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

microsphere benchmark

The microrsphere benchmark runs a system of star polymers in an explicit solvent using DPD. These organize into a microspherical droplet. This model is used in the research article: Zhang et. al. Simultaneous Nano- and Microscale Control of Nanofibrous Microspheres Self-Assembled from Star-Shaped Polymers. Advanced Materials, pages 3947–3952 , 2015.

Parameters:

  • $N = 1,428,364$
  • $r_\mathrm{cut} = 1.0$
  • DPD pair force
    • See bmark.py for full force field specification.
  • Harmonic bond force
  • Integration: DPD thermostat
    • $T=1.0$
    • $\delta t = 0.01$

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 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz Tesla P100-PCIE-16GB 4 14.91
2018/01/15 comet gcc 4.9.2 8.0 2.2.2 double 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz Tesla P100-PCIE-16GB 16 24.17
2018/01/15 comet gcc 4.9.2 8.0 2.2.2 double 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz Tesla P100-PCIE-16GB 1 26.15
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla P100-PCIE-16GB 16 7.35
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K80 64 7.65
2016/10/24 titan gcc 4.9.3 7.5 2.1.1 double 1,428,364 6-Core AMD Opteron(tm) Processor 23 (D0) Tesla K20X 16 15.80
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla P100-PCIE-16GB 4 15.89
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K80 16 17.52
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla P100-PCIE-16GB 1 25.79
2016/10/24 titan gcc 4.9.3 7.5 2.1.1 double 1,428,364 6-Core AMD Opteron(tm) Processor 23 (D0) Tesla K20X 4 37.61
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K40m 4 38.06
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K80 4 43.68
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K80 1 81.98
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K40m 1 100.15
2016/10/24 titan gcc 4.9.3 7.5 2.1.1 double 1,428,364 6-Core AMD Opteron(tm) Processor 23 (D0) Tesla K20X 1 101.71
2016/10/23 psg gcc 4.8.5 8.0 2.1.1 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla M40 24GB 1 143.05
2016/10/12 psg gcc 4.8.5 8.0 2.1.0 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla P100-PCIE-16GB 4 16.22
2016/10/12 psg gcc 4.8.5 8.0 2.1.0 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K80 8 22.50
2016/10/12 psg gcc 4.8.5 8.0 2.1.0 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla P100-PCIE-16GB 1 25.74
2016/10/13 psg gcc 4.8.5 7.5 2.1.0 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K40m 4 38.11
2016/10/13 psg gcc 4.8.5 7.5 2.1.0 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla M40 24GB 4 39.15
2016/10/12 psg gcc 4.8.5 8.0 2.1.0 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla K80 1 82.40
2016/10/13 psg gcc 4.8.5 7.5 2.1.0 double 1,428,364 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz Tesla M40 24GB 1 146.81
2016/09/13 flux gcc 4.9.3 7.5 2.0.3 double 1,428,364 6-Core AMD Opteron(tm) Processor 23 (D0) Tesla K20X 64 8.67
2016/09/13 collins gcc 4.8.5 7.5 2.0.3 double 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 77.84
2016/09/13 collins gcc 4.8.5 7.5 2.0.3 double 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz TITAN X 1 83.06
2016/09/13 collins gcc 4.8.5 7.5 2.0.3 double 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 155.31
2015/12/15 collins gcc 4.9.3 7.5 1.3.0 single 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 37.94
2015/12/15 collins gcc 4.9.3 7.5 1.3.0 single 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 59.75
2015/12/15 collins gcc 4.9.3 7.5 1.3.0 double 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 88.60
2015/12/15 collins gcc 4.9.3 7.5 1.3.0 double 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 166.13
2015/12/15 collins gcc 4.9.3 7.5 1.3.0 single 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 202.82
2015/12/15 collins gcc 4.9.3 7.5 1.3.0 double 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 356.29
2015/12/15 collins gcc 4.9.3 7.5 1.2.1 single 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 37.42
2015/12/15 collins gcc 4.9.3 7.5 1.2.1 single 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 59.90
2015/12/15 collins gcc 4.9.3 7.5 1.2.1 single 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 204.49
2015/12/15 collins gcc 4.9.3 7.5 1.1.1 single 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Quadro M6000 1 25.20
2015/12/15 collins gcc 4.9.3 7.5 1.1.1 single 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla K40c 1 41.72
2015/12/15 collins gcc 4.9.3 7.5 1.1.1 single 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz GeForce GTX 680 1 77.66
2015/12/15 collins gcc 4.9.3 7.5 1.1.1 single 1,428,364 Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Tesla C2070 1 131.49
In [4]:
from IPython.display import HTML

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