From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Dec 04 2015 - 16:52:30 CST
This is fixed in 2.11b2, which is just now available for download.
I'll post the formal 2.11b2 release announcement over the weekend.
Jim
On Thu, 3 Dec 2015, Jeff Comer wrote:
> Dear NAMD developers,
>
> For small systems (3400 atoms), I've been getting "FATAL ERROR:
> Incorrect number of exclusions detected" with NAMD2.11b1, while the
> same systems run without problem in NAMD2.10. The patch grid in both
> cases is 3 (PERIODIC) BY 1 (PERIODIC) BY 3 (PERIODIC).
>
> I can get NAMD2.11b1 to run these systems by using "margin 4", which
> gives a patch grid of 2 (PERIODIC) BY 2 (PERIODIC) BY 2 (PERIODIC),
> but here I get worse performance:
>
> NAMD2.11b1, margin 0, procs 6, gpus 1: FAILS
> NAMD2.11b1, margin 4, procs 6, gpus 1: 74 ns/day
>
> NAMD2.10, margin 0, procs 6, gpus 1: 77 ns/day
> NAMD2.10, margin 4, procs 6, gpus 1: 56 ns/day
>
> I can also get NAMD2.11b1 to run by using more cores. I have
> hyperthreading on, but using more than the number of physical cores
> (6) usually leads to performance loss, as it also does in this case:
>
> PATCH GRID IS 3 (PERIODIC) BY 3 (PERIODIC) BY 3 (PERIODIC)
> NAMD2.11b1, margin 0, procs 12, gpus 1: 45 ns/day
> NAMD2.11b1, margin 0, procs 10, gpus 1: 60 ns/day
> NAMD2.11b1, margin 0, procs 8, gpus 1: FAILS
>
> Is there any other way to avoid using "margin" or increasing the
> number of cores with NAMD2.11b1? Some other information that might be
> useful is below.
>
> Thanks,
> Jeff
>
> Build: NAMD_2.11b1_Linux-x86_64-multicore-CUDA
> Processor: Intel E5-1650v2 3.5GHz 6-core
> switchDist 8
> cutoff 9
> pairListDist 11
> pmeGridSpacing 1.2
>
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
>
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