Performance in RFD4-Proteina NIM#

Execution Backends#

The RFD4-Proteina NIM can run three execution backends, selected per deployment (refer to Configuration Alternatives):

  • oss_eager: the upstream reference network, uncompiled.

  • oss_torch_compile: the same network under torch.compile.

  • bioir: an NVIDIA-accelerated trunk built on the BioNeMo Inference Runtime, with its own fused kernels and CUDA-graph capture.

Every response reports which backend actually ran it in model.execution_backend, alongside runtime.cuda_graphs and runtime.cuda_graph_cache, which describe what the loaded runtime currently holds. Results are comparable in kind across backends but not bit-identical, since compilation and BioIR’s own kernels both change floating-point numerics.

Benchmark Configuration#

The table in this section comes from a single release-candidate sweep of the synthetic latency suite, 1.0.0-rc.20261012093607, measured 2026-10-12.

Parameter

Setting

Task

generation

Input

synthetic poly-glycine backbone, annotated_cif

sampling.recycle_strategy

thinking_medium — the checkpoint default, 60 steps over 185 trunk passes

sampling.num_replicates, sampling.batch_size

1, 2, and 4, swept at every token bucket

output.structure_format

none

Token buckets

128, 160, 192, 224, 256, 288, 320, 352, 384, 448, 512, 640, 768, 896, 1024

Runs per shape

3, of which the cold first run is discarded and the warm median reported

Backends

oss_eager, oss_torch_compile, bioir

Design time is the client’s end-to-end wall clock around one HTTP request. It therefore covers input parsing, sampling, metrics, and response encoding, not only the trunk forward passes. Because the cold run is excluded, these are steady-state figures; refer to Cold-Start Behavior for what the first request into a bucket costs instead.

Replicates are batched into one forward pass, so a batch-n request is a single request returning n designs. Divide by the batch size for a per-design cost. Refer to Replicates and Batching.

Five GPUs sweep batch 1 only — GB10, both 40 GB A100s, L40S, and RTX 6000 Ada Generation — so their tabs carry 15 rows rather than 45, and each one says so.

Performance Across Execution Backends#

All three execution backends over the full sweep, at every token bucket and every batch size that GPU was swept at. Select a GPU to switch the table; the two rightmost columns are bioir’s speedup over each OSS baseline, where higher means bioir is faster. A dash marks a shape that did not complete.

