Re: [PyMOL] Performance of extended commands vs python function

[Thomas H. <tho...@sc...>]

Hi Lorenzo,

Thanks for the script, and great that you could identify cmd.sync() as the culprit. I looked at the code, cmd.do("cmd.sync()") literally blocks itself until it times out after 1 second. cmd.do() puts commands in a queue, and cmd.sync() tries to ensure that all queued commands have been executed. PyMOL calls cmd.sync() in a few places right before capturing an image for example.

Not sure how this could be improved. Maybe cmd.sync() should print a warning if it times out, that would help to notice a self-lock.

Cheers,
  Thomas


> On Dec 17, 2019, at 11:42 AM, Lorenzo Gaifas <br...@gm...> wrote:
> 
> After playing around with it a bit longer, it's clear that I misunderstood. The issue was not with `cmd.alter` nor with `cmd.show_as`, but with `cmd.sync`.
> 
> I was calling many times a smaller function that contained `cmd.sync()`, which resulted - it seems - in all these calls piling up.
> 
> Still, I don't know if it's intended behaviour for `sync` to be so much slower if it's called as a pymol function. Attached you will find a minimal working example to show the difference.
> 
> 
> Il giorno lun 16 dic 2019 alle ore 17:52 Thomas Holder <tho...@sc...> ha scritto:
> OK thanks. I haven't seen such performance differences before and couldn't reproduce it so far. Could you share your script (and data files if possible) with me?
> 
> Thanks,
>   Thomas
> 
> 
> > On Dec 16, 2019, at 5:42 PM, Lorenzo Gaifas <br...@gm...> wrote:
> > 
> > Yes, it does. Both cases are with the GUI and ewual graphical representation.
> > 
> > On Mon, Dec 16, 2019, 17:37 Thomas Holder <tho...@sc...> wrote:
> > Hi Lorenzo,
> > 
> > When you say "run from a python script", is that with the graphical GUI? That "instant update", does that include instant update of visual representations?
> > 
> > Thanks,
> >   Thomas
> > 
> > 
> > > On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas <br...@gm...> wrote:
> > > 
> > > Dear Pymol users,
> > > 
> > > I just discovered something I did not expect: the same python function can have extremely different performance when called as a python function or using the pymol api.
> > > 
> > > To be more specific: I have a function func that (among other things) uses cmd.alter several times over a big system to change the properties and representation.
> > > 
> > > If I run it calling func() from a python script, its effects are almost instant. If I call it with cmd.do('func') (or directly from within pymol with func), it’s extremely slow (up to 10 seconds) and Pymol freezes completely during this time.
> > > 
> > > I expected this to be due to an overhead of the api itself, but when I do the same thing with a simpler function, I see no noticeable difference.
> > > 
> > > Why exactly is this happening? And more importantly, how can I get the performance of func even when I call it from within pymol?
> > > 
> > > Thank you,
> > > Lorenzo
> > > 
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> > 
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> > 
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> <slow.py>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.