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 <[email protected]> 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
> <[email protected]> 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 <[email protected]> wrote:
> >
> > Yes, it does. Both cases are with the GUI and ewual graphical
> > representation.
> >
> > On Mon, Dec 16, 2019, 17:37 Thomas Holder <[email protected]>
> > 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 <[email protected]> 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
> > >
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > Archives: http://www.mail-archive.com/[email protected]
> > > Unsubscribe:
> > > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> >
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> >
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
> <slow.py>
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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