Dear,
Thanks for you advice , I will have a try.
Best wishes
2013/3/18 Gerald Monard <Gerald.Monard.univ-lorraine.fr>
> Hi,
>
> It seems that you have set ntc=2 with ntf=2 (which is what the doc asks
> you to do :-)). Try ntf=1. Sometimes, when collisions occur, the SHAKE
> part has some problems. With the GPU is then give a "cudaMemcpy" error.
> It worked for me.
> Best,
>
> Gerald.
>
> On 03/16/2013 10:49 AM, Ϳ־Ƽ wrote:
> > Dear all,
> > I have made the version number in the output file correct.but the error
> > cudaMemcpy GpuBuffer:::Download failed unspecified
> > launch failure still happends.I want to ask how can I restraint the atoms
> > of protein chain within a fixed distance ,like a cylinder ,using the
> amber
> > original program?
> > Thanks a lot.
> > Tu
> >
> > 2013/3/10 Jason Swails <jason.swails.gmail.com>
> >
> >> Did you recompile? The updates only affect the source code, not the
> >> compiled binaries. Make sure to reconfigure and recompile after the
> updates
> >> were applied.
> >>
> >> If you have done this correctly, the version number in the output file
> >> will be correct.
> >> Goo luck,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project
> >> University of Florida
> >> Ph.D. Candidate
> >> 352-392-4032
> >>
> >> On Mar 10, 2013, at 10:20 AM, 涂志萍 <tuzhiping711.gmail.com> wrote:
> >>
> >>> Dear all,
> >>> The result of "./patch_amber.py --patch-level" is:
> >>> Latest patch applied to AmberTools12: 35
> >>> Latest patch applied to Amber12: 15
> >>> so I am sure I have patched the all bugfixs, I think I should tell you
> >>> that we had added some tube control files to the program. But after I
> >> have
> >>> updated the patches.the mdout file still shows the version of GUP
> pmemd
> >>> 12.1 and the error cudaMemcpy GpuBuffer:::Download failed unspecified
> >>> launch failure happends
> >>> I don't know why? Any help ? Thanks a lot.
> >>>
> >>> Yours
> >>> Tu
> >>> 2013/3/8 Jason Swails <jason.swails.gmail.com>
> >>>
> >>>> On Thu, Mar 7, 2013 at 11:51 PM, 涂志萍 <tuzhiping711.gmail.com> wrote:
> >>>>
> >>>>> Dear all ,
> >>>>> I'm sorry for unclear formulation . Yes, I had patched the latest
> bug
> >>>>> fixes applied to my
> >>>>> AMBER 12 installation four days ago.Section of my mdout file as
> below:
> >>>>
> >>>> Note it is not enough to simply run patch_amber.py to 'update' amber.
> >> You
> >>>> also have to re-build. Furthermore, you really should post the
> results
> >> of
> >>>> "./patch_amber.py --patch-level" so we can see exactly what patches
> have
> >>>> been applied---especially when that has been requested (note the
> >> difference
> >>>> between that and "I've applied all patches." ;-) ).
> >>>>
> >>>> It is important for people providing help remotely to have an exact
> >> picture
> >>>> (or as close as possible) to the conditions leading to the failure in
> >> order
> >>>> to provide help.
> >>>>
> >>>> Good luck,
> >>>> 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
> >>
> >> _______________________________________________
> >> 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
> >
>
> --
>
> ____________________________________________________________________________
>
> Prof. Gerald MONARD
> Theoretical Chemistry and Biochemistry Group
> SRSMC, Université de Lorraine, CNRS
> Boulevard des Aiguillettes B.P. 70239
> F-54506 Vandoeuvre-les-Nancy, FRANCE
>
> e-mail : Gerald.Monard.univ-lorraine.fr
> tel. : +33 (0)383.684.381
> fax : +33 (0)383.684.371
> web : http://www.monard.info
>
>
> ____________________________________________________________________________
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Received on Sun Mar 17 2013 - 20:30:03 PDT
