Disk full warning?


Just ran into (not for the first time) a disk completely filling up because users were unaware how full it was getting, and now (after making some space) the cryosparc database won’t start properly. The database issue I will try to figure out separately, but in general I think it would be very useful to:

  1. Warn users when the disk where the current project resides starts getting full (with a user-settable threshold, say 0.5TB)
  2. Add an option to automatically put the instance into admin mode (no new jobs) if there is less than a certain amount of disk space remaining.


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Would be useful, although you keep your processing and database on the same mount? How large is the database?

I dodged something similar to this recently; a new postdoc started a motion correction run up on a system with [not enough space]… I spotted it when the drive had about 20GB left. As I really didn’t feel like making them waste the time to redo motion correction of the 13,000 micrographs which had already been completed, some rapid cleanup of other projects made just enough room for the motion correction job to complete.

Can’t say I was super happy, but all life is a learning process. :rofl:

A “continue” option would be very useful for motion correction, too!

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Yep on same mount (66T, database is only 0.6T)

Re motion correction you kind of can continue - if it dies, just run a second job with the incomplete mics, then combine outputs.

Long running refinement and classification jobs on the other hand…

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I keep telling the new users

  1. Patch motion correction always enable check the Save results in 16-bit floating point
  2. Any Particle extraction jobs always enable Save results in 16-bit floating point
  3. Importing movies from our Falcon 4i in .eer format the upsampling is 2 by default, but why do they need that ?

That has made a huge difference for us and it could help if these were set by default.


100% to all three, agreed

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Agreed, we’ve already requested in the past the ability to set global defaults for certain options. I think the team are working on it. :wink:

Actually, upsampling 2 is quite useful, although it does catch some users by surprise. I’ve had a rush of samples recently which have hit physical Nyquist at our “normal” mag with me barely trying. It’s always fun to hit <1.8A from data which would top out at 1.9A. :smiley: That said, if RBMC had the option with EER to resample the input, we could work at 4K and move to 8K if necessary…

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Thanks @olibclarke. We recorded your suggestions.

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