Couldn't stop/restart Cryosaprc: cryosparc.sock refused connection

Troubleshooting
1

Hi there,

I couldn’t stop/restart Cryosparc on the cluster when I run cryosparcm stop/restart.

qchen@flash:~$ cryosparcm stop
CryoSPARC is running.
Stopping cryoSPARC
unix:///run/user/27067/cryosparc.sock refused connection

Can you help with this? Thanks very much.

2

The initial problem was that I couldn’t run the import job. So I tried to restart my cryosparc. I got an error like this:

image
image942×73 11.3 KB

Then I manged to kill the supervisord process like this:
ps -aux|grep supervisor
image
image938×30 6.79 KB

kill -9 3669533

And then I tried to restart the Cryosparc.
image

I don’t know how to fix this issue.

3

You may want to try the extended CryoSPARC shutdown procedure.
Your CryoSPARC installation may include a customized socket file path. What is the output of the command

cryosparcm env | grep SOCK

?

You may want to avoid using the -9 (SIGKILL) signal when terminating processes as this signal may cause unnecessary disruption.

4

Thanks, solved by removing the sock file.

Somehow kill 3669533 (without -9) didn’t work for killing the supervisord process.

5

supervisord may need several seconds to “clean up” CryoSPARC service processes before exiting. SIGKILL might interrupt the cleanup and leave stale processes behind.