VMD-L Mailing List

From: Corenflos, Steven Charles (scorenfl_at_indiana.edu)
Date: Mon Oct 15 2007 - 11:30:04 CDT

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