pymongo.errors.ServerSelectionTimeoutError: localhost:XXXXX: [Errno 111] Connection refused

[wtempel]

I have not seen a combination of errors and warnings quite like this, and am not sure how or if they may be related, for example:

Uncaught exception in 'FileNotOpen: Failed to open interim file
WARNING: soft rlimits too low. rlimits set to 10240 processes, 131072 files. Number of processes should be at least 65536 : 0.5 times number of files.
WiredTiger error (5) [1648057320:747508][12287:0x7fd05f1b0700], file:WiredTiger.wt, WT_SESSION.checkpoint: /oak/stanford/groups/kornberg/donghuac/cryosparc2_database/WiredTiger.turtle.set: handle-write: pwrite: failed to write 1029 bytes at offset 0: Input/output error

My suggestion at this point:

1. Ensure the directory /oak/stanford/groups/kornberg/donghuac/cryosparc2_database

   • (and its content) is owned and writeable by Linux user that “owns” the cryoSPARC instance
   • did not/does not become full or otherwise unavailable (network issues?)

2. Create two kinds of database backups (because each kind has its limitations)

   • using cryosparcm backup
   • using rsync (modify source and target directories according to your circumstances). This method requires that the database is not being modified during the backup (MongoDB Backup Methods — MongoDB Manual). Ensure cryoSPARC and the associated mongod process(es) are stopped.

3. Repair the database (see forum post, mongo docs)

4. Attempt cryosparcm start