Can you do minimization using 4 CPUs? I could only use 2 CPUs in
minimization processes.
On Tue, 11 Nov 2008, Lachele Foley wrote:
> PS to the previous... the minimization was run on four processors... Sorry for any confusion.
>
>
> :-) 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: Lachele Foley
> [mailto:lfoley.ccrc.uga.edu]
> To: amber-developers.scripps.edu
> Sent: Tue, 11
> Nov 2008 13:27:09 -0500
> Subject: Re: amber-developers: Extra Points
> Calculation
>
>
> > > We thought it does, but Lachele discovered more problems yesterday
> > > evening; he was going to take a look today.
> >
> > I kept having jobs fail... I could only get them to behave on 2 processors.
> > I hadn't even looked, graphically, at the output. Silly me.
> >
> > The minimization isn't doing quite what I expect. Load the attached
> > topology and restart into vmd or something and you will find, if you twirl
> > the system the right way, a lovely rift between two halves of the solvent,
> > with the sucrose molecule spanning the gap, more or less. The starting
> > coordinates look like a standard array of water molecules dropped around a
> > solvent, so this is something the minimization is doing. Also attached is
> > my MIN.in file in case there is some EP-relevant keyword I didn't set
> > properly. If I had to make a blind guess, I'd say the two processors aren't
> > talking to each other in quite the way they should -- like half the solvent
> > went to one, and half went to the other, and neither knows exactly where the
> > other is. Or something.
> >
> > And, for what it's worth, The CP running on two processors seems to be
> > slowly correcting the problem. It's over 100,000 steps and the coordinates
> > look pretty good now. At first, it was what you'd expect. I can send some
> > or all of that output if anyone wants to see it.
> >
> > :-) 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 07:20:07 -0500
> > Subject: Re: amber-developers: Extra Points
> > Calculation
> >
> >
> > > > Does it solve Lachele's problem (the sucrose_EP test case)?
> > >
> > > We thought it does, but Lachele discovered more problems yesterday
> > > evening; he was going to take a look today.
> > >
> > > > As far as I can see, that example does not include any "LP" atoms,
> > > > and I don't think we should be expanding to that...my recollection
> > > > was that "LP" atoms (still found in
> > > > some old parameter/topology files) were *not* treated as extra points,
> > but
> > > > as real atoms.
> > >
> > > I see. Then probably the 'LP ' part is unneeded indeed. I am not a
> > > right person to judge here.
> > >
> > > > I tried to expand the size of max14 (not as much as you did), and was
> > > > still getting segfaults on Lachele's example.
> > >
> > > This is because of too short nb14_list and i14 (their sizes are
> > proportional
> > > to the max14, but max14 is not used in the corresponding allocate()).
> > >
> > > Volodymyr
> > >
> > >
>
>
--
Ilyas Yildirim, Ph.D.
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Received on Fri Dec 05 2008 - 14:28:34 PST