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

6.82

3.12

1.17

5.83x

2.67x

128

2

7.04

3.35

1.44

4.88x

2.33x

128

4

8.25

3.93

2.44

3.39x

1.61x

160

1

6.85

3.26

1.23

5.56x

2.65x

160

2

7.09

3.51

2.00

3.54x

1.75x

160

4

8.87

4.74

3.34

2.66x

1.42x

192

1

6.87

3.35

1.49

4.60x

2.24x

192

2

8.71

3.75

2.39

3.64x

1.57x

192

4

9.14

5.62

4.12

2.22x

1.36x

224

1

6.93

3.40

1.65

4.19x

2.06x

224

2

11.10

4.51

2.76

4.02x

1.63x

224

4

10.69

6.86

5.02

2.13x

1.37x

256

1

8.05

3.88

1.91

4.22x

2.03x

256

2

8.67

4.79

3.28

2.64x

1.46x

256

4

13.18

8.36

6.09

2.16x

1.37x

288

1

8.20

3.96

2.28

3.60x

1.74x

288

2

8.90

5.70

3.99

2.23x

1.43x

288

4

16.00

10.17

7.55

2.12x

1.35x

320

1

8.24

4.02

2.63

3.14x

1.53x

320

2

10.32

6.50

4.73

2.18x

1.37x

320

4

19.13

11.87

8.90

2.15x

1.33x

352

1

8.30

4.49

2.94

2.82x

1.53x

352

2

12.00

7.57

5.36

2.24x

1.41x

352

4

22.57

13.88

10.40

2.17x

1.34x

384

1

8.53

4.74

3.30

2.59x

1.44x

384

2

13.81

8.47

6.18

2.24x

1.37x

384

4

26.29

16.15

11.85

2.22x

1.36x

448

1

9.75

5.93

4.21

2.32x

1.41x

448

2

18.03

10.97

7.95

2.27x

1.38x

448

4

34.64

21.48

15.61

2.22x

1.38x

512

1

12.02

7.29

5.17

2.32x

1.41x

512

2

22.79

13.62

9.98

2.28x

1.36x

512

4

44.20

26.46

19.32

2.29x

1.37x

640

1

17.69

10.56

7.79

2.27x

1.36x

640

2

34.38

20.32

15.00

2.29x

1.35x

640

4

67.22

39.86

29.35

2.29x

1.36x

768

1

24.65

14.58

10.68

2.31x

1.37x

768

2

48.16

28.44

20.57

2.34x

1.38x

768

4

95.19

55.93

40.69

2.34x

1.37x

896

1

32.82

19.45

14.36

2.29x

1.35x

896

2

65.12

38.30

28.10

2.32x

1.36x

896

4

128.90

75.59

56.00

2.30x

1.35x

1024

1

42.05

24.74

17.89

2.35x

1.38x

1024

2

83.45

49.12

35.31

2.36x

1.39x

1024

4

166.68

97.17

69.98

2.38x

1.39x

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

6.15

2.66

0.91

6.79x

2.93x

128

2

6.12

2.84

1.30

4.70x

2.18x

128

4

7.42

3.35

2.16

3.43x

1.55x

160

1

6.01

2.81

1.10

5.47x

2.55x

160

2

6.25

3.05

1.75

3.57x

1.74x

160

4

7.73

3.95

2.88

2.69x

1.37x

192

1

6.03

2.86

1.32

4.57x

2.16x

192

2

7.82

3.14

2.08

3.76x

1.51x

192

4

7.99

4.62

3.62

2.21x

1.28x

224

1

6.01

2.94

1.44

4.17x

2.04x

224

2

9.99

3.64

2.44

4.10x

1.50x

224

4

9.55

5.82

4.45

2.15x

1.31x

256

1

7.11

3.37

1.69

4.20x

1.99x

256

2

7.65

3.97

2.90

2.64x

1.37x

256

4

11.73

6.97

5.43

2.16x

1.28x

288

1

7.23

3.48

2.00

3.62x

1.74x

288

2

7.92

4.72

3.56

2.23x

1.33x

288

4

14.33

8.52

6.79

2.11x

1.25x

320

1

7.24

3.48

2.33

3.11x

1.49x

320

2

9.18

5.38

4.21

2.18x

1.28x

320

4

17.05

10.11

7.98

2.14x

1.27x

352

1

6.99

3.67

2.60

2.69x

1.41x

352

2

10.72

6.33

4.81

2.23x

1.32x

352

4

20.16

11.91

9.29

2.17x

1.28x

384

1

7.50

4.09

2.94

2.55x

1.39x

384

2

12.40

7.32

5.53

2.24x

1.32x

384

4

23.42

13.67

10.71

2.19x

1.28x

448

1

8.76

5.04

3.77

2.32x

1.34x

448

2

16.10

9.29

7.22

2.23x

1.29x

448

4

30.90

18.13

14.18

2.18x

1.28x

512

1

10.85

6.15

4.67

2.32x

1.32x

512

2

20.41

11.71

9.01

2.26x

1.30x

512

4

39.49

22.50

17.74

2.23x

1.27x

640

1

15.86

9.11

7.16

2.22x

1.27x

640

2

30.93

17.50

13.88

2.23x

1.26x

640

4

60.43

34.44

27.37

2.21x

1.26x

768

1

22.10

12.57

9.72

2.27x

1.29x

768

2

43.42

24.79

19.34

2.24x

1.28x

768

4

85.86

48.55

38.26

2.24x

1.27x

896

1

29.54

16.98

13.35

2.21x

1.27x

896

2

59.09

33.23

26.32

2.25x

1.26x

896

4

116.96

66.69

52.88

2.21x

1.26x

1024

1

38.02

21.71

16.95

2.24x

1.28x

1024

2

75.89

42.80

33.74

2.25x

1.27x

1024

4

151.45

84.61

67.08

2.26x

1.26x

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

9.63

4.17

1.75

5.51x

2.39x

128

2

9.95

4.14

2.82

3.53x

1.47x

128

4

13.31

6.16

4.84

2.75x

1.27x

160

1

9.67

4.00

2.25

4.29x

1.78x

160

2

10.81

4.99

3.82

2.83x

1.31x

160

4

19.42

8.57

6.98

2.78x

1.23x

192

1

9.68

4.52

2.81

3.44x

1.61x

192

2

14.77

6.25

4.97

2.97x

1.26x

192

4

27.22

11.41

9.35

2.91x

1.22x

224

1

11.28

5.97

3.50

3.23x

1.71x

224

2

20.34

7.95

6.25

3.25x

1.27x

224

4

38.45

14.64

11.81

3.26x

1.24x

256

1

14.87

7.53

4.17

3.57x

1.81x

256

2

27.42

9.69

7.61

3.60x

1.27x

256

4

52.48

18.04

14.71

3.57x

1.23x

288

1

17.21

8.69

5.12

3.36x

1.70x

288

2

32.31

12.12

9.76

3.31x

1.24x

288

4

62.39

22.79

18.63

3.35x

1.22x

320

1

20.40

10.36

6.04

3.38x

1.72x

320

2

38.61

14.11

11.47

3.37x

1.23x

320

4

75.90

27.19

22.31

3.40x

1.22x

352

1

