[phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS

Nathaniel Echols nechols at lbl.gov
Mon Nov 11 08:38:26 PST 2013

On Mon, Nov 11, 2013 at 7:12 AM, Jan Gebauer <jan.gebauer at uni-koeln.de>wrote:

> just to let you know:
> For 1 processor, 600 Aa and 4 copy per asu, and ~60% solvent, my Ubuntu
> needed 4.8GB of RAM and additionally 60% of the 1.4 GB Swap.
> If I used more than one processor, RAM and Swap was completly filled and
> execution failed with "Failed memory alloc" after a while.
> Unfortunately Ubuntu tends to generate small swap partitions, a solution
> might be to add a swap file (additionally to the partition...) [
> http://goo.gl/RSLqT]
> Just watch you "system  monitor"...

That seems a little excessive - we may be doing something inefficient with
map handling.  We tend to buy and use much more powerful systems than what
the average user has access to, which occasionally allows us to miss the
signs of memory bloat in our code.

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