Refused connection after computer restart

Troubleshooting
1

Hi,
I installed cryoSPARC as a user (Centos 7) and managed to run it in the browser. I then encountered problems with jobs that could not start because of issues with ksshaskpass. After many failed attempts to solve this I restarted the computer, however now I get a ‘refused connection’ message for whatever I do and cannot start cryoSPARC at all.

Here are examples:

$cryosparcm stop
CryoSPARC is running.
Stopping cryosparc.
unix:///tmp/cryosparc-supervisor–6410667835282660811.sock refused connection
ERROR: unix:///tmp/cryosparc-supervisor–6410667835282660811.sock refused connection (already shut down?)

$ cryosparcm restart
CryoSPARC is running.
Stopping cryosparc.
unix:///tmp/cryosparc-supervisor–6410667835282660811.sock refused connection
ERROR: unix:///tmp/cryosparc-supervisor–6410667835282660811.sock refused connection (already shut down?)
Starting cryoSPARC System master process…
CryoSPARC is already running.
If you would like to restart, use cryosparcm restart

I realize that a similar issue has been discussed in this forum, but I could not find any solution.

Thanks
Nadav

2

Hi @nadav,

Can you please try cryosparcm stop

Then, delete the /tmp/cryosparc-supervisor–6410667835282660811.sock file.

Finally, you may need to kill any other remaining processes that may be interfering. You can find the process IDs using:

ps -ax | grep “supervisord” (kill only the process that is running from your cryosparc2 install, not cryosparc v0 if you have that running too)
ps -ax | grep “cryosparc2_command” (kill all the matching processes)
ps -ax | grep “mongod” (kill only the process running your cryosparc2 database, not cryosparc v0 if you have that running too)

Then you should be able to start cryosparc again: cryosparcm start

Please let us know if that works.

8 Likes
3

This worked, many thanks!

4

hi

i am also facing the same issue frequently

I tried the way @spunjani has said before

I am attaching the output i obtained.

(base) radha@radha-SYS-7048GR-TR:~$ **cryosparcm stop** 
CryoSPARC is running.
Stopping cryoSPARC 
unix:///tmp/cryosparc-supervisor-1566b74c3f9891e2acf9ca6357f42d58.sock refused connection
(base) radha@radha-SYS-7048GR-TR:~$ ps xww | grep -e cryosparc -e mongo
 **758311 pts/0    S+     0:00 grep --color=auto -e cryosparc -e mongo**
(base) radha@radha-SYS-7048GR-TR:~$

Thanks
Aswathy

5

Because ps xww lists only processes of the user who runs the the ps command, please ensure that ps xww is run by the user under whose Linux account CryoSPARC runs.
Given the “empty” (except the grep command itself) output of the ps command and assuming that the interfering
/tmp/cryosparc-supervisor-1566b74c3f9891e2acf9ca6357f42d58.sock
file is owned by Linux user radha (please confirm), cryosparc-supervisor-1566b74c3f9891e2acf9ca6357f42d58.sock could be a “leftover” from an abrupt computer shutdown. In that case, you can remove
cryosparc-supervisor-1566b74c3f9891e2acf9ca6357f42d58.sock
and try cryosparcm start.
Suggestions/Reminders for the benefit of others visiting this forum topic:

  • avoid computer shutdowns while cryosparc_master software is running
  • always confirm, as @aswathy did, that no cryosparc_master (or mongo) processes are running before removing any CryoSPARC-related supervisor or mongo *.sock file
7

hi, where can I find the .sock file?

8

You should find them in the /tmp/ directory, but only manipulate or delete them under exceptional circumstances and after confirming that related processes are no longer running.