Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent

From: Scott Le Grand <varelse2005.gmail.com>
Date: Fri, 30 Jan 2015 09:38:54 -0800

If you look in gb_ene, this happens in the FORTRAN code as well. It's just
that there's an else clause that keeps it from doing something doofy...

I think normally one never hits that clause, but perhaps the FORTRAN code
should have some sort of WTF write statement there...


On Fri, Jan 30, 2015 at 9:24 AM, Ross Walker <ross.rosswalker.co.uk> wrote:

> FYI, Scott found a race condition in the code - occurring because of an
> initialized variable that can occur when the GB parameters are invalid.
> Essentially giving zero radii - why this happens I have not had time to
> investigate. But having the code always initialize the variable fixes the
> race condition (it was in both DPFP and SPFP but only tended to manifest in
> DPFP, likely because the unititialized variable tended to be zero anyway
> for the SPFP memory layout). A bugfix for this will be released shortly.
>
> No why this problem doesn't show up with any of our test cases but did
> with this specific one (as in what is unique about the system Rosie
> provided) is something that needs more investigation.
>
> All the best
> Ross
>
> > On Jan 30, 2015, at 7:11 AM, Ilyas Yildirim <iy222.cam.ac.uk> wrote:
> >
> > To MODERATOR: I've sent the same email today early morning with some
> attachments, but the size of the attachments were too big, which required
> the moderator to decide to post or not. I am re-sending the email without
> the attachments; thus, please discard and do not send the previous email to
> the list.
> >
> > Dear Jason, Scott, Dave, and Ross,
> >
> > I have been reading this thread since Rosie described the problem with
> the energies coming out different at each new calculation. Scott and Jason
> were talking about the problem arising due to the GB model, or the method
> it is being used by cuda. So, I provided Rosie with a new prmtop/inpcrd
> input set directly created with ff12SB force field. The new set seems to
> work fine. The previous one was created with new frcmod/lib files loaded
> over ff12SB. The new frcmod has new atom types in it, and it seems that
> those are the ones causing the problem (though it is not clear yet to me
> why energies are different at the end). You can check out the
> prmtop.notworking and prmtop.working from the following address:
> >
> > http://www-wales.ch.cam.ac.uk/rosie/new_input/
> >
> > While creating the prmtop.notworking file, I used the following leap
> script to create it.
> >
> > ---------- xleap.in -----------
> > source leaprc.ff12SB
> > addPdbAtomMap {
> > { "OP1" "O1P" } { "OP2" "O2P" }
> > { "HO5'" "H5T" } { "HO3'" "H3T" }
> > { "H5'" "H5'1" } { "H5''" "H5'2" }
> > { "H2'" "H2'1" } { "H2''" "H2'2" }
> > }
> > addAtomTypes {
> > { "DH" "H" "sp3" }
> > { "C1" "C" "sp2" }
> > { "C2" "C" "sp2" }
> > { "C3" "C" "sp2" }
> > { "C4" "C" "sp2" }
> > { "C5" "C" "sp2" }
> > { "C6" "C" "sp2" }
> > { "C7" "C" "sp2" }
> > { "C8" "C" "sp2" }
> > { "CI" "C" "sp3" }
> > { "OZ" "O" "sp3" }
> > }
> > loadamberparams ./libraries/frcmod.parmCHI
> > loadamberparams ./libraries/frcmod.ionsjc_tip3p
> > loadoff ./libraries/dna.parm99chi.parmbsc.off
> > loadoff ./libraries/ions08.lib
> > set default PBradii mbondi2
> > mol = loadpdb model.pdb
> > saveAmberParm mol prmtop.notworking inpcrd
> > quit
> > ------------------------------------------------
> >
> > If someone wants to use a GB model on a modified system (or let's say a
> model with revised force field) I am not sure what else needs to be defined
> in the leap input file. In the cuda version of pmemd, is there a specific
> file that has info on the GB model which needs to be modified in order make
> sure that the new atom types are recognized by AMBER 14 DPFP runs (so that
> the GB model won't complain about it)? It seems that usage of new atoms
> types somehow creates this whole problem. Thanks.
> >
> > Best regards,
> >
> > Ilyas Yildirim, Ph.D.
> > -----------------------------------------------------------
> > = Department of Chemistry | University of Cambridge =
> > = Lensfield Road (Room # 380) | Cambridge, UK CB2 1EW =
> > = Ph.: +44-1223-336-353 | E-mail: iy222.cam.ac.uk =
> > = Website: http://ilyasyildirim.wordpress.com =
> > = ------------------------------------------------------- =
> > = http://www.linkedin.com/in/yildirimilyas =
> > = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
> > -----------------------------------------------------------
> >
> >
> > On Thu, 29 Jan 2015, Jason Swails wrote:
> >
> >> On Thu, Jan 29, 2015 at 9:14 PM, Scott Le Grand <varelse2005.gmail.com>
> >> wrote:
> >>> Hey Jason, I found the root cause and checked in a fix.
> >>> If I put a printf into any CUDA kernel, that's the end of its
> performance.
> >>> Printf is a hog. It's only useful for debugging purposes.
> >> ‚ÄčThat's what I was suggesting it be used for. Basically what I was
> curious
> >> about was whether or not any of the GB tests in our test suite hit the
> code
> >> path where dr didn't get initialized. If it did, that would seem (to
> me)
> >> to be clear evidence that that code path is not illegal/unusual (i.e.,
> >> indicative of bad parameters). If that printf is never triggered during
> >> the test suite, the parameters may be unusual. I certainly wasn't
> >> suggesting it be left in permanently. I'll take a look if I have time.
> >>
> >>> The beginning
> >>> of this thread has links to the data to repro this behavior. It's
> weird
> >>> that we never saw this before.
> >>> Just initialializing PMEFloat dr does the trick. The bug is fixed.
> >> ‚ÄčI saw the commit log :).
> >> Thanks,
> >> Jason
> >> --
> >> Jason M. Swails
> >> BioMaPS,
> >> Rutgers University
> >> Postdoctoral Researcher
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 30 2015 - 10:00:02 PST
Custom Search