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
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
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>>
>
>
>
> --
> 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 - 18:00:03 PDT
