Update failure from 2.2 --> 2.3

Install, Configure and Update
1

Hi,

I have update from 2.1 to 2.2 in the past and all work OK.
I have try to update to 2.3 and got this error:

Deleting old files…
rm: cannot remove ‘cryosparc2_command/command_core/.nfs0000000051213359000c1e48’: Device or resource busy
rm: cannot remove ‘cryosparc2_webapp/nodejs/bin/.nfs00000000480cf309000c1e49’: Device or resource busy
rm: cannot remove ‘cryosparc2_webapp/bundle/programs/server/npm/node_modules/bcrypt/lib/binding/.nfs000000005ffc060f000c1e4a’: Device or resource busy
rm: cannot remove ‘cryosparc2_webapp/bundle/programs/server/node_modules/fibers/bin/linux-x64-57/.nfs000000005121590e000c1e4b’: Device or resource busy

and the update failed

cryosparcm status give me

CryoSPARC System master node installed at
/home/emguest/software/cryosparc2_master
Current cryoSPARC version: v2.2.0

when I’m trying to start I get this error:

cryosparcm start
Starting cryoSPARC System master process…
CryoSPARC is not already running.
database: started
command_core: ERROR (spawn error)
cryosparc command core startup complete.
command_vis: ERROR (spawn error)
command_proxy: ERROR (spawn error)
webapp: ERROR (no such file)

CryoSPARC master started.
From this machine, access the webapp at
http://localhost:39000
From other machines on the network, access at
http://cryogpu2:39000

Do I need to delete and re-install cryospac?

Thanks,

2

Hi @Elad,

It looks like the update process couldn’t delete the directory properly (cryosparc was still somehow running/ another user had a session open?) You data should be fine, but I’d recommend stopping cryoSPARC completely (cryosparcm stop), ensuring any processes aren’t alive (ps -ax | grep "supervisord", kill any cryoSPARC 2 PID’s) manually deleting only the cryosparc2_master directory, and then reinstalling cryoSPARC.

3

Thanks for your help. It fix the problem and now it has bin update and work.