VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 18 2021 - 12:13:47 CDT

Hi,
  I'm guessing that you've run out of open file handles, which tends
to happen at around 1000 files or so unless you're careful to prevent
this from happening by processing a limited number of files at a time
and ensuring their loading is entirely complete before continuing to
open new files.

Since there isn't a "canonical" animatedcds script in the script library,
I'm not sure exactly what your script is doing, and whether or not
it is using "waitfor all" to force loading to complete before adding
each subsequent DCD file, etc.

I'm assuming you're running on a Unix system and that you're system
is set to limit you to 1024 open file handles, e.g.:
% ulimit -n
1024

You can query other system-enforced per-process limits like this:
% ulimit -a
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 512639
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 512639
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Oct 10, 2021 at 08:27:00AM -0700, Ryan Woltz wrote:
> Dear community,
> I've seen a few threads regarding this error but can't find a
> anything about my situation as it seems to be a gui interface problem but
> I don't have any more verbose to go off of from here.
> I have a completed MD simulation that has ~1106 dcd files to load
> in sequence. I"m using the community posted tcl script to do this called
> animatedcds and I've been using the same script for a year now with no
> issues so I don't think the problem is coming from there. I have multiple
> steps with 106 dcd files being loaded in the equilibration phase and 1000
> dcds being loaded in the production phase. The issue is it stops loading
> at file 995 in the production phase. I then load manually file 996 to
> using the GUI file load menu but get the error:
> X_ChangeProperty: BadValue (integer parameter out of range for operation)
> 0x40
> I'm not running out of RAM as I have 128 GB and I'm only using 43 GB. Any
> suggestions on what the problem is? Does VMD only load 1100 files and I
> need to combine them into sections? I'm really confused why this would
> happen as there was never any failures loading files to check how the
> simulation was going before completion (less than 950 production dcd
> files).
> Thank you,
> Ryan 

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