Alternative MongoDB repair

[wtempel]

@ldlamini If error messages in the database log
cryosparcm log database
confirm corruption, I recommend:

1. If possible, harden the server against power failures:
   • “uninterruptible” power
   • redundant power supplies
2. As @btsewell suggested, rebuild a new database from your project directories. The procedure is described in a related post:

@wtempel

1. updating the CRYOSPARC_DB_PATH= definition inside /XXX/cryosparc_master/config.sh with a new, suitable path.
2. then running
   cryosparcm start
   which should start CryoSPARC with a bank database.
3. re-creating CryoSPARC users in the database with
   cryosparcm createuser
   commands (guide)
4. registering CryoSPARC workers in the database with
   cryosparcw connect commands (on the worker(s), guide) or
   cryosparcm cluster connect command(s) (guide), as applicable.
5. attaching project directories. You may have to delete the cs.lock file from any given project directory before attachment because the instance id stored in the new, blank database differs from the old instance id stored in the old database. This is an exception from the rule that cs.lock files should generally not be deleted.

[edited for spelling 2024-04-12]