25.21

12.49

6.91

3.65x

1.81x

352

2

48.20

16.61

13.24

3.64x

1.25x

352

4

94.67

31.67

26.34

3.59x

1.20x

384

1

29.69

14.44

8.00

3.71x

1.81x

384

2

56.99

19.20

15.32

3.72x

1.25x

384

4

112.61

36.72

30.72

3.67x

1.20x

448

1

41.48

20.53

10.64

3.90x

1.93x

448

2

81.03

25.39

20.65

3.92x

1.23x

448

4

160.89

49.59

40.79

3.94x

1.22x

512

1

58.76

31.01

13.34

4.41x

2.33x

512

2

116.25

32.01

26.01

4.47x

1.23x

512

4

231.44

63.17

52.27

4.43x

1.21x

640

1

99.39

56.56

20.50

4.85x

2.76x

640

2

198.37

49.26

40.74

4.87x

1.21x

640

4

396.50

97.48

80.69

4.91x

1.21x

768

1

147.68

84.16

29.08

5.08x

2.89x

768

2

294.72

70.07

57.69

5.11x

1.21x

768

4

589.56

138.93

115.12

5.12x

1.21x

896

1

200.99

114.39

39.60

5.08x

2.89x

896

2

402.19

95.22

78.92

5.10x

1.21x

896

4

805.30

189.86

157.50

5.11x

1.21x

1024

1

262.70

149.65

51.28

5.12x

2.92x

1024

2

525.71

124.05

102.48

5.13x

1.21x

1024

4

1055.63

247.65

205.40

5.14x

1.21x

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

5.10

2.33

0.93

5.49x

2.51x

128

2

5.42

2.56

1.18

4.59x

2.17x

128

4

5.80

2.95

1.93

3.00x

1.53x

160

1

5.22

2.44

0.99

5.27x

2.47x

160

2

5.41

2.65

1.48

3.65x

1.79x

160

4

8.11

3.11

2.51

3.23x

1.24x

192

1

5.26

2.47

1.17

4.50x

2.12x

192

2

6.03

2.74

1.85

3.26x

1.48x

192

4

7.31

3.85

3.14

2.33x

1.23x

224

1

5.32

2.52

1.35

3.94x

1.87x

224

2

7.71

2.81

2.18

3.53x

1.29x

224

4

7.47

4.10

3.92

1.91x

1.05x

256

1

5.36

2.57

1.55

3.45x

1.66x

256

2

7.01

3.56

2.57

2.72x

1.38x

256

4

8.94

4.92

4.77

1.87x

1.03x

288

1

6.46

2.93

1.80

3.59x

1.63x

288

2

7.08

3.69

3.07

2.30x

1.20x

288

4

10.88

5.91

5.80

1.88x

1.02x

320

1

7.63

2.96

2.01

3.79x

1.47x

320

2

7.13

3.79

3.55

2.01x

1.07x

320

4

12.96

6.84

6.81

1.90x

1.00x

352

1

8.91

3.38

2.29

3.88x

1.47x

352

2

8.12

4.42

4.12

1.97x

1.07x

352

4

15.13

7.93

7.99

1.89x

0.99x

384

1

6.77

3.27

2.58

2.63x

1.27x

384

2

9.33

4.85

4.79

1.95x

1.01x

384

4

17.63

9.11

9.16

1.92x

0.99x

448

1

6.84

3.54

3.22

2.12x

1.10x

448

2

12.15

6.19

6.36

1.91x

0.97x

448

4

23.40

11.88

11.94

1.96x

1.00x

512

1

8.10

4.16

4.03

2.01x

1.03x

512

2

15.26

7.72

7.67

1.99x

1.01x

512

4

29.54

14.92

15.04

1.96x

0.99x

640

1

11.91

6.04

5.97

1.99x

1.01x

640

2

22.98

11.50

11.54

1.99x

1.00x

640

4

45.33

22.50

22.75

1.99x

0.99x

768

1

16.41

8.15

8.31

1.97x

0.98x

768

2

32.05

15.74

15.89

2.02x

0.99x

768

4

63.90

31.16

31.77

2.01x

0.98x

896

1

21.91

11.07

11.02

1.99x

1.00x

896

2

43.37

21.43

21.65

2.00x

0.99x

896

4

86.71

42.62

43.32

2.00x

0.98x

1024

1

27.89

13.66

13.85

2.01x

0.99x

1024

2

56.12

27.10

27.12

2.07x

1.00x

1024

4

112.14

54.03

54.62

2.05x

0.99x

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

9.08

3.90

1.10

8.23x

3.53x

128

2

5.38

4.33

1.11

4.85x

3.91x

128

4

5.76

4.96

1.70

3.40x

2.93x

160

1

5.31

4.13

0.89

5.99x

4.66x

160

2

5.47

4.48

1.31

4.18x

3.42x

160

4

7.76

5.33

2.26

3.43x

2.36x

192

1

5.31

4.32

1.16

4.59x

3.73x

192

2

7.65

4.78

2.20

3.47x

2.17x

192

4

12.52

6.55

3.74

3.34x

1.75x

224

1

9.14

4.36

1.61

5.68x

2.71x

224

2

9.76

4.89

2.60

3.76x

1.88x

224

4

12.79

6.99

4.60

2.78x

1.52x

256

1

9.19

4.38

1.81

5.07x

2.41x

256

2

11.92

5.96

3.04

3.92x

1.96x

256

4

13.02

7.28

4.23

3.08x

1.72x

288

1

9.32

4.45

1.67

5.59x

2.67x

288

2

12.14

6.19

2.76

4.39x

2.24x

288

4

13.34

7.59

5.15

2.59x

1.47x

320

1

9.35

4.64

1.85

5.06x

2.51x

320

2

12.26

6.34

4.00

3.07x

1.59x

320

4

13.84

8.07

7.61

1.82x

1.06x

352

1

9.49

4.57

2.66

3.57x

1.72x

352

2

12.31

6.51

4.61

2.67x

1.41x

352

4

16.20

9.26

8.71

1.86x

1.06x

384

1

11.67

6.19

2.87

4.07x

2.16x

384

2

12.35

6.68

5.33

2.32x

1.25x

384

4

18.65

8.75

10.03

1.86x

0.87x

448

1

11.76

3.51

3.57

3.30x

0.99x

448

2

12.83

6.42

6.59

1.95x

0.97x

448

4

24.37

11.13

12.70

1.92x

0.88x

512

1

11.91

5.83

4.29

2.77x

1.36x

512

2

15.82

8.56

8.15

1.94x

1.05x

512

4

30.52

14.99

15.98

1.91x

0.94x

640

1

12.30

6.62

8.13

1.51x

0.81x

640

2

23.45

10.72

11.98

1.96x

0.89x

640

4

46.00

21.02

20.68

2.22x

1.02x

768

1

16.69

7.60

7.33

2.28x

1.04x

768

2

32.49

16.84

14.40

2.26x

1.17x

768

4

62.31

33.02

30.41

2.05x

1.09x

896

1

22.11

11.41

9.93

2.23x

1.15x

896

2

43.57

22.38

19.61

2.22x

1.14x

896

4

86.16

45.55

39.16

2.20x

1.16x

1024

1

28.02

14.18

