Cytoscape.js GPU benchmarks

v4 executor 'cpu' vs 'gpu' · times are per-call p50 · 2026-08-13 01:30 · 0d3561de (v4) · chromium v24.18.0 · algorithms-gpu profile

CPU	Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
Cores	8 physical / 16 logical · 3.6 GHz base · 5 GHz max
Memory	62.6 GiB
GPU	CoffeeLake-S GT2 [UHD Graphics 630] i915 Ellesmere [Radeon RX 470/480/570/570X/580/580X/590] (8.0 GiB) amdgpu
Adapter	amd gcn-4
Browser	chromium 149.0.7827.55
OS	Fedora Linux 43 (Workstation Edition) · 6.19.14-200.fc43.x86_64 · x64
Node	v24.18.0 (v8 13.6.233.17-node.50)
Commit	0d3561de merge: the round 69/70 algorithm matrix into v4
Machine id	5cf3f79c

Speedup overview cpu p50 ÷ gpu p50, log scale · right of the 1× line = gpu faster

heatKernel @ 1.024k

2264×

markovClustering @ 1.024k

652×

heatKernel @ 512

427×

markovClustering @ 512

286×

rwrProximity @ 1.024k

283×

kMedoids @ 4.096k

165×

simRank @ 1.024k

147×

rwrProximity @ 512

125×

simRank @ 512

88×

heatKernel @ 256

83×

kMedoids @ 2.048k

82×

markovClustering @ 256

70×

fuzzyCMeans @ 65.536k

69×

fuzzyCMeans @ 16.384k

48×

closenessCentralityNormalized @ 1.024k

47×

effectiveResistance @ 1.024k

43×

simRank @ 256

33×

floydWarshall @ 1.024k

33×

rwrProximity @ 256

30×

fuzzyCMeans @ 4.096k

28×

motifCensus @ 2.048k

23×

kMeans @ 65.536k

22×

closenessCentralityNormalized @ 512

21×

kMedoids @ 1.024k

19×

betweennessCentrality @ 2.048k

18×

effectiveResistance @ 512

17×

kMeans @ 16.384k

16×

floydWarshall @ 512

12×

betweennessCentrality @ 1.024k

10×

triangleCount @ 2.048k

8.6×

motifCensus @ 1.024k

8.2×

kMeans @ 4.096k

7.4×

effectiveResistance @ 256

6.8×

closenessCentralityNormalized @ 256

6.7×

neighborhoodSimilarity @ 2.048k

6.6×

triangleCount @ 1.024k

4.8×

betweennessCentrality @ 512

4.0×

neighborhoodSimilarity @ 1.024k

3.9×

affinityPropagation @ 1.024k

3.7×

floydWarshall @ 256

3.7×

affinityPropagation @ 256

2.6×

triangleCount @ 512

2.3×

motifCensus @ 512

2.1×

neighborhoodSimilarity @ 512

1.97×

affinityPropagation @ 512

1.80×

hierarchicalClustering @ 4.096k

0.97×

hierarchicalClustering @ 1.024k

0.95×

hierarchicalClustering @ 2.048k

0.90×

pageRankDense @ 2.048k

0.19×

pageRankDense @ 1.024k

0.18×

pageRankDense @ 512

0.14×

katzCentrality @ 512

0.08×

pageRank @ 512

0.06×

pageRank @ 1.024k

0.02×

katzCentrality @ 2.048k

0.01×

pageRank @ 2.048k

0.01×

katzCentrality @ 1.024k

0.01×

0.001×0.01×0.1×1×10×100×1000×10000×

Scaling speedup vs graph size

algorithms-gpu

group	× @ N=256	× @ N=512	× @ N=1.024k	× @ N=2.048k	× @ N=4.096k	× @ N=16.384k	× @ N=65.536k
markovClustering	70×	286×	652×	–	–	–	–
floydWarshall	3.7×	12×	33×	–	–	–	–
affinityPropagation	2.6×	1.80×	3.7×	–	–	–	–
