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Table 1 Average running time (in seconds) of LSODA and LASSIE – and corresponding speed-up value – required for the execution of the set of 30 synthetic reaction-based models of size M×N (with M=N), considering 10, 50, 100, 500, 1000 samples of the system dynamics of all chemical species

From: LASSIE: simulating large-scale models of biochemical systems on GPUs

 

10 samples

50 samples

100 samples

500 samples

1000 samples

M×N

LSODA

LASSIE

Speed-up

LSODA

LASSIE

Speed-up

LSODA

LASSIE

Speed-up

LSODA

LASSIE

Speed-up

LSODA

LASSIE

Speed-up

64×64

0.257

0.519

0.495

0.288

0.541

0.532

0.220

0.557

0.395

0.307

0.665

0.462

0.303

0.839

0.361

128×128

0.393

0.613

0.641

0.473

0.635

0.745

0.507

0.644

0.787

0.674

0.786

0.858

0.498

0.958

0.520

256×256

1.277

0.669

1.909

1.486

0.696

2.135

1.293

0.727

1.779

1.319

0.905

1.456

1.277

1.122

1.138

512×512

4.313

0.792

5.446

4.629

0.841

5.504

4.559

0.915

4.982

4.300

1.215

3.539

4.669

1.526

3.060

1024×1024

15.753

0.955

16.495

15.707

1.056

14.874

16.201

1.201

13.490

15.982

1.809

8.835

16.647

2.407

6.916

2048×2048

61.824

1.662

37.199

61.748

1.987

31.076

61.762

2.397

25.766

62.307

3.721

14.745

62.742

5.479

11.451

4096×4096

249.839

2.713

92.090*

248.234

4.571

54,306

249.422

5.665

44.029

249.546

12.407

20.113

254.416

17.393

14.627

8192×8192

NA

14.134

NA

NA

26.051

NA

NA

38.058

NA

NA

101.91

NA

NA

129.755

NA

  1. *Maximum speed-up value