From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Feb 12 2007 - 11:07:50 CST
Hi Michel,
the rate limiting step for ionize is the initial grid calculation, not
the ion placements. Once your grid is done the ion placements are
practically free. As of VMD 1.8.6 cionize is going to be included with
VMD (similar to catdcd); in the meantime I'll send you a newer version
off list that should give you somewhat better performance and give you
more detailed timing and processor usage info so you can make sure it's
using all the processors. My guess would be that a system that big
should have finished in 2 days on 24 processors, which is why I'm puzzled...
BTW, if the bladecenter a shared memory machine? If not you certainly
won't be running in parallel.
Peter
L. Michel Espinoza-Fonseca wrote:
> Hi,
>
> I've started to use the IONIZE program (kindly provided by Peter
> Freddolino) to add ions to a 2-million atom system. The net charge of
> my system is -3,600 e. I tried to neutralize such system by using 50
> processors (Altix) for 2 days, and nothing happened. Then I tried to
> do it on 100 processors, and the job was killed. Now I'm trying to do
> it with 500 processors (BladeCenter, AMD Opteron) and I'm waiting to
> see if this time the job will be completed. So here is my question: do
> you have any idea of how much time it could take to add such a big
> amount of ions?
>
> Thanks!
>
> Michel
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