Benchmarks for CNS 1.1 test suite

A comparison of the times for the standard CNS input files from CNS 1.1


Opteron data from station05 over NFS at IRIC


Data for SGI, 1.8 GHz Athlon and 2.8 GHz Xeon taken from NIH site



All jobs were ran on 1 CPU

Click here for some graphical representations

Bottom line: Opteron outperforms other CPU's. Sometimes twice as fast as the next fastest CPU, e.g nmr_calc/ensemble_cv_1.inp

Times given in seconds

Test suite program

SGI 600 MHz
R14000 IP30

AMD OPTERON

optimised by Savoirefaire 32-bit

1.8 GHz Athlon
(Biowulf cluster)

2.8 GHz Xeon
(Biowulf cluster)

general/alternate.inp

0.4

0.06

0.1

0.1

general/bfactor_plot.inp

0.4

0.14

0.4

0.3

general/buried_surface.inp

5.5

2.34

4.9

4.4

general/cis_peptide.inp

30.3

11.48

64.7

55.6

general/cns_to_o.inp

1.0

0.38

0.7

0.7

general/contact.inp

105.6

39.17

219.6

189.4

general/delete_atoms.inp

0.3

0.05

0.1

0.1

general/delta_phipsi.inp

2.7

0.94

4.9

4.0

general/difference_distance.inp

25.3

8

27.0

22.2

general/fractional_transform.inp

0.7

0.28

0.7

0.6

general/generate.inp

2.5

0.89

3.9

3.3

general/generate_easy.inp

42.8

15.61

84.3

71.3

general/generate_seq.inp

1.0

0.3

0.9

0.8

general/get_ncs_matrices.inp

0.6

0.22

0.4

0.3

general/hydrogen_bonds.inp

20.4

7.63

39.2

33.1

general/merge_structures.inp

1.5

0.42

1.4

1.1

general/model_anneal.inp

38.4

17.69

29.5

24.2

general/model_mask.inp

1.0

0.41

0.8

0.8

general/model_minimize.inp

8.5

3.84

6.6

5.4

general/model_rigid.inp

2.0

0.86

1.8

1.4

general/molecule_extent.inp

0.7

0.27

1.1

0.9

general/mtf_to_psf.inp

0.1

0.01

0.0

0.0

general/neighbours.inp

10.6

3.9

20.1

17.5

general/psf_to_mtf.inp

0.3

0.03

0.1

0.0

general/ramachandran.inp

2.3

0.82

4.5

3.7

general/realspace_transform.inp

1.3

0.51

1.1

1.0

general/rename_segid.inp

2.1

0.32

0.7

0.6

general/rms_fit.inp

0.1

0.04

0.1

0.0

general/rmsd.inp

0.5

0.15

0.5

0.4

general/shift_molecules.inp

92.1

34.38

162.0

139.7

general/split_structure.inp

7.2

1.98

2.8

2.4

general/surface_plot.inp

0.7

0.25

0.8

0.6

nmr_calc/accept.inp

411.0

181.60

275.6

381.7

nmr_calc/anneal.inp

3972.3

1520.820

2563.7

2216.4

nmr_calc/anneal_1.inp

1881.7

635.28

1208.4

982.9

nmr_calc/anneal_2.inp

2765.2

1032.07

2004.5

1482.3

nmr_calc/anneal_3.inp

1110.3

450.29

870.0

686.0

nmr_calc/anneal_cv.inp

10758.3

3911.98

7117.1

5429.7

nmr_calc/dg_sa.inp

1886.7

627.41

1259.0

947.5

nmr_calc/dg_sa_1.inp

334.7

171.42

680.2

333.0

nmr_calc/ensemble.inp

1289.0

457.7

917.6

818.8

nmr_calc/ensemble_1.inp

860.2

267.75

548.5

550.2

nmr_calc/ensemble_cv.inp

3827.9

1365.79

2783.8

2475.1

nmr_calc/ensemble_cv_1.inp

8660.1

2513.48

5309.9

5512.9

nmr_calc/generate_extended.inp

115.8

19.01

37.6

49.3

nmr_calc/generate_extended_1.inp

71.4

21.68

25.1

20.5

nmr_calc/pmrefine.inp

875.9

441.89

770.0

809.2

nmr_calc/pmrefine_1.inp

598.3

285.54

444.6

474.9

nmr_calc/rmsd_pm.inp

8.2

2.990

12.2

10.6

nmr_calc/rmsd_pm_1.inp

8.5

3.17

11.7

10.3

xtal_mr/cross_rotation.inp

1737.6

871.04

1434.2

1643.0

xtal_mr/cross_rotation_1.inp

541.0

175.13

544.3

393.1

xtal_mr/self_rotation.inp

65.5

21.2

67.2

50.6

xtal_mr/translation.inp

224.8

106.31

219.9

234.6

xtal_mr/translation_1.inp

971.4

493.4

868.2

983.3

xtal_mr/translation_2.inp

202.7

94.23

206.0

212.2

xtal_patterson/heavy_search.inp

413.3


283.6

364.3

xtal_patterson/patterson_map.inp

17.6


18.7

16.7

xtal_patterson/patterson_map_1.inp

20.5


20.7

18.5

xtal_patterson/patterson_refine.inp

22.7


20.7

20.6

xtal_patterson/predict_patterson.inp

1.7


1.7

1.6

xtal_phase/cns_to_sdb.inp

0.1


0.0

0.0

xtal_phase/delete_sites.inp

0.1


0.1

0.1

xtal_phase/density_modify.inp

36.2


29.6

26.8

