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
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>>
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--
____________________________________________________________________________
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 - 14:30:03 PDT
