CyoSPARC v4 update permission denied

Does anyone know the issue with the permission denied? I have used “cryosparcm update” to update the cryosparc from 3.4.0 to 4.0.3… For the first time, I forgot to stop the cryosparc (cryosparcm stop) and run the update with errors. So I stopped for the second time and the update was successful. However, when I open the webapp, it shows no versions (null) and I could not open any jobs because permission was denied.
Any ideas?
Thank you so much.


Which Linux account “owns” and runs the CryoSPARC installation?
Could there have been a “slip up” and an operation like cryosparcm start or cryosparcm update was run under a different Linux account?

I am not sure who is the ower. Our node is on HPC and IT helped us install the system and cryosparc. However I am the primary user and can create user for others on the node. Another node which is assigned for another person, can be updated by the user. Is there any way to check?

There are various ways in which a CryoSPARC instance (or multiple CryoSPARC instances) may be installed on a computer. I would typically expect that a CryoSPARC instance continues to be operated and maintained (and updated, as applicable) under the Linux account under which it was installed.
Please ask your IT support under which Linux account (the “intended” account) they installed the CryoSPARC instance in question, and who is responsible for its maintenance.
You can check for the actual owner of CryoSPARC processes with
ps axuww | grep -e cryosparc -e mongod. The actual Linux account that owns CryoSPARC software files can be displayed using ls -l.
Do the “intented” and “actual” account(s) match?
Please keep in mind that files and processes displayed may correspond to another CryoSPARC instance than the one in question.

I appreciate your help. However, it only shows my name for both.

I have requested IT to help me solve the problem.
Thanks again.

The IT said on their side, it looks normal. So any one has suggestions? I also checked the instance showing nothing.
Thank you so much.

Your process list still includes a reference to a March 21 process. You may want to try as tinghai.xu:

  1. cryosparcm stop
  2. ps xww | grep cryosparc. Take note of the ids of CryoSPARC-related processes that may still be running.
  3. kill (but not kill -9) relevant progresses.
  4. ps xww | grep cryosparc to confirm there are no more CryoSPARC-related processes.
  5. Repeat the software update according to the instructions and to the type of your CryoSPARC instance, recording all screen output to a file. For example (to illustrate capturing the output to a file):
    cryosparcm update 2>&1 | tee update_$(date +%F).out
  6. cryosparcm start. Does CryoSPARC work now?

After killing all the CryoSPARC-related processes and restarting it, finally, the new version of CryoSPARC works. Thank you.