In [1]:
import util
import os
from IPython.core.display import Markdown
benchmark = 'quasicrystal'
In [2]:
Markdown(open(os.path.join(benchmark, 'README.md'), 'r').read())
Out[2]:

quasicrystal benchmark

The quasicrystal benchmark runs a system of particles with an oscillatory pair potential that forms an icosahedral quasicrystal. This model is used in the research article: Engel M, et. al. (2015) Computational self-assembly of a one-component icosahedral quasicrystal, Nature materials 14(January), p. 109-116,

Parameters:

  • $N = 100000$
  • $\rho = 0.03$
  • Tabulated pair force
    • $$V = \frac{1}{r^{15}} + \frac{\cos(k (r - 1.25) - \phi)}{r^3}$$
    • $k = 6.25$
    • $\phi = 0.62$
  • Integration: Nosé-Hoover NVT
    • $T=0.18$
    • $\tau=1.0$
    • $\delta t = 0.01$

Performance data

Performance results are reported in hours to complete ten million time steps.

In [3]:
rows = util.read_rows(benchmark)
table = util.make_table(rows)
Markdown(table)
Out[3]:
Date System Compiler CUDA HOOMD Precision N CPU GPU Ranks Time for 10e6 steps (hours)
2018/01/15 comet gcc 4.9.2 8.0 2.2.2 double 100,000 Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz Tesla P100-PCIE-16GB 1 3.45
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 100,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla P100-PCIE-16GB 1 3.27
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 100,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K80 1 10.07
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 100,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K40m 1 10.93
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 100,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla M40 24GB 1 18.58
2016/10/12 psg gcc 4.8.5 8.0 2.1.0 double 100,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla P100-PCIE-16GB 1 3.34
2016/10/12 psg gcc 4.8.5 8.0 2.1.0 double 100,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K80 1 10.22
2016/10/13 psg gcc 4.8.5 7.5 2.1.0 double 100,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K40m 1 11.64
2016/10/13 psg gcc 4.8.5 7.5 2.1.0 double 100,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla M40 24GB 1 19.53
2016/09/13 collins gcc 4.8.5 7.5 2.0.3 double 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 10.27
2016/09/13 collins gcc 4.8.5 7.5 2.0.3 double 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz TITAN X 1 11.28
2016/09/13 collins gcc 4.8.5 7.5 2.0.3 double 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 21.24
2016/09/13 collins gcc 4.8.5 7.5 2.0.3 double 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz GeForce GTX 680 1 31.29
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 5.51
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 8.28
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 double 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 10.70
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz GeForce GTX 680 1 15.79
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 double 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 22.75
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 23.29
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 double 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 31.43
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 double 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz GeForce GTX 680 1 32.27
2015/12/14 collins gcc 4.9.3 7.5 1.2.1 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 5.23
2015/12/14 collins gcc 4.9.3 7.5 1.2.1 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 8.45
2015/12/14 collins gcc 4.9.3 7.5 1.2.1 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz GeForce GTX 680 1 16.18
2015/12/14 collins gcc 4.9.3 7.5 1.2.1 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 23.54
2015/12/14 collins gcc 4.9.3 7.5 1.1.1 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 3.18
2015/12/14 collins gcc 4.9.3 7.5 1.1.1 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 4.84
2015/12/14 collins gcc 4.9.3 7.5 1.1.1 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz GeForce GTX 680 1 7.05
2015/12/14 collins gcc 4.9.3 7.5 1.1.1 single 100,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 13.05
In [4]:
from IPython.display import HTML

#Hide code blocks
HTML('''<script>
code_show=true; 
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 if (code_show){
 $('div.input').hide();
 } else {
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$( document ).ready(code_toggle);
</script>
The raw code for this IPython notebook is by default hidden for easier reading.To toggle on/off the raw code, click <a href="javascript:code_toggle()">here</a>.''')
Out[4]:
The raw code for this IPython notebook is by default hidden for easier reading.To toggle on/off the raw code, click here.
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