VMD-L Mailing List

From: Windle,Stephen (snw42_at_drexel.edu)
Date: Wed Jan 31 2018 - 14:21:17 CST

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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