closenessCentralityNormalized	6.7×	21×	47×	–	–	–	–
effectiveResistance	6.8×	17×	43×	–	–	–	–
simRank	33×	88×	147×	–	–	–	–
rwrProximity	30×	125×	283×	–	–	–	–
heatKernel	83×	427×	2264×	–	–	–	–
pageRank	–	0.06×	0.02×	0.01×	–	–	–
pageRankDense	–	0.14×	0.18×	0.19×	–	–	–
betweennessCentrality	–	4.0×	10×	18×	–	–	–
triangleCount	–	2.3×	4.8×	8.6×	–	–	–
neighborhoodSimilarity	–	1.97×	3.9×	6.6×	–	–	–
katzCentrality	–	0.08×	0.01×	0.01×	–	–	–
motifCensus	–	2.1×	8.2×	23×	–	–	–
kMedoids	–	–	19×	82×	165×	–	–
hierarchicalClustering	–	–	0.95×	0.90×	0.97×	–	–
kMeans	–	–	–	–	7.4×	16×	22×
fuzzyCMeans	–	–	–	–	28×	48×	69×

algorithms-gpu N=256 · 9.4 sv4 (gpu) v4 (cpu)

markovClustering

70×

floydWarshall

3.7×

affinityPropagation

2.6×

closenessCentralityNormalized

6.7×

effectiveResistance

6.8×

simRank

33×

rwrProximity

30×

heatKernel

83×

1 ms10 ms100 ms1 s

All stats (table view)

group	bench	p50	avg	p99	min	samples
markovClustering	cpu	617 ms	621 ms	632 ms	610 ms	5
markovClustering	gpu	8.80 ms	9.18 ms	9.00 ms	8.60 ms	5
markovClustering	gpu first call	26.7 ms	26.7 ms	26.7 ms	26.7 ms	1
floydWarshall	cpu	23.4 ms	33.3 ms	49.3 ms	21.0 ms	5
floydWarshall	gpu	6.40 ms	6.52 ms	6.60 ms	6.30 ms	5
floydWarshall	gpu first call	20.6 ms	20.6 ms	20.6 ms	20.6 ms	1
affinityPropagation	cpu	40.6 ms	42.6 ms	42.6 ms	39.6 ms	5
affinityPropagation	gpu	15.4 ms	15.7 ms	15.6 ms	14.8 ms	5
affinityPropagation	gpu first call	25.5 ms	25.5 ms	25.5 ms	25.5 ms	1
closenessCentralityNormalized	cpu	24.1 ms	23.9 ms	24.2 ms	23.4 ms	5
closenessCentralityNormalized	gpu	3.60 ms	3.66 ms	3.80 ms	3.50 ms	5
closenessCentralityNormalized	gpu first call	7.50 ms	7.50 ms	7.50 ms	7.50 ms	1
effectiveResistance	cpu	51.7 ms	51.8 ms	51.9 ms	51.1 ms	5
effectiveResistance	gpu	7.60 ms	7.90 ms	8.70 ms	6.90 ms	5
effectiveResistance	gpu first call	18.2 ms	18.2 ms	18.2 ms	18.2 ms	1
simRank	cpu	146 ms	205 ms	149 ms	145 ms	5
simRank	gpu	4.50 ms	4.84 ms	5.10 ms	4.20 ms	5
simRank	gpu first call	15.9 ms	15.9 ms	15.9 ms	15.9 ms	1
rwrProximity	cpu	173 ms	173 ms	173 ms	170 ms	5
rwrProximity	gpu	5.80 ms	6.24 ms	5.90 ms	5.60 ms	5
rwrProximity	gpu first call	13.5 ms	13.5 ms	13.5 ms	13.5 ms	1
heatKernel	cpu	308 ms	308 ms	309 ms	306 ms	5
heatKernel	gpu	3.70 ms	4.36 ms	4.50 ms	3.50 ms	5
heatKernel	gpu first call	14.5 ms	14.5 ms	14.5 ms	14.5 ms	1

algorithms-gpu N=512 · 1.4 minv4 (gpu) v4 (cpu)

markovClustering

286×

pageRank

0.06×

pageRankDense

0.14×

floydWarshall

12×

betweennessCentrality

4.0×

affinityPropagation

1.80×

closenessCentralityNormalized

21×

triangleCount

2.3×

neighborhoodSimilarity

1.97×

katzCentrality

0.08×

effectiveResistance

17×

simRank

88×

rwrProximity

125×

heatKernel

427×

motifCensus

2.1×

100 µs1 ms10 ms100 ms1 s10 s

All stats (table view)

