I don't get the hard cap part.
For my system I have (right now) 64,000 atoms, and the NPT (npt=1, ntb=2) ensemble fails and spits out that error. The NVT (ntb=1, npt=0) works fine.
But I also ran the FactorIX_Production_NPT (with 90,000+ atoms) and FactorIX_Production_NVT and both ran fine.
Or are you saying it's the molecules (residue) number? Then I have 4000 molecules. I'm not sure about the FactorIX benchmark molecules.
Regards,
Farid Ismail
________________________________________
From: Scott Le Grand [varelse2005.gmail.com]
Sent: Tuesday, August 09, 2011 12:28 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Failure kReduceSoluteCOM with GPU
The problem they're hitting here is that C1060 is hard-capped to 460 solute
molecules and C20xx is capped to 1535.
I've fixed that but it's still in testing. That said, what would be useful
here is for you guys to tell me the maximum number of atoms you'll generally
use in these alternate solvent molecules so I can optimize performance for
these down the road.
Scott
On Tue, Aug 9, 2011 at 9:15 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Aug 9, 2011 at 10:47 AM, Ismail, Mohd F. <farid.ou.edu> wrote:
>
> > I have also stumbled into this error. My system is a 64,000 atom system
> > made of 4000 dimethoxy ethane molecule.
> >
> > My system is a dual opteron with GTX 590, cuda 3.2, Nvidia driver 280.16,
> > and gfortran.
> >
> > If I run the system with NPT ensembles, it fails. But if I run with NVT
> > ensemble, it works fine. I never test it with NVE calculation. Both
> system
> > works when run on CPU. The weird thing is the benchmark system
> > Factorial....NPT runs fine. The only different I found is the benchmark
> > system uses the old parameter file, whereas the my system run the new
> > parameter file (the part in the mdout that says "New format PARM file
> being
> > parsed.")
> >
> > I assume the old format PARM is for AmberTools <1.5, no?
> >
>
> No. Old parm format is actually < Amber 7, which is pretty severely
> outdated at this point (not sure exactly when it was released -- maybe
> ~2004
> or so?).
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Aug 09 2011 - 11:30:02 PDT
