[chimera-dev] source of ~10x slowdown in opening of Molecules in lastest chimera

[Eric Pettersen]

Obviously, the code for sortedAtoms() hasn't changed in a long time.  
So one way to look at it is that the "problem" is the new pre-fetching 
behavior of wrappy.  So is it true that with the new behavior of wrappy 
it is effectively impossible to have a lazily-evaluated attribute of a 
Molecule (or Atom or Bond for that matter)?  I think I already ran 
afoul of this new behavior when I couldn't make primaryBonds() or 
allLocations() into attributes.

sortedAtoms() was being used in my analysis of trajectories, where the 
molecules in question were hundreds or atoms in size and performance as 
is was more than acceptable.  Now that sortedAtoms is forcibly executed 
no matter what, then you have it operating on molecules that are many 
thousands of atoms and you get what you see now.

Perhaps we need a discussion before we commit to never having 
lazily-evaluated attributes.

--Eric

On Tuesday, June 3, 2003, at 02:44 PM, Greg Couch wrote:

> After much digging, it turns out that the slowdown occurs when the
> PDBio wrapper returns the new molecules to chimera.  Due to wrappy's
> C++/Python reference count caching, the molecule's attributes are
> fetched at that time, and one of those attributes, sortedAtoms, takes a
> long time to compute (for 4371 atoms it takes 4.1 seconds on socrates,
> 3.2 on spin and 5.9 on my home P4).  With a timing script, we can see
> that sortedAtoms isn't any slower in the lastest chimera, and
> sortedAtoms has been an attribute since 2000/05/02, so an optimization
> to speed up the initial sorting of atoms seems to have been lost
> recently.  So far, I have been unable to find it, so I'm hoping Eric
> or Conrad will chime in.
>
> In the mean time, making sortedAtoms a member function instead of an
> attribute (which wrappy much prefers anyway) avoids the delay.  Luckily
> no .py file in /usr/local/src/chimera calls sortedAtoms, so it is a
> fairly safe fix.
>
> 	- Greg
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