12.54

2.24x

1.13x

1024

2

55.42

27.61

26.00

2.13x

1.06x

1024

4

111.25

56.06

50.61

2.20x

1.11x

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

9.84

5.44

1.16

8.50x

4.70x

128

2

10.14

5.56

1.35

7.52x

4.12x

128

4

10.35

6.97

2.10

4.94x

3.32x

160

1

10.14

6.13

1.08

9.35x

5.65x

160

2

10.31

6.61

1.59

6.46x

4.14x

160

4

10.82

7.68

2.59

4.18x

2.97x

192

1

10.27

6.26

1.30

7.92x

4.83x

192

2

10.21

5.79

1.95

5.25x

2.98x

192

4

12.98

8.09

3.21

4.05x

2.52x

224

1

10.20

6.56

1.51

6.77x

4.36x

224

2

10.65

6.85

2.33

4.58x

2.94x

224

4

12.69

8.43

3.81

3.33x

2.21x

256

1

10.09

5.96

1.69

5.95x

3.52x

256

2

11.97

7.99

2.68

4.47x

2.98x

256

4

12.79

8.75

4.56

2.80x

1.92x

288

1

10.06

6.24

1.89

5.33x

3.30x

288

2

12.29

7.21

3.03

4.05x

2.38x

288

4

12.85

9.02

5.49

2.34x

1.64x

320

1

10.26

6.56

2.10

4.90x

3.13x

320

2

12.58

7.69

3.48

3.61x

2.21x

320

4

13.86

10.08

6.47

2.14x

1.56x

352

1

10.36

6.27

2.44

4.25x

2.57x

352

2

12.39

8.27

3.99

3.11x

2.07x

352

4

14.67

9.21

7.60

1.93x

1.21x

384

1

12.51

7.90

2.73

4.59x

2.90x

384

2

12.99

8.59

4.56

2.85x

1.89x

384

4

16.80

10.38

8.60

1.95x

1.21x

448

1

11.93

7.18

3.12

3.82x

2.30x

448

2

12.78

7.92

5.69

2.24x

1.39x

448

4

21.97

12.62

11.01

2.00x

1.15x

512

1

12.04

8.04

3.79

3.18x

2.12x

512

2

14.53

9.18

7.13

2.04x

1.29x

512

4

28.12

15.09

13.73

2.05x

1.10x

640

1

12.62

7.53

9.30

1.36x

0.81x

640

2

21.73

11.43

10.64

2.04x

1.07x

640

4

42.19

21.79

20.70

2.04x

1.05x

768

1

15.51

8.64

9.05

1.71x

0.95x

768

2

30.07

15.66

14.78

2.03x

1.06x

768

4

59.00

29.94

28.91

2.04x

1.04x

896

1

20.65

10.99

10.15

2.04x

1.08x

896

2

40.62

20.28

19.82

2.05x

1.02x

896

4

79.96

39.62

39.03

2.05x

1.02x

1024

1

26.13

13.00

12.61

2.07x

1.03x

1024

2

51.82

25.27

25.09

2.07x

1.01x

1024

4

102.82

51.02

49.89

2.06x

1.02x

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

11.04

4.25

1.12

9.85x

3.79x

128

2

11.79

4.67

1.31

8.99x

3.56x

128

4

12.35

5.20

1.96

6.29x

2.65x

160

1

11.72

4.70

1.06

11.04x

4.43x

160

2

12.05

5.58

1.56

7.73x

3.58x

160

4

12.14

5.79

2.65

4.58x

2.19x

192

1

11.50

5.41

1.33

8.67x

4.07x

192

2

12.33

5.01

1.94

6.36x

2.59x

192

4

15.55

6.99

3.15

4.93x

2.21x

224

1

11.22

4.91

1.46

7.66x

3.35x

224

2

12.62

5.45

2.28

5.54x

2.39x

224

4

14.87

6.64

3.86

3.85x

1.72x

256

1

10.70

4.93

1.78

6.03x

2.77x

256

2

13.65

5.75

2.58

5.28x

2.22x

256

4

14.61

7.59

4.52

3.23x

1.68x

288

1

12.53

5.68

1.89

6.65x

3.01x

288

2

15.02

7.01

3.01

4.98x

2.33x

288

4

15.16

7.64

5.43

2.79x

1.41x

320

1

13.00

5.04

2.11

6.15x

2.38x

320

2

14.81

6.45

3.45

4.29x

1.87x

320

4

16.28

7.77

6.32

2.57x

1.23x

352

1

12.45

5.64

2.45

5.09x

2.31x

352

2

15.00

6.64

3.99

3.76x

1.66x

352

4

16.70

8.49

7.25

2.30x

1.17x

384

1

13.61

6.05

2.59

5.26x

2.34x

384

2

14.67

7.02

4.44

3.30x

1.58x

384

4

17.53

9.09

8.28

2.12x

1.10x

448

1

13.81

6.39

3.09

4.46x

2.07x

448

2

14.12

6.94

5.58

2.53x

1.24x

448

4

22.30

11.18

10.45

2.13x

1.07x

512

1

13.69

7.95

3.69

3.71x

2.16x

512

2

14.95

7.57

6.92

2.16x

1.10x

512

4

28.24

13.77

13.04

2.17x

1.06x

640

1

13.43

6.07

8.81

1.52x

0.69x

640

2

21.87

11.61

10.25

2.13x

1.13x

640

4

42.51

20.56

19.36

2.20x

1.06x

768

1

15.73

7.55

8.86

1.77x

0.85x

768

2

30.30

14.16

13.56

2.23x

1.04x

768

4

59.17

29.05

26.46

2.24x

1.10x

896

1

21.00

10.49

9.51

2.21x

1.10x

896

2

40.63

19.03

18.31

2.22x

1.04x

896

4

80.21

37.40

35.96

2.23x

1.04x

1024

1

26.40

12.16

11.64

2.27x

1.05x

1024

2

52.08

23.69

22.55

2.31x

1.05x

1024

4

103.28

45.49

45.10

2.29x

1.01x

This SKU’s benchmark sweeps batch 1 only.

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

11.08

6.38

6.23

1.78x

1.03x

160

1

18.70

10.21

10.69

1.75x

0.95x

192

1

27.06

14.23

15.53

1.74x

0.92x

224

1

36.49

19.29

21.21

1.72x

0.91x

256

1

47.35

25.01

27.58

1.72x

0.91x

288

1

60.26

31.65

35.10

1.72x

0.90x

320

1

74.05

39.65

44.15

1.68x

0.90x

352

1

89.95

47.84

53.98

1.67x

0.89x

384

1

107.38

56.81

64.74

1.66x

0.88x

448

1

165.16

100.91

116.68

1.42x

0.86x

512

1

272.33

192.18

195.32

1.39x

0.98x

640

1

440.08

296.56

332.75

1.32x

0.89x

768

1

618.50

414.79

465.30

1.33x

0.89x

896

1

850.69

572.41

649.30

1.31x

0.88x

1024

1

1131.61

774.21

833.86

1.36x

0.93x

This SKU’s benchmark sweeps batch 1 only.