xtal_phase/density_modify_1.inp

430.4


319.4

250.2

xtal_phase/flip_sites.inp

0.7


0.8

0.7

xtal_phase/generate_sdb.inp

0.1


0.1

0.1

xtal_phase/ir_phase.inp

97.1


68.2

81.8

xtal_phase/ir_phase_1.inp

334.2


375.6

290.1

xtal_phase/ir_phase_2.inp

175.9


120.6

151.8

xtal_phase/ir_phase_3.inp

312.6


365.1

281.4

xtal_phase/mad_bijvoet_ave.inp

15.8


16.7

15.0

xtal_phase/mad_phase.inp

2331.5


1305.0

1814.2

xtal_phase/mad_phase_1.inp

227.0


155.6

199.7

xtal_phase/mad_phase_2.inp

207.7


145.2

182.8

xtal_phase/optimize_ncsop.inp

380.5


243.6

176.0

xtal_phase/pdb_to_sdb.inp

0.1


0.1

0.1

xtal_phase/sdb_manipulate.inp

0.5


0.6

0.5

xtal_phase/sdb_split.inp

0.4


0.5

0.3

xtal_phase/sdb_to_pdb.inp

0.2


0.2

0.2

xtal_phase/sdb_to_sdb.inp

0.2


0.2

0.2

xtal_phase/shift_sites.inp

3.6


4.0

3.5

xtal_phase/solvent_mask.inp

6.8


5.6

4.8

xtal_phase/solvent_mask_1.inp

6.8


6.0

5.0

xtal_refine/anneal.inp

177.6


155.3

160.1

xtal_refine/anneal_1.inp

102.0


102.4

80.5

xtal_refine/anneal_2.inp

27.6


25.5

24.1

xtal_refine/bdomain.inp

10.3


8.6

9.9

xtal_refine/bgroup.inp

11.3


9.3

10.7

xtal_refine/bindividual.inp

11.1


9.2

10.5

xtal_refine/composite_omit_map.inp

1543.5


1423.7

1430.4

xtal_refine/fo-fo_map.inp

5.8


5.2

4.8

xtal_refine/fp_fdp_group.inp

4.4


3.8

4.1

xtal_refine/map_cover.inp

2.6


2.6

2.3

xtal_refine/minimize.inp

60.0


49.1

58.8

xtal_refine/model_map.inp

4.7


4.0

3.4

xtal_refine/model_map_1.inp

4.4


3.9

3.3

xtal_refine/model_stats.inp

18.6


24.3

21.9

xtal_refine/ncs_average_map.inp

245.3


218.7

199.0

xtal_refine/ncs_average_map_1.inp

131.7


118.0

100.8

xtal_refine/optimize_average.inp

2.1


2.0

1.7

xtal_refine/optimize_rweight.inp

43.0


34.4

41.0

xtal_refine/optimize_wa.inp

641.6


552.4

594.9

xtal_refine/qgroup.inp

4.5


3.9

4.1

xtal_refine/qindividual.inp

10.6


8.7

10.0

xtal_refine/refine.inp

52.5


50.4

46.3

xtal_refine/rigid.inp

8.2


6.9

7.8

xtal_refine/sa_omit_map.inp

49.8


44.3

43.7

xtal_refine/shift_solvent.inp

11.8


13.2

11.0

xtal_refine/water_delete.inp

5.8


4.5

4.0

xtal_refine/water_pick.inp

49.7


37.0

43.1

xtal_twin/anneal_twin.inp

3252.3


2855.5

2414.2

xtal_twin/bdomain_twin.inp

148.7


130.8

112.1

xtal_twin/bgroup_twin.inp

152.7


133.6

116.9

xtal_twin/bindividual_twin.inp

153.0


136.0

117.6

xtal_twin/detect_twinning.inp

10.2


6.8

5.8

xtal_twin/detwin_partial.inp

9.3


6.3

5.6

xtal_twin/detwin_perfect.inp

20.7


16.5

14.0

xtal_twin/make_cv_twin.inp

4.5


3.8

3.4

xtal_twin/minimize_twin.inp

921.6


822.9

703.3

xtal_twin/model_map_twin.inp

57.9


41.1

32.8

xtal_twin/model_stats_twin.inp

109.0


134.6

119.0

xtal_twin/rigid_twin.inp

109.0


97.1

84.2

xtal_twin/twin_fraction.inp

16.7


13.9

12.0

xtal_twin/water_pick_twin.inp

626.6


580.4

483.3

xtal_util/analyse.inp

53.2


40.9

35.0

xtal_util/analyse_1.inp

15.4


12.2

10.7

xtal_util/average_friedels.inp

12.7


12.9

11.7

xtal_util/average_map.inp

9.5


6.7

5.1

xtal_util/combine.inp

5.5


5.8

5.2

xtal_util/flip_friedels.inp

17.4


17.3

15.5

xtal_util/fourier_map.inp

28.7


30.9

27.9

xtal_util/fourier_map_1.inp

38.3


36.5

34.1

xtal_util/hlcoeff_blur.inp

2.1


2.1

2.0

xtal_util/make_cv.inp

1.3


1.3

1.2

xtal_util/make_hlcoeff.inp

2.1


2.1

2.0

xtal_util/manipulate.inp

13.6


13.3

11.9

xtal_util/manipulate_1.inp

15.7


14.1

12.7

xtal_util/mask_map.inp

3.6


2.8

2.3

xtal_util/matthews_coef.inp

0.5


0.5

0.5

xtal_util/merge.inp

23.0


21.6

19.2

xtal_util/merge_1.inp

23.0


21.7

19.2

xtal_util/merge_2.inp

13.5


13.5

12.0

xtal_util/model_fcalc.inp

1.1


0.9

0.8

xtal_util/model_phase.inp

2.6


2.3

2.0

xtal_util/scale.inp

25.8


21.9

21.0

xtal_util/transform_map.inp

5.9


4.0

3.0