Re: ionize (big, big, big system!)

From: Peter Freddolino (
Date: Mon Feb 12 2007 - 13:07:08 CST

He's talking about our new, improved, parallel ionize overlords
(, which will be
included in VMD 1.8.6.

Cesar Luis Avila wrote:
> You should check previous messages on the list, but as long as I can
> recall, the ionize routine was not parallelized. So, it doesn't matter
> how many processors you send the task for, you will be using only one.
> Regards
> Cesar
> L. Michel Espinoza-Fonseca escribió:
>> 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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