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

6.55

4.88

2.08

3.16x

2.35x

160

1

6.57

4.95

2.56

2.56x

1.93x

192

1

8.77

5.24

3.38

2.60x

1.55x

224

1

11.79

7.14

4.08

2.89x

1.75x

256

1

15.58

8.70

4.94

3.15x

1.76x

288

1

18.44

10.13

6.11

3.02x

1.66x

320

1

22.11

11.89

7.37

3.00x

1.61x

352

1

27.21

14.71

8.39

3.24x

1.75x

384

1

32.37

17.15

9.74

3.32x

1.76x

448

1

45.69

24.62

13.00

3.52x

1.89x

512

1

65.67

36.29

16.44

4.00x

2.21x

640

1

114.42

68.76

25.49

4.49x

2.70x

768

1

169.72

102.43

36.24

4.68x

2.83x

896

1

231.09

139.09

49.20

4.70x

2.83x

1024

1

302.18

181.64

64.80

4.66x

2.80x

This SKU’s benchmark sweeps batch 1 only.

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

10.42

4.33

1.92

5.42x

2.25x

160

1

10.50

4.44

2.36

4.45x

1.88x

192

1

10.51

4.79

2.93

3.58x

1.63x

224

1

11.92

6.30

3.60

3.31x

1.75x

256

1

15.57

8.04

4.34

3.59x

1.85x

288

1

18.11

9.23

5.28

3.43x

1.75x

320

1

21.52

10.86

6.22

3.46x

1.75x

352

1

26.54

13.45

7.11

3.73x

1.89x

384

1

31.37

15.44

8.24

3.81x

1.87x

448

1

44.16

22.24

10.89

4.06x

2.04x

512

1

63.31

33.73

13.66

4.63x

2.47x

640

1

111.98

67.36

21.11

5.31x

3.19x

768

1

166.56

100.33

29.86

5.58x

3.36x

896

1

226.38

136.43

40.47

5.59x

3.37x

1024

1

295.86

178.09

52.76

5.61x

3.38x

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

8.69

3.77

1.76

4.95x

2.15x

128

2

8.93

3.84

2.76

3.23x

1.39x

128

4

13.48

6.25

4.88

2.76x

1.28x

160

1

9.02

3.83

2.21

4.07x

1.73x

160

2

10.90

5.10

3.82

2.85x

1.33x

160

4

19.96

8.73

7.20

2.77x

1.21x

192

1

8.86

4.54

2.85

3.11x

1.59x

192

2

15.04

6.44

5.04

2.99x

1.28x

192

4

28.39

11.59

9.45

3.00x

1.23x

224

1

11.35

6.02

3.52

3.22x

1.71x

224

2

20.73

8.14

6.46

3.21x

1.26x

224

4

39.69

14.98

12.21

3.25x

1.23x

256

1

14.92

7.64

4.25

3.51x

1.80x

256

2

27.87

10.05

7.95

3.51x

1.27x

256

4

54.16

18.80

15.39

3.52x

1.22x

288

1

17.55

9.03

5.33

3.29x

1.69x

288

2

33.28

12.76

10.18

3.27x

1.25x

288

4

64.88

23.70

19.64

3.30x

1.21x

320

1

20.89

10.48

6.31

3.31x

1.66x

320

2

40.17

14.86

12.09

3.32x

1.23x

320

4

78.76

28.51

23.73

3.32x

1.20x

352

1

25.73

13.19

7.27

3.54x

1.81x

352

2

49.98

17.49

14.26

3.50x

1.23x

352

4

98.47

33.47

27.64

3.56x

1.21x

384

1

30.41

15.09

8.42

3.61x

1.79x

384

2

59.27

20.12

16.43

3.61x

1.23x

384

4

117.63

39.04

32.12

3.66x

1.22x

448

1

42.84

21.84

11.28

3.80x

1.94x

448

2

84.39

26.93

22.09

3.82x

1.22x

448

4

168.09

52.98

43.73

3.84x

1.21x

512

1

60.71

32.09

14.28

4.25x

2.25x

512

2

120.97

34.24

28.07

4.31x

1.22x

512

4

241.06

67.74

55.62

4.33x

1.22x

640

1

103.00

58.53

22.12

4.66x

2.65x

640

2

205.48

52.94

43.69

4.70x

1.21x

640

4

410.53

104.66

86.81

4.73x

1.21x

768

1

152.80

86.93

31.47

4.85x

2.76x

768

2

304.74

75.43

62.38

4.88x

1.21x

768

4

611.95

150.51

124.35

4.92x

1.21x

896

1

208.04

118.37

42.66

4.88x

2.77x

896

2

415.65

102.95

84.90

4.90x

1.21x

896

4

838.80

204.82

170.07

4.93x

1.20x

1024

1

271.61

154.49

55.85

4.86x

2.77x

1024

2

545.38

133.94

111.49

4.89x

1.20x

1024

4

1101.63

267.61

222.79

4.94x

1.20x

This SKU’s benchmark sweeps batch 1 only.

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

6.58

2.91

1.42

4.63x

2.05x

160

1

6.67

3.51

1.81

3.67x

1.93x

192

1

7.42

4.70

2.49

2.98x

1.89x

224

1

10.62

6.35

3.36

3.16x

1.89x

256

1

15.49

8.28

4.42

3.51x

1.88x

288

1

20.30

10.53

5.79

3.50x

1.82x

320

1

25.75

13.36

7.16

3.60x

1.87x

352

1

31.95

16.81

10.02

3.19x

1.68x

384

1

38.58

20.22

12.92

2.99x

1.56x

448

1

53.22

27.86

14.15

3.76x

1.97x

512

1

71.50

37.42

18.29

3.91x

2.05x

640

1

110.99

58.05

28.17

3.94x

2.06x

768

1

163.30

85.47

41.57

3.93x

2.06x

896

1

272.86

171.07

57.52

4.74x

2.97x

1024

1

449.06

307.58

76.08

5.90x

4.04x

This SKU’s benchmark sweeps batch 1 only.

