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-- 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 13:45:51 -0500 Subject: Re: amber-developers: Extra Points Calculation > Yep... Even the mdout file agrees: > > > Number of triangulated 3-point waters found: 623 > | Atom division among processors: > | 0 797 1592 2387 3182 > > Sum of charges from parm topology file = 0.00000000 > Forcing neutrality... > | Running AMBER/MPI version on 4 nodes > > > I'll try running it on 2 nodes now and see if the output looks better. > > > :-) 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: Ilyas Yildirim > [mailto:yildirim.pas.rochester.edu] > To: amber-developers.scripps.edu > Sent: > Tue, 11 Nov 2008 13:41:50 -0500 > Subject: Re: amber-developers: Extra Points > Calculation > > > > 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. > > --------------------------------------------------------------- > > = Hutchison Hall B#10 - Department of Chemistry = > > = - University of Rochester = > > = 585-275-6766 (office) - = > > = http://www.pas.rochester.edu/~yildirim/ = > > --------------------------------------------------------------- > > > > >Received on Fri Dec 05 2008 - 14:28:43 PST