Is Leginon on Windows using 7-zip?
Added by Patrick Goetz about 6 years ago
We've had an intermittent problem where periodically rawtransfer.py stops transferring images from the CIFS-mounted camera PC to the frames folder, and the Camera PC SSD rapidly starts to run out of space. Yesterday I was finally able to track down the cause of this problem. Monitoring the rawtransfer.py log, I noticed that it was getting stuck trying to delete a particular .mrc file from the CIFS share:
Nov 15 17:05:39 kraken rawtransfer.py24990: rm: cannot remove '/local/krios-k2-frames/20181114_23595273.mrc': Device or resource busy
Nov 15 17:06:58 kraken rawtransfer.py24990: rm: cannot remove '/local/krios-k2-frames/20181114_23595273.mrc': Device or resource busy
This image was collected on a previous day and was part of a different data set. I tracked the problem down to the file being open on the Windows camera PC. When the lab manager tried to deleted the file (directly from the camera PC), we got the following message in a dialog box:
The action can't be completed because the file is open in 7-Zip Console. Close the file and try again.
A compression process is getting stuck somehow, leaving the file locked on the Windows box. My question is who is using 7-zip? There are really only 2 user processes running on this machine, leginon, and DigitalMicrograph, so I'm trying to track the source of this issue.
Thanks.
Replies (3)
RE: Is Leginon on Windows using 7-zip? - Added by Anchi Cheng about 6 years ago
Leginon does not use 7-Zip. Could it be a backup process initiated from Gatan ?
RE: Is Leginon on Windows using 7-zip? - Added by Patrick Goetz about 6 years ago
Must be something like that, in which case the only solution is for the user to either kill the 7z.exe processes or log out and log back in. In the interim I spoke with a colleague who is a windows expert and he noted that in his experience 7-zip has this problem (will periodically hang).
Thanks for the quick response! Hopefully this ticket will help someone else, as I'm sure most leginon users have Gatan stuff as well.
RE: Is Leginon on Windows using 7-zip? - Added by Christopher Lilienthal almost 6 years ago
Sorry to be late to the discussion.
We have seen the exact same behavior with one of our two K2 controlling PCs. Apparently Digital Micrograph on the controlling PC collects logs and diagnostics at midnight every night and uses 7z.exe to compress the data. Occasionally, and we have not been able to determine why this happens it pulls in an image a user captures and never lets go of the file handle. The way we were able to continue is to quit Digital Micrograph and then things were happy once more.