I was trying to update from v2.12.4 to v3.0.1 of cryoSPARC following the instructions page. It shows the message- successfully updated master to v3.0.1 but then gives the error- “database: ERROR(spawn error)”.
the output of cryosparcm log database seems to run in a loop (
Any help on how to fix this is appreciated.
It’s a recurrent problem, I believe.
Check the existing posts How to recover from Database Spawn error
Once I’m not sure there are no remnants of a failing run (
ps -ax | grep "supervisord") I tend to do this:
- stop cryosparc
- copy the database folder onto another folder (something like
cp -rav cryosparc2_database cryosparc_database_backup )
- remove the original folder
rm -rf cryosparc2_database
- start cryosparc --> this will recreate the database
- stop cryosparc, do
rsync cryosparc2_database_backup cryosparc2_database --delete-after --progress
- start cryosparc again
After that I have my database back. Of course, no warranties
Thanks a lot. Moving mongod.lock file to tmp folder and restarting cryosparc had sorted the issue for me.
Same problem, after the recent update database got corrupted. Spawn Error when I restarted the cryosparc.
Moved mongod.lock to /tmp, however, the. error still remains.
Please suggest if there’s any other way. Re-installing every time this error comes is really inconvenient.
Hi @diffracteD, there are a few strategies for avoiding this database issue on updates:
- Update your system to include the latest system packages, updates, etc.
- Stop cryoSPARC before proceeding with the update.
- Ensure no cryoSPARC or cryoSPARC related processes are running:
If you see any processes related to cryoSPARC or Mongo DB, read the process ID from the beginning of each output line and use it to kill the process
ps -ax | grep cryosparc
Additional details here
- Delete the mongod.lock file, as others have noted
- Proceed with the update
- Restart your machine
- Start cryoSPARC
Hope that helps,