group	bench	p50	avg	p99	min	samples
markovClustering	cpu	4.77 s	4.78 s	4.78 s	4.76 s	5
markovClustering	gpu	16.7 ms	17.4 ms	16.9 ms	15.8 ms	5
markovClustering	gpu first call	33.0 ms	33.0 ms	33.0 ms	33.0 ms	1
pageRank	cpu	400 µs	420 µs	500 µs	200 µs	5
pageRank	gpu	6.60 ms	6.76 ms	6.90 ms	6.30 ms	5
pageRank	gpu first call	13.7 ms	13.7 ms	13.7 ms	13.7 ms	1
pageRankDense	cpu	1.00 ms	960 µs	1.00 ms	900 µs	5
pageRankDense	gpu	7.40 ms	7.42 ms	7.60 ms	7.10 ms	5
pageRankDense	gpu first call	27.8 ms	27.8 ms	27.8 ms	27.8 ms	1
floydWarshall	cpu	180 ms	181 ms	182 ms	179 ms	5
floydWarshall	gpu	15.3 ms	15.5 ms	15.8 ms	14.3 ms	5
floydWarshall	gpu first call	15.9 ms	15.9 ms	15.9 ms	15.9 ms	1
betweennessCentrality	cpu	36.4 ms	36.8 ms	36.4 ms	35.5 ms	5
betweennessCentrality	gpu	9.00 ms	9.30 ms	9.10 ms	8.90 ms	5
betweennessCentrality	gpu first call	19.1 ms	19.1 ms	19.1 ms	19.1 ms	1
affinityPropagation	cpu	204 ms	204 ms	204 ms	202 ms	5
affinityPropagation	gpu	114 ms	114 ms	114 ms	113 ms	5
affinityPropagation	gpu first call	117 ms	117 ms	117 ms	117 ms	1
closenessCentralityNormalized	cpu	180 ms	175 ms	181 ms	164 ms	5
closenessCentralityNormalized	gpu	8.50 ms	11.4 ms	10.9 ms	8.20 ms	5
closenessCentralityNormalized	gpu first call	9.00 ms	9.00 ms	9.00 ms	9.00 ms	1
triangleCount	cpu	16.2 ms	16.5 ms	16.3 ms	15.5 ms	5
triangleCount	gpu	7.10 ms	7.10 ms	7.10 ms	7.00 ms	5
triangleCount	gpu first call	27.0 ms	27.0 ms	27.0 ms	27.0 ms	1
neighborhoodSimilarity	cpu	14.6 ms	14.6 ms	14.8 ms	14.2 ms	5
neighborhoodSimilarity	gpu	7.40 ms	7.30 ms	7.50 ms	6.90 ms	5
neighborhoodSimilarity	gpu first call	42.7 ms	42.7 ms	42.7 ms	42.7 ms	1
katzCentrality	cpu	500 µs	500 µs	600 µs	400 µs	5
katzCentrality	gpu	6.40 ms	5.96 ms	6.50 ms	4.90 ms	5
katzCentrality	gpu first call	8.70 ms	8.70 ms	8.70 ms	8.70 ms	1
effectiveResistance	cpu	413 ms	610 ms	899 ms	408 ms	5
effectiveResistance	gpu	24.9 ms	23.4 ms	25.1 ms	18.2 ms	5
effectiveResistance	gpu first call	20.6 ms	20.6 ms	20.6 ms	20.6 ms	1
simRank	cpu	1.05 s	1.52 s	1.07 s	1.04 s	5
simRank	gpu	12.0 ms	13.0 ms	12.4 ms	11.5 ms	5
simRank	gpu first call	43.3 ms	43.3 ms	43.3 ms	43.3 ms	1
rwrProximity	cpu	1.31 s	1.31 s	1.31 s	1.30 s	5
rwrProximity	gpu	10.5 ms	11.7 ms	10.5 ms	10.3 ms	5
rwrProximity	gpu first call	33.6 ms	33.6 ms	33.6 ms	33.6 ms	1
heatKernel	cpu	4.74 s	4.75 s	4.76 s	4.74 s	5
heatKernel	gpu	11.1 ms	11.8 ms	11.2 ms	10.4 ms	5
heatKernel	gpu first call	29.4 ms	29.4 ms	29.4 ms	29.4 ms	1
motifCensus	cpu	42.3 ms	41.1 ms	42.6 ms	38.3 ms	5
motifCensus	gpu	20.1 ms	19.8 ms	23.0 ms	10.0 ms	5
motifCensus	gpu first call	48.5 ms	48.5 ms	48.5 ms	48.5 ms	1

