# Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability

From: Marc van der Kamp <marcvanderkamp.gmail.com>
Date: Tue, 20 Dec 2011 10:03:05 +0000

Hi Ross,

Thanks, I noticed that bugfix.20 is there now!

I applied it and compiled a fresh pmemd.cuda_SPDP.
However, when I ran my test job with this, I got the same issue as I had
before: energies increase (and VIRIAL decreases) signficantly in 200 steps
of NPT MD (but not 200 steps of NVT MD).

See the attached files, run with pmemd (*.cpu) and with pmemd.cuda_SPDP
(*.SPDP)

I will try doing a completely clean installation, including AmberTools 1.5,
next.

Thanks,
Marc

On 19 December 2011 17:31, Ross Walker <ross.rosswalker.co.uk> wrote:

> Hi Marc,
>
> We are just testing the patch - it will fix three known bugs at the same
> time so we just want to make sure it is working properly before making it
> public.
>
> - Fix for "GPU Runs with IWRAP die with NAN for KE immediately after the
> first molecule is wrapped".
>
> - Fix for "Possible hang at MPI_Win_fence(0,gpu->MPIPMEForceWindow); in
> gpu_gather_pme_forces_() "
> casued by the presence of vacuum bubbles in the solvent.
>
> - Fix for "Problems running pmemd.cuda with a chamber prmtop and NPT"
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Marc van der Kamp [mailto:marcvanderkamp.gmail.com]
> > Sent: Monday, December 19, 2011 1:54 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is
> > causing serious instability
> >
> > Hi there,
> >
> > Any ETA on the bugfix yet?
> > I appreciate things get busy, but it would be great if you could post
> > the
> > fix soon (so I can start using it over the X-mas holidays).
> > If this is difficult, could Scot perhaps give us the changes he made in
> > the
> > code (or is it too involved)?
> >
> > Many thanks, and (both) your efforts with pmemd.cuda are immensely
> > appreciated!
> > Marc
> >
> > On 1 December 2011 17:23, Scott Le Grand <varelse2005.gmail.com> wrote:
> >
> > > Why don't you hold on that long enough to throw in the netfrc fix
> > along
> > > with it?
> > >
> > >
> > > On Thu, Dec 1, 2011 at 9:15 AM, Ross Walker <ross.rosswalker.co.uk>
> > wrote:
> > >
> > > > Hi Marc,
> > > >
> > > > > Great to hear a fix is on the way! Thanks, Scott.
> > > > >
> > > > > How/when will I be able to apply the fix? Just wait until it
> > appears on
> > > > > http://ambermd.org/bugfixes11.html, or could there be another
> > (faster)
> > > > > way?
> > > >
> > > > I'll post a bugfix in a few days once I have had a chance to test
> > it
> > > > properly.
> > > >
> > > > All the best
> > > > Ross
> > > >
> > > > /\
> > > > \/
> > > > |\oss Walker
> > > >
> > > > ---------------------------------------------------------
> > > > | Assistant Research Professor |
> > > > | San Diego Supercomputer Center |
> > > > | Adjunct Assistant Professor |
> > > > | Dept. of Chemistry and Biochemistry |
> > > > | University of California San Diego |
> > > > | NVIDIA Fellow |
> > > > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> > > > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > > > ---------------------------------------------------------
> > > >
> > > > Note: Electronic Mail is not secure, has no guarantee of delivery,
> > may
> > > not
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> > issues.
> > > >
> > > >
> > > >
> > > >
> > > >
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Received on Tue Dec 20 2011 - 02:30:02 PST
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