I experienced similar symptoms a while back.  The notebook frequently
backs up individual worksheets in a "snapshots" directory and you may
have millions of them, but I don't think this was the root of the
problem.  There is also a  .sage/sage_notebook/nb.sobj file that gets
backed-up regularly (every 30 seconds, every new cell) into a backups
subdirectory alongside the original file.  My "personal" version of
this file is 30 MB and is run off an external drive, so I noticed
delays.

I don't think I ever checked CPU usage relative to this effect.
William is aware of this, I believe, so maybe he has a reason to
believe this is not the explanation here.

You can set the delay time on this (mine is now 20 minutes or an hour)
and then for me the symptoms went away.  At the command line, you need
to instantiate a notebook object, set the right attribute and then
save it, or something like that.

Read the docstring on the patch at:  
http://trac.sagemath.org/sage_trac/ticket/5371
for a detailed how-to.

More hints are at http://trac.sagemath.org/sage_trac/ticket/5459 and
there are other relevant trac tickets.

The various save intervals have names that are somewhat confusing -
hopefully this all gets reorganized in the next overhaul of the
notebook.

Rob


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