algorithms-gpu N=1,024 · 13.4 minv4 (gpu) v4 (cpu)

markovClustering

652×

pageRank

0.02×

pageRankDense

0.18×

floydWarshall

33×

betweennessCentrality

10×

affinityPropagation

3.7×

kMedoids

19×

hierarchicalClustering

0.95×

closenessCentralityNormalized

47×

triangleCount

4.8×

neighborhoodSimilarity

3.9×

katzCentrality

0.01×

effectiveResistance

43×

simRank

147×

rwrProximity

283×

heatKernel

2264×

motifCensus

8.2×

100 µs1 ms10 ms100 ms1 s10 s100 s

All stats (table view)

group	bench	p50	avg	p99	min	samples
markovClustering	cpu	30.4 s	30.3 s	30.4 s	30.2 s	5
markovClustering	gpu	46.6 ms	50.2 ms	46.8 ms	46.2 ms	5
markovClustering	gpu first call	62.7 ms	62.7 ms	62.7 ms	62.7 ms	1
pageRank	cpu	400 µs	520 µs	700 µs	300 µs	5
pageRank	gpu	18.1 ms	18.4 ms	18.1 ms	17.6 ms	5
pageRank	gpu first call	20.3 ms	20.3 ms	20.3 ms	20.3 ms	1
pageRankDense	cpu	3.80 ms	3.86 ms	3.90 ms	3.80 ms	5
pageRankDense	gpu	21.2 ms	21.3 ms	21.5 ms	20.6 ms	5
pageRankDense	gpu first call	105 ms	105 ms	105 ms	105 ms	1
floydWarshall	cpu	1.43 s	1.43 s	1.43 s	1.42 s	5
floydWarshall	gpu	43.9 ms	43.0 ms	45.7 ms	35.4 ms	5
floydWarshall	gpu first call	44.6 ms	44.6 ms	44.6 ms	44.6 ms	1
betweennessCentrality	cpu	153 ms	152 ms	153 ms	151 ms	5
betweennessCentrality	gpu	15.2 ms	16.3 ms	15.3 ms	14.8 ms	5
betweennessCentrality	gpu first call	16.6 ms	16.6 ms	16.6 ms	16.6 ms	1
affinityPropagation	cpu	1.10 s	1.49 s	2.11 s	1.06 s	5
affinityPropagation	gpu	296 ms	295 ms	296 ms	292 ms	5
affinityPropagation	gpu first call	301 ms	301 ms	301 ms	301 ms	1
kMedoids	cpu	80.2 ms	77.3 ms	80.4 ms	67.4 ms	5
kMedoids	gpu	4.20 ms	3.84 ms	4.20 ms	3.00 ms	5
kMedoids	gpu first call	13.1 ms	13.1 ms	13.1 ms	13.1 ms	1
hierarchicalClustering	cpu	27.9 ms	29.9 ms	34.9 ms	25.5 ms	5
hierarchicalClustering	gpu	29.5 ms	29.1 ms	29.8 ms	27.5 ms	5
hierarchicalClustering	gpu first call	31.4 ms	31.4 ms	31.4 ms	31.4 ms	1
closenessCentralityNormalized	cpu	1.29 s	1.30 s	1.30 s	1.29 s	5
closenessCentralityNormalized	gpu	27.7 ms	29.9 ms	31.9 ms	26.5 ms	5
closenessCentralityNormalized	gpu first call	33.2 ms	33.2 ms	33.2 ms	33.2 ms	1
triangleCount	cpu	107 ms	157 ms	115 ms	104 ms	5
triangleCount	gpu	22.3 ms	22.8 ms	23.4 ms	21.5 ms	5
triangleCount	gpu first call	95.0 ms	95.0 ms	95.0 ms	95.0 ms	1
neighborhoodSimilarity	cpu	90.3 ms	139 ms	212 ms	89.5 ms	5
neighborhoodSimilarity	gpu	23.3 ms	23.6 ms	24.0 ms	22.8 ms	5
neighborhoodSimilarity	gpu first call	92.3 ms	92.3 ms	92.3 ms	92.3 ms	1
katzCentrality	cpu	100 µs	140 µs	200 µs	100 µs	5
katzCentrality	gpu	12.1 ms	12.5 ms	12.3 ms	12.0 ms	5
katzCentrality	gpu first call	13.0 ms	13.0 ms	13.0 ms	13.0 ms	1
effectiveResistance	cpu	3.44 s	3.43 s	3.44 s	3.40 s	5
effectiveResistance	gpu	79.5 ms	82.1 ms	82.5 ms	78.7 ms	5
effectiveResistance	gpu first call	82.0 ms	82.0 ms	82.0 ms	82.0 ms	1
simRank	cpu	8.45 s	8.44 s	8.45 s	8.39 s	5
simRank	gpu	57.6 ms	57.5 ms	58.1 ms	53.6 ms	5
simRank	gpu first call	142 ms	142 ms	142 ms	142 ms	1
rwrProximity	cpu	10.4 s	10.4 s	10.4 s	10.3 s	5
rwrProximity	gpu	36.6 ms	39.3 ms	41.8 ms	35.7 ms	5
rwrProximity	gpu first call	120 ms	120 ms	120 ms	120 ms	1
heatKernel	cpu	75.4 s	75.4 s	75.4 s	75.1 s	5
heatKernel	gpu	33.3 ms	36.3 ms	33.6 ms	33.1 ms	5
heatKernel	gpu first call	127 ms	127 ms	127 ms	127 ms	1
motifCensus	cpu	311 ms	362 ms	327 ms	301 ms	5
motifCensus	gpu	38.2 ms	36.1 ms	40.6 ms	30.2 ms	5
motifCensus	gpu first call	137 ms	137 ms	137 ms	137 ms	1