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

8.04

3.33

1.39

5.79x

2.39x

160

1

8.00

3.54

1.95

4.09x

1.81x

192

1

8.11

4.65

2.62

3.10x

1.77x

224

1

10.20

6.49

3.63

2.81x

1.79x

256

1

14.30

8.32

4.86

2.95x

1.71x

288

1

18.64

10.78

6.36

2.93x

1.70x

320

1

23.18

13.07

8.05

2.88x

1.63x

352

1

28.56

16.56

10.59

2.70x

1.56x

384

1

34.18

19.73

12.82

2.67x

1.54x

448

1

47.39

27.22

17.33

2.73x

1.57x

512

1

63.69

36.58

22.72

2.80x

1.61x

640

1

99.74

57.80

36.52

2.73x

1.58x

768

1

148.09

86.48

53.80

2.75x

1.61x

896

1

246.66

160.44

74.02

3.33x

2.17x

1024

1

407.31

292.16

97.86

4.16x

2.99x

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

6.89

2.82

1.23

5.60x

2.29x

128

2

7.06

3.07

1.72

4.10x

1.78x

128

4

10.29

4.54

2.86

3.60x

1.59x

160

1

7.00

3.05

1.30

5.39x

2.34x

160

2

8.28

3.67

2.22

3.73x

1.66x

160

4

8.98

6.00

3.99

2.25x

1.50x

192

1

7.06

3.14

1.62

4.35x

1.93x

192

2

11.08

4.60

2.88

3.85x

1.60x

192

4

11.07

6.97

5.21

2.13x

1.34x

224

1

7.94

3.46

2.03

3.92x

1.71x

224

2

8.47

5.14

3.50

2.42x

1.47x

224

4

14.27

8.98

6.46

2.21x

1.39x

256

1

7.96

3.57

2.41

3.31x

1.48x

256

2

9.62

6.03

4.24

2.27x

1.42x

256

4

18.11

11.30

8.06

2.25x

1.40x

288

1

8.09

4.34

2.88

2.81x

1.51x

288

2

11.80

7.43

5.34

2.21x

1.39x

288

4

22.43

13.71

10.05

2.23x

1.36x

320

1

8.39

5.02

3.42

2.45x

1.47x

320

2

14.16

8.59

6.31

2.24x

1.36x

320

4

27.48

16.56

12.02

2.29x

1.38x

352

1

9.81

5.84

3.92

2.50x

1.49x

352

2

16.77

10.36

7.35

2.28x

1.41x

352

4

32.38

19.55

14.29

2.27x

1.37x

384

1

10.37

6.37

4.54

2.29x

1.40x

384

2

19.54

11.72

8.62

2.27x

1.36x

384

4

37.90

22.82

16.70

2.27x

1.37x

448

1

13.50

8.15

5.83

2.31x

1.40x

448

2

25.89

15.50

11.23

2.31x

1.38x

448

4

50.71

29.99

22.01

2.30x

1.36x

512

1

17.11

10.34

7.42

2.31x

1.39x

512

2

33.26

19.78

14.20

2.34x

1.39x

512

4

65.47

38.62

28.02

2.34x

1.38x

640

1

25.80

15.24

11.27

2.29x

1.35x

640

2

50.77

29.69

21.81

2.33x

1.36x

640

4

100.71

58.66

43.06

2.34x

1.36x

768

1

36.41

21.62

15.44

2.36x

1.40x

768

2

72.20

41.99

30.09

2.40x

1.40x

768

4

143.25

83.43

61.09

2.35x

1.37x

896

1

49.10

28.61

21.23

2.31x

1.35x

896

2

98.27

56.92

42.12

2.33x

1.35x

896

4

195.63

112.82

84.84

2.31x

1.33x

1024

1

63.56

36.92

27.02

2.35x

1.37x

1024

2

127.40

73.16

53.87

2.36x

1.36x

1024

4

255.10

146.18

108.00

2.36x

1.35x

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

6.74

2.78

1.06

6.33x

2.61x

128

2

7.06

2.94

1.43

4.92x

2.05x

128

4

8.31

3.48

2.50

3.32x

1.39x

160

1

6.76

2.89

1.22

5.56x

2.38x

160

2

7.41

3.11

2.25

3.29x

1.38x

160

4

8.42

4.46

3.53

2.38x

1.26x

192

1

7.04

2.96

1.49

4.74x

1.99x

192

2

8.81

3.50

2.50

3.53x

1.40x

192

4

8.89

5.60

4.45

2.00x

1.26x

224

1

7.00

3.10

1.72

4.06x

1.80x

224

2

11.47

4.44

3.03

3.79x

1.47x

224

4

11.46

7.14

5.58

2.05x

1.28x

256

1

7.70

3.26

2.04

3.77x

1.60x

256

2

8.27

4.76

3.68

2.25x

1.30x

256

4

14.40

8.86

6.91

