VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 02 2004 - 11:24:43 CDT

Shirley,
  I was hoping you'd show me all of what you're getting from top, not just
the process stats. Unless you have much more than 512MB, I'm guessing
that your machine is paging and this is the reason for slow performance.
How much swap is in use on your machine when you get those numbers?
For example, look at the two 'top' results below. In order to determine
if you're causing the machine to run out of ram, you need to look at how
much is free, how much VMD is using, AND how much swap is being used.
The output from top depends on which OS you're running on, but the concepts
are essentially the same regardless.

Linux:
Mem: 1030856k av, 578164k used, 452692k free, 0k shrd, 101448k buff
                    345384k actv, 36568k in_d, 3772k in_c
Swap: 2096472k av, 2116k used, 2094356k free 197464k cached

  PID USER PRI NI SIZE RSS SHARE STAT %CPU %MEM TIME CPU COMMAND
19820 johns 23 0 208M 15M 6360 R 9.8 1.5 0:00 0 vmd_LINUX

64-bit Solaris:
Memory: 32G real, 30G free, 683M swap in use, 30G swap free
   PID USERNAME LWP PRI NICE SIZE RES STATE TIME CPU COMMAND
 27067 johns 1 59 0 780M 594M sleep 20:27 0.00% vmd_SOLARIS2_64

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 02, 2004 at 08:14:34AM -0700, Shirley Li wrote:
> Hi John,
>
> When the machaine becomes unreponsive at step "Encoding", "top"gives the usage of %MEM/SIZE/RSS as 82.3%/530M/413M. After the "Encoding"step is done, the usage changes into 1.5%/70960/8204.
>
> Thank you.
>
> Have a great day.
>
> Shirley
>
>
> John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> When you saw those total/used/free values, what was your swap size?
> I.e. what does 'top' give for memory usage stats when the machine
> is unresponsive as you're describing. It is quite possible that the
> "free" memory is only due to large amounts of swap being used... :)
>
> John Stone
> vmd_at_ks.uiuc.edu
>
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-- 
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