algorithms-gpu N=2,048 · 45.4 sv4 (gpu) v4 (cpu)

pageRank

0.01×

pageRankDense

0.19×

betweennessCentrality

18×

kMedoids

82×

hierarchicalClustering

0.90×

triangleCount

8.6×

neighborhoodSimilarity

6.6×

katzCentrality

0.01×

motifCensus

23×

100 µs1 ms10 ms100 ms1 s10 s

All stats (table view)

group	bench	p50	avg	p99	min	samples
pageRank	cpu	600 µs	620 µs	600 µs	500 µs	5
pageRank	gpu	72.4 ms	73.0 ms	73.0 ms	68.3 ms	5
pageRank	gpu first call	88.0 ms	88.0 ms	88.0 ms	88.0 ms	1
pageRankDense	cpu	15.3 ms	15.4 ms	15.3 ms	15.1 ms	5
pageRankDense	gpu	80.6 ms	80.9 ms	80.9 ms	80.2 ms	5
pageRankDense	gpu first call	392 ms	392 ms	392 ms	392 ms	1
betweennessCentrality	cpu	648 ms	665 ms	665 ms	642 ms	5
betweennessCentrality	gpu	35.3 ms	37.9 ms	37.8 ms	35.0 ms	5
betweennessCentrality	gpu first call	42.3 ms	42.3 ms	42.3 ms	42.3 ms	1
kMedoids	cpu	386 ms	386 ms	405 ms	344 ms	5
kMedoids	gpu	4.70 ms	5.56 ms	5.90 ms	3.50 ms	5
kMedoids	gpu first call	4.50 ms	4.50 ms	4.50 ms	4.50 ms	1
hierarchicalClustering	cpu	99.7 ms	101 ms	100 ms	99.3 ms	5
hierarchicalClustering	gpu	111 ms	110 ms	111 ms	105 ms	5
hierarchicalClustering	gpu first call	119 ms	119 ms	119 ms	119 ms	1
triangleCount	cpu	769 ms	1.54 s	2.71 s	756 ms	5
triangleCount	gpu	89.4 ms	91.5 ms	96.0 ms	86.2 ms	5
triangleCount	gpu first call	417 ms	417 ms	417 ms	417 ms	1
neighborhoodSimilarity	cpu	630 ms	630 ms	630 ms	614 ms	5
neighborhoodSimilarity	gpu	95.0 ms	99.6 ms	101 ms	92.2 ms	5
neighborhoodSimilarity	gpu first call	419 ms	419 ms	419 ms	419 ms	1
katzCentrality	cpu	300 µs	360 µs	400 µs	300 µs	5
katzCentrality	gpu	36.0 ms	36.0 ms	36.2 ms	35.2 ms	5
katzCentrality	gpu first call	38.3 ms	38.3 ms	38.3 ms	38.3 ms	1
motifCensus	cpu	2.86 s	3.43 s	4.45 s	2.58 s	5
motifCensus	gpu	127 ms	124 ms	128 ms	112 ms	5
motifCensus	gpu first call	453 ms	453 ms	453 ms	453 ms	1