2.08x

1.28x

288

1

7.85

3.44

2.49

3.16x

1.38x

288

2

9.41

5.93

4.58

2.05x

1.30x

288

4

18.01

10.93

8.66

2.08x

1.26x

320

1

7.85

3.90

2.99

2.63x

1.31x

320

2

11.29

6.86

5.43

2.08x

1.26x

320

4

21.79

13.16

10.39

2.10x

1.27x

352

1

7.87

4.61

3.38

2.33x

1.36x

352

2

13.32

8.19

6.20

2.15x

1.32x

352

4

25.97

15.43

12.12

2.14x

1.27x

384

1

8.22

4.96

3.78

2.17x

1.31x

384

2

15.57

9.25

7.15

2.18x

1.29x

384

4

30.26

17.90

14.01

2.16x

1.28x

448

1

10.72

6.49

4.93

2.17x

1.32x

448

2

20.82

12.24

9.74

2.14x

1.26x

448

4

40.83

24.18

18.88

2.16x

1.28x

512

1

13.62

8.07

6.12

2.22x

1.32x

512

2

26.55

15.48

12.04

2.20x

1.29x

512

4

52.54

30.45

23.85

2.20x

1.28x

640

1

20.70

12.13

9.51

2.18x

1.28x

640

2

40.66

23.92

18.54

2.19x

1.29x

640

4

80.70

47.71

36.99

2.18x

1.29x

768

1

29.19

17.05

13.15

2.22x

1.30x

768

2

57.88

34.16

26.21

2.21x

1.30x

768

4

114.95

68.55

53.13

2.16x

1.29x

896

1

39.69

23.34

18.01

2.20x

1.30x

896

2

79.05

46.67

35.90

2.20x

1.30x

896

4

157.34

92.67

73.74

2.13x

1.26x

1024

1

51.19

30.12

23.25

2.20x

1.30x

1024

2

102.52

60.16

46.91

2.19x

1.28x

1024

4

204.19

120.15

94.36

2.16x

1.27x

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

4.92

2.86

0.96

5.13x

2.98x

128

2

5.10

2.93

1.33

3.84x

2.21x

128

4

7.74

3.94

2.13

3.64x

1.85x

160

1

4.97

2.94

1.27

3.91x

2.31x

160

2

6.31

2.97

1.80

3.50x

1.65x

160

4

6.56

3.98

2.90

2.26x

1.37x

192

1

5.22

2.99

1.36

3.85x

2.20x

192

2

8.23

3.30

2.10

3.93x

1.57x

192

4

7.89

4.80

3.58

2.21x

1.34x

224

1

6.05

2.93

1.50

4.04x

1.96x

224

2

10.53

3.87

2.49

4.23x

1.56x

224

4

9.95

5.96

4.44

2.24x

1.34x

256

1

5.98

3.21

1.73

3.45x

1.85x

256

2

6.90

4.19

2.96

2.33x

1.42x

256

4

12.34

7.32

5.50

2.24x

1.33x

288

1

6.16

3.35

2.05

3.00x

1.63x

288

2

8.29

4.94

3.65

2.27x

1.35x

288

4

15.13

8.83

6.87

2.20x

1.29x

320

1

6.12

3.50

2.44

2.51x

1.43x

320

2

9.74

5.61

4.31

2.26x

1.30x

320

4

18.10

10.45

8.19

2.21x

1.28x

352

1

6.77

3.94

2.72

2.49x

1.45x

352

2

11.34

6.59

4.94

2.29x

1.33x

352

4

21.43

12.26

9.57

2.24x

1.28x

384

1

7.23

4.20

3.02

2.39x

1.39x

384

2

13.13

7.52

5.71

2.30x

1.32x

384

4

25.00

14.24

11.04

2.27x

1.29x

448

1

9.24

5.34

3.95

2.34x

1.35x

448

2

17.22

9.76

7.50

2.30x

1.30x

448

4

33.13

18.88

14.68

2.26x

1.29x

512

1

11.50

6.52

4.82

2.39x

1.35x

512

2

21.83

12.24

9.40

2.32x

1.30x

512

4

42.43

23.71

18.44

2.30x

1.29x

640

1

17.07

10.26

7.55

2.26x

1.36x

640

2

33.01

18.40

14.57

2.27x

1.26x

640

4

65.15

36.41

28.75

2.27x

1.27x

768

1

23.84

13.49

10.19

2.34x

1.32x

768

2

46.91

26.10

20.15

2.33x

1.29x

768

4

93.03

51.79

40.47

2.30x

1.28x

896

1

31.95

17.93

14.04

2.28x

1.28x

896

2

64.49

36.09

27.81

2.32x

1.30x

896

4

128.13

71.59

56.06

2.29x

1.28x

1024

1

41.27

22.97

17.93

2.30x

1.28x

1024

2

82.18

45.80

35.87

2.29x

1.28x

1024

4

164.67

92.02

71.87

2.29x

1.28x

Tokens

Batch

oss_eager (s)

oss_torch_compile (s)

bioir (s)

