restart there is database: ERROR (spawn error)
Sometimes when cryoSPARC master is shut down it can not restart due to database error. It leads to
CryoSPARC is not already running. If you would like to restart, use cryosparcm restart Starting cryoSPARC System master process.. CryoSPARC is not already running. database: ERROR (spawn error)
In such case you should check logs for errors
main log in
~/.cryosparc/log/run/command_core.log
database logless ~/.cryosparc/log/run/command_core.log
supervisor log in
~/.cryosparc/log/run/supervisord.log
database logless ~/.cryosparc/log/run/supervisord.log
database log in
~/.cryosparc/log/run/database.log
database logless ~/.cryosparc/log/run/database.log
- if there is information that database is "node is not in primary or recovering state" i.e. belowcryoSPARC log with error
AssertionError: {'code': 500, 'data': None, 'message': "OtherError: node is not in primary or recovering state, full error: {'ok': 0.0, 'errmsg': 'node is not in primary or recovering state', 'code': 13436, 'codeName': 'NotMasterOrSecondary'}
then:
backup of cryoSPARC projects
Backup all your projects and data before removing cryoSPARC database. Usually it should not be a problem to import them without backup but you should backup projects just in case. You have to remember that each cryoSPARC database start naming projects from P1, therefore it is best to backup projects to i.e.
$PLG_GROUPS_STORAGE/<your-plggteam>
space.you have to move current cryoSPARC database
database logmv ~/.cryosparc/cryosparc_database ~/.cryosparc/cryosparc_database-$(date+"%Y-%m-%d")
rerun configuration of cryoSPARC to rebuild database
- import projects that you want working with