Restore database after crash

Install, Configure and Update
2

Assuming

  1. an intact database at /path/to/old/cryosparc_database
  2. a new cryosparc_master installation with the same $CRYOSPARC_BASE_PORT but different $CRYOSPARC_DB_PATH as the old instance
  3. the old and the new CryoSPARC instance have been stopped and the absence of CryoSPARC-related processes has been confirmed with suitable ps command(s)

one should be able to define

export CRYOSPARC_DB_PATH="/path/to/old/cryosparc_database"

inside the new instance’s cryosparc_master/config.sh and start the new instance with the old database.
The description of your recovery attempts so far suggests that the first assumption does not apply and the content of the old database directory has been corrupted. In this case, your only remedy may be to (see lower part of Warning: Could not get database status (attempt 1/3) - issue after storage outage - #4 by wtempel):

  1. define worker targets and CryoSPARC users in a fresh database.
  2. attach project directories to the new CryoSPARC instance.

In CryoSPARC v4.3.1, you may increase the resilience of your database against unexpected shutdowns by including (with space between quotes)

export CRYOSPARC_MONGO_EXTRA_FLAGS=" "

inside cryosparc_master/config.sh (and restarting CryoSPARC).

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