Bug refinement "forgets" symmetry parameter and runs on default

Troubleshooting
1

Hi,
Sometimes I’ll queue a job with symmetry imposed and then come back to find that it’s running with C1. I’m not sure if it happens to other parameters since I’m only changing symmetry, but it’s been happening consistently for a while.
-Aaron

2

Hi @user123,

To help me further troubleshoot, can you send me following:

  • The contents of the refinement job’s “Metadata” tab
  • A screenshot of the parameters where you see
  • How are you connecting to the cryoSPARC interface? e.g., SSH tunnel or locally on a workstation?

Thanks,

Nick

3

Hi Nick,
I sent you that metadata info you requested in a DM.
The problem still occurs. I send a bunch of homogeneous and heterogeneous refinements to run overnight and they all ran with default settings despite putting in sym param and het box size param.
The GPU can be a bit slow and laggy in setting up jobs, so I wonder if it’s not catching these parameters before I queue the job.
-Aaron

4

Hi Aaron, I got your information shortly before I went on leave but unfortunately lost track of the investigation after I returned - sorry about! I’m looking into this now.

5

Looking at your job document, it looks like the parameters indeed did not get get saved before you queued the job. I have sometimes seen this when one or more parameters are not set to valid values or when the job is queued to fast and does not get a chance to save.

To avoid this, try pressing “Enter” after you set a parameter, which should prompt cryoSPARC to commit the value. You can also check that the parameter is set correctly by pressing “Cancel” to get out of Builder mode and then press “B” on your keyboard to go back to builder mode. If the parameter has the same value that you set, then you may safely queue it. We’ll likely improve how this work sin a future version of cryoSPARC.

Hope that helps.

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6

Hi Nick, thanks for having a look. I realize that the gui is laggy and I need to wait for the box to turn green. I think I was submitting the job before the box turned green and it hadn’t properly saved the parameter.
-Aaron

1 Like