VMD-L Mailing List

From: Ryan Woltz (rlwoltz_at_ucdavis.edu)
Date: Fri Oct 22 2021 - 14:41:40 CDT

Thank you John,

        Yes, that is most likely the issue. I do have 1024 with that ulimit
command, very interesting. I don't have a "waitfor all" in my loading
command (script pasted below) and even after all dcds are loaded from that
initial script if I try to load manually it'll throw the error. It's also
strange because I'm actually loading 1106 (106 equilibration/ 1000
production) dcd files and it loads 1101 since it stops at 995 of the
production. My solution, which is a little annoying on the time for
processing side, is to load as many as I can -> save that as one dcd ->
reload that one large dcd -> load remaining 5 dcds. Is there a more
efficient way to merge multiple dcd files?

Thanks again for the advice,

Ryan

animatedcds script:
#Name:
# animatepdbs
#Synopsis:
# A Tcl script to load a consecutively numbered
# sequence of PDB files into VMD for animation purposes.
#Version:
# 1.0
#Uses VMD Version:
# 1.1
#Parameters:
# start - "frame number" of first PDB file in sequence
# end - "frame number" of last PDB file in sqeuence
# format - a Tcl format string which describes the filename/numbering
# used.
#
#Examples:
# To load a sequence of PDB files named 0.pdb 1.pdb 2.pdb 3.pdb
# one would call this proc with: animatepdbs 0 3 "%d.pdb"
#
# To load a sequence of PDB files named foo0000.pdb foo0001.pdb foo0002.pdb
# one would call this proc with: animatepdbs 0 2 "foo%04d.pdb"
#
#Author:
# John Stone $lt;johns_at_ks.uiuc.edu>
#
proc animatedcds {start end fileformat} {
  set filename [format $fileformat [expr $start]]
# incr start
# puts "Reading initial frame in PDB sequence $filename"
# mol load dcd $filename

  puts "Reading PDB files as an animation..."
  for {set i $start} {$i <= $end} {incr i 1} {
    set filename [format $fileformat [expr $i]]
    animate read dcd $filename 0
  }
}

animatedcd.tcl run in tk console:

source animatedcds
animatedcds 1 6 "step6.%d_equilibration.dcd"
animatedcds 1 5 "step7.1_%d_production.dcd"
animatedcds 1 5 "step7.2_%d_production.dcd"
animatedcds 1 10 "step7.3_%d_production.dcd"
animatedcds 1 5 "step7.4_%d_production.dcd"
animatedcds 1 10 "step7.5_%d_production.dcd"
animatedcds 1 10 "step7.6_%d_production.dcd"
animatedcds 1 10 "step7.7_%d_production.dcd"
animatedcds 1 5 "step7.8_%d_production.dcd"
animatedcds 1 10 "step7.9_%d_production.dcd"
animatedcds 1 5 "step7.10_%d_production.dcd"
animatedcds 1 5 "step7.11_%d_production.dcd"
animatedcds 1 10 "step7.12_%d_production.dcd"
animatedcds 1 10 "step7.13_%d_production.dcd"
animatedcds 1 1000 "step7.14_%d_production.dcd"

On Mon, Oct 18, 2021 at 11:02 AM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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
> > animatedcdsĀ and I've been using the same script for a year now with
> no
> > issues so I don't think the problem is comingĀ 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--000000000000e7190605cef6331e--