Re: amber-developers: Extra Points Calculation

From: Lachele Foley <lfoley.ccrc.uga.edu>
Date: Tue, 11 Nov 2008 15:31:52 -0500

> These look perfectly fine, i.e., the output does not depend on the
> number of cpus, which is good.

But, the end result of the minimization, after 14,000 steps, most certainly is not fine. In fact, it is very bad. It has a great big gap running down the middle of it.

So, my guess about the different processors was wrong... and I don't know enough about the code to make any other guesses. I have no clue why it would do that, but it does look sort-of as if it divided the waters into two sets and minimized them separately, and the sucrose separately, still.


:-) Lachele

--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
----- Original Message -----
From: Volodymyr Babin
[mailto:vbabin.ncsu.edu]
To: amber-developers.scripps.edu
Sent: Tue, 11 Nov
2008 15:17:39 -0500
Subject: Re: amber-developers: Extra Points
Calculation
> On Tue, November 11, 2008 15:00, Lachele Foley wrote:
> > I made clean first.
> 
> I probably misunderstood you then.
> 
> > I just did a serial run (despite any complaints about not being able to
> > get to it).  It gives the same, or very similar, 14000-step result.
> 
> Strange.
> 
> > Attached is input and output from a short series of 14-step runs (serial,
> > MPI with one proc, MPI with 2 procs, MPI with 4 procs).  Let me know if I
> > misunderstood you and there was some other set of runs that would be
> > better.  It hardly looks as if it's done anything.
> 
> These look perfectly fine, i.e., the output does not depend on the
> number of cpus, which is good.
> 
> Volodymyr
> 

Received on Fri Dec 05 2008 - 14:30:14 PST