After some trial and error we managed to restore our DB using a snapshot of the DB folder taken before the outage. As the snapshot was not a proper mongodb dump this required another step of running
mongod --dbpath /XXX/db --repair
before being able to use it in cryosparc again, similar as described here.
The mongod executable shipped with cryosparc can be found here:
XXX/cryosparc_master/deps/external/mongodb/bin/mongod
Thanks for the help.
Sidnote:
I would not remove the
mongod.lockfile at this time, but only (and possibly, as I do not recall encountering such a situation) after confirming that the mere presence ofmongod.lockis a problem and there are no other, underlying problems.
As suggested by @wtempel in the first reply, removing or emptying the mongod.lock did not help.