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

lj-liquid benchmark

The Lennard-Jones liquid benchmark is a classic benchmark for general-purpose MD simulations. It is representative of the performance HOOMD-blue achieves with straight pair potential simulations.

Parameters:

  • $N = 64000$
  • $\rho = 0.382$
  • Lennard-Jones pair force
    • $r_\mathrm{cut} = 3.0$
    • $\epsilon = 1.0$
    • $\sigma = 1.0$
    • $\delta t = 0.005$
  • Integration: Nosé-Hoover NVT
    • $T=1.2$
    • $\tau=0.5$

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 64,000 Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz Tesla P100-PCIE-16GB 1 1.25
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 64,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla P100-PCIE-16GB 1 1.22
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 64,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K80 1 3.81
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 64,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K40m 1 4.00
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 64,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla M40 24GB 1 9.38
2016/10/12 psg gcc 4.8.5 8.0 2.1.0 double 64,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla P100-PCIE-16GB 1 1.23
2016/10/12 psg gcc 4.8.5 8.0 2.1.0 double 64,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K80 1 3.85
2016/10/13 psg gcc 4.8.5 7.5 2.1.0 double 64,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K40m 1 4.00
2016/10/13 psg gcc 4.8.5 7.5 2.1.0 double 64,000 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla M40 24GB 1 9.39
2016/09/13 collins gcc 4.8.5 7.5 2.0.3 double 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 3.40
2016/09/13 collins gcc 4.8.5 7.5 2.0.3 double 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz TITAN X 1 5.18
2016/09/13 collins gcc 4.8.5 7.5 2.0.3 double 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 10.37
2016/09/13 collins gcc 4.8.5 7.5 2.0.3 double 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz GeForce GTX 680 1 15.06
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 1.60
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 2.70
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 double 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 3.55
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz GeForce GTX 680 1 3.74
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 7.68
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 double 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 9.96
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 double 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 10.53
2015/12/14 collins gcc 4.9.3 7.5 1.3.0 double 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz GeForce GTX 680 1 15.19
2015/12/14 collins gcc 4.9.3 7.5 1.2.1 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 1.64
2015/12/14 collins gcc 4.9.3 7.5 1.2.1 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 2.80
2015/12/14 collins gcc 4.9.3 7.5 1.2.1 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz GeForce GTX 680 1 3.86
2015/12/14 collins gcc 4.9.3 7.5 1.2.1 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 7.86
2015/12/14 collins gcc 4.9.3 7.5 1.1.1 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 1.41
2015/12/14 collins gcc 4.9.3 7.5 1.1.1 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 2.37
2015/12/14 collins gcc 4.9.3 7.5 1.1.1 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz GeForce GTX 680 1 3.31
2015/12/14 collins gcc 4.9.3 7.5 1.1.1 single 64,000 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 6.12
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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