VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 31 2018 - 18:06:57 CST

Hi,
  Yes, you can often increase file descriptor limits, but most systems max
out at about 1024 descriptors, so you're already there. Yes, you should use
the command:
  mol new $pdb waitfor all

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 31, 2018 at 08:21:17PM +0000, Windle,Stephen wrote:
> Hey,
>
> So the error is: "Unable to load file '2ado.pdb' using file type 'pdb'."
> It originally was doing it with 2yjb.pdb, so I went in an removed that
> file from the folder, then it did it again with the 2ado.pdb file. In both
> cases, it loaded 1011 molecules into VMD. The code I'm using is:
>
> set pdblist [glob *.pdb]
> foreach pdb $pdblist {
> mol new $pdb
> }
>
> ...should this be "mol new $pdb waitfor all"? I can see in the command
> terminal that it is definitely loading the file info in the background.
> I'm not sure what the max number of file descriptors is for my OS (Ubuntu
> 16.04.2 LTS), but I think it's possible to raise it using the ulimit
> command? Thanks!
>
> -Steve
>
> --------------------------------------------------------------------------
>
> From: John Stone <johns_at_ks.uiuc.edu>
> Sent: Tuesday, January 30, 2018 12:23:33 AM
> To: Vermaas, Joshua
> Cc: Windle,Stephen; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Molecule limit
>
> Hi,
> This sounds to me like a case where the maximum number of open file
> descriptors has been hit, and is not really a limitation of VMD itself.
> This is typically caused by loading a huge number of molecules but
> not using "waitfor all" in the mol new/addfile commands. This can
> cause VMD to have a large number of files open at once, and that may
> cause the OS to run out of file descriptors. Generally speaking if
> the "waitfor all" flags are present with the "mol" commands, this
> problem shouldn't normally crop up.
>
> Other than the possibility of running out of file descriptors, the
> only other issues I'm aware of relate to running VMD with the GUI
> enabled when having tens of thousands of molecules loaded at once
> (e.g. if you load the entire set of all PDBs into VMD at once on a machine
> with sufficient memory to do so).
> The VMD FLTK GUI does act a bit squirrelly when you get a few tens
> of thousands of molecules loaded due to some internal limits that exist
> in the FLTK GUI components, but I think that for just a few thousand
> molecules those should not be an issue. I think I was able to load about
> 30 or 40,000 molecules into VMD myself previously without any problem,
> even with the GUI enabled. But it has been a while since I needed to do
> that.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Jan 30, 2018 at 01:44:42AM +0000, Vermaas, Joshua wrote:
> > Hi Steve,
> >
> > I don't think so. Here is a little test I ran:
> >
> > for { set i 0 } { $i < 10000 } { incr i } {
> > mol new
> > }
> >
> > This creates 10000 (empty) molecules. You could just as easily do this
> with one specific pdb, and I think you'll find that there is nothing
> stopping you from simultaneously loading an egregious number of files at
> once. There is instead probably something fishy about 1 out of your 2000
> pdbs, and VMD's tcl interpreter catches the error returned and halts
> execution of the rest of the script, which is why VMD works fine for the
> loaded files rather than segfaulting like it would if you ran it out of
> memory. What is the error message, if any?
> >
> > -Josh
> >
> > On 01/29/2018 06:31 PM, Windle,Stephen wrote:
> >
> > Hey all,
> >
> >
> > I have a script that loads all the molecules into VMD. I have two
> folders, one with close to 2,000 pdb files and another with over 6,000. In
> each case, I get an error on a pdb file after it's successfully loaded
> 1,011 files into VMD. The loaded files work fine. Is this the max number
> of allowable molecules for VMD? Thank you!
> >
> >
> > -Steve
> >
>
> --
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-- 
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/