VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 21 2003 - 16:36:02 CST

Joe,
  Depending on how you're performing your atom selections, you
may be causing Tcl to leak atom selection memory. If you're making
many atom selections inside of a loop, make sure you call '$sel delete'
so that the selection is destroyed when you're finished with it.
Without seeing your code I'm not positive this is the cause, but that's
probably 90% likelihood... If you need more help, send us a copy of
your script so we can see what you're actually doing.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 20, 2003 at 01:02:48PM -0600, Joe Huang wrote:
> Dear VMD users,
> I am running a kind of RMSD comparisons (segment by segment on Protein
> or RNA) with TCL script under VMD1.8.
> The system is huge and the calculations can be ~ (1500 X 1500) RMSD
> calculations (i.e., 2.25 E6 or more than 2 million RMSD calculations).
> In the beginning, my calculations would crash due to the consumptions
> of virtual SWAP memory in the system after ~ 4 rounds of RMSD
> calculations (i.e., ~[4x1500] out of more than 2 million calculations);
> later, I checked the VMD-L archive and found out that I need to unset
> the atom selections after each RMSD comparison to solve this problem.
> Therefore, I unset the atomselections (e.g., "unset
> upproc_var_$compare" and "unset upproc_var_$reference") and also unset
> all the variables (e.g., "unset trans_mat", "unset rmsd", ...etc.)
> after their usages on each cycle; in this case, the calculations could
> go on more than (400x1500) comparisons, but the virtual SWAP memory was
> still decreasing in a much slower slower degree and eventually the
> calculations would still crash in the middle to the finish line!
> Although I could rerun VMD and recontinue the job several times to
> finish the whole calculations, I prefer to finish it just by one session
> of VMD calculations with TCL script. So, does anyone know what causes
> the calculations to slowly consume the SWAP memory and also know the
> solution to it?
> Your help will be much appreciated!!
>
>
> Joe
>
> --
> *****************************************
> Hung-Chung Huang, M. T., M. Sc., Ph. D.
> Department of Biology and Biochemistry
> University of Houston, Houston, TX 77204
> Tel: (713) 743-8365, Fax: (713) 743-8351
> e-mail: HCHuang_at_uh.edu
> http://prion.bchs.uh.edu/~jhuang
> *****************************************
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078