VMD-L Mailing List

From: Johannes Müllegger (hannes_at_zymeworks.com)
Date: Tue Feb 19 2008 - 11:19:04 CST

axel,

        I had to use 'array unset dist' instead of what you proposed but
that did not work either.
when I unset the array variable right after I set it in the inner
most loop the memory usage stays low, but that's obviously of no use.
I'll try to find a workaround for now using an array with only two
dimensions.
thanks
-h-

On Feb 19, 2008, at 5:35 AM, Axel Kohlmeyer wrote:

>
> On Mon, 18 Feb 2008, Johannes Müllegger wrote:
>
> JM> Dear VMD users/developers,
> JM>
> JM> I've modified the original ca-dist.tcl script
> JM> (http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/ca-
> dist-v2.0/)
>
> JM> so I can use it on a trajectory and average the CA distances
> over all
> JM> frames. The new tcl function that I have does not exit clean
> but leaves a
> JM> huge memory behind. This is to the best of my knowledge not due
> to an
> JM> undeleted atomselection but has to do with the array of
> distances that is
> JM> used. I was able to narrow the problem down to second for loop
> in the script
> JM> below. The array, as expected is deleted after the procedure
> exits,
> JM> additional, just to confirm, I've added a unset line, which
> does however not
> JM> change anything.
>
> johannes,
> can you try using:
>
> array dist unset
>
> instead. perhaps there is a bug in tcl with the reference
> counting of the array elements?
>
> cheers,
> axel.
>
> JM> My system has ~ 200 amino acids in two separate chains,
> depending on how
> JM> many frames I run the script on I see different percentages of
> the memory
> JM> used up. Rerunning the script increases the memory use but only
> marginally.
> JM> Any suggestion of what's going wrong here is appreciated.
> JM>
> JM> Our system:
> JM> Linux node004 2.6.17-gentoo-r4 #5 SMP Thu Jun 21 14:15:34 PDT
> 2007 x86_64
> JM> Dual Core AMD Opteron(tm) Processor 275 AuthenticAMD GNU/Linux
> JM>
> JM> VMD:
> JM> >Main< (feb08.data.1) 61 % vmdinfo versionmsg
> JM> VMD for LINUX, version 1.8.6 (July 18, 2007)
> JM>
> JM> Thanks,
> JM> -hannes-
> JM>
> JM>
> JM> proc ca_average {main_sel start_frame end_frame} {
> JM>
> JM> set sel [atomselect top "$main_sel and name CA"]
> JM> set list1 [$sel list]
> JM> set list2 $list1
> JM> for {set i $start_frame} {$i < $end_frame} {incr i 1} {
> JM> $sel frame $i
> JM> set coords($i) [$sel get {x y z}]
> JM> }
> JM> $sel delete
> JM>
> JM> for {set i $start_frame} {$i < $end_frame} {incr i 1} {
> JM> set list2 $list1
> JM> foreach atom1 $coords($i) id1 $list1 {
> JM> foreach atom2 $coords($i) id2 $list2 {
> JM> set dist($i,$id1,$id2) [veclength [vecsub
> $atom2
> JM> $atom1]]
> JM> }
> JM> lvarpop list2
> JM> lvarpop coords($i)
> JM> }
> JM> }
> JM> puts "Array before deletion: [array size dist]"
> JM> unset dist
> JM> puts "Array after deletion: [array size dist]"
> JM> }
> JM>
> JM>
> JM> Tk Console output:
> JM> loading history file ... 48 events added
> JM> Main console display active (Tcl8.4.9 / Tk8.4.9)
> JM> (feb08.data.1) 49 % source ~/Tcl_scripts/test.tcl
> JM> >Main< (feb08.data.1) 50 % ca_average protein 0 200
> JM> Array before deletion: 5130200
> JM> Array after deletion: 0
> JM> >Main< (feb08.data.1) 51 %
> JM>
> JM> top output for VMD before I run the script:
> JM> 4680 hannes 15 0 223m 39m 7620 S 0 2.0 0:02.77
> vmd_LINUX
> JM>
> JM> and after:
> JM> 4680 hannes 15 0 1165m 982m 7912 S 0 48.8 0:21.61
> vmd_LINUX
> JM>
> JM>
> JM> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
> JM>
> JM> Dr. Johannes Müllegger
> JM> Zymeworks Inc.
> JM> 201 - 1401 West Broadway
> JM> Vancouver, BC, Canada
> JM> V6H 1H6
> JM> Phone: 604 678 1388 -124
> JM> Fax: 604 737 7077
> JM> www.zymeworks.com
> JM>
> JM> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
> JM>
> JM>
> JM>
> JM>
> JM>
> JM>
> JM>
> JM>
> JM>
> JM> Notice of Confidentiality: The information transmitted is
> intended only for
> JM> the
> JM> person or entity to which it is addressed and may contain
> confidential
> JM> and/or
> JM> privileged material. Any review, re-transmission, dissemination
> or other use
> JM> of
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> JM>
> JM>
> JM>
>
> --
> ======================================================================
> =
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
> www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> ======================================================================
> =
> If you make something idiot-proof, the universe creates a better
> idiot.

_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/

Dr. Johannes Müllegger
Senior Scientist - Protein Engineering
Zymeworks Inc.
201 - 1401 West Broadway
Vancouver, BC, Canada
V6H 1H6
Phone: 604 678 1388 -124
Fax: 604 737 7077
www.zymeworks.com

_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/

Notice of Confidentiality: The information transmitted is intended only for the
person or entity to which it is addressed and may contain confidential and/or
privileged material. Any review, re-transmission, dissemination or other use of
or taking of any action in reliance upon this information by persons or entities
other than the intended recipient is prohibited. If you received this in error
please contact the sender immediately by return electronic transmission and then
immediately delete this transmission including all attachments without copying,
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