eager÷bioir

compile÷bioir

128

1

10.37

6.55

1.13

9.18x

5.81x

128

2

10.88

6.26

1.43

7.59x

4.37x

128

4

11.48

7.00

2.35

4.89x

2.98x

160

1

11.12

7.01

1.29

8.64x

5.44x

160

2

12.54

6.17

1.99

6.31x

3.11x

160

4

12.38

8.47

3.16

3.92x

2.68x

192

1

10.86

7.12

1.51

7.19x

4.71x

192

2

11.09

7.03

2.21

5.01x

3.18x

192

4

12.70

9.29

3.79

3.35x

2.45x

224

1

10.52

6.64

1.57

6.71x

4.24x

224

2

11.15

7.83

2.63

4.23x

2.97x

224

4

13.21

8.96

4.63

2.85x

1.93x

256

1

11.30

7.02

1.83

6.17x

3.84x

256

2

12.02

7.57

3.02

3.98x

2.51x

256

4

13.68

8.59

5.52

2.48x

1.56x

288

1

11.65

7.42

2.18

5.35x

3.41x

288

2

12.47

8.33

3.81

3.27x

2.19x

288

4

15.34

10.48

7.07

2.17x

1.48x

320

1

12.25

7.64

2.51

4.89x

3.05x

320

2

12.75

7.59

4.32

2.95x

1.76x

320

4

17.60

11.30

8.34

2.11x

1.35x

352

1

11.94

7.16

2.87

4.16x

2.49x

352

2

13.56

8.34

5.00

2.71x

1.67x

352

4

20.48

13.61

9.61

2.13x

1.42x

384

1

14.44

8.04

3.11

4.65x

2.59x

384

2

14.89

9.39

5.67

2.63x

1.66x

384

4

23.90

14.77

10.92

2.19x

1.35x

448

1

14.41

7.27

4.00

3.60x

1.82x

448

2

16.36

10.60

7.38

2.22x

1.44x

448

4

31.27

18.71

14.61

2.14x

1.28x

512

1

14.54

9.78

4.85

3.00x

2.02x

512

2

20.65

13.07

9.35

2.21x

1.40x

512

4

39.52

24.54

18.06

2.19x

1.36x

640

1

16.22

10.27

7.60

2.13x

1.35x

640

2

31.33

19.43

14.30

2.19x

1.36x

640

4

60.65

35.94

28.02

2.16x

1.28x

768

1

22.41

13.71

10.39

2.16x

1.32x

768

2

43.82

25.98

19.78

2.22x

1.31x

768

4

86.53

50.59

39.22

2.21x

1.29x

896

1

29.90

18.10

13.83

2.16x

1.31x

896

2

59.05

34.63

26.99

2.19x

1.28x

896

4

117.42

69.20

54.31

2.16x

1.27x

1024

1

38.37

22.61

17.47

2.20x

1.29x

1024

2

76.44

45.74

34.73

2.20x

1.32x

1024

4

152.35

88.67

68.90

2.21x

1.29x

Three things the grid shows.

Design time is super-linear in token count, because the pair track is quadratic: on H100 80GB HBM3 with bioir at batch 1, an eightfold rise in tokens, 128 to 1024, costs 15.3x the time. The spread between GPUs widens with it. At 128 tokens the datacenter parts are about 2.3x apart; at 1024 they fall into bands — 11.6 to 13.9 s on the Blackwell datacenter parts, 16.9 to 27.0 s on Hopper, 51.3 to 64.8 s on Ampere, and 76.1 to 97.9 s on the Ada-generation parts. GPU choice therefore matters far more for long designs than for short ones. The GB10 (DGX Spark) sits well outside those bands at 833.9 s, which is what a desktop part costs on the longest design this suite sends.

Batching is close to free at short lengths and close to linear at long ones. On H100 at 128 tokens, oss_eager returns four designs in 8.25 s against 6.82 s for one — 1.21x the time for 4x the output. bioir starts from a far lower per-request floor and so saturates sooner, at 2.08x. By 1024 tokens the GPU is saturated either way and batch 4 costs about 3.9x on both. A deployment serving short designs should batch; one serving long designs gains throughput from batching but little latency.

bioir leads on most parts, by a margin that narrows with both length and batch. On H100 it is 5.83x over oss_eager and 2.67x over oss_torch_compile at 128 tokens and batch 1, 3.39x and 1.61x at the same length and batch 4, and settles near 2.3x and 1.38x from 512 tokens upward regardless of batch. The short-length, batch-1 figures are the most flattering ones and should not be quoted as the general case.

Accuracy Across Execution Backends#

The eval suite’s structural-quality metrics, on one H100 80GB HBM3, from the same release candidate as the performance table above. Each backend ran the same 87 conditioned designs. n is how many of those 87 the metric is defined on.

Metric

Better

n

oss_eager

oss_torch_compile

bioir

success_rate

higher

87

1.000

1.000

1.000

clash_frac mean

lower

87

0.0134

0.0105

0.0106

clash_frac max

lower

87

0.917

0.833

0.917

bond_length_unreasonable mean

lower

87

0.00023

0.00025

0.00031

bond_length_unreasonable max

lower

87

0.0082

0.0108

0.0041

sequence_adherence mean

higher

57

1.000

1.000

0.994

ss_conditioning_accuracy mean

higher

1

0.663

0.807

0.659

Every design completed on every backend, and the structural-quality means sit within a few thousandths of one another. Results are comparable in kind across backends but not bit-identical — compilation and BioIR’s own kernels both change floating-point numerics — so small differences between the three columns are expected and none of the gaps here is larger than that.

Warning

These are means over a small evaluation set, not a published accuracy benchmark, and two rows are weaker than the rest. sequence_adherence is defined on 57 of the 87 designs, and ss_conditioning_accuracy on exactly one — the spread from 0.659 to 0.807 in that last row is a single design and carries no information about backend quality. Do not select a backend on these numbers.

Cold-Start Behavior#

The NIM reports ready as soon as its weights are loaded; it does not pre-warm every token-count bucket the oss_torch_compile backend compiles for. This means the first request against a given token bucket after startup pays a Triton JIT compilation cost, once per bucket per container start, and later requests against the same (or a smaller, same-bucket) size run at steady-state speed. This is a deliberate trade: a NIM that is servable in well under a minute, with the compile cost spread across a handful of early requests, versus one that is uniformly fast but takes several minutes to report ready.

Measured on one H100, thinking_medium (the checkpoint’s default recycle strategy), one design:

Tokens

Bucket

Cold (first request in bucket)

Steady state

Penalty

100

128

30.3 s

3.1 s

9.8x

150

160

22.2 s

3.6 s

6.2x

250

256

21.9 s

4.4 s

5.0x

650

768

54.9 s

28.4 s

1.9x

694

768 (already warm from 650)

28.5 s

28.4 s

1.0x

Two things follow from this table. First, the penalty is per bucket, not “the first request ever”: a deployment serving a wide range of input sizes pays this cost once per distinct bucket its clients exercise, scattered across whichever requests happen to land first. Second, after a bucket is warm, a smaller request that rounds up into that same bucket (694 tokens padding to the 768 bucket already warmed by a 650-token request) pays nothing extra.

If a deployment or a demo needs a specific input size to respond quickly from the first request, send one request of that size to warm its bucket before the size matters.

Memory Footprint#

This NIM ships with no refolding oracle built in (refer to Oracles), so the design model’s own memory footprint is what a deployment plans capacity around. That footprint grows with the square of the token count and with the batch size, and sampling.batch_size defaults to sampling.num_replicates: a multi-replicate request is a single large forward pass unless it says otherwise. Refer to Replicates and Batching. A mounted oracle that calls out to an independently hosted structure-prediction NIM (the reference implementations this NIM ships against OpenFold3 and Boltz-2 both work this way) adds no GPU memory cost of its own here, since the model it calls lives entirely in that other service.