VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 03 2011 - 13:02:04 CDT

Benjamin,
 Your "inner loop" proc is creating an atom selection that it is
not getting deleted either within the proc that makes it, nor within
the outer loop that calls it. This is likely the cause of your slowdown.

Cheers,
  John Stone
  johns_at_ks.uiuc.edu

On Fri, Jun 03, 2011 at 05:23:25PM +0100, Benjamin Hall wrote:
>
> On 2 Jun 2011, at 12:27, Axel Kohlmeyer wrote:
>
> > On Thu, Jun 2, 2011 at 4:39 AM, Benjamin Hall
> > <benjamin.hall_at_bioch.ox.ac.uk> wrote:
> >> Hi
> >>
> >> I've encountered an odd problem with for loops in tcl in VMD, whereby over the course of extended loops (>10000 iterations) in subroutines the individual loops seem to become slower as the loop progresses. The scripts are typically looping through frames in a trajectory in a manner similar to the below structure
> >>
> >> for { set i 0 } { $i < [molinfo top get numframes] } { incr i } {
> >> some_other_function $i
> >> puts "."
> >> }
> >>
> >> As the loop progresses, the rate of printing "." visibly slows. I've not noticed any memory leaks (the some_other_function typically contains several atomselect commands), but I've seen this happen in a couple of unrelated scripts which do the same kind of looping through frames. If I rerun the loop, the initial speeds appear the same. I've not been able to sensibly benchmark the script, though I would if someone could suggest a benchmarking tool for tcl. Has anyone else observed this kind of behaviour, and could anyone suggest a likely cause/solution for the problem?
> >
> > no, i have not seen this. however, there are a lot of possible reasons
> > why "some_other_function" can slow down over the course of iterations,
> > e.g. by inefficiently walking or searching growing lists. memory leaks
> > is a less likely option, but the slowdown would be drastic when you run
> > out of available memory and go into swap.
> >
> > timing in tcl can be done with the "clock" command. check out the
> > tcl/tk wiki (you can find it from www.tcl.tk) which contains lots of little
> > useful codelets and discussions on how to do things in tcl.
> >
>
> Thanks. I've used time in the below example; unfortunately this produces values in realtime rather than cputime, but it seems to reproduce what I can see when running scripts which do something similar. I get up to a ~10% slow down after ~1000 cycles, and this appears to increase steadily with more cycles (I'm running loops with > 40000 repeats). Apologies if I'm doing something foolish but I'd appreciate any pointers or tips. I don't think it is CPU throttling as running "outerloop; outerloop" shows an initial speed up
>
> proc outerloop { } {
> set outfile [open benchmark.txt w]
> set numframes 5000
> set increment 1
>
> for {set i 0} {$i < $numframes} {incr i $increment} {
> set bm [inner_loop]
> puts $outfile "$bm"
> if { [expr ($i/$increment) % 2] == 0} {
> set linestring "-"
> } else {
> set linestring "|"
> }
>
> puts -nonewline "\r$linestring"
> }
> close $outfile
> }
>
> proc inner_loop { } {
> set bm [time { for {set i 0} {$i < 20 } {incr i } {
> set DPPC_number [atomselect top "all" frame 0]
> } } ]
> return $bm
> }
>
> Thanks
>
> Ben
>
>
> > cheers,
> > axel.
> >
> >> Thanks
> >>
> >> Ben
> >> ************************************************************************
> >> Benjamin A. Hall
> >> Structural Bioinformatics & Computational Biochemistry Unit / OCISB
> >> University of Oxford
> >> http://sbcb.bioch.ox.ac.uk/hall.php
> >> +44 (0)1865 613304
> >> benjamin.hall_at_bioch.ox.ac.uk
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com http://goo.gl/1wk0
> >
> > Institute for Computational Molecular Science
> > Temple University, Philadelphia PA, USA.
>
> ************************************************************************
> Benjamin A. Hall
> Structural Bioinformatics & Computational Biochemistry Unit / OCISB
> University of Oxford
> http://sbcb.bioch.ox.ac.uk/hall.php
> +44 (0)1865 613304
> benjamin.hall_at_bioch.ox.ac.uk
>
>
>
>
>
>
> 

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