VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 15 2007 - 15:26:55 CDT

Hi,
  It sounds to me like VMD is running your system out of virtual memory
when you load the 3.5 GB DX file. There are two likely possibilities here:
  1) If you're running a 32-bit version of VMD, it won't be able to
     successfully load a DX file that large, even if your system has
     several gigabytes of physical memory. You _must_ use the 64-bit
     version of VMD for datasets that large.

  2) If your system doesn't have sufficient physical memory, you'll either
     begin paging the system to death (if you have significantly more
     virtual memory), or the memory allocations will fail and the program
     will either return an error or terminate depending on where and how
     the allocation failure occurs.

Since you didn't say anything about getting warnings or seeing the system
run out of physical/virtual memory, I suspect that your problem is 1), and
that you need to run the 64-bit version of VMD.

Let me know if you need more help with this.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Oct 15, 2007 at 12:30:04PM -0400, Corenflos, Steven Charles wrote:
> First of all I apologize if I don't convey the necessary information. I'm doing technical support for a chemistry lab which has brought me to this mailing list.
>
> I open VMD and go to File->New Molecule.
> I have two molecules I'm working with: one is a 177 MB .dx file, and the other is a 3.5 GB .dx file.
> The 177 MB file (we can call it A), opens just fine.
> Attempting to open the 3.5 GB file (which we'll call B) causes top to show 100% CPU usage on one of the CPUs, and variable memory usage usually in the range of 15-17%. This continues for several minutes until the program spontaneously terminates.
>
> I'm running this on a dual-processor, dual-core Xeon 3.06 GHz server with 6 GB of RAM, running Gentoo Linux.
>
> In case it's relevent I also want to point out that it's only using 100% of one core; top shows only 25% total CPU usage. Also I'm running this on one of our servers because the same file caused an out-of-memory error on the workstation that was originally processing it, which had only 1 GB of RAM. I realize it theoretically should be able to allocate any additional memory it needs from swap, but since one file opens and the other doesn't (and since I wasn't 100% certain vmd wasn't allocating memory directly instead of through system calls) I decided to try it on our server.
>
> Please let me know what additional information I can provide to help figure this problem out.
>
> Thanks,
> -Steve 

-- 
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
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