Ed
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This can be quite frustrating, as there does not appear to be an apparent cause, and the only symptom is that you are within a quite large and complex project.
If this sounds familiar, the cause could be a related to your autosave settings.
CAUSE
Within Nuke the preset autosave time is set to 5 seconds. If your script is quite large and complex, the amount of time it can take to save can take longer that this default duration allows.
This occurs as the Nuke script (.nk) save file itself is taking longer to generate than than the time given to write the autosave file (.autosave). As a byproduct of this process, Nuke lags for a second as it waits for both processes to finish concurrently.
RESOLUTION
We suggest to alter the the force comp autosave to a higher amount to allow sufficient time for the Nuke script to save, before the autosave saves.
This can be changed with the Preferences menu, under the 'General' tab within the 'force comp autosave after' field.
If the slowness still occurs after this change, this may also be related to a full disk cache. In this situation we would suggest checking and clearing the disk cache using the following instructions:
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SYMPTOMS
When working within Nuke, there can be points in time where the user interface seemingly hangs/freezes briefly and then resumes.