Apologies Heather, my Amber 12 repository was not fully up-to-date when I
checked (I should have followed my own advice to check for updates). The
real results should be:
$ ./patch_amber.py --patch-level
Latest patch applied to AmberTools12: 26
Latest patch applied to Amber12: 12
I just wanted to update in case you got worried about your results
differing from the ones I reported.
All the best,
Jason
On Fri, Oct 19, 2012 at 12:46 PM, <mhclewett.msn.com> wrote:
>
> Jason,
> As I have:
> Latest patch applied to AmberTools12: 24Latest patch applied to Amber12:
> 9
> I will update per your suggestion.
> THANK YOU!Heather
>
> > Date: Fri, 19 Oct 2012 10:49:50 -0400
> > From: jason.swails.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] NaN question
> >
> > On Fri, Oct 19, 2012 at 10:36 AM, <mhclewett.msn.com> wrote:
> >
> > >
> > > Hello and thank you in advance for your help,
> > > I have a NaN error that does not seem to respond to the posted
> > > fixes/suggestions. I will provide as much information as would be
> helpful.
> > > My guess of what is helpful follows.
> > > I am operating Amber12 on a 2 GPU system that follows the Ross Walker
> > > recommendation for all hardware. The command nvidia-smi returns a
> > > temperature of 80 C for GPU0 and 85 C for GPU1.
> > > My bugfixes are current through bugfix.24.
> > >
> >
> > There are two sets of bug fixes available. One is for Amber and the
> other
> > for AmberTools. When reporting patch levels (which is important in this
> > case), give us the result of the following command:
> >
> > cd $AMBERHOME && ./patch_amber.py --patch-level
> >
> > This will tell us how many patches have been applied to both packages.
> For
> > reference, the fully-updated tree should return this:
> >
> > $ ./patch_amber.py --patch-level
> > Latest patch applied to AmberTools12: 25
> > Latest patch applied to Amber12: 11
> >
> > Note, you can also use patch_amber.py to quickly check for available
> > updates using "./patch_amber.py --check" (see a full listing of options
> > using --help).
> >
> > Most notably, bugfix.11 for Amber12 I believe fixes parallel GPU
> > simulations which may have given NaNs before.
> >
> > HTH,
> > Jason
> >
> > --
> > 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Oct 19 2012 - 10:30:03 PDT