algorithms-gpu N=4,096 · 16.4 sv4 (gpu) v4 (cpu)

kMeans

7.4×

fuzzyCMeans

28×

kMedoids

165×

hierarchicalClustering

0.97×

1 ms10 ms100 ms1 s10 s

All stats (table view)

group	bench	p50	avg	p99	min	samples
kMeans	cpu	29.7 ms	30.6 ms	29.9 ms	29.4 ms	5
kMeans	gpu	4.00 ms	4.06 ms	4.10 ms	3.80 ms	5
kMeans	gpu first call	14.8 ms	14.8 ms	14.8 ms	14.8 ms	1
fuzzyCMeans	cpu	156 ms	157 ms	158 ms	155 ms	5
fuzzyCMeans	gpu	5.60 ms	5.54 ms	5.80 ms	4.80 ms	5
fuzzyCMeans	gpu first call	18.5 ms	18.5 ms	18.5 ms	18.5 ms	1
kMedoids	cpu	1.65 s	1.65 s	1.66 s	1.41 s	5
kMedoids	gpu	10.0 ms	12.9 ms	12.1 ms	8.80 ms	5
kMedoids	gpu first call	12.3 ms	12.3 ms	12.3 ms	12.3 ms	1
hierarchicalClustering	cpu	431 ms	432 ms	435 ms	430 ms	5
hierarchicalClustering	gpu	447 ms	451 ms	448 ms	442 ms	5
hierarchicalClustering	gpu first call	500 ms	500 ms	500 ms	500 ms	1

Cytoscape.js GPU benchmarks

Speedup overview cpu p50 ÷ gpu p50, log scale · right of the 1× line = gpu faster

Scaling speedup vs graph size

algorithms-gpu

algorithms-gpu N=256 · 9.4 sv4 (gpu) v4 (cpu)

algorithms-gpu N=512 · 1.4 minv4 (gpu) v4 (cpu)

algorithms-gpu N=1,024 · 13.4 minv4 (gpu) v4 (cpu)

algorithms-gpu N=2,048 · 45.4 sv4 (gpu) v4 (cpu)

algorithms-gpu N=4,096 · 16.4 sv4 (gpu) v4 (cpu)

algorithms-gpu N=16,384 · 4.7 sv4 (gpu) v4 (cpu)

algorithms-gpu N=65,536 · 20.2 sv4 (gpu) v4 (cpu)

group	bench	p50	avg	p99	min	samples
kMeans	cpu	126 ms	126 ms	126 ms	124 ms	5
kMeans	gpu	7.70 ms	8.80 ms	8.10 ms	7.40 ms	5
kMeans	gpu first call	16.4 ms	16.4 ms	16.4 ms	16.4 ms	1
fuzzyCMeans	cpu	612 ms	610 ms	612 ms	603 ms	5
fuzzyCMeans	gpu	12.8 ms	18.2 ms	12.8 ms	11.2 ms	5
fuzzyCMeans	gpu first call	22.8 ms	22.8 ms	22.8 ms	22.8 ms	1

group	bench	p50	avg	p99	min	samples
kMeans	cpu	630 ms	620 ms	636 ms	593 ms	5
kMeans	gpu	28.3 ms	27.9 ms	28.4 ms	25.9 ms	5
kMeans	gpu first call	77.5 ms	77.5 ms	77.5 ms	77.5 ms	1
fuzzyCMeans	cpu	2.64 s	2.64 s	2.68 s	2.54 s	5
fuzzyCMeans	gpu	38.0 ms	40.3 ms	43.9 ms	37.7 ms	5
fuzzyCMeans	gpu first call	85.4 ms	85.4 ms	85.4 ms	85.4 ms	1