Figured this out, fix in a couple days... Or, ironically, just fill all
that empty space up with atomic goodness and the problem will fix itself
(for now)...
On Thu, Aug 8, 2013 at 5:31 PM, Scott Le Grand <varelse2005.gmail.com>wrote:
> Reproduced at my end, guessing it's somehow due to lots of empty space in
> the simulation box, but that still shouldn't crash....
>
>
>
> On Thu, Aug 8, 2013 at 7:12 AM, Kyle Sutherland-Cash <khs26.cam.ac.uk>wrote:
>
>> Hello Scott,
>>
>> I've attached working and failing input (they only differ by the value of
>> the cut off). Let me know if there's anything else you need.
>>
>> Thanks,
>>
>> Kyle
>>
>>
>> On 7 August 2013 18:28, Scott Le Grand <varelse2005.gmail.com> wrote:
>>
>>> Send me the input files?
>>> On Aug 7, 2013 10:14 AM, "Kyle Sutherland-Cash" <khs26.cam.ac.uk> wrote:
>>>
>>> > Hello,
>>> >
>>> > I had an issue that has been mentioned before at:
>>> > http://archive.ambermd.org/201307/0514.html
>>> >
>>> > This occurs when running a minimisation for an 80,000 atom system with
>>> cut
>>> > offs over a certain size (10.0 and 11.0 work fine, but 12.0 and larger
>>> do
>>> > not). The error is reported as GpuBuffer::Download failed unspecified
>>> > launch error (i.e. probably a CUDA segfault).
>>> >
>>> > I ran pmemd.cuda through cuda-memcheck and it highlighted calls to
>>> > kNLBuildNeighborListOrthogonal16_kernel. All of the errors were of the
>>> > following form:
>>> >
>>> > ========= Invalid __global__ write of size 4
>>> > ========= at 0x00000e38 in
>>> > kNLBuildNeighborListOrthogonal16_kernel(void)
>>> > ========= by thread (527,0,0) in block (0,0,0)
>>> > ========= Address 0x70eaede3c is out of bounds
>>> >
>>> > The threads in question were threads (512-527,0,0) in block (0,0,0) and
>>> > (192-207,0,0) in block (7,0,0). I tried looking at kBNL.h, but I don't
>>> > really know CUDA well enough to work out where the indexing might have
>>> gone
>>> > awry.
>>> >
>>> > If it helps, I can upload input files as well.
>>> >
>>> > The code was built yesterday with all the available bugfixes using CUDA
>>> > 5.5, ifort and the Intel MKL.
>>> >
>>> > Thanks,
>>> >
>>> > Kyle
>>> > _______________________________________________
>>> > 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
>>>
>>
>>
>>
>> --
>> Kyle Sutherland-Cash
>> PhD student, Wales group
>>
>> Department of Chemistry
>> University of Cambridge
>> Cambridge
>> United Kingdom
>> CB2 1DQ
>>
>
>
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Received on Thu Aug 08 2013 - 20:30:02 PDT
