Cryosparc won't start after migrating the database to a new location

[wtempel]

@Yehuda

file:WiredTiger.wt, connection: __wt_block_read_off, 291: WiredTiger.wt: read checksum error for 4096B block at offset 147456: block header checksum of 809334881 doesn’t match expected checksum of 2553729618

Given the evidence of database corruption, I recommend

1. a confirmed shutdown of CryoSPARC

2. a database rebuild

   @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 blank 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.

   Before project attachment (step 5. in the quoted instructions): If your CryoSPARC version is below 4.3, I recommend upgrading. If your CryoSPARC version is 4.3.*, I recommend appending to the file
   /path/to/cryosparc_master/config.sh the line

   export CRYOSPARC_MONGO_EXTRA_FLAGS=" "
   

   (the space between the quotes is important). Upgrade to v4.4 or, in v4.3, setting CRYOSPARC_MONGO_EXTRA_FLAGS would enable database journalling that should increase the new database’s robustness against corruption. I CryoSPARC restart is required to activate changes of /path/to/cryosparc_master/config.sh.

3. continuous monitoring of the available capacity of the filesystem that holds the database

4. regular database backups via
   cryosparcm backup (guide) or, once database journalling is enabled, filesystem snapshots.