Unresponsive "cleanup workspace data" tool

Data Management
1

Hi,
I used the “Cleanup Workspace Data” tool after data processing in one for my workspaces. It has been running for quite a long time, and seems unresponsive (no jobs have been cleared/deleted in the workspace). Is there any safe way to force clear it ?
Thank you,
Iliass

2

Welcome to the forum @Iliass_i .
Which options did you select in the Cleanup Workspace Data dialog?

3

Hi,
I selected options 2 and 3, in order to only keep jobs marked as final.

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4

@Iliass_i Please can you share with us the tgz file created by the command
cryosparcm snaplogs.
If the oldest timestamp printed by the command

cryosparcm log command_core | head -n 20

is newer than when you ran the Cleanup Workspace tool, we would also like to look at a copy of the file
/path/to/cryosparc_master/run/command_core.log.1
I will send you a private message regarding file transfer arrangements.

5

Thanks @Iliass_i for sending the logs. Do you remember the date and time when

  • Cleanup Workspace Data was initiated?
  • you found the cleanup task had become unresponsive?
6

I think it was on May 5th but I’m not sure unfortunately. I don’t exactly know when it became unresponsive, but I figured that it became unresponsive because it had been running for a couple of weeks and is still running currently.

Thank you.

7

A brief update on this issue:

The command_core log you shared with us show, among other errors,

  • a permissions error when trying to remove files related to job P62.J54
  • and, approx 50 min later, a Disk quota exceeded error

Errors of these kind could cause the cleanup tool to fail.

The command core log includes additional errors that suggest problems that may go beyond just the failure of the cleanup tool. One may browse recent command_core log entries with the command

cryosparcm log command_core | less

or identify “problem spots” (for subsequent inspection of context) with the command

cryosparcm log command_core | grep -i error

Have any additional problems been observed on the CryoSPARC instance?

8

Thank you for your reply.

I’m not sure I understood the second part of your reply :

Could you please rephrase it ?

9

When we inspected the command_core log you sent us for errors possibly related to the Cleanup Data tool, we found additional errors related to data storage. These errors were dated after you first posted under this topic and may affect the Cleanup Data tool, or other CryoSPARC functions. Some errors occurred May 21 or May 28, for example. You may inspect the logs using the